Daily Papers

Streamlining content discovery within media archives requires integrating advanced data representations and effective visualization techniques for clear communication of video topics to users. The proposed system addresses the challenge of efficiently navigating large video collections by exploiting a fusion of visual, audio, and textual features to accurately index and categorize video content through a text-based method. Additionally, semantic embeddings are employed to provide contextually relevant information and recommendations to users, resulting in an intuitive and engaging exploratory experience over our topics ontology map using OpenAI GPT-4.

We propose the LLMs4OL approach, which utilizes Large Language Models (LLMs) for Ontology Learning (OL). LLMs have shown significant advancements in natural language processing, demonstrating their ability to capture complex language patterns in different knowledge domains. Our LLMs4OL paradigm investigates the following hypothesis: Can LLMs effectively apply their language pattern capturing capability to OL, which involves automatically extracting and structuring knowledge from natural language text? To test this hypothesis, we conduct a comprehensive evaluation using the zero-shot prompting method. We evaluate nine different LLM model families for three main OL tasks: term typing, taxonomy discovery, and extraction of non-taxonomic relations. Additionally, the evaluations encompass diverse genres of ontological knowledge, including lexicosemantic knowledge in WordNet, geographical knowledge in GeoNames, and medical knowledge in UMLS.

OpenStreetMap (OSM) is currently the richest publicly available information source on geographic entities (e.g., buildings and roads) worldwide. However, using OSM entities in machine learning models and other applications is challenging due to the large scale of OSM, the extreme heterogeneity of entity annotations, and a lack of a well-defined ontology to describe entity semantics and properties. This paper presents GeoVectors - a unique, comprehensive world-scale linked open corpus of OSM entity embeddings covering the entire OSM dataset and providing latent representations of over 980 million geographic entities in 180 countries. The GeoVectors corpus captures semantic and geographic dimensions of OSM entities and makes these entities directly accessible to machine learning algorithms and semantic applications. We create a semantic description of the GeoVectors corpus, including identity links to the Wikidata and DBpedia knowledge graphs to supply context information. Furthermore, we provide a SPARQL endpoint - a semantic interface that offers direct access to the semantic and latent representations of geographic entities in OSM.

Existing domain-specific Large Language Models (LLMs) are typically developed by fine-tuning general-purposed LLMs with large-scale domain-specific corpora. However, training on large-scale corpora often fails to effectively organize domain knowledge of LLMs, leading to fragmented understanding. Inspired by how humans connect concepts and organize knowledge through mind maps, we aim to emulate this approach by using ontology with hierarchical conceptual knowledge to reorganize LLM's domain knowledge. From this perspective, we propose an ontology-driven self-training framework called OntoTune, which aims to align LLMs with ontology through in-context learning, enabling the generation of responses guided by the ontology. We leverage in-context learning to identify whether the LLM has acquired the specific concept's ontology knowledge, and select the entries not yet mastered by LLM as the training set to further align the LLM with ontology. Compared to existing domain LLMs based on newly collected large-scale domain-specific corpora, our OntoTune, which relies on the existing, long-term developed ontology and LLM itself, significantly reduces data maintenance costs and offers improved generalization ability. We conduct our study in the medical domain to evaluate the effectiveness of OntoTune, utilizing a standardized medical ontology, SNOMED CT as our ontology source. Experimental results demonstrate that OntoTune achieves state-of-the-art performance in both in-ontology task hypernym discovery and out-of-ontology task medical domain QA. Moreover, compared to the latest direct ontology injection method TaxoLLaMA, our OntoTune better preserves original knowledge of LLM. The code and data are available at https://github.com/zjukg/OntoTune.

This work investigates the applicability of recent generative Large Language Models (LLMs), such as the GPT series and Flan-T5, to ontology alignment for identifying concept equivalence mappings across ontologies. To test the zero-shot performance of Flan-T5-XXL and GPT-3.5-turbo, we leverage challenging subsets from two equivalence matching datasets of the OAEI Bio-ML track, taking into account concept labels and structural contexts. Preliminary findings suggest that LLMs have the potential to outperform existing ontology alignment systems like BERTMap, given careful framework and prompt design.

We design a new technique for the distributional semantic modeling with a neural network-based approach to learn distributed term representations (or term embeddings) - term vector space models as a result, inspired by the recent ontology-related approach (using different types of contextual knowledge such as syntactic knowledge, terminological knowledge, semantic knowledge, etc.) to the identification of terms (term extraction) and relations between them (relation extraction) called semantic pre-processing technology - SPT. Our method relies on automatic term extraction from the natural language texts and subsequent formation of the problem-oriented or application-oriented (also deeply annotated) text corpora where the fundamental entity is the term (includes non-compositional and compositional terms). This gives us an opportunity to changeover from distributed word representations (or word embeddings) to distributed term representations (or term embeddings). This transition will allow to generate more accurate semantic maps of different subject domains (also, of relations between input terms - it is useful to explore clusters and oppositions, or to test your hypotheses about them). The semantic map can be represented as a graph using Vec2graph - a Python library for visualizing word embeddings (term embeddings in our case) as dynamic and interactive graphs. The Vec2graph library coupled with term embeddings will not only improve accuracy in solving standard NLP tasks, but also update the conventional concept of automated ontology development. The main practical result of our work is the development kit (set of toolkits represented as web service APIs and web application), which provides all necessary routines for the basic linguistic pre-processing and the semantic pre-processing of the natural language texts in Ukrainian for future training of term vector space models.

Humans have a natural ability to perform semantic associations with the surrounding objects in the environment. This allows them to create a mental map of the environment, allowing them to navigate on-demand when given linguistic instructions. A natural goal in Vision Language Navigation (VLN) research is to impart autonomous agents with similar capabilities. Recent works take a step towards this goal by creating a semantic spatial map representation of the environment without any labeled data. However, their representations are limited for practical applicability as they do not distinguish between different instances of the same object. In this work, we address this limitation by integrating instance-level information into spatial map representation using a community detection algorithm and utilizing word ontology learned by large language models (LLMs) to perform open-set semantic associations in the mapping representation. The resulting map representation improves the navigation performance by two-fold (233%) on realistic language commands with instance-specific descriptions compared to the baseline. We validate the practicality and effectiveness of our approach through extensive qualitative and quantitative experiments.

We present KNOW--the Knowledge Navigator Ontology for the World--the first ontology designed to capture everyday knowledge to augment large language models (LLMs) in real-world generative AI use cases such as personal AI assistants. Our domain is human life, both its everyday concerns and its major milestones. We have limited the initial scope of the modeled concepts to only established human universals: spacetime (places, events) plus social (people, groups, organizations). The inclusion criteria for modeled concepts are pragmatic, beginning with universality and utility. We compare and contrast previous work such as Schema.org and Cyc--as well as attempts at a synthesis of knowledge graphs and language models--noting how LLMs already encode internally much of the commonsense tacit knowledge that took decades to capture in the Cyc project. We also make available code-generated software libraries for the 12 most popular programming languages, enabling the direct use of ontology concepts in software engineering. We emphasize simplicity and developer experience in promoting AI interoperability.

We introduce semantic towers, an extrinsic knowledge representation method, and compare it to intrinsic knowledge in large language models for ontology learning. Our experiments show a trade-off between performance and semantic grounding for extrinsic knowledge compared to a fine-tuned model intrinsic knowledge. We report our findings on the Large Language Models for Ontology Learning (LLMs4OL) 2024 challenge.

Maps are fundamental medium to visualize and represent the real word in a simple and 16 philosophical way. The emergence of the 3rd wave information has made a proportion of maps are available to be generated ubiquitously, which would significantly enrich the dimensions and perspectives to understand the characteristics of the real world. However, a majority of map dataset have never been discovered, acquired and effectively used, and the map data used in many applications might not be completely fitted for the authentic demands of these applications. This challenge is emerged due to the lack of numerous well-labelled benchmark datasets for implementing the deep learning approaches into identifying complicated map content. Thus, we develop a large-scale benchmark dataset that includes well-labelled dataset for map text annotation recognition, map scene classification, map super-resolution reconstruction, and map style transferring. Furthermore, these well-labelled datasets would facilitate the state-of-the-art machine intelligence technologies to conduct map feature detection, map pattern recognition and map content retrieval. We hope our efforts would be useful for AI-enhanced cartographical applications.

Since long, corporations are looking for knowledge sources which can provide structured description of data and can focus on meaning and shared understanding. Structures which can facilitate open world assumptions and can be flexible enough to incorporate and recognize more than one name for an entity. A source whose major purpose is to facilitate human communication and interoperability. Clearly, databases fail to provide these features and ontologies have emerged as an alternative choice, but corporations working on same domain tend to make different ontologies. The problem occurs when they want to share their data/knowledge. Thus we need tools to merge ontologies into one. This task is termed as ontology matching. This is an emerging area and still we have to go a long way in having an ideal matcher which can produce good results. In this paper we have shown a framework to matching ontologies using graphs.

In this paper we introduce the olog, or ontology log, a category-theoretic model for knowledge representation (KR). Grounded in formal mathematics, ologs can be rigorously formulated and cross-compared in ways that other KR models (such as semantic networks) cannot. An olog is similar to a relational database schema; in fact an olog can serve as a data repository if desired. Unlike database schemas, which are generally difficult to create or modify, ologs are designed to be user-friendly enough that authoring or reconfiguring an olog is a matter of course rather than a difficult chore. It is hoped that learning to author ologs is much simpler than learning a database definition language, despite their similarity. We describe ologs carefully and illustrate with many examples. As an application we show that any primitive recursive function can be described by an olog. We also show that ologs can be aligned or connected together into a larger network using functors. The various methods of information flow and institutions can then be used to integrate local and global world-views. We finish by providing several different avenues for future research.

The core obstacle towards a large-scale deployment of autonomous vehicles currently lies in the long tail of rare events. These are extremely challenging since they do not occur often in the utilized training data for deep neural networks. To tackle this problem, we propose the generation of additional synthetic training data, covering a wide variety of corner case scenarios. As ontologies can represent human expert knowledge while enabling computational processing, we use them to describe scenarios. Our proposed master ontology is capable to model scenarios from all common corner case categories found in the literature. From this one master ontology, arbitrary scenario-describing ontologies can be derived. In an automated fashion, these can be converted into the OpenSCENARIO format and subsequently executed in simulation. This way, also challenging test and evaluation scenarios can be generated.

The exponential growth of scientific literature requires effective management and extraction of valuable insights. While existing scientific search engines excel at delivering search results based on relational databases, they often neglect the analysis of collaborations between scientific entities and the evolution of ideas, as well as the in-depth analysis of content within scientific publications. The representation of heterogeneous graphs and the effective measurement, analysis, and mining of such graphs pose significant challenges. To address these challenges, we present AceMap, an academic system designed for knowledge discovery through academic graph. We present advanced database construction techniques to build the comprehensive AceMap database with large-scale academic entities that contain rich visual, textual, and numerical information. AceMap also employs innovative visualization, quantification, and analysis methods to explore associations and logical relationships among academic entities. AceMap introduces large-scale academic network visualization techniques centered on nebular graphs, providing a comprehensive view of academic networks from multiple perspectives. In addition, AceMap proposes a unified metric based on structural entropy to quantitatively measure the knowledge content of different academic entities. Moreover, AceMap provides advanced analysis capabilities, including tracing the evolution of academic ideas through citation relationships and concept co-occurrence, and generating concise summaries informed by this evolutionary process. In addition, AceMap uses machine reading methods to generate potential new ideas at the intersection of different fields. Exploring the integration of large language models and knowledge graphs is a promising direction for future research in idea evolution. Please visit https://www.acemap.info for further exploration.

This paper presents OG-RAG, an Ontology-Grounded Retrieval Augmented Generation method designed to enhance LLM-generated responses by anchoring retrieval processes in domain-specific ontologies. While LLMs are widely used for tasks like question answering and search, they struggle to adapt to specialized knowledge, such as industrial workflows or knowledge work, without expensive fine-tuning or sub-optimal retrieval methods. Existing retrieval-augmented models, such as RAG, offer improvements but fail to account for structured domain knowledge, leading to suboptimal context generation. Ontologies, which conceptually organize domain knowledge by defining entities and their interrelationships, offer a structured representation to address this gap. OG-RAG constructs a hypergraph representation of domain documents, where each hyperedge encapsulates clusters of factual knowledge grounded using domain-specific ontology. An optimization algorithm then retrieves the minimal set of hyperedges that constructs a precise, conceptually grounded context for the LLM. This method enables efficient retrieval while preserving the complex relationships between entities. OG-RAG applies to domains where fact-based reasoning is essential, particularly in tasks that require workflows or decision-making steps to follow predefined rules and procedures. These include industrial workflows in healthcare, legal, and agricultural sectors, as well as knowledge-driven tasks such as news journalism, investigative research, consulting and more. Our evaluations demonstrate that OG-RAG increases the recall of accurate facts by 55% and improves response correctness by 40% across four different LLMs. Additionally, OG-RAG enables 30% faster attribution of responses to context and boosts fact-based reasoning accuracy by 27% compared to baseline methods.

Scientific knowledge is growing rapidly, making it challenging to track progress and high-level conceptual links across broad disciplines. While existing tools like citation networks and search engines make it easy to access a few related papers, they fundamentally lack the flexible abstraction needed to represent the density of activity in various scientific subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that allows for the categorization of scientific work across varying levels of abstraction, from very broad fields to very specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve the goals of SCIENCE HIERARCHOGRAPHY, we develop a range of algorithms. Our primary approach combines fast embedding-based clustering with LLM-based prompting to balance the computational efficiency of embedding methods with the semantic precision offered by LLM prompting. We demonstrate that this approach offers the best trade-off between quality and speed compared to methods that heavily rely on LLM prompting, such as iterative tree construction with LLMs. To better reflect the interdisciplinary and multifaceted nature of research papers, our hierarchy captures multiple dimensions of categorization beyond simple topic labels. We evaluate the utility of our framework by assessing how effectively an LLM-based agent can locate target papers using the hierarchy. Results show that this structured approach enhances interpretability, supports trend discovery, and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo: https://github.com/JHU-CLSP/science-hierarchography{https://github.com/JHU-CLSP/science-hierarchography}

Investigating whether pre-trained language models (LMs) can function as knowledge bases (KBs) has raised wide research interests recently. However, existing works focus on simple, triple-based, relational KBs, but omit more sophisticated, logic-based, conceptualised KBs such as OWL ontologies. To investigate an LM's knowledge of ontologies, we propose OntoLAMA, a set of inference-based probing tasks and datasets from ontology subsumption axioms involving both atomic and complex concepts. We conduct extensive experiments on ontologies of different domains and scales, and our results demonstrate that LMs encode relatively less background knowledge of Subsumption Inference (SI) than traditional Natural Language Inference (NLI) but can improve on SI significantly when a small number of samples are given. We will open-source our code and datasets.

With the web getting bigger and assimilating knowledge about different concepts and domains, it is becoming very difficult for simple database driven applications to capture the data for a domain. Thus developers have come out with ontology based systems which can store large amount of information and can apply reasoning and produce timely information. Thus facilitating effective knowledge management. Though this approach has made our lives easier, but at the same time has given rise to another problem. Two different ontologies assimilating same knowledge tend to use different terms for the same concepts. This creates confusion among knowledge engineers and workers, as they do not know which is a better term then the other. Thus we need to merge ontologies working on same domain so that the engineers can develop a better application over it. This paper shows the development of one such matcher which merges the concepts available in two ontologies at two levels; 1) at string level and 2) at semantic level; thus producing better merged ontologies. We have used a graph matching technique which works at the core of the system. We have also evaluated the system and have tested its performance with its predecessor which works only on string matching. Thus current approach produces better results.

Emotions have played an important part in many sectors, including psychology, medicine, mental health, computer science, and so on, and categorizing them has proven extremely useful in separating one emotion from another. Emotions can be classified using the following two methods: (1) The supervised method's efficiency is strongly dependent on the size and domain of the data collected. A categorization established using relevant data from one domain may not work well in another. (2) An unsupervised method that uses either domain expertise or a knowledge base of emotion types already exists. Though this second approach provides a suitable and generic categorization of emotions and is cost-effective, the literature doesn't possess a publicly available knowledge base that can be directly applied to any emotion categorization-related task. This pushes us to create a knowledge base that can be used for emotion classification across domains, and ontology is often used for this purpose. In this study, we provide TONE, an emotion-based ontology that effectively creates an emotional hierarchy based on Dr. Gerrod Parrot's group of emotions. In addition to ontology development, we introduce a semi-automated vocabulary construction process to generate a detailed collection of terms for emotions at each tier of the hierarchy. We also demonstrate automated methods for establishing three sorts of dependencies in order to develop linkages between different emotions. Our human and automatic evaluation results show the ontology's quality. Furthermore, we describe three distinct use cases that demonstrate the applicability of our ontology.

Historical maps contain detailed geographic information difficult to find elsewhere covering long-periods of time (e.g., 125 years for the historical topographic maps in the US). However, these maps typically exist as scanned images without searchable metadata. Existing approaches making historical maps searchable rely on tedious manual work (including crowd-sourcing) to generate the metadata (e.g., geolocations and keywords). Optical character recognition (OCR) software could alleviate the required manual work, but the recognition results are individual words instead of location phrases (e.g., "Black" and "Mountain" vs. "Black Mountain"). This paper presents an end-to-end approach to address the real-world problem of finding and indexing historical map images. This approach automatically processes historical map images to extract their text content and generates a set of metadata that is linked to large external geospatial knowledge bases. The linked metadata in the RDF (Resource Description Framework) format support complex queries for finding and indexing historical maps, such as retrieving all historical maps covering mountain peaks higher than 1,000 meters in California. We have implemented the approach in a system called mapKurator. We have evaluated mapKurator using historical maps from several sources with various map styles, scales, and coverage. Our results show significant improvement over the state-of-the-art methods. The code has been made publicly available as modules of the Kartta Labs project at https://github.com/kartta-labs/Project.

In applications such as personal assistants, large language models (LLMs) must consider the user's personal information and preferences. However, LLMs lack the inherent ability to learn from user interactions. This paper explores capturing personal information from user prompts using ontology and knowledge-graph approaches. We use a subset of the KNOW ontology, which models personal information, to train the language model on these concepts. We then evaluate the success of knowledge capture using a specially constructed dataset. Our code and datasets are publicly available at https://github.com/HaltiaAI/paper-PTODSKC

The recent advances in large language models (LLM) and foundation models with emergent capabilities have been shown to improve the performance of many NLP tasks. LLMs and Knowledge Graphs (KG) can complement each other such that LLMs can be used for KG construction or completion while existing KGs can be used for different tasks such as making LLM outputs explainable or fact-checking in Neuro-Symbolic manner. In this paper, we present Text2KGBench, a benchmark to evaluate the capabilities of language models to generate KGs from natural language text guided by an ontology. Given an input ontology and a set of sentences, the task is to extract facts from the text while complying with the given ontology (concepts, relations, domain/range constraints) and being faithful to the input sentences. We provide two datasets (i) Wikidata-TekGen with 10 ontologies and 13,474 sentences and (ii) DBpedia-WebNLG with 19 ontologies and 4,860 sentences. We define seven evaluation metrics to measure fact extraction performance, ontology conformance, and hallucinations by LLMs. Furthermore, we provide results for two baseline models, Vicuna-13B and Alpaca-LoRA-13B using automatic prompt generation from test cases. The baseline results show that there is room for improvement using both Semantic Web and Natural Language Processing techniques.

LLMs usually exhibit limitations in their ability to incorporate new knowledge, the generation of hallucinations, and the transparency of their decision-making process. In this paper, we explore how to prompt LLMs with knowledge graphs (KG), working as a remedy to engage LLMs with up-to-date knowledge and elicit the reasoning pathways from LLMs. Specifically, we build a prompting pipeline that endows LLMs with the capability of comprehending KG inputs and inferring with a combined implicit knowledge and the retrieved external knowledge. In addition, we investigate eliciting the mind map on which LLMs perform the reasoning and generate the answers. It is identified that the produced mind map exhibits the reasoning pathways of LLMs grounded on the ontology of knowledge, hence bringing the prospects of probing and gauging LLM inference in production. The experiments on three question & answering datasets also show that MindMap prompting leads to a striking empirical gain. For instance, prompting a GPT-3.5 with MindMap yields an overwhelming performance over GPT-4 consistently. We also demonstrate that with structured facts retrieved from KG, MindMap can outperform a series of prompting-with-document-retrieval methods, benefiting from more accurate, concise, and comprehensive knowledge from KGs. To reproduce our results and extend the framework further, we make our codebase available at https://github.com/wyl.willing/MindMap.

Document clustering is a text mining technique used to provide better document search and browsing in digital libraries or online corpora. A lot of research has been done on biomedical document clustering that is based on using existing ontology. But, associations and co-occurrences of the medical concepts are not well represented by using ontology. In this research, a vector representation of concepts of diseases and similarity measurement between concepts are proposed. They identify the closest concepts of diseases in the context of a corpus. Each document is represented by using the vector space model. A weight scheme is proposed to consider both local content and associations between concepts. A Self-Organizing Map is used as document clustering algorithm. The vector projection and visualization features of SOM enable visualization and analysis of the clusters distributions and relationships on the two dimensional space. The experimental results show that the proposed document clustering framework generates meaningful clusters and facilitate visualization of the clusters based on the concepts of diseases.

Creating knowledge bases and ontologies is a time consuming task that relies on a manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrary complex nested knowledge schemas. Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning (ZSL) and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against GPT-3+ to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for all matched elements. We present examples of use of SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease causation graphs. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction (RE) methods, but has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. SPIRES is available as part of the open source OntoGPT package: https://github.com/ monarch-initiative/ontogpt.

The ability to summarize and organize knowledge into abstract concepts is key to learning and reasoning. Many industrial applications rely on the consistent and systematic use of concepts, especially when dealing with decision-critical knowledge. However, we demonstrate that, when methodically questioned, large language models (LLMs) often display and demonstrate significant inconsistencies in their knowledge. Computationally, the basic aspects of the conceptualization of a given domain can be represented as Is-A hierarchies in a knowledge graph (KG) or ontology, together with a few properties or axioms that enable straightforward reasoning. We show that even simple ontologies can be used to reveal conceptual inconsistencies across several LLMs. We also propose strategies that domain experts can use to evaluate and improve the coverage of key domain concepts in LLMs of various sizes. In particular, we have been able to significantly enhance the performance of LLMs of various sizes with openly available weights using simple knowledge-graph (KG) based prompting strategies.

We study the task of semantic mapping - specifically, an embodied agent (a robot or an egocentric AI assistant) is given a tour of a new environment and asked to build an allocentric top-down semantic map ("what is where?") from egocentric observations of an RGB-D camera with known pose (via localization sensors). Towards this goal, we present SemanticMapNet (SMNet), which consists of: (1) an Egocentric Visual Encoder that encodes each egocentric RGB-D frame, (2) a Feature Projector that projects egocentric features to appropriate locations on a floor-plan, (3) a Spatial Memory Tensor of size floor-plan length x width x feature-dims that learns to accumulate projected egocentric features, and (4) a Map Decoder that uses the memory tensor to produce semantic top-down maps. SMNet combines the strengths of (known) projective camera geometry and neural representation learning. On the task of semantic mapping in the Matterport3D dataset, SMNet significantly outperforms competitive baselines by 4.01-16.81% (absolute) on mean-IoU and 3.81-19.69% (absolute) on Boundary-F1 metrics. Moreover, we show how to use the neural episodic memories and spatio-semantic allocentric representations build by SMNet for subsequent tasks in the same space - navigating to objects seen during the tour("Find chair") or answering questions about the space ("How many chairs did you see in the house?"). Project page: https://vincentcartillier.github.io/smnet.html.

A variety of knowledge graph embedding approaches have been developed. Most of them obtain embeddings by learning the structure of the knowledge graph within a link prediction setting. As a result, the embeddings reflect only the semantics of a single knowledge graph, and embeddings for different knowledge graphs are not aligned, e.g., they cannot be used to find similar entities across knowledge graphs via nearest neighbor search. However, knowledge graph embedding applications such as entity disambiguation require a more global representation, i.e., a representation that is valid across multiple sources. We propose to learn universal knowledge graph embeddings from large-scale interlinked knowledge sources. To this end, we fuse large knowledge graphs based on the owl:sameAs relation such that every entity is represented by a unique identity. We instantiate our idea by computing universal embeddings based on DBpedia and Wikidata yielding embeddings for about 180 million entities, 15 thousand relations, and 1.2 billion triples. Moreover, we develop a convenient API to provide embeddings as a service. Experiments on link prediction show that universal knowledge graph embeddings encode better semantics compared to embeddings computed on a single knowledge graph. For reproducibility purposes, we provide our source code and datasets open access at https://github.com/dice-group/Universal_Embeddings

Ontology Alignment (OA) is fundamental for achieving semantic interoperability across diverse knowledge systems. We present OntoAligner, a comprehensive, modular, and robust Python toolkit for ontology alignment, designed to address current limitations with existing tools faced by practitioners. Existing tools are limited in scalability, modularity, and ease of integration with recent AI advances. OntoAligner provides a flexible architecture integrating existing lightweight OA techniques such as fuzzy matching but goes beyond by supporting contemporary methods with retrieval-augmented generation and large language models for OA. The framework prioritizes extensibility, enabling researchers to integrate custom alignment algorithms and datasets. This paper details the design principles, architecture, and implementation of the OntoAligner, demonstrating its utility through benchmarks on standard OA tasks. Our evaluation highlights OntoAligner's ability to handle large-scale ontologies efficiently with few lines of code while delivering high alignment quality. By making OntoAligner open-source, we aim to provide a resource that fosters innovation and collaboration within the OA community, empowering researchers and practitioners with a toolkit for reproducible OA research and real-world applications.

Ontology engineering (OE) in large projects poses a number of challenges arising from the heterogeneous backgrounds of the various stakeholders, domain experts, and their complex interactions with ontology designers. This multi-party interaction often creates systematic ambiguities and biases from the elicitation of ontology requirements, which directly affect the design, evaluation and may jeopardise the target reuse. Meanwhile, current OE methodologies strongly rely on manual activities (e.g., interviews, discussion pages). After collecting evidence on the most crucial OE activities, we introduce OntoChat, a framework for conversational ontology engineering that supports requirement elicitation, analysis, and testing. By interacting with a conversational agent, users can steer the creation of user stories and the extraction of competency questions, while receiving computational support to analyse the overall requirements and test early versions of the resulting ontologies. We evaluate OntoChat by replicating the engineering of the Music Meta Ontology, and collecting preliminary metrics on the effectiveness of each component from users. We release all code at https://github.com/King-s-Knowledge-Graph-Lab/OntoChat.

In many scientific fields, large language models (LLMs) have revolutionized the way text and other modalities of data (e.g., molecules and proteins) are handled, achieving superior performance in various applications and augmenting the scientific discovery process. Nevertheless, previous surveys on scientific LLMs often concentrate on one or two fields or a single modality. In this paper, we aim to provide a more holistic view of the research landscape by unveiling cross-field and cross-modal connections between scientific LLMs regarding their architectures and pre-training techniques. To this end, we comprehensively survey over 260 scientific LLMs, discuss their commonalities and differences, as well as summarize pre-training datasets and evaluation tasks for each field and modality. Moreover, we investigate how LLMs have been deployed to benefit scientific discovery. Resources related to this survey are available at https://github.com/yuzhimanhua/Awesome-Scientific-Language-Models.

Recently, Large Language Models (LLMs) have demonstrated great potential in robotic applications by providing essential general knowledge for situations that can not be pre-programmed beforehand. Generally speaking, mobile robots need to understand maps to execute tasks such as localization or navigation. In this letter, we address the problem of enabling LLMs to comprehend Area Graph, a text-based map representation, in order to enhance their applicability in the field of mobile robotics. Area Graph is a hierarchical, topometric semantic map representation utilizing polygons to demark areas such as rooms, corridors or buildings. In contrast to commonly used map representations, such as occupancy grid maps or point clouds, osmAG (Area Graph in OpensStreetMap format) is stored in a XML textual format naturally readable by LLMs. Furthermore, conventional robotic algorithms such as localization and path planning are compatible with osmAG, facilitating this map representation comprehensible by LLMs, traditional robotic algorithms and humans. Our experiments show that with a proper map representation, LLMs possess the capability to understand maps and answer queries based on that understanding. Following simple fine-tuning of LLaMA2 models, it surpassed ChatGPT-3.5 in tasks involving topology and hierarchy understanding. Our dataset, dataset generation code, fine-tuned LoRA adapters can be accessed at https://github.com/xiefujing/LLM-osmAG-Comprehension.

Large language models (LLMs) have unlocked new capabilities of task planning from human instructions. However, prior attempts to apply LLMs to real-world robotic tasks are limited by the lack of grounding in the surrounding scene. In this paper, we develop NLMap, an open-vocabulary and queryable scene representation to address this problem. NLMap serves as a framework to gather and integrate contextual information into LLM planners, allowing them to see and query available objects in the scene before generating a context-conditioned plan. NLMap first establishes a natural language queryable scene representation with Visual Language models (VLMs). An LLM based object proposal module parses instructions and proposes involved objects to query the scene representation for object availability and location. An LLM planner then plans with such information about the scene. NLMap allows robots to operate without a fixed list of objects nor executable options, enabling real robot operation unachievable by previous methods. Project website: https://nlmap-saycan.github.io

Recent work within the Argument Mining community has shown the applicability of Natural Language Processing systems for solving problems found within competitive debate. One of the most important tasks within competitive debate is for debaters to create high quality debate cases. We show that effective debate cases can be constructed using constrained shortest path traversals on Argumentative Semantic Knowledge Graphs. We study this potential in the context of a type of American Competitive Debate, called Policy Debate, which already has a large scale dataset targeting it called DebateSum. We significantly improve upon DebateSum by introducing 53180 new examples, as well as further useful metadata for every example, to the dataset. We leverage the txtai semantic search and knowledge graph toolchain to produce and contribute 9 semantic knowledge graphs built on this dataset. We create a unique method for evaluating which knowledge graphs are better in the context of producing policy debate cases. A demo which automatically generates debate cases, along with all other code and the Knowledge Graphs, are open-sourced and made available to the public here: https://github.com/Hellisotherpeople/DebateKG

We present NLU++, a novel dataset for natural language understanding (NLU) in task-oriented dialogue (ToD) systems, with the aim to provide a much more challenging evaluation environment for dialogue NLU models, up to date with the current application and industry requirements. NLU++ is divided into two domains (BANKING and HOTELS) and brings several crucial improvements over current commonly used NLU datasets. 1) NLU++ provides fine-grained domain ontologies with a large set of challenging multi-intent sentences, introducing and validating the idea of intent modules that can be combined into complex intents that convey complex user goals, combined with finer-grained and thus more challenging slot sets. 2) The ontology is divided into domain-specific and generic (i.e., domain-universal) intent modules that overlap across domains, promoting cross-domain reusability of annotated examples. 3) The dataset design has been inspired by the problems observed in industrial ToD systems, and 4) it has been collected, filtered and carefully annotated by dialogue NLU experts, yielding high-quality annotated data. Finally, we benchmark a series of current state-of-the-art NLU models on NLU++; the results demonstrate the challenging nature of the dataset, especially in low-data regimes, the validity of `intent modularisation', and call for further research on ToD NLU.

This work introduces BioLORD, a new pre-training strategy for producing meaningful representations for clinical sentences and biomedical concepts. State-of-the-art methodologies operate by maximizing the similarity in representation of names referring to the same concept, and preventing collapse through contrastive learning. However, because biomedical names are not always self-explanatory, it sometimes results in non-semantic representations. BioLORD overcomes this issue by grounding its concept representations using definitions, as well as short descriptions derived from a multi-relational knowledge graph consisting of biomedical ontologies. Thanks to this grounding, our model produces more semantic concept representations that match more closely the hierarchical structure of ontologies. BioLORD establishes a new state of the art for text similarity on both clinical sentences (MedSTS) and biomedical concepts (MayoSRS).

In this work, we focus on the problem of retrieving relevant arguments for a query claim covering diverse aspects. State-of-the-art methods rely on explicit mappings between claims and premises, and thus are unable to utilize large available collections of premises without laborious and costly manual annotation. Their diversity approach relies on removing duplicates via clustering which does not directly ensure that the selected premises cover all aspects. This work introduces a new multi-step approach for the argument retrieval problem. Rather than relying on ground-truth assignments, our approach employs a machine learning model to capture semantic relationships between arguments. Beyond that, it aims to cover diverse facets of the query, instead of trying to identify duplicates explicitly. Our empirical evaluation demonstrates that our approach leads to a significant improvement in the argument retrieval task even though it requires less data.

Of primary importance in formulating a response to the increasing prevalence and power of artificial intelligence (AI) applications in society are questions of ontology. Questions such as: What "are" these systems? How are they to be regarded? How does an algorithm come to be regarded as an agent? We discuss three factors which hinder discussion and obscure attempts to form a clear ontology of AI: (1) the various and evolving definitions of AI, (2) the tendency for pre-existing technologies to be assimilated and regarded as "normal," and (3) the tendency of human beings to anthropomorphize. This list is not intended as exhaustive, nor is it seen to preclude entirely a clear ontology, however, these challenges are a necessary set of topics for consideration. Each of these factors is seen to present a 'moving target' for discussion, which poses a challenge for both technical specialists and non-practitioners of AI systems development (e.g., philosophers and theologians) to speak meaningfully given that the corpus of AI structures and capabilities evolves at a rapid pace. Finally, we present avenues for moving forward, including opportunities for collaborative synthesis for scholars in philosophy and science.

The volume of scientific output is creating an urgent need for automated tools to help scientists keep up with developments in their field. Semantic Scholar (S2) is an open data platform and website aimed at accelerating science by helping scholars discover and understand scientific literature. We combine public and proprietary data sources using state-of-the-art techniques for scholarly PDF content extraction and automatic knowledge graph construction to build the Semantic Scholar Academic Graph, the largest open scientific literature graph to-date, with 200M+ papers, 80M+ authors, 550M+ paper-authorship edges, and 2.4B+ citation edges. The graph includes advanced semantic features such as structurally parsed text, natural language summaries, and vector embeddings. In this paper, we describe the components of the S2 data processing pipeline and the associated APIs offered by the platform. We will update this living document to reflect changes as we add new data offerings and improve existing services.

Large Language Models (LLMs) have generated considerable interest and debate regarding their potential emergence of Theory of Mind (ToM). Several recent inquiries reveal a lack of robust ToM in these models and pose a pressing demand to develop new benchmarks, as current ones primarily focus on different aspects of ToM and are prone to shortcuts and data leakage. In this position paper, we seek to answer two road-blocking questions: (1) How can we taxonomize a holistic landscape of machine ToM? (2) What is a more effective evaluation protocol for machine ToM? Following psychological studies, we taxonomize machine ToM into 7 mental state categories and delineate existing benchmarks to identify under-explored aspects of ToM. We argue for a holistic and situated evaluation of ToM to break ToM into individual components and treat LLMs as an agent who is physically situated in environments and socially situated in interactions with humans. Such situated evaluation provides a more comprehensive assessment of mental states and potentially mitigates the risk of shortcuts and data leakage. We further present a pilot study in a grid world setup as a proof of concept. We hope this position paper can facilitate future research to integrate ToM with LLMs and offer an intuitive means for researchers to better position their work in the landscape of ToM. Project page: https://github.com/Mars-tin/awesome-theory-of-mind

Complex hierarchical structures composed of simple nanoscale building blocks form the basis of most biological materials. Here we demonstrate how analogies between seemingly different fields enable the understanding of general principles by which functional properties in hierarchical systems emerge, similar to an analogy learning process. Specifically, natural hierarchical materials like spider silk exhibit properties comparable to classical music in terms of their hierarchical structure and function. As a comparative tool here we apply hierarchical ontology logs (olog) that follow a rigorous mathematical formulation based on category theory to provide an insightful system representation by expressing knowledge in a conceptual map. We explain the process of analogy creation, draw connections at several levels of hierarchy and identify similar patterns that govern the structure of the hierarchical systems silk and music and discuss the impact of the derived analogy for nanotechnology.

In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.

As robots become increasingly capable, users will want to describe high-level missions and have robots infer the relevant details. because pre-built maps are difficult to obtain in many realistic settings, accomplishing such missions will require the robot to map and plan online. while many semantic planning methods operate online, they are typically designed for well specified missions such as object search or exploration. recently, large language models (LLMs) have demonstrated powerful contextual reasoning abilities over a range of robotic tasks described in natural language. however, existing LLM-enabled planners typically do not consider online planning or complex missions; rather, relevant subtasks and semantics are provided by a pre-built map or a user. we address these limitations via spine, an online planner for missions with incomplete mission specifications provided in natural language. the planner uses an LLM to reason about subtasks implied by the mission specification and then realizes these subtasks in a receding horizon framework. tasks are automatically validated for safety and refined online with new map observations. we evaluate spine in simulation and real-world settings with missions that require multiple steps of semantic reasoning and exploration in cluttered outdoor environments of over 20,000m^2. compared to baselines that use existing LLM-enabled planning approaches, our method is over twice as efficient in terms of time and distance, requires less user interactions, and does not require a full map. Additional resources are provided at: https://zacravichandran.github.io/SPINE.

Knowledge Graph (KG) and its variant of ontology have been widely used for knowledge representation, and have shown to be quite effective in augmenting Zero-shot Learning (ZSL). However, existing ZSL methods that utilize KGs all neglect the intrinsic complexity of inter-class relationships represented in KGs. One typical feature is that a class is often related to other classes in different semantic aspects. In this paper, we focus on ontologies for augmenting ZSL, and propose to learn disentangled ontology embeddings guided by ontology properties to capture and utilize more fine-grained class relationships in different aspects. We also contribute a new ZSL framework named DOZSL, which contains two new ZSL solutions based on generative models and graph propagation models, respectively, for effectively utilizing the disentangled ontology embeddings. Extensive evaluations have been conducted on five benchmarks across zero-shot image classification (ZS-IMGC) and zero-shot KG completion (ZS-KGC). DOZSL often achieves better performance than the state-of-the-art, and its components have been verified by ablation studies and case studies. Our codes and datasets are available at https://github.com/zjukg/DOZSL.

Electronic maps consist of diverse entities, such as points of interest (POIs), road networks, and land parcels, playing a vital role in applications like ITS and LBS. Map entity representation learning (MapRL) generates versatile and reusable data representations, providing essential tools for efficiently managing and utilizing map entity data. Despite the progress in MapRL, two key challenges constrain further development. First, existing research is fragmented, with models classified by the type of map entity, limiting the reusability of techniques across different tasks. Second, the lack of unified benchmarks makes systematic evaluation and comparison of models difficult. To address these challenges, we propose a novel taxonomy for MapRL that organizes models based on functional module-such as encoders, pre-training tasks, and downstream tasks-rather than by entity type. Building on this taxonomy, we present a taxonomy-driven library, VecCity, which offers easy-to-use interfaces for encoding, pre-training, fine-tuning, and evaluation. The library integrates datasets from nine cities and reproduces 21 mainstream MapRL models, establishing the first standardized benchmarks for the field. VecCity also allows users to modify and extend models through modular components, facilitating seamless experimentation. Our comprehensive experiments cover multiple types of map entities and evaluate 21 VecCity pre-built models across various downstream tasks. Experimental results demonstrate the effectiveness of VecCity in streamlining model development and provide insights into the impact of various components on performance. By promoting modular design and reusability, VecCity offers a unified framework to advance research and innovation in MapRL. The code is available at https://github.com/Bigscity-VecCity/VecCity.

This paper presents the formal release of MedMentions, a new manually annotated resource for the recognition of biomedical concepts. What distinguishes MedMentions from other annotated biomedical corpora is its size (over 4,000 abstracts and over 350,000 linked mentions), as well as the size of the concept ontology (over 3 million concepts from UMLS 2017) and its broad coverage of biomedical disciplines. In addition to the full corpus, a sub-corpus of MedMentions is also presented, comprising annotations for a subset of UMLS 2017 targeted towards document retrieval. To encourage research in Biomedical Named Entity Recognition and Linking, data splits for training and testing are included in the release, and a baseline model and its metrics for entity linking are also described.

This paper describes the KnowledgeHub tool, a scientific literature Information Extraction (IE) and Question Answering (QA) pipeline. This is achieved by supporting the ingestion of PDF documents that are converted to text and structured representations. An ontology can then be constructed where a user defines the types of entities and relationships they want to capture. A browser-based annotation tool enables annotating the contents of the PDF documents according to the ontology. Named Entity Recognition (NER) and Relation Classification (RC) models can be trained on the resulting annotations and can be used to annotate the unannotated portion of the documents. A knowledge graph is constructed from these entity and relation triples which can be queried to obtain insights from the data. Furthermore, we integrate a suite of Large Language Models (LLMs) that can be used for QA and summarisation that is grounded in the included documents via a retrieval component. KnowledgeHub is a unique tool that supports annotation, IE and QA, which gives the user full insight into the knowledge discovery pipeline.

Failure mode and effects analysis (FMEA) is a critical tool for mitigating potential failures, particular during ramp-up phases of new products. However, its effectiveness is often limited by the missing reasoning capabilities of the FMEA tools, which are usually tabular structured. Meanwhile, large language models (LLMs) offer novel prospects for fine-tuning on custom datasets for reasoning within FMEA contexts. However, LLMs face challenges in tasks that require factual knowledge, a gap that retrieval-augmented generation (RAG) approaches aim to fill. RAG retrieves information from a non-parametric data store and uses a language model to generate responses. Building on this idea, we propose to advance the non-parametric data store with a knowledge graph (KG). By enhancing the RAG framework with a KG, our objective is to leverage analytical and semantic question-answering capabilities on FMEA data. This paper contributes by presenting a new ontology for FMEA observations, an algorithm for creating vector embeddings from the FMEA KG, and a KG enhanced RAG framework. Our approach is validated through a human study and we measure the performance of the context retrieval recall and precision.

Ontologies and knowledge graphs (KGs) are general-purpose computable representations of some domain, such as human anatomy, and are frequently a crucial part of modern information systems. Most of these structures change over time, incorporating new knowledge or information that was previously missing. Managing these changes is a challenge, both in terms of communicating changes to users, and providing mechanisms to make it easier for multiple stakeholders to contribute. To fill that need, we have created KGCL, the Knowledge Graph Change Language, a standard data model for describing changes to KGs and ontologies at a high level, and an accompanying human-readable controlled natural language. This language serves two purposes: a curator can use it to request desired changes, and it can also be used to describe changes that have already happened, corresponding to the concepts of "apply patch" and "diff" commonly used for managing changes in text documents and computer programs. Another key feature of KGCL is that descriptions are at a high enough level to be useful and understood by a variety of stakeholders--for example, ontology edits can be specified by commands like "add synonym 'arm' to 'forelimb'" or "move 'Parkinson disease' under 'neurodegenerative disease'". We have also built a suite of tools for managing ontology changes. These include an automated agent that integrates with and monitors GitHub ontology repositories and applies any requested changes, and a new component in the BioPortal ontology resource that allows users to make change requests directly from within the BioPortal user interface. Overall, the KGCL data model, its controlled natural language, and associated tooling allow for easier management and processing of changes associated with the development of ontologies and KGs.

A research division plays an important role of driving innovation in an organization. Drawing insights, following trends, keeping abreast of new research, and formulating strategies are increasingly becoming more challenging for both researchers and executives as the amount of information grows in both velocity and volume. In this paper we present a use case of how a corporate research community, IBM Research, utilizes Semantic Web technologies to induce a unified Knowledge Graph from both structured and textual data obtained by integrating various applications used by the community related to research projects, academic papers, datasets, achievements and recognition. In order to make the Knowledge Graph more accessible to application developers, we identified a set of common patterns for exploiting the induced knowledge and exposed them as APIs. Those patterns were born out of user research which identified the most valuable use cases or user pain points to be alleviated. We outline two distinct scenarios: recommendation and analytics for business use. We will discuss these scenarios in detail and provide an empirical evaluation on entity recommendation specifically. The methodology used and the lessons learned from this work can be applied to other organizations facing similar challenges.

In this paper, we propose OpenSatMap, a fine-grained, high-resolution satellite dataset for large-scale map construction. Map construction is one of the foundations of the transportation industry, such as navigation and autonomous driving. Extracting road structures from satellite images is an efficient way to construct large-scale maps. However, existing satellite datasets provide only coarse semantic-level labels with a relatively low resolution (up to level 19), impeding the advancement of this field. In contrast, the proposed OpenSatMap (1) has fine-grained instance-level annotations; (2) consists of high-resolution images (level 20); (3) is currently the largest one of its kind; (4) collects data with high diversity. Moreover, OpenSatMap covers and aligns with the popular nuScenes dataset and Argoverse 2 dataset to potentially advance autonomous driving technologies. By publishing and maintaining the dataset, we provide a high-quality benchmark for satellite-based map construction and downstream tasks like autonomous driving.

Task-oriented dialog (TOD) systems typically manage structured knowledge (e.g. ontologies and databases) to guide the goal-oriented conversations. However, they fall short of handling dialog turns grounded on unstructured knowledge (e.g. reviews and documents). In this paper, we formulate a task of modeling TOD grounded on both structured and unstructured knowledge. To address this task, we propose a TOD system with hybrid knowledge management, HyKnow. It extends the belief state to manage both structured and unstructured knowledge, and is the first end-to-end model that jointly optimizes dialog modeling grounded on these two kinds of knowledge. We conduct experiments on the modified version of MultiWOZ 2.1 dataset, where dialogs are grounded on hybrid knowledge. Experimental results show that HyKnow has strong end-to-end performance compared to existing TOD systems. It also outperforms the pipeline knowledge management schemes, with higher unstructured knowledge retrieval accuracy.

MultiWOZ is a well-known task-oriented dialogue dataset containing over 10,000 annotated dialogues spanning 8 domains. It is extensively used as a benchmark for dialogue state tracking. However, recent works have reported presence of substantial noise in the dialogue state annotations. MultiWOZ 2.1 identified and fixed many of these erroneous annotations and user utterances, resulting in an improved version of this dataset. This work introduces MultiWOZ 2.2, which is a yet another improved version of this dataset. Firstly, we identify and fix dialogue state annotation errors across 17.3% of the utterances on top of MultiWOZ 2.1. Secondly, we redefine the ontology by disallowing vocabularies of slots with a large number of possible values (e.g., restaurant name, time of booking). In addition, we introduce slot span annotations for these slots to standardize them across recent models, which previously used custom string matching heuristics to generate them. We also benchmark a few state of the art dialogue state tracking models on the corrected dataset to facilitate comparison for future work. In the end, we discuss best practices for dialogue data collection that can help avoid annotation errors.

LLMs are bound to transform healthcare with advanced decision support and flexible chat assistants. However, LLMs are prone to generate inaccurate medical content. To ground LLMs in high-quality medical knowledge, LLMs have been equipped with external knowledge via RAG, where unstructured medical knowledge is split into small text chunks that can be selectively retrieved and integrated into the LLMs context. Yet, existing RAG pipelines rely on raw, unstructured medical text, which can be noisy, uncurated and difficult for LLMs to effectively leverage. Systematic approaches to organize medical knowledge to best surface it to LLMs are generally lacking. To address these challenges, we introduce MIRIAD, a large-scale, curated corpus of 5,821,948 medical QA pairs, each rephrased from and grounded in a passage from peer-reviewed medical literature using a semi-automated pipeline combining LLM generation, filtering, grounding, and human annotation. Unlike prior medical corpora, which rely on unstructured text, MIRIAD encapsulates web-scale medical knowledge in an operationalized query-response format, which enables more targeted retrieval. Experiments on challenging medical QA benchmarks show that augmenting LLMs with MIRIAD improves accuracy up to 6.7% compared to unstructured RAG baselines with the same source corpus and with the same amount of retrieved text. Moreover, MIRIAD improved the ability of LLMs to detect medical hallucinations by 22.5 to 37% (increase in F1 score). We further introduce MIRIAD-Atlas, an interactive map of MIRIAD spanning 56 medical disciplines, enabling clinical users to visually explore, search, and refine medical knowledge. MIRIAD promises to unlock a wealth of down-stream applications, including medical information retrievers, enhanced RAG applications, and knowledge-grounded chat interfaces, which ultimately enables more reliable LLM applications in healthcare.

We present a new knowledge-base of hasPart relationships, extracted from a large corpus of generic statements. Complementary to other resources available, it is the first which is all three of: accurate (90% precision), salient (covers relationships a person may mention), and has high coverage of common terms (approximated as within a 10 year old's vocabulary), as well as having several times more hasPart entries than in the popular ontologies ConceptNet and WordNet. In addition, it contains information about quantifiers, argument modifiers, and links the entities to appropriate concepts in Wikipedia and WordNet. The knowledge base is available at https://allenai.org/data/haspartkb

Knowledge graph embedding (KGE) is an increasingly popular technique that aims to represent entities and relations of knowledge graphs into low-dimensional semantic spaces for a wide spectrum of applications such as link prediction, knowledge reasoning and knowledge completion. In this paper, we provide a systematic review of existing KGE techniques based on representation spaces. Particularly, we build a fine-grained classification to categorise the models based on three mathematical perspectives of the representation spaces: (1) Algebraic perspective, (2) Geometric perspective, and (3) Analytical perspective. We introduce the rigorous definitions of fundamental mathematical spaces before diving into KGE models and their mathematical properties. We further discuss different KGE methods over the three categories, as well as summarise how spatial advantages work over different embedding needs. By collating the experimental results from downstream tasks, we also explore the advantages of mathematical space in different scenarios and the reasons behind them. We further state some promising research directions from a representation space perspective, with which we hope to inspire researchers to design their KGE models as well as their related applications with more consideration of their mathematical space properties.

The exponential growth of scientific literature necessitates advanced tools for effective knowledge exploration. We present Knowledge Navigator, a system designed to enhance exploratory search abilities by organizing and structuring the retrieved documents from broad topical queries into a navigable, two-level hierarchy of named and descriptive scientific topics and subtopics. This structured organization provides an overall view of the research themes in a domain, while also enabling iterative search and deeper knowledge discovery within specific subtopics by allowing users to refine their focus and retrieve additional relevant documents. Knowledge Navigator combines LLM capabilities with cluster-based methods to enable an effective browsing method. We demonstrate our approach's effectiveness through automatic and manual evaluations on two novel benchmarks, CLUSTREC-COVID and SCITOC. Our code, prompts, and benchmarks are made publicly available.

Electronic health record (EHR) systems are used extensively throughout the healthcare domain. However, data interchangeability between EHR systems is limited due to the use of different coding standards across systems. Existing methods of mapping coding standards based on manual human experts mapping, dictionary mapping, symbolic NLP and classification are unscalable and cannot accommodate large scale EHR datasets. In this work, we present Text2Node, a cross-domain mapping system capable of mapping medical phrases to concepts in a large taxonomy (such as SNOMED CT). The system is designed to generalize from a limited set of training samples and map phrases to elements of the taxonomy that are not covered by training data. As a result, our system is scalable, robust to wording variants between coding systems and can output highly relevant concepts when no exact concept exists in the target taxonomy. Text2Node operates in three main stages: first, the lexicon is mapped to word embeddings; second, the taxonomy is vectorized using node embeddings; and finally, the mapping function is trained to connect the two embedding spaces. We compared multiple algorithms and architectures for each stage of the training, including GloVe and FastText word embeddings, CNN and Bi-LSTM mapping functions, and node2vec for node embeddings. We confirmed the robustness and generalisation properties of Text2Node by mapping ICD-9-CM Diagnosis phrases to SNOMED CT and by zero-shot training at comparable accuracy. This system is a novel methodological contribution to the task of normalizing and linking phrases to a taxonomy, advancing data interchangeability in healthcare. When applied, the system can use electronic health records to generate an embedding that incorporates taxonomical medical knowledge to improve clinical predictive models.

Large language models (LLMs), such as ChatGPT and GPT4, are making new waves in the field of natural language processing and artificial intelligence, due to their emergent ability and generalizability. However, LLMs are black-box models, which often fall short of capturing and accessing factual knowledge. In contrast, Knowledge Graphs (KGs), Wikipedia and Huapu for example, are structured knowledge models that explicitly store rich factual knowledge. KGs can enhance LLMs by providing external knowledge for inference and interpretability. Meanwhile, KGs are difficult to construct and evolving by nature, which challenges the existing methods in KGs to generate new facts and represent unseen knowledge. Therefore, it is complementary to unify LLMs and KGs together and simultaneously leverage their advantages. In this article, we present a forward-looking roadmap for the unification of LLMs and KGs. Our roadmap consists of three general frameworks, namely, 1) KG-enhanced LLMs, which incorporate KGs during the pre-training and inference phases of LLMs, or for the purpose of enhancing understanding of the knowledge learned by LLMs; 2) LLM-augmented KGs, that leverage LLMs for different KG tasks such as embedding, completion, construction, graph-to-text generation, and question answering; and 3) Synergized LLMs + KGs, in which LLMs and KGs play equal roles and work in a mutually beneficial way to enhance both LLMs and KGs for bidirectional reasoning driven by both data and knowledge. We review and summarize existing efforts within these three frameworks in our roadmap and pinpoint their future research directions.

We present a new dataset, Functional Map of the World (fMoW), which aims to inspire the development of machine learning models capable of predicting the functional purpose of buildings and land use from temporal sequences of satellite images and a rich set of metadata features. The metadata provided with each image enables reasoning about location, time, sun angles, physical sizes, and other features when making predictions about objects in the image. Our dataset consists of over 1 million images from over 200 countries. For each image, we provide at least one bounding box annotation containing one of 63 categories, including a "false detection" category. We present an analysis of the dataset along with baseline approaches that reason about metadata and temporal views. Our data, code, and pretrained models have been made publicly available.

There is increasing evidence that question-answering (QA) systems with Large Language Models (LLMs), which employ a knowledge graph/semantic representation of an enterprise SQL database (i.e. Text-to-SPARQL), achieve higher accuracy compared to systems that answer questions directly on SQL databases (i.e. Text-to-SQL). Our previous benchmark research showed that by using a knowledge graph, the accuracy improved from 16% to 54%. The question remains: how can we further improve the accuracy and reduce the error rate? Building on the observations of our previous research where the inaccurate LLM-generated SPARQL queries followed incorrect paths, we present an approach that consists of 1) Ontology-based Query Check (OBQC): detects errors by leveraging the ontology of the knowledge graph to check if the LLM-generated SPARQL query matches the semantic of ontology and 2) LLM Repair: use the error explanations with an LLM to repair the SPARQL query. Using the chat with the data benchmark, our primary finding is that our approach increases the overall accuracy to 72% including an additional 8% of "I don't know" unknown results. Thus, the overall error rate is 20%. These results provide further evidence that investing knowledge graphs, namely the ontology, provides higher accuracy for LLM powered question answering systems.

This paper introduces 26 guiding principles designed to streamline the process of querying and prompting large language models. Our goal is to simplify the underlying concepts of formulating questions for various scales of large language models, examining their abilities, and enhancing user comprehension on the behaviors of different scales of large language models when feeding into different prompts. Extensive experiments are conducted on LLaMA-1/2 (7B, 13B and 70B), GPT-3.5/4 to verify the effectiveness of the proposed principles on instructions and prompts design. We hope that this work can provide a better guide for researchers working on the prompting of large language models. Project page is available at https://github.com/VILA-Lab/ATLAS.

Retrieval from graph data is crucial for augmenting large language models (LLM) with both open-domain knowledge and private enterprise data, and it is also a key component in the recent GraphRAG system (edge et al., 2024). Despite decades of research on knowledge graphs and knowledge base question answering, leading LLM frameworks (e.g. Langchain and LlamaIndex) have only minimal support for retrieval from modern encyclopedic knowledge graphs like Wikidata. In this paper, we analyze the root cause and suggest that modern RDF knowledge graphs (e.g. Wikidata, Freebase) are less efficient for LLMs due to overly large schemas that far exceed the typical LLM context window, use of resource identifiers, overlapping relation types and lack of normalization. As a solution, we propose property graph views on top of the underlying RDF graph that can be efficiently queried by LLMs using Cypher. We instantiated this idea on Wikidata and introduced CypherBench, the first benchmark with 11 large-scale, multi-domain property graphs with 7.8 million entities and over 10,000 questions. To achieve this, we tackled several key challenges, including developing an RDF-to-property graph conversion engine, creating a systematic pipeline for text-to-Cypher task generation, and designing new evaluation metrics.

Objective: To transform heterogeneous clinical data from electronic health records into clinically meaningful constructed features using data driven method that rely, in part, on temporal relations among data. Materials and Methods: The clinically meaningful representations of medical concepts and patients are the key for health analytic applications. Most of existing approaches directly construct features mapped to raw data (e.g., ICD or CPT codes), or utilize some ontology mapping such as SNOMED codes. However, none of the existing approaches leverage EHR data directly for learning such concept representation. We propose a new way to represent heterogeneous medical concepts (e.g., diagnoses, medications and procedures) based on co-occurrence patterns in longitudinal electronic health records. The intuition behind the method is to map medical concepts that are co-occuring closely in time to similar concept vectors so that their distance will be small. We also derive a simple method to construct patient vectors from the related medical concept vectors. Results: For qualitative evaluation, we study similar medical concepts across diagnosis, medication and procedure. In quantitative evaluation, our proposed representation significantly improves the predictive modeling performance for onset of heart failure (HF), where classification methods (e.g. logistic regression, neural network, support vector machine and K-nearest neighbors) achieve up to 23% improvement in area under the ROC curve (AUC) using this proposed representation. Conclusion: We proposed an effective method for patient and medical concept representation learning. The resulting representation can map relevant concepts together and also improves predictive modeling performance.

The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.

The knowledge of city exploration trails of people is in short supply because of the complexity in defining meaningful trails representative of individual behaviours and in the access to actionable data. Existing datasets have only recorded isolated check-ins of activities featured by opaque venue types. In this paper, we fill the gaps in defining what is a semantic trail of city exploration and how it can be generated by integrating different data sources. Furthermore, we publicly release two datasets holding millions of semantic trails each and we discuss their most salient characteristics. We finally present an application using these datasets to build a recommender system meant to guide tourists while exploring a city.

Deep learning models are increasingly data-hungry, requiring significant resources to collect and compile the datasets needed to train them, with Earth Observation (EO) models being no exception. However, the landscape of datasets in EO is relatively atomised, with interoperability made difficult by diverse formats and data structures. If ever larger datasets are to be built, and duplication of effort minimised, then a shared framework that allows users to combine and access multiple datasets is needed. Here, Major TOM (Terrestrial Observation Metaset) is proposed as this extensible framework. Primarily, it consists of a geographical indexing system based on a set of grid points and a metadata structure that allows multiple datasets with different sources to be merged. Besides the specification of Major TOM as a framework, this work also presents a large, open-access dataset, MajorTOM-Core, which covers the vast majority of the Earth's land surface. This dataset provides the community with both an immediately useful resource, as well as acting as a template for future additions to the Major TOM ecosystem. Access: https://huggingface.co/Major-TOM

For centuries, researchers have sought out ways to connect disparate areas of knowledge. While early scholars (Galileo, da Vinci, etc.) were experts across fields, specialization has taken hold later. With the advent of Artificial Intelligence, we can now explore relationships across areas (e.g., mechanics-biology) or disparate domains (e.g., failure mechanics-art). To achieve this, we use a fine-tuned Large Language Model (LLM), here for a subset of knowledge in multiscale materials failure. The approach includes the use of a general-purpose LLM to distill question-answer pairs from raw sources followed by LLM fine-tuning. The resulting MechGPT LLM foundation model is used in a series of computational experiments to explore its capacity for knowledge retrieval, various language tasks, hypothesis generation, and connecting knowledge across disparate areas. While the model has some ability to recall knowledge from training, we find that LLMs are particularly useful to extract structural insights through Ontological Knowledge Graphs. These interpretable graph structures provide explanatory insights, frameworks for new research questions, and visual representations of knowledge that also can be used in retrieval-augmented generation. Three versions of MechGPT are discussed, featuring different sizes from 13 billion to 70 billion parameters, and reaching context lengths of more than 10,000 tokens. This provides ample capacity for sophisticated retrieval augmented strategies, as well as agent-based modeling where multiple LLMs interact collaboratively and/or adversarially, the incorporation of new data from the literature or web searches, as well as multimodality.

Finding relevant literature underpins the practice of evidence-based medicine. From 2014 to 2016, TREC conducted a clinical decision support track, wherein participants were tasked with finding articles relevant to clinical questions posed by physicians. In total, 87 teams have participated over the past three years, generating 395 runs. During this period, each team has trialled a variety of methods. While there was significant overlap in the methods employed by different teams, the results were varied. Due to the diversity of the platforms used, the results arising from the different techniques are not directly comparable, reducing the ability to build on previous work. By using a stable platform, we have been able to compare different document and query processing techniques, allowing us to experiment with different search parameters. We have used our system to reproduce leading teams runs, and compare the results obtained. By benchmarking our indexing and search techniques, we can statistically test a variety of hypotheses, paving the way for further research.

Geologic map, as a fundamental diagram in geology science, provides critical insights into the structure and composition of Earth's subsurface and surface. These maps are indispensable in various fields, including disaster detection, resource exploration, and civil engineering. Despite their significance, current Multimodal Large Language Models (MLLMs) often fall short in geologic map understanding. This gap is primarily due to the challenging nature of cartographic generalization, which involves handling high-resolution map, managing multiple associated components, and requiring domain-specific knowledge. To quantify this gap, we construct GeoMap-Bench, the first-ever benchmark for evaluating MLLMs in geologic map understanding, which assesses the full-scale abilities in extracting, referring, grounding, reasoning, and analyzing. To bridge this gap, we introduce GeoMap-Agent, the inaugural agent designed for geologic map understanding, which features three modules: Hierarchical Information Extraction (HIE), Domain Knowledge Injection (DKI), and Prompt-enhanced Question Answering (PEQA). Inspired by the interdisciplinary collaboration among human scientists, an AI expert group acts as consultants, utilizing a diverse tool pool to comprehensively analyze questions. Through comprehensive experiments, GeoMap-Agent achieves an overall score of 0.811 on GeoMap-Bench, significantly outperforming 0.369 of GPT-4o. Our work, emPowering gEologic mAp holistiC undErstanding (PEACE) with MLLMs, paves the way for advanced AI applications in geology, enhancing the efficiency and accuracy of geological investigations.

Machine learning models often learn latent embedding representations that capture the domain semantics of their training data. These embedding representations are valuable for interpreting trained models, building new models, and analyzing new datasets. However, interpreting and using embeddings can be challenging due to their opaqueness, high dimensionality, and the large size of modern datasets. To tackle these challenges, we present WizMap, an interactive visualization tool to help researchers and practitioners easily explore large embeddings. With a novel multi-resolution embedding summarization method and a familiar map-like interaction design, WizMap enables users to navigate and interpret embedding spaces with ease. Leveraging modern web technologies such as WebGL and Web Workers, WizMap scales to millions of embedding points directly in users' web browsers and computational notebooks without the need for dedicated backend servers. WizMap is open-source and available at the following public demo link: https://poloclub.github.io/wizmap.

Large Language Models (LLMs) have demonstrated remarkable capabilities in important tasks such as natural language understanding, language generation, and complex reasoning and have the potential to make a substantial impact on our society. Such capabilities, however, come with the considerable resources they demand, highlighting the strong need to develop effective techniques for addressing their efficiency challenges. In this survey, we provide a systematic and comprehensive review of efficient LLMs research. We organize the literature in a taxonomy consisting of three main categories, covering distinct yet interconnected efficient LLMs topics from model-centric, data-centric, and framework-centric perspective, respectively. We have also created a GitHub repository where we compile the papers featured in this survey at https://github.com/AIoT-MLSys-Lab/EfficientLLMs, and will actively maintain this repository and incorporate new research as it emerges. We hope our survey can serve as a valuable resource to help researchers and practitioners gain a systematic understanding of the research developments in efficient LLMs and inspire them to contribute to this important and exciting field.

We introduce ParaNames, a multilingual parallel name resource consisting of 118 million names spanning across 400 languages. Names are provided for 13.6 million entities which are mapped to standardized entity types (PER/LOC/ORG). Using Wikidata as a source, we create the largest resource of this type to-date. We describe our approach to filtering and standardizing the data to provide the best quality possible. ParaNames is useful for multilingual language processing, both in defining tasks for name translation/transliteration and as supplementary data for tasks such as named entity recognition and linking. We demonstrate an application of ParaNames by training a multilingual model for canonical name translation to and from English. Our resource is released under a Creative Commons license (CC BY 4.0) at https://github.com/bltlab/paranames.

This research presents a comprehensive methodology for utilizing an ontology-driven structured prompts system in interplay with ChatGPT, a widely used large language model (LLM). The study develops formal models, both information and functional, and establishes the methodological foundations for integrating ontology-driven prompts with ChatGPT's meta-learning capabilities. The resulting productive triad comprises the methodological foundations, advanced information technology, and the OntoChatGPT system, which collectively enhance the effectiveness and performance of chatbot systems. The implementation of this technology is demonstrated using the Ukrainian language within the domain of rehabilitation. By applying the proposed methodology, the OntoChatGPT system effectively extracts entities from contexts, classifies them, and generates relevant responses. The study highlights the versatility of the methodology, emphasizing its applicability not only to ChatGPT but also to other chatbot systems based on LLMs, such as Google's Bard utilizing the PaLM 2 LLM. The underlying principles of meta-learning, structured prompts, and ontology-driven information retrieval form the core of the proposed methodology, enabling their adaptation and utilization in various LLM-based systems. This versatile approach opens up new possibilities for NLP and dialogue systems, empowering developers to enhance the performance and functionality of chatbot systems across different domains and languages.

Advancements in Large Language Models (LLMs) drive interest in scientific applications, necessitating specialized benchmarks such as Earth science. Existing benchmarks either present a general science focus devoid of Earth science specificity or cover isolated subdomains, lacking holistic evaluation. Furthermore, current benchmarks typically neglect the assessment of LLMs' capabilities in open-ended scientific exploration. In this paper, we present a comprehensive and professional benchmark for the Earth sciences, designed to evaluate the capabilities of LLMs in scientific exploration within this domain, spanning from fundamental to advanced levels. Leveraging a corpus of 100,000 research papers, we first construct two Question Answering (QA) datasets: Earth-Iron, which offers extensive question coverage for broad assessment, and Earth-Silver, which features a higher level of difficulty to evaluate professional depth. These datasets encompass five Earth spheres, 114 disciplines, and 11 task categories, assessing foundational knowledge crucial for scientific exploration. Most notably, we introduce Earth-Gold with new metrics, a dataset comprising open-ended multi-turn dialogues specifically designed to evaluate the advanced capabilities of LLMs in scientific exploration, including methodology induction, limitation analysis, and concept proposal. Extensive experiments reveal limitations in 11 leading LLMs across different domains and tasks, highlighting considerable room for improvement in their scientific exploration capabilities. The benchmark is available on https://huggingface.co/ai-earth .

Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction towards cognition and human-level intelligence. In this survey, we provide a comprehensive review of knowledge graph covering overall research topics about 1) knowledge graph representation learning, 2) knowledge acquisition and completion, 3) temporal knowledge graph, and 4) knowledge-aware applications, and summarize recent breakthroughs and perspective directions to facilitate future research. We propose a full-view categorization and new taxonomies on these topics. Knowledge graph embedding is organized from four aspects of representation space, scoring function, encoding models, and auxiliary information. For knowledge acquisition, especially knowledge graph completion, embedding methods, path inference, and logical rule reasoning, are reviewed. We further explore several emerging topics, including meta relational learning, commonsense reasoning, and temporal knowledge graphs. To facilitate future research on knowledge graphs, we also provide a curated collection of datasets and open-source libraries on different tasks. In the end, we have a thorough outlook on several promising research directions.

In recent years, the rapid advancement of Large Language Models (LLMs) has transformed the landscape of scientific research, offering unprecedented support across various stages of the research cycle. This paper presents the first systematic survey dedicated to exploring how LLMs are revolutionizing the scientific research process. We analyze the unique roles LLMs play across four critical stages of research: hypothesis discovery, experiment planning and implementation, scientific writing, and peer reviewing. Our review comprehensively showcases the task-specific methodologies and evaluation benchmarks. By identifying current challenges and proposing future research directions, this survey not only highlights the transformative potential of LLMs, but also aims to inspire and guide researchers and practitioners in leveraging LLMs to advance scientific inquiry. Resources are available at the following repository: https://github.com/du-nlp-lab/LLM4SR

With the rapid development of IT operations, it has become increasingly crucial to efficiently manage and analyze large volumes of data for practical applications. The techniques of Natural Language Processing (NLP) have shown remarkable capabilities for various tasks, including named entity recognition, machine translation and dialogue systems. Recently, Large Language Models (LLMs) have achieved significant improvements across various NLP downstream tasks. However, there is a lack of specialized LLMs for IT operations. In this paper, we introduce the OWL, a large language model trained on our collected OWL-Instruct dataset with a wide range of IT-related information, where the mixture-of-adapter strategy is proposed to improve the parameter-efficient tuning across different domains or tasks. Furthermore, we evaluate the performance of our OWL on the OWL-Bench established by us and open IT-related benchmarks. OWL demonstrates superior performance results on IT tasks, which outperforms existing models by significant margins. Moreover, we hope that the findings of our work will provide more insights to revolutionize the techniques of IT operations with specialized LLMs.

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

Different entities with the same name can be difficult to distinguish. Handling confusing entity mentions is a crucial skill for language models (LMs). For example, given the question "Where was Michael Jordan educated?" and a set of documents discussing different people named Michael Jordan, can LMs distinguish entity mentions to generate a cohesive answer to the question? To test this ability, we introduce a new benchmark, AmbigDocs. By leveraging Wikipedia's disambiguation pages, we identify a set of documents, belonging to different entities who share an ambiguous name. From these documents, we generate questions containing an ambiguous name and their corresponding sets of answers. Our analysis reveals that current state-of-the-art models often yield ambiguous answers or incorrectly merge information belonging to different entities. We establish an ontology categorizing four types of incomplete answers and automatic evaluation metrics to identify such categories. We lay the foundation for future work on reasoning across multiple documents with ambiguous entities.

The proposed research aims to develop an innovative semantic query processing system that enables users to obtain comprehensive information about research works produced by Computer Science (CS) researchers at the Australian National University (ANU). The system integrates Large Language Models (LLMs) with the ANU Scholarly Knowledge Graph (ASKG), a structured repository of all research-related artifacts produced at ANU in the CS field. Each artifact and its parts are represented as textual nodes stored in a Knowledge Graph (KG). To address the limitations of traditional scholarly KG construction and utilization methods, which often fail to capture fine-grained details, we propose a novel framework that integrates the Deep Document Model (DDM) for comprehensive document representation and the KG-enhanced Query Processing (KGQP) for optimized complex query handling. DDM enables a fine-grained representation of the hierarchical structure and semantic relationships within academic papers, while KGQP leverages the KG structure to improve query accuracy and efficiency with LLMs. By combining the ASKG with LLMs, our approach enhances knowledge utilization and natural language understanding capabilities. The proposed system employs an automatic LLM-SPARQL fusion to retrieve relevant facts and textual nodes from the ASKG. Initial experiments demonstrate that our framework is superior to baseline methods in terms of accuracy retrieval and query efficiency. We showcase the practical application of our framework in academic research scenarios, highlighting its potential to revolutionize scholarly knowledge management and discovery. This work empowers researchers to acquire and utilize knowledge from documents more effectively and provides a foundation for developing precise and reliable interactions with LLMs.

In real world applications, knowledge graphs (KG) are widely used in various domains (e.g. medical applications and dialogue agents). However, for fact verification, KGs have not been adequately utilized as a knowledge source. KGs can be a valuable knowledge source in fact verification due to their reliability and broad applicability. A KG consists of nodes and edges which makes it clear how concepts are linked together, allowing machines to reason over chains of topics. However, there are many challenges in understanding how these machine-readable concepts map to information in text. To enable the community to better use KGs, we introduce a new dataset, FactKG: Fact Verification via Reasoning on Knowledge Graphs. It consists of 108k natural language claims with five types of reasoning: One-hop, Conjunction, Existence, Multi-hop, and Negation. Furthermore, FactKG contains various linguistic patterns, including colloquial style claims as well as written style claims to increase practicality. Lastly, we develop a baseline approach and analyze FactKG over these reasoning types. We believe FactKG can advance both reliability and practicality in KG-based fact verification.

This work presents a unified knowledge protocol, called UKnow, which facilitates knowledge-based studies from the perspective of data. Particularly focusing on visual and linguistic modalities, we categorize data knowledge into five unit types, namely, in-image, in-text, cross-image, cross-text, and image-text, and set up an efficient pipeline to help construct the multimodal knowledge graph from any data collection. Thanks to the logical information naturally contained in knowledge graph, organizing datasets under UKnow format opens up more possibilities of data usage compared to the commonly used image-text pairs. Following UKnow protocol, we collect, from public international news, a large-scale multimodal knowledge graph dataset that consists of 1,388,568 nodes (with 571,791 vision-related ones) and 3,673,817 triplets. The dataset is also annotated with rich event tags, including 11 coarse labels and 9,185 fine labels. Experiments on four benchmarks demonstrate the potential of UKnow in supporting common-sense reasoning and boosting vision-language pre-training with a single dataset, benefiting from its unified form of knowledge organization. Code, dataset, and models will be made publicly available.

In this study, we investigate the potential of Large Language Models to complement biomedical knowledge graphs in the training of semantic models for the biomedical and clinical domains. Drawing on the wealth of the UMLS knowledge graph and harnessing cutting-edge Large Language Models, we propose a new state-of-the-art approach for obtaining high-fidelity representations of biomedical concepts and sentences, consisting of three steps: an improved contrastive learning phase, a novel self-distillation phase, and a weight averaging phase. Through rigorous evaluations via the extensive BioLORD testing suite and diverse downstream tasks, we demonstrate consistent and substantial performance improvements over the previous state of the art (e.g. +2pts on MedSTS, +2.5pts on MedNLI-S, +6.1pts on EHR-Rel-B). Besides our new state-of-the-art biomedical model for English, we also distill and release a multilingual model compatible with 50+ languages and finetuned on 7 European languages. Many clinical pipelines can benefit from our latest models. Our new multilingual model enables a range of languages to benefit from our advancements in biomedical semantic representation learning, opening a new avenue for bioinformatics researchers around the world. As a result, we hope to see BioLORD-2023 becoming a precious tool for future biomedical applications.

Large Language Models (LLMs) have made great strides in recent years to achieve unprecedented performance across different tasks. However, due to commercial interest, the most competitive models like GPT, Gemini, and Claude have been gated behind proprietary interfaces without disclosing the training details. Recently, many institutions have open-sourced several strong LLMs like LLaMA-3, comparable to existing closed-source LLMs. However, only the model's weights are provided with most details (e.g., intermediate checkpoints, pre-training corpus, and training code, etc.) being undisclosed. To improve the transparency of LLMs, the research community has formed to open-source truly open LLMs (e.g., Pythia, Amber, OLMo), where more details (e.g., pre-training corpus and training code) are being provided. These models have greatly advanced the scientific study of these large models including their strengths, weaknesses, biases and risks. However, we observe that the existing truly open LLMs on reasoning, knowledge, and coding tasks are still inferior to existing state-of-the-art LLMs with similar model sizes. To this end, we open-source MAP-Neo, a highly capable and transparent bilingual language model with 7B parameters trained from scratch on 4.5T high-quality tokens. Our MAP-Neo is the first fully open-sourced bilingual LLM with comparable performance compared to existing state-of-the-art LLMs. Moreover, we open-source all details to reproduce our MAP-Neo, where the cleaned pre-training corpus, data cleaning pipeline, checkpoints, and well-optimized training/evaluation framework are provided. Finally, we hope our MAP-Neo will enhance and strengthen the open research community and inspire more innovations and creativities to facilitate the further improvements of LLMs.

Large language models have demonstrated remarkable potential in various tasks, however, there remains a significant scarcity of open-source models and data for specific domains. Previous works have primarily focused on manually specifying resources and collecting high-quality data on specific domains, which significantly consume time and effort. To address this limitation, we propose an efficient data collection method~Query of CC based on large language models. This method bootstraps seed information through a large language model and retrieves related data from public corpora. It not only collects knowledge-related data for specific domains but unearths the data with potential reasoning procedures. Through the application of this method, we have curated a high-quality dataset called~Knowledge Pile, encompassing four major domains, including stem and humanities sciences, among others. Experimental results demonstrate that~Knowledge Pile significantly improves the performance of large language models in mathematical and knowledge-related reasoning ability tests. To facilitate academic sharing, we open-source our dataset and code, providing valuable support to the academic community.

In this paper, we propose a new mixed-integer linear programming (MILP) model ontology and a novel constraint typology of MILP formulations. MILP is a commonly used mathematical programming technique for modelling and solving real-life scheduling, routing, planning, resource allocation, and timetabling optimization problems providing optimized business solutions for industry sectors such as manufacturing, agriculture, defence, healthcare, medicine, energy, finance, and transportation. Despite the numerous real-life Combinatorial Optimization Problems found and solved and millions yet to be discovered and formulated, the number of types of constraints (the building blocks of a MILP) is relatively small. In the search for a suitable machine-readable knowledge representation structure for MILPs, we propose an optimization modelling tree built based upon an MILP model ontology that can be used as a guide for automated systems to elicit an MILP model from end-users on their combinatorial business optimization problems. Our ultimate aim is to develop a machine-readable knowledge representation for MILP that allows us to map an end-user's natural language description of the business optimization problem to an MILP formal specification as a first step towards automated mathematical modelling.

Large datasets have become commonplace in NLP research. However, the increased emphasis on data quantity has made it challenging to assess the quality of data. We introduce Data Maps---a model-based tool to characterize and diagnose datasets. We leverage a largely ignored source of information: the behavior of the model on individual instances during training (training dynamics) for building data maps. This yields two intuitive measures for each example---the model's confidence in the true class, and the variability of this confidence across epochs---obtained in a single run of training. Experiments across four datasets show that these model-dependent measures reveal three distinct regions in the data map, each with pronounced characteristics. First, our data maps show the presence of "ambiguous" regions with respect to the model, which contribute the most towards out-of-distribution generalization. Second, the most populous regions in the data are "easy to learn" for the model, and play an important role in model optimization. Finally, data maps uncover a region with instances that the model finds "hard to learn"; these often correspond to labeling errors. Our results indicate that a shift in focus from quantity to quality of data could lead to robust models and improved out-of-distribution generalization.

We present the system description for our submission towards the Key Point Analysis Shared Task at ArgMining 2021. Track 1 of the shared task requires participants to develop methods to predict the match score between each pair of arguments and keypoints, provided they belong to the same topic under the same stance. We leveraged existing state of the art pre-trained language models along with incorporating additional data and features extracted from the inputs (topics, key points, and arguments) to improve performance. We were able to achieve mAP strict and mAP relaxed score of 0.872 and 0.966 respectively in the evaluation phase, securing 5th place on the leaderboard. In the post evaluation phase, we achieved a mAP strict and mAP relaxed score of 0.921 and 0.982 respectively. All the codes to generate reproducible results on our models are available on Github.

Knowledge Graphs (KGs) play a pivotal role in advancing various AI applications, with the semantic web community's exploration into multi-modal dimensions unlocking new avenues for innovation. In this survey, we carefully review over 300 articles, focusing on KG-aware research in two principal aspects: KG-driven Multi-Modal (KG4MM) learning, where KGs support multi-modal tasks, and Multi-Modal Knowledge Graph (MM4KG), which extends KG studies into the MMKG realm. We begin by defining KGs and MMKGs, then explore their construction progress. Our review includes two primary task categories: KG-aware multi-modal learning tasks, such as Image Classification and Visual Question Answering, and intrinsic MMKG tasks like Multi-modal Knowledge Graph Completion and Entity Alignment, highlighting specific research trajectories. For most of these tasks, we provide definitions, evaluation benchmarks, and additionally outline essential insights for conducting relevant research. Finally, we discuss current challenges and identify emerging trends, such as progress in Large Language Modeling and Multi-modal Pre-training strategies. This survey aims to serve as a comprehensive reference for researchers already involved in or considering delving into KG and multi-modal learning research, offering insights into the evolving landscape of MMKG research and supporting future work.

Efficient molecular modeling and design are crucial for the discovery and exploration of novel molecules, and the incorporation of deep learning methods has revolutionized this field. In particular, large language models (LLMs) offer a fresh approach to tackle scientific problems from a natural language processing (NLP) perspective, introducing a research paradigm called scientific language modeling (SLM). However, two key issues remain: how to quantify the match between model and data modalities and how to identify the knowledge-learning preferences of models. To address these challenges, we propose a multi-modal benchmark, named ChEBI-20-MM, and perform 1263 experiments to assess the model's compatibility with data modalities and knowledge acquisition. Through the modal transition probability matrix, we provide insights into the most suitable modalities for tasks. Furthermore, we introduce a statistically interpretable approach to discover context-specific knowledge mapping by localized feature filtering. Our pioneering analysis offers an exploration of the learning mechanism and paves the way for advancing SLM in molecular science.

Recently, the emergence of pre-trained models (PTMs) has brought natural language processing (NLP) to a new era. In this survey, we provide a comprehensive review of PTMs for NLP. We first briefly introduce language representation learning and its research progress. Then we systematically categorize existing PTMs based on a taxonomy with four perspectives. Next, we describe how to adapt the knowledge of PTMs to the downstream tasks. Finally, we outline some potential directions of PTMs for future research. This survey is purposed to be a hands-on guide for understanding, using, and developing PTMs for various NLP tasks.

Semantic role labeling (SRL) is a central natural language processing (NLP) task aiming to understand the semantic roles within texts, facilitating a wide range of downstream applications. While SRL has garnered extensive and enduring research, there is currently a lack of a comprehensive survey that thoroughly organizes and synthesizes the field. This paper aims to review the entire research trajectory of the SRL community over the past two decades. We begin by providing a complete definition of SRL. To offer a comprehensive taxonomy, we categorize SRL methodologies into four key perspectives: model architectures, syntax feature modeling, application scenarios, and multi-modal extensions. Further, we discuss SRL benchmarks, evaluation metrics, and paradigm modeling approaches, while also exploring practical applications across various domains. Finally, we analyze future research directions in SRL, addressing the evolving role of SRL in the age of large language models (LLMs) and its potential impact on the broader NLP landscape. We maintain a public repository and consistently update related resources at: https://github.com/DreamH1gh/Awesome-SRL

A heuristic extending the Squarified Treemap technique for the representation of hierarchical information as treemaps is presented. The original technique gives high quality treemap views, since items are laid out with rectangles that approximate squares, allowing easy comparison and selection operations. New key steps, with a low computational impact, have been introduced to yield treemaps with even better aspect ratios and higher homogeneity among items.

With the exponential growth of research facilitated by modern technology and improved accessibility, scientific discoveries have become increasingly fragmented within and across fields. This makes it challenging to assess the significance, novelty, incremental findings, and equivalent ideas between related works, particularly those from different research communities. Large language models (LLMs) have recently demonstrated strong quantitative and qualitative reasoning abilities, and multi-agent LLM debates have shown promise in handling complex reasoning tasks by exploring diverse perspectives and reasoning paths. Inspired by this, we introduce Tree-of-Debate (ToD), a framework which converts scientific papers into LLM personas that debate their respective novelties. To emphasize structured, critical reasoning rather than focusing solely on outcomes, ToD dynamically constructs a debate tree, enabling fine-grained analysis of independent novelty arguments within scholarly articles. Through experiments on scientific literature across various domains, evaluated by expert researchers, we demonstrate that ToD generates informative arguments, effectively contrasts papers, and supports researchers in their literature review.

Asking questions about a situation is an inherent step towards understanding it. To this end, we introduce the task of role question generation, which, given a predicate mention and a passage, requires producing a set of questions asking about all possible semantic roles of the predicate. We develop a two-stage model for this task, which first produces a context-independent question prototype for each role and then revises it to be contextually appropriate for the passage. Unlike most existing approaches to question generation, our approach does not require conditioning on existing answers in the text. Instead, we condition on the type of information to inquire about, regardless of whether the answer appears explicitly in the text, could be inferred from it, or should be sought elsewhere. Our evaluation demonstrates that we generate diverse and well-formed questions for a large, broad-coverage ontology of predicates and roles.

Digital Twins are digital representations of systems in the Internet of Things (IoT) that are often based on AI models that are trained on data from those systems. Semantic models are used increasingly to link these datasets from different stages of the IoT systems life-cycle together and to automatically configure the AI modelling pipelines. This combination of semantic models with AI pipelines running on external datasets raises unique challenges particular if rolled out at scale. Within this paper we will discuss the unique requirements of applying semantic graphs to automate Digital Twins in different practical use cases. We will introduce the benchmark dataset DTBM that reflects these characteristics and look into the scaling challenges of different knowledge graph technologies. Based on these insights we will propose a reference architecture that is in-use in multiple products in IBM and derive lessons learned for scaling knowledge graphs for configuring AI models for Digital Twins.

Introduction: The scientific publishing landscape is expanding rapidly, creating challenges for researchers to stay up-to-date with the evolution of the literature. Natural Language Processing (NLP) has emerged as a potent approach to automating knowledge extraction from this vast amount of publications and preprints. Tasks such as Named-Entity Recognition (NER) and Named-Entity Linking (NEL), in conjunction with context-dependent semantic interpretation, offer promising and complementary approaches to extracting structured information and revealing key concepts. Results: We present the SourceData-NLP dataset produced through the routine curation of papers during the publication process. A unique feature of this dataset is its emphasis on the annotation of bioentities in figure legends. We annotate eight classes of biomedical entities (small molecules, gene products, subcellular components, cell lines, cell types, tissues, organisms, and diseases), their role in the experimental design, and the nature of the experimental method as an additional class. SourceData-NLP contains more than 620,000 annotated biomedical entities, curated from 18,689 figures in 3,223 papers in molecular and cell biology. We illustrate the dataset's usefulness by assessing BioLinkBERT and PubmedBERT, two transformers-based models, fine-tuned on the SourceData-NLP dataset for NER. We also introduce a novel context-dependent semantic task that infers whether an entity is the target of a controlled intervention or the object of measurement. Conclusions: SourceData-NLP's scale highlights the value of integrating curation into publishing. Models trained with SourceData-NLP will furthermore enable the development of tools able to extract causal hypotheses from the literature and assemble them into knowledge graphs.

Recent works in Event Argument Extraction (EAE) have focused on improving model generalizability to cater to new events and domains. However, standard benchmarking datasets like ACE and ERE cover less than 40 event types and 25 entity-centric argument roles. Limited diversity and coverage hinder these datasets from adequately evaluating the generalizability of EAE models. In this paper, we first contribute by creating a large and diverse EAE ontology. This ontology is created by transforming FrameNet, a comprehensive semantic role labeling (SRL) dataset for EAE, by exploiting the similarity between these two tasks. Then, exhaustive human expert annotations are collected to build the ontology, concluding with 115 events and 220 argument roles, with a significant portion of roles not being entities. We utilize this ontology to further introduce GENEVA, a diverse generalizability benchmarking dataset comprising four test suites, aimed at evaluating models' ability to handle limited data and unseen event type generalization. We benchmark six EAE models from various families. The results show that owing to non-entity argument roles, even the best-performing model can only achieve 39% F1 score, indicating how GENEVA provides new challenges for generalization in EAE. Overall, our large and diverse EAE ontology can aid in creating more comprehensive future resources, while GENEVA is a challenging benchmarking dataset encouraging further research for improving generalizability in EAE. The code and data can be found at https://github.com/PlusLabNLP/GENEVA.

This paper presents a systematic literature review in Computer Science that provide an overview of the initiatives related to digital misinformation. This is an exploratory study that covers research from 1993 to 2020, focusing on the investigation of the phenomenon of misinformation. The review consists of 788 studies from SCOPUS, IEEE, and ACM digital libraries, synthesizing the primary research directions and sociotechnical challenges. These challenges are classified into Physical, Empirical, Syntactic, Semantic, Pragmatic, and Social dimensions, drawing from Organizational Semiotics. The mapping identifies issues related to the concept of misinformation, highlights deficiencies in mitigation strategies, discusses challenges in approaching stakeholders, and unveils various sociotechnical aspects relevant to understanding and mitigating the harmful effects of digital misinformation. As contributions, this study present a novel categorization of mitigation strategies, a sociotechnical taxonomy for classifying types of false information and elaborate on the inter-relation of sociotechnical aspects and their impacts.

Despite the widespread success of self-supervised learning via masked language models (MLM), accurately capturing fine-grained semantic relationships in the biomedical domain remains a challenge. This is of paramount importance for entity-level tasks such as entity linking where the ability to model entity relations (especially synonymy) is pivotal. To address this challenge, we propose SapBERT, a pretraining scheme that self-aligns the representation space of biomedical entities. We design a scalable metric learning framework that can leverage UMLS, a massive collection of biomedical ontologies with 4M+ concepts. In contrast with previous pipeline-based hybrid systems, SapBERT offers an elegant one-model-for-all solution to the problem of medical entity linking (MEL), achieving a new state-of-the-art (SOTA) on six MEL benchmarking datasets. In the scientific domain, we achieve SOTA even without task-specific supervision. With substantial improvement over various domain-specific pretrained MLMs such as BioBERT, SciBERTand and PubMedBERT, our pretraining scheme proves to be both effective and robust.

Biomedical knowledge graphs (BioMedKGs) are essential infrastructures for biomedical and healthcare big data and artificial intelligence (AI), facilitating natural language processing, model development, and data exchange. For decades, these knowledge graphs have been developed via expert curation; however, this method can no longer keep up with today's AI development, and a transition to algorithmically generated BioMedKGs is necessary. In this work, we introduce the Biomedical Informatics Ontology System (BIOS), the first large-scale publicly available BioMedKG generated completely by machine learning algorithms. BIOS currently contains 4.1 million concepts, 7.4 million terms in two languages, and 7.3 million relation triplets. We present the methodology for developing BIOS, including the curation of raw biomedical terms, computational identification of synonymous terms and aggregation of these terms to create concept nodes, semantic type classification of the concepts, relation identification, and biomedical machine translation. We provide statistics on the current BIOS content and perform preliminary assessments of term quality, synonym grouping, and relation extraction. The results suggest that machine learning-based BioMedKG development is a viable alternative to traditional expert curation.

We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials. Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the `PICO' elements). These spans are further annotated at a more granular level, e.g., individual interventions within them are marked and mapped onto a structured medical vocabulary. We acquired annotations from a diverse set of workers with varying levels of expertise and cost. We describe our data collection process and the corpus itself in detail. We then outline a set of challenging NLP tasks that would aid searching of the medical literature and the practice of evidence-based medicine.

We introduce ParaNames, a massively multilingual parallel name resource consisting of 140 million names spanning over 400 languages. Names are provided for 16.8 million entities, and each entity is mapped from a complex type hierarchy to a standard type (PER/LOC/ORG). Using Wikidata as a source, we create the largest resource of this type to date. We describe our approach to filtering and standardizing the data to provide the best quality possible. ParaNames is useful for multilingual language processing, both in defining tasks for name translation/transliteration and as supplementary data for tasks such as named entity recognition and linking. We demonstrate the usefulness of ParaNames on two tasks. First, we perform canonical name translation between English and 17 other languages. Second, we use it as a gazetteer for multilingual named entity recognition, obtaining performance improvements on all 10 languages evaluated.

We provide here a dataset for tasks related to natural language understanding and natural language inference. The dataset contains logical puzzles in natural language from three domains: comparing puzzles, knighs and knaves, and zebra puzzles. Each puzzle is associated with the entire set of atomic questions that can be generated based on the relations and individuals occurring in the text. For each question we provide the correct answer: entailment, contradiction or ambiguity. The answer's correctness is verified against theorem provers. Good puzzles have two properties: (i) each piece of information is necessary and (ii) no unnecessary information is provided. These properties make puzzles interesting candidates for machine comprehension tasks.

We utilize a recently developed topic modeling method called SeNMFk, extending the standard Non-negative Matrix Factorization (NMF) methods by incorporating the semantic structure of the text, and adding a robust system for determining the number of topics. With SeNMFk, we were able to extract coherent topics validated by human experts. From these topics, a few are relatively general and cover broad concepts, while the majority can be precisely mapped to specific scientific effects or measurement techniques. The topics also differ by ubiquity, with only three topics prevalent in almost 40 percent of the abstract, while each specific topic tends to dominate a small subset of the abstracts. These results demonstrate the ability of SeNMFk to produce a layered and nuanced analysis of large scientific corpora.

Vision-and-language navigation (VLN) enables the agent to navigate to a remote location following the natural language instruction in 3D environments. To represent the previously visited environment, most approaches for VLN implement memory using recurrent states, topological maps, or top-down semantic maps. In contrast to these approaches, we build the top-down egocentric and dynamically growing Grid Memory Map (i.e., GridMM) to structure the visited environment. From a global perspective, historical observations are projected into a unified grid map in a top-down view, which can better represent the spatial relations of the environment. From a local perspective, we further propose an instruction relevance aggregation method to capture fine-grained visual clues in each grid region. Extensive experiments are conducted on both the REVERIE, R2R, SOON datasets in the discrete environments, and the R2R-CE dataset in the continuous environments, showing the superiority of our proposed method.

Traditional similarity-based schema matching methods are incapable of resolving semantic ambiguities and conflicts in domain-specific complex mapping scenarios due to missing commonsense and domain-specific knowledge. The hallucination problem of large language models (LLMs) also makes it challenging for LLM-based schema matching to address the above issues. Therefore, we propose a Knowledge Graph-based Retrieval-Augmented Generation model for Schema Matching, referred to as the KG-RAG4SM. In particular, KG-RAG4SM introduces novel vector-based, graph traversal-based, and query-based graph retrievals, as well as a hybrid approach and ranking schemes that identify the most relevant subgraphs from external large knowledge graphs (KGs). We showcase that KG-based retrieval-augmented LLMs are capable of generating more accurate results for complex matching cases without any re-training. Our experimental results show that KG-RAG4SM outperforms the LLM-based state-of-the-art (SOTA) methods (e.g., Jellyfish-8B) by 35.89% and 30.50% in terms of precision and F1 score on the MIMIC dataset, respectively; KG-RAG4SM with GPT-4o-mini outperforms the pre-trained language model (PLM)-based SOTA methods (e.g., SMAT) by 69.20% and 21.97% in terms of precision and F1 score on the Synthea dataset, respectively. The results also demonstrate that our approach is more efficient in end-to-end schema matching, and scales to retrieve from large KGs. Our case studies on the dataset from the real-world schema matching scenario exhibit that the hallucination problem of LLMs for schema matching is well mitigated by our solution.

Knowledge graph embedding involves learning representations of entities -- the vertices of the graph -- and relations -- the edges of the graph -- such that the resulting representations encode the known factual information represented by the knowledge graph and can be used in the inference of new relations. We show that knowledge graph embedding is naturally expressed in the topological and categorical language of cellular sheaves: a knowledge graph embedding can be described as an approximate global section of an appropriate knowledge sheaf over the graph, with consistency constraints induced by the knowledge graph's schema. This approach provides a generalized framework for reasoning about knowledge graph embedding models and allows for the expression of a wide range of prior constraints on embeddings. Further, the resulting embeddings can be easily adapted for reasoning over composite relations without special training. We implement these ideas to highlight the benefits of the extensions inspired by this new perspective.

Large language models (LLMs) have grown in their usage to provide support for question answering across numerous disciplines. The models on their own have already shown promise for answering basic questions, however fail quickly where expert domain knowledge is required or the question is nuanced. Scientific research often involves searching for relevant literature, distilling pertinent information from that literature and analysing how the findings support or contradict one another. The information is often encapsulated in the full text body of research articles, rather than just in the abstracts. Statements within these articles frequently require the wider article context to be fully understood. We have built an LLM-based system that performs such search and distillation of information encapsulated in scientific literature, and we evaluate our keyword based search and information distillation system against a set of biology related questions from previously released literature benchmarks. We demonstrate sparse retrieval methods exhibit results close to state of the art without the need for dense retrieval, with its associated infrastructure and complexity overhead. We also show how to increase the coverage of relevant documents for literature review generation.

We propose MultiDoc2Dial, a new task and dataset on modeling goal-oriented dialogues grounded in multiple documents. Most previous works treat document-grounded dialogue modeling as a machine reading comprehension task based on a single given document or passage. In this work, we aim to address more realistic scenarios where a goal-oriented information-seeking conversation involves multiple topics, and hence is grounded on different documents. To facilitate such a task, we introduce a new dataset that contains dialogues grounded in multiple documents from four different domains. We also explore modeling the dialogue-based and document-based context in the dataset. We present strong baseline approaches and various experimental results, aiming to support further research efforts on such a task.

Previous works on knowledge-to-text generation take as input a few RDF triples or key-value pairs conveying the knowledge of some entities to generate a natural language description. Existing datasets, such as WIKIBIO, WebNLG, and E2E, basically have a good alignment between an input triple/pair set and its output text. However, in practice, the input knowledge could be more than enough, since the output description may only cover the most significant knowledge. In this paper, we introduce a large-scale and challenging dataset to facilitate the study of such a practical scenario in KG-to-text. Our dataset involves retrieving abundant knowledge of various types of main entities from a large knowledge graph (KG), which makes the current graph-to-sequence models severely suffer from the problems of information loss and parameter explosion while generating the descriptions. We address these challenges by proposing a multi-graph structure that is able to represent the original graph information more comprehensively. Furthermore, we also incorporate aggregation methods that learn to extract the rich graph information. Extensive experiments demonstrate the effectiveness of our model architecture.

We define deriving semantic class targets as a novel multi-modal task. By doing so, we aim to improve classification schemes in the physical sciences which can be severely abstracted and obfuscating. We address this task for upcoming radio astronomy surveys and present the derived semantic radio galaxy morphology class targets.

In recent years, graph representation learning has undergone a paradigm shift, driven by the emergence and proliferation of graph neural networks (GNNs) and their heterogeneous counterparts. Heterogeneous GNNs have shown remarkable success in extracting low-dimensional embeddings from complex graphs that encompass diverse entity types and relationships. While meta-path-based techniques have long been recognized for their ability to capture semantic affinities among nodes, their dependence on manual specification poses a significant limitation. In contrast, matrix-focused methods accelerate processing by utilizing structural cues but often overlook contextual richness. In this paper, we challenge the current paradigm by introducing ontology as a fundamental semantic primitive within complex graphs. Our goal is to integrate the strengths of both matrix-centric and meta-path-based approaches into a unified framework. We propose perturbation Ontology-based Graph Attention Networks (POGAT), a novel methodology that combines ontology subgraphs with an advanced self-supervised learning paradigm to achieve a deep contextual understanding. The core innovation of POGAT lies in our enhanced homogeneous perturbing scheme designed to generate rigorous negative samples, encouraging the model to explore minimal contextual features more thoroughly. Through extensive empirical evaluations, we demonstrate that POGAT significantly outperforms state-of-the-art baselines, achieving a groundbreaking improvement of up to 10.78\% in F1-score for the critical task of link prediction and 12.01\% in Micro-F1 for the critical task of node classification.

Medication Extraction and Mining play an important role in healthcare NLP research due to its practical applications in hospital settings, such as their mapping into standard clinical knowledge bases (SNOMED-CT, BNF, etc.). In this work, we investigate state-of-the-art LLMs in text mining tasks on medications and their related attributes such as dosage, route, strength, and adverse effects. In addition, we explore different ensemble learning methods (Stack-Ensemble and Voting-Ensemble) to augment the model performances from individual LLMs. Our ensemble learning result demonstrated better performances than individually fine-tuned base models BERT, RoBERTa, RoBERTa-L, BioBERT, BioClinicalBERT, BioMedRoBERTa, ClinicalBERT, and PubMedBERT across general and specific domains. Finally, we build up an entity linking function to map extracted medical terminologies into the SNOMED-CT codes and the British National Formulary (BNF) codes, which are further mapped to the Dictionary of Medicines and Devices (dm+d), and ICD. Our model's toolkit and desktop applications are publicly available at https://github.com/HECTA-UoM/ensemble-NER.

A key challenge in artificial intelligence is the creation of systems capable of autonomously advancing scientific understanding by exploring novel domains, identifying complex patterns, and uncovering previously unseen connections in vast scientific data. In this work, we present SciAgents, an approach that leverages three core concepts: (1) the use of large-scale ontological knowledge graphs to organize and interconnect diverse scientific concepts, (2) a suite of large language models (LLMs) and data retrieval tools, and (3) multi-agent systems with in-situ learning capabilities. Applied to biologically inspired materials, SciAgents reveals hidden interdisciplinary relationships that were previously considered unrelated, achieving a scale, precision, and exploratory power that surpasses traditional human-driven research methods. The framework autonomously generates and refines research hypotheses, elucidating underlying mechanisms, design principles, and unexpected material properties. By integrating these capabilities in a modular fashion, the intelligent system yields material discoveries, critique and improve existing hypotheses, retrieve up-to-date data about existing research, and highlights their strengths and limitations. Our case studies demonstrate scalable capabilities to combine generative AI, ontological representations, and multi-agent modeling, harnessing a `swarm of intelligence' similar to biological systems. This provides new avenues for materials discovery and accelerates the development of advanced materials by unlocking Nature's design principles.

The exponential growth of knowledge and the increasing complexity of interdisciplinary research pose significant challenges for researchers, including information overload and difficulties in exploring novel ideas. The advancements in large language models (LLMs), such as GPT-4, have shown great potential in enhancing idea proposals, but how to effectively utilize large models for reasonable idea proposal has not been thoroughly explored. This paper proposes a scientific paper idea proposer (SciPIP). Based on a user-provided research background, SciPIP retrieves helpful papers from a literature database while leveraging the capabilities of LLMs to generate more novel and feasible ideas. To this end, 1) we construct a literature retrieval database, extracting lots of papers' multi-dimension information for fast access. Then, a literature retrieval method based on semantics, entity, and citation co-occurrences is proposed to search relevant literature from multiple aspects based on the user-provided background. 2) After literature retrieval, we introduce dual-path idea proposal strategies, where one path infers solutions from the retrieved literature and the other path generates original ideas through model brainstorming. We then combine the two to achieve a good balance between feasibility and originality. Through extensive experiments on the natural language processing (NLP) field, we demonstrate that SciPIP can retrieve citations similar to those of existing top conference papers and generate many ideas consistent with them. Additionally, we evaluate the originality of other ideas generated by SciPIP using large language models, further validating the effectiveness of our proposed method. The code and the database are released at https://github.com/cheerss/SciPIP.

Diderot's Encyclop\'edie is a reference work from XVIIIth century in Europe that aimed at collecting the knowledge of its era. Wikipedia has the same ambition with a much greater scope. However, the lack of digital connection between the two encyclopedias may hinder their comparison and the study of how knowledge has evolved. A key element of Wikipedia is Wikidata that backs the articles with a graph of structured data. In this paper, we describe the annotation of more than 10,300 of the Encyclop\'edie entries with Wikidata identifiers enabling us to connect these entries to the graph. We considered geographic and human entities. The Encyclop\'edie does not contain biographic entries as they mostly appear as subentries of locations. We extracted all the geographic entries and we completely annotated all the entries containing a description of human entities. This represents more than 2,600 links referring to locations or human entities. In addition, we annotated more than 9,500 entries having a geographic content only. We describe the annotation process as well as application examples. This resource is available at https://github.com/pnugues/encyclopedie_1751

Question processing is a fundamental step in a question answering (QA) application, and its quality impacts the performance of QA application. The major challenging issue in processing question is how to extract semantic of natural language questions (NLQs). A human language is ambiguous. Ambiguity may occur at two levels; lexical and syntactic. In this paper, we propose a new approach for resolving lexical ambiguity problem by integrating context knowledge and concepts knowledge of a domain, into shallow natural language processing (SNLP) techniques. Concepts knowledge is modeled using ontology, while context knowledge is obtained from WordNet, and it is determined based on neighborhood words in a question. The approach will be applied to a university QA system.

The exploitation of syntactic graphs (SyGs) as a word's context has been shown to be beneficial for distributional semantic models (DSMs), both at the level of individual word representations and in deriving phrasal representations via composition. However, notwithstanding the potential performance benefit, the syntactically-aware DSMs proposed to date have huge numbers of parameters (compared to conventional DSMs) and suffer from data sparsity. Furthermore, the encoding of the SyG links (i.e., the syntactic relations) has been largely limited to linear maps. The knowledge graphs' literature, on the other hand, has proposed light-weight models employing different geometric transformations (GTs) to encode edges in a knowledge graph (KG). Our work explores the possibility of adopting this family of models to encode SyGs. Furthermore, we investigate which GT better encodes syntactic relations, so that these representations can be used to enhance phrase-level composition via syntactic contextualisation.

Pre-trained Language Models (PLMs) are trained on vast unlabeled data, rich in world knowledge. This fact has sparked the interest of the community in quantifying the amount of factual knowledge present in PLMs, as this explains their performance on downstream tasks, and potentially justifies their use as knowledge bases. In this work, we survey methods and datasets that are used to probe PLMs for factual knowledge. Our contributions are: (1) We propose a categorization scheme for factual probing methods that is based on how their inputs, outputs and the probed PLMs are adapted; (2) We provide an overview of the datasets used for factual probing; (3) We synthesize insights about knowledge retention and prompt optimization in PLMs, analyze obstacles to adopting PLMs as knowledge bases and outline directions for future work.

Scientific literature searches are often exploratory, whereby users are not yet familiar with a particular field or concept but are interested in learning more about it. However, existing systems for scientific literature search are typically tailored to keyword-based lookup searches, limiting the possibilities for exploration. We propose NLP-KG, a feature-rich system designed to support the exploration of research literature in unfamiliar natural language processing (NLP) fields. In addition to a semantic search, NLP-KG allows users to easily find survey papers that provide a quick introduction to a field of interest. Further, a Fields of Study hierarchy graph enables users to familiarize themselves with a field and its related areas. Finally, a chat interface allows users to ask questions about unfamiliar concepts or specific articles in NLP and obtain answers grounded in knowledge retrieved from scientific publications. Our system provides users with comprehensive exploration possibilities, supporting them in investigating the relationships between different fields, understanding unfamiliar concepts in NLP, and finding relevant research literature. Demo, video, and code are available at: https://github.com/NLP-Knowledge-Graph/NLP-KG-WebApp.

In this work, we explore the use of Large Language Models (LLMs) for knowledge engineering tasks in the context of the ISWC 2023 LM-KBC Challenge. For this task, given subject and relation pairs sourced from Wikidata, we utilize pre-trained LLMs to produce the relevant objects in string format and link them to their respective Wikidata QIDs. We developed a pipeline using LLMs for Knowledge Engineering (LLMKE), combining knowledge probing and Wikidata entity mapping. The method achieved a macro-averaged F1-score of 0.701 across the properties, with the scores varying from 1.00 to 0.328. These results demonstrate that the knowledge of LLMs varies significantly depending on the domain and that further experimentation is required to determine the circumstances under which LLMs can be used for automatic Knowledge Base (e.g., Wikidata) completion and correction. The investigation of the results also suggests the promising contribution of LLMs in collaborative knowledge engineering. LLMKE won Track 2 of the challenge. The implementation is available at https://github.com/bohuizhang/LLMKE.

Topic modeling is used for discovering latent semantic structure, usually referred to as topics, in a large collection of documents. The most widely used methods are Latent Dirichlet Allocation and Probabilistic Latent Semantic Analysis. Despite their popularity they have several weaknesses. In order to achieve optimal results they often require the number of topics to be known, custom stop-word lists, stemming, and lemmatization. Additionally these methods rely on bag-of-words representation of documents which ignore the ordering and semantics of words. Distributed representations of documents and words have gained popularity due to their ability to capture semantics of words and documents. We present top2vec, which leverages joint document and word semantic embedding to find topic vectors. This model does not require stop-word lists, stemming or lemmatization, and it automatically finds the number of topics. The resulting topic vectors are jointly embedded with the document and word vectors with distance between them representing semantic similarity. Our experiments demonstrate that top2vec finds topics which are significantly more informative and representative of the corpus trained on than probabilistic generative models.

We present M2D2, a fine-grained, massively multi-domain corpus for studying domain adaptation in language models (LMs). M2D2 consists of 8.5B tokens and spans 145 domains extracted from Wikipedia and Semantic Scholar. Using ontologies derived from Wikipedia and ArXiv categories, we organize the domains in each data source into 22 groups. This two-level hierarchy enables the study of relationships between domains and their effects on in- and out-of-domain performance after adaptation. We also present a number of insights into the nature of effective domain adaptation in LMs, as examples of the new types of studies M2D2 enables. To improve in-domain performance, we show the benefits of adapting the LM along a domain hierarchy; adapting to smaller amounts of fine-grained domain-specific data can lead to larger in-domain performance gains than larger amounts of weakly relevant data. We further demonstrate a trade-off between in-domain specialization and out-of-domain generalization within and across ontologies, as well as a strong correlation between out-of-domain performance and lexical overlap between domains.

Large language models (LLMs) are a class of language models that have demonstrated outstanding performance across a range of natural language processing (NLP) tasks and have become a highly sought-after research area, because of their ability to generate human-like language and their potential to revolutionize science and technology. In this study, we conduct bibliometric and discourse analyses of scholarly literature on LLMs. Synthesizing over 5,000 publications, this paper serves as a roadmap for researchers, practitioners, and policymakers to navigate the current landscape of LLMs research. We present the research trends from 2017 to early 2023, identifying patterns in research paradigms and collaborations. We start with analyzing the core algorithm developments and NLP tasks that are fundamental in LLMs research. We then investigate the applications of LLMs in various fields and domains including medicine, engineering, social science, and humanities. Our review also reveals the dynamic, fast-paced evolution of LLMs research. Overall, this paper offers valuable insights into the current state, impact, and potential of LLMs research and its applications.

We propose a framework for classifying the capabilities and behavior of Artificial General Intelligence (AGI) models and their precursors. This framework introduces levels of AGI performance, generality, and autonomy, providing a common language to compare models, assess risks, and measure progress along the path to AGI. To develop our framework, we analyze existing definitions of AGI, and distill six principles that a useful ontology for AGI should satisfy. With these principles in mind, we propose "Levels of AGI" based on depth (performance) and breadth (generality) of capabilities, and reflect on how current systems fit into this ontology. We discuss the challenging requirements for future benchmarks that quantify the behavior and capabilities of AGI models against these levels. Finally, we discuss how these levels of AGI interact with deployment considerations such as autonomy and risk, and emphasize the importance of carefully selecting Human-AI Interaction paradigms for responsible and safe deployment of highly capable AI systems.

The emergence of vision-language models has transformed medical AI, enabling unprecedented advances in diagnostic capability and clinical applications. However, progress in dermatology has lagged behind other medical domains due to the lack of standard image-text pairs. Existing dermatological datasets are limited in both scale and depth, offering only single-label annotations across a narrow range of diseases instead of rich textual descriptions, and lacking the crucial clinical context needed for real-world applications. To address these limitations, we present Derm1M, the first large-scale vision-language dataset for dermatology, comprising 1,029,761 image-text pairs. Built from diverse educational resources and structured around a standard ontology collaboratively developed by experts, Derm1M provides comprehensive coverage for over 390 skin conditions across four hierarchical levels and 130 clinical concepts with rich contextual information such as medical history, symptoms, and skin tone. To demonstrate Derm1M potential in advancing both AI research and clinical application, we pretrained a series of CLIP-like models, collectively called DermLIP, on this dataset. The DermLIP family significantly outperforms state-of-the-art foundation models on eight diverse datasets across multiple tasks, including zero-shot skin disease classification, clinical and artifacts concept identification, few-shot/full-shot learning, and cross-modal retrieval. Our dataset and code will be public.

As there are now millions of publicly available neural networks, searching and analyzing large model repositories becomes increasingly important. Navigating so many models requires an atlas, but as most models are poorly documented charting such an atlas is challenging. To explore the hidden potential of model repositories, we chart a preliminary atlas representing the documented fraction of Hugging Face. It provides stunning visualizations of the model landscape and evolution. We demonstrate several applications of this atlas including predicting model attributes (e.g., accuracy), and analyzing trends in computer vision models. However, as the current atlas remains incomplete, we propose a method for charting undocumented regions. Specifically, we identify high-confidence structural priors based on dominant real-world model training practices. Leveraging these priors, our approach enables accurate mapping of previously undocumented areas of the atlas. We publicly release our datasets, code, and interactive atlas.

This work presents an unsupervised method for automatically constructing and expanding topic taxonomies by using instruction-based fine-tuned LLMs (Large Language Models). We apply topic modeling and keyword extraction techniques to create initial topic taxonomies and LLMs to post-process the resulting terms and create a hierarchy. To expand an existing taxonomy with new terms, we use zero-shot prompting to find out where to add new nodes, which, to our knowledge, is the first work to present such an approach to taxonomy tasks. We use the resulting taxonomies to assign tags that characterize merchants from a retail bank dataset. To evaluate our work, we asked 12 volunteers to answer a two-part form in which we first assessed the quality of the taxonomies created and then the tags assigned to merchants based on that taxonomy. The evaluation revealed a coherence rate exceeding 90% for the chosen taxonomies, while the average coherence for merchant tagging surpassed 80%.

The Airbnb search system grapples with many unique challenges as it continues to evolve. We oversee a marketplace that is nuanced by geography, diversity of homes, and guests with a variety of preferences. Crafting an efficient search system that can accommodate diverse guest needs, while showcasing relevant homes lies at the heart of Airbnb's success. Airbnb search has many challenges that parallel other recommendation and search systems but it has a unique information retrieval problem, upstream of ranking, called location retrieval. It requires defining a topological map area that is relevant to the searched query for homes listing retrieval. The purpose of this paper is to demonstrate the methodology, challenges, and impact of building a machine learning based location retrieval product from the ground up. Despite the lack of suitable, prevalent machine learning based approaches, we tackle cold start, generalization, differentiation and algorithmic bias. We detail the efficacy of heuristics, statistics, machine learning, and reinforcement learning approaches to solve these challenges, particularly for systems that are often unexplored by current literature.

Large Language Models (LLMs) are catalyzing a paradigm shift in scientific discovery, evolving from task-specific automation tools into increasingly autonomous agents and fundamentally redefining research processes and human-AI collaboration. This survey systematically charts this burgeoning field, placing a central focus on the changing roles and escalating capabilities of LLMs in science. Through the lens of the scientific method, we introduce a foundational three-level taxonomy-Tool, Analyst, and Scientist-to delineate their escalating autonomy and evolving responsibilities within the research lifecycle. We further identify pivotal challenges and future research trajectories such as robotic automation, self-improvement, and ethical governance. Overall, this survey provides a conceptual architecture and strategic foresight to navigate and shape the future of AI-driven scientific discovery, fostering both rapid innovation and responsible advancement. Github Repository: https://github.com/HKUST-KnowComp/Awesome-LLM-Scientific-Discovery.

Recent breakthroughs in large language models (LLMs) exemplified by the impressive mathematical and scientific reasoning capabilities of the o1 model have spotlighted the critical importance of high-quality training data in advancing LLM performance across STEM disciplines. While the mathematics community has benefited from a growing body of curated datasets, the scientific domain at the higher education level has long suffered from a scarcity of comparable resources. To address this gap, we present SCP-116K, a new large-scale dataset of 116,756 high-quality problem-solution pairs, automatically extracted from heterogeneous sources using a streamlined and highly generalizable pipeline. Our approach involves stringent filtering to ensure the scientific rigor and educational level of the extracted materials, while maintaining adaptability for future expansions or domain transfers. By openly releasing both the dataset and the extraction pipeline, we seek to foster research on scientific reasoning, enable comprehensive performance evaluations of new LLMs, and lower the barrier to replicating the successes of advanced models like o1 in the broader science community. We believe SCP-116K will serve as a critical resource, catalyzing progress in high-level scientific reasoning tasks and promoting further innovations in LLM development. The dataset and code are publicly available at https://github.com/AQA6666/SCP-116K-open.

This paper embarks on an exploration into the Large Language Model (LLM) datasets, which play a crucial role in the remarkable advancements of LLMs. The datasets serve as the foundational infrastructure analogous to a root system that sustains and nurtures the development of LLMs. Consequently, examination of these datasets emerges as a critical topic in research. In order to address the current lack of a comprehensive overview and thorough analysis of LLM datasets, and to gain insights into their current status and future trends, this survey consolidates and categorizes the fundamental aspects of LLM datasets from five perspectives: (1) Pre-training Corpora; (2) Instruction Fine-tuning Datasets; (3) Preference Datasets; (4) Evaluation Datasets; (5) Traditional Natural Language Processing (NLP) Datasets. The survey sheds light on the prevailing challenges and points out potential avenues for future investigation. Additionally, a comprehensive review of the existing available dataset resources is also provided, including statistics from 444 datasets, covering 8 language categories and spanning 32 domains. Information from 20 dimensions is incorporated into the dataset statistics. The total data size surveyed surpasses 774.5 TB for pre-training corpora and 700M instances for other datasets. We aim to present the entire landscape of LLM text datasets, serving as a comprehensive reference for researchers in this field and contributing to future studies. Related resources are available at: https://github.com/lmmlzn/Awesome-LLMs-Datasets.

Large language models (LLMs) have significantly advanced the field of natural language processing (NLP), providing a highly useful, task-agnostic foundation for a wide range of applications. However, directly applying LLMs to solve sophisticated problems in specific domains meets many hurdles, caused by the heterogeneity of domain data, the sophistication of domain knowledge, the uniqueness of domain objectives, and the diversity of the constraints (e.g., various social norms, cultural conformity, religious beliefs, and ethical standards in the domain applications). Domain specification techniques are key to make large language models disruptive in many applications. Specifically, to solve these hurdles, there has been a notable increase in research and practices conducted in recent years on the domain specialization of LLMs. This emerging field of study, with its substantial potential for impact, necessitates a comprehensive and systematic review to better summarize and guide ongoing work in this area. In this article, we present a comprehensive survey on domain specification techniques for large language models, an emerging direction critical for large language model applications. First, we propose a systematic taxonomy that categorizes the LLM domain-specialization techniques based on the accessibility to LLMs and summarizes the framework for all the subcategories as well as their relations and differences to each other. Second, we present an extensive taxonomy of critical application domains that can benefit dramatically from specialized LLMs, discussing their practical significance and open challenges. Last, we offer our insights into the current research status and future trends in this area.

Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic notations, with emerging extensions to incorporate multi-modal inputs. To advance the new field of LLM for molecular discovery, this survey provides an up-to-date and forward-looking review of the emerging use of LLMs for two central tasks: molecule generation and molecule optimization. Based on our proposed taxonomy for both problems, we analyze representative techniques in each category, highlighting how LLM capabilities are leveraged across different learning settings. In addition, we include the commonly used datasets and evaluation protocols. We conclude by discussing key challenges and future directions, positioning this survey as a resource for researchers working at the intersection of LLMs and molecular science. A continuously updated reading list is available at https://github.com/REAL-Lab-NU/Awesome-LLM-Centric-Molecular-Discovery.

Identifying keyphrases (KPs) from text documents is a fundamental task in natural language processing and information retrieval. Vast majority of the benchmark datasets for this task are from the scientific domain containing only the document title and abstract information. This limits keyphrase extraction (KPE) and keyphrase generation (KPG) algorithms to identify keyphrases from human-written summaries that are often very short (approx 8 sentences). This presents three challenges for real-world applications: human-written summaries are unavailable for most documents, the documents are almost always long, and a high percentage of KPs are directly found beyond the limited context of title and abstract. Therefore, we release two extensive corpora mapping KPs of ~1.3M and ~100K scientific articles with their fully extracted text and additional metadata including publication venue, year, author, field of study, and citations for facilitating research on this real-world problem.

Biomedical research is growing at such an exponential pace that scientists, researchers, and practitioners are no more able to cope with the amount of published literature in the domain. The knowledge presented in the literature needs to be systematized in such a way that claims and hypotheses can be easily found, accessed, and validated. Knowledge graphs can provide such a framework for semantic knowledge representation from literature. However, in order to build a knowledge graph, it is necessary to extract knowledge as relationships between biomedical entities and normalize both entities and relationship types. In this paper, we present and compare few rule-based and machine learning-based (Naive Bayes, Random Forests as examples of traditional machine learning methods and DistilBERT, PubMedBERT, T5 and SciFive-based models as examples of modern deep learning transformers) methods for scalable relationship extraction from biomedical literature, and for the integration into the knowledge graphs. We examine how resilient are these various methods to unbalanced and fairly small datasets. Our experiments show that transformer-based models handle well both small (due to pre-training on a large dataset) and unbalanced datasets. The best performing model was the PubMedBERT-based model fine-tuned on balanced data, with a reported F1-score of 0.92. DistilBERT-based model followed with F1-score of 0.89, performing faster and with lower resource requirements. BERT-based models performed better then T5-based generative models.

Accurate mapping of the built asset information to established data classification systems and taxonomies is crucial for effective asset management, whether for compliance at project handover or ad-hoc data integration scenarios. Due to the complex nature of built asset data, which predominantly comprises technical text elements, this process remains largely manual and reliant on domain expert input. Recent breakthroughs in contextual text representation learning (text embedding), particularly through pre-trained large language models, offer promising approaches that can facilitate the automation of cross-mapping of the built asset data. However, no comprehensive evaluation has yet been conducted to assess these models' ability to effectively represent the complex semantics specific to built asset technical terminology. This study presents a comparative benchmark of state-of-the-art text embedding models to evaluate their effectiveness in aligning built asset information with domain-specific technical concepts. Our proposed datasets are derived from two renowned built asset data classification dictionaries. The results of our benchmarking across six proposed datasets, covering three tasks of clustering, retrieval, and reranking, highlight the need for future research on domain adaptation techniques. The benchmarking resources are published as an open-source library, which will be maintained and extended to support future evaluations in this field.

The rapid expansion of scientific literature in computer science presents challenges in tracking research trends and extracting key insights. Existing datasets provide metadata but lack structured summaries that capture core contributions and methodologies. We introduce CS-PaperSum, a large-scale dataset of 91,919 papers from 31 top-tier computer science conferences, enriched with AI-generated structured summaries using ChatGPT. To assess summary quality, we conduct embedding alignment analysis and keyword overlap analysis, demonstrating strong preservation of key concepts. We further present a case study on AI research trends, highlighting shifts in methodologies and interdisciplinary crossovers, including the rise of self-supervised learning, retrieval-augmented generation, and multimodal AI. Our dataset enables automated literature analysis, research trend forecasting, and AI-driven scientific discovery, providing a valuable resource for researchers, policymakers, and scientific information retrieval systems.

The Land Matrix initiative (https://landmatrix.org) and its global observatory aim to provide reliable data on large-scale land acquisitions to inform debates and actions in sectors such as agriculture, extraction, or energy in low- and middle-income countries. Although these data are recognized in the academic world, they remain underutilized in public policy, mainly due to the complexity of access and exploitation, which requires technical expertise and a good understanding of the database schema. The objective of this work is to simplify access to data from different database systems. The methods proposed in this article are evaluated using data from the Land Matrix. This work presents various comparisons of Large Language Models (LLMs) as well as combinations of LLM adaptations (Prompt Engineering, RAG, Agents) to query different database systems (GraphQL and REST queries). The experiments are reproducible, and a demonstration is available online: https://github.com/tetis-nlp/landmatrix-graphql-python.

Keyphrase generation has primarily been explored within the context of academic research articles, with a particular focus on scientific domains and the English language. In this work, we present EUROPA, a dataset for multilingual keyphrase generation in the legal domain. It is derived from legal judgments from the Court of Justice of the European Union (EU), and contains instances in all 24 EU official languages. We run multilingual models on our corpus and analyze the results, showing room for improvement on a domain-specific multilingual corpus such as the one we present.

Many mathematical models have been leveraged to design embeddings for representing Knowledge Graph (KG) entities and relations for link prediction and many downstream tasks. These mathematically-inspired models are not only highly scalable for inference in large KGs, but also have many explainable advantages in modeling different relation patterns that can be validated through both formal proofs and empirical results. In this paper, we make a comprehensive overview of the current state of research in KG completion. In particular, we focus on two main branches of KG embedding (KGE) design: 1) distance-based methods and 2) semantic matching-based methods. We discover the connections between recently proposed models and present an underlying trend that might help researchers invent novel and more effective models. Next, we delve into CompoundE and CompoundE3D, which draw inspiration from 2D and 3D affine operations, respectively. They encompass a broad spectrum of techniques including distance-based and semantic-based methods. We will also discuss an emerging approach for KG completion which leverages pre-trained language models (PLMs) and textual descriptions of entities and relations and offer insights into the integration of KGE embedding methods with PLMs for KG completion.

Autonomous agents have long been a prominent research focus in both academic and industry communities. Previous research in this field often focuses on training agents with limited knowledge within isolated environments, which diverges significantly from human learning processes, and thus makes the agents hard to achieve human-like decisions. Recently, through the acquisition of vast amounts of web knowledge, large language models (LLMs) have demonstrated remarkable potential in achieving human-level intelligence. This has sparked an upsurge in studies investigating LLM-based autonomous agents. In this paper, we present a comprehensive survey of these studies, delivering a systematic review of the field of LLM-based autonomous agents from a holistic perspective. More specifically, we first discuss the construction of LLM-based autonomous agents, for which we propose a unified framework that encompasses a majority of the previous work. Then, we present a comprehensive overview of the diverse applications of LLM-based autonomous agents in the fields of social science, natural science, and engineering. Finally, we delve into the evaluation strategies commonly used for LLM-based autonomous agents. Based on the previous studies, we also present several challenges and future directions in this field. To keep track of this field and continuously update our survey, we maintain a repository of relevant references at https://github.com/Paitesanshi/LLM-Agent-Survey.

Recent progress in large language models (LLMs) has enabled the deployment of many generative NLP applications. At the same time, it has also led to a misleading public discourse that ``it's all been solved.'' Not surprisingly, this has, in turn, made many NLP researchers -- especially those at the beginning of their careers -- worry about what NLP research area they should focus on. Has it all been solved, or what remaining questions can we work on regardless of LLMs? To address this question, this paper compiles NLP research directions rich for exploration. We identify fourteen different research areas encompassing 45 research directions that require new research and are not directly solvable by LLMs. While we identify many research areas, many others exist; we do not cover areas currently addressed by LLMs, but where LLMs lag behind in performance or those focused on LLM development. We welcome suggestions for other research directions to include: https://bit.ly/nlp-era-llm

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine. In experiments with 19 researchers and clinicians using our system, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain and to AI papers, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org/

Text-rich Graph Knowledge Bases (TG-KBs) have become increasingly crucial for answering queries by providing textual and structural knowledge. However, current retrieval methods often retrieve these two types of knowledge in isolation without considering their mutual reinforcement and some hybrid methods even bypass structural retrieval entirely after neighboring aggregation. To fill in this gap, we propose a Mixture of Structural-and-Textual Retrieval (MoR) to retrieve these two types of knowledge via a Planning-Reasoning-Organizing framework. In the Planning stage, MoR generates textual planning graphs delineating the logic for answering queries. Following planning graphs, in the Reasoning stage, MoR interweaves structural traversal and textual matching to obtain candidates from TG-KBs. In the Organizing stage, MoR further reranks fetched candidates based on their structural trajectory. Extensive experiments demonstrate the superiority of MoR in harmonizing structural and textual retrieval with insights, including uneven retrieving performance across different query logics and the benefits of integrating structural trajectories for candidate reranking. Our code is available at https://github.com/Yoega/MoR.

Although large language models (LLMs) are impressive in solving various tasks, they can quickly be outdated after deployment. Maintaining their up-to-date status is a pressing concern in the current era. This paper provides a comprehensive review of recent advances in aligning LLMs with the ever-changing world knowledge without re-training from scratch. We categorize research works systemically and provide in-depth comparisons and discussion. We also discuss existing challenges and highlight future directions to facilitate research in this field. We release the paper list at https://github.com/hyintell/awesome-refreshing-llms

Knowledge Graph-to-Text (G2T) generation involves verbalizing structured knowledge graphs into natural language text. Recent advancements in Pretrained Language Models (PLMs) have improved G2T performance, but their effectiveness depends on datasets with precise graph-text alignment. However, the scarcity of high-quality, general-domain G2T generation datasets restricts progress in the general-domain G2T generation research. To address this issue, we introduce Wikipedia Ontology-Free Graph-text dataset (WikiOFGraph), a new large-scale G2T dataset generated using a novel method that leverages Large Language Model (LLM) and Data-QuestEval. Our new dataset, which contains 5.85M general-domain graph-text pairs, offers high graph-text consistency without relying on external ontologies. Experimental results demonstrate that PLM fine-tuned on WikiOFGraph outperforms those trained on other datasets across various evaluation metrics. Our method proves to be a scalable and effective solution for generating high-quality G2T data, significantly advancing the field of G2T generation.

Large language models (LLMs) have emerged as powerful tools in chemistry, significantly impacting molecule design, property prediction, and synthesis optimization. This review highlights LLM capabilities in these domains and their potential to accelerate scientific discovery through automation. We also review LLM-based autonomous agents: LLMs with a broader set of tools to interact with their surrounding environment. These agents perform diverse tasks such as paper scraping, interfacing with automated laboratories, and synthesis planning. As agents are an emerging topic, we extend the scope of our review of agents beyond chemistry and discuss across any scientific domains. This review covers the recent history, current capabilities, and design of LLMs and autonomous agents, addressing specific challenges, opportunities, and future directions in chemistry. Key challenges include data quality and integration, model interpretability, and the need for standard benchmarks, while future directions point towards more sophisticated multi-modal agents and enhanced collaboration between agents and experimental methods. Due to the quick pace of this field, a repository has been built to keep track of the latest studies: https://github.com/ur-whitelab/LLMs-in-science.

Large Language Models (LLMs) have demonstrated unprecedented prowess across various natural language processing tasks in various application domains. Recent studies show that LLMs can be leveraged to perform lexical semantic tasks, such as Knowledge Base Completion (KBC) or Ontology Learning (OL). However, it has not effectively been verified whether their success is due to their ability to reason over unstructured or semi-structured data, or their effective learning of linguistic patterns and senses alone. This unresolved question is particularly crucial when dealing with domain-specific data, where the lexical senses and their meaning can completely differ from what a LLM has learned during its training stage. This paper investigates the following question: Do LLMs really adapt to domains and remain consistent in the extraction of structured knowledge, or do they only learn lexical senses instead of reasoning? To answer this question and, we devise a controlled experiment setup that uses WordNet to synthesize parallel corpora, with English and gibberish terms. We examine the differences in the outputs of LLMs for each corpus in two OL tasks: relation extraction and taxonomy discovery. Empirical results show that, while adapting to the gibberish corpora, off-the-shelf LLMs do not consistently reason over semantic relationships between concepts, and instead leverage senses and their frame. However, fine-tuning improves the performance of LLMs on lexical semantic tasks even when the domain-specific terms are arbitrary and unseen during pre-training, hinting at the applicability of pre-trained LLMs for OL.

The existing search tools for exploring the NASA Astrophysics Data System (ADS) can be quite rich and empowering (e.g., similar and trending operators), but researchers are not yet allowed to fully leverage semantic search. For example, a query for "results from the Planck mission" should be able to distinguish between all the various meanings of Planck (person, mission, constant, institutions and more) without further clarification from the user. At ADS, we are applying modern machine learning and natural language processing techniques to our dataset of recent astronomy publications to train astroBERT, a deeply contextual language model based on research at Google. Using astroBERT, we aim to enrich the ADS dataset and improve its discoverability, and in particular we are developing our own named entity recognition tool. We present here our preliminary results and lessons learned.

Knowledge Bases (KBs) find applications in many knowledge-intensive tasks and, most notably, in information retrieval. Wikidata is one of the largest public general-purpose KBs. Yet, its collaborative nature has led to a convoluted schema and taxonomy. The YAGO 4 KB cleaned up the taxonomy by incorporating the ontology of Schema.org, resulting in a cleaner structure amenable to automated reasoning. However, it also cut away large parts of the Wikidata taxonomy, which is essential for information retrieval. In this paper, we extend YAGO 4 with a large part of the Wikidata taxonomy - while respecting logical constraints and the distinction between classes and instances. This yields YAGO 4.5, a new, logically consistent version of YAGO that adds a rich layer of informative classes. An intrinsic and an extrinsic evaluation show the value of the new resource.

Structured knowledge bases (KBs) are the backbone of many know\-ledge-intensive applications, and their automated construction has received considerable attention. In particular, open information extraction (OpenIE) is often used to induce structure from a text. However, although it allows high recall, the extracted knowledge tends to inherit noise from the sources and the OpenIE algorithm. Besides, OpenIE tuples contain an open-ended, non-canonicalized set of relations, making the extracted knowledge's downstream exploitation harder. In this paper, we study the problem of mapping an open KB into the fixed schema of an existing KB, specifically for the case of commonsense knowledge. We propose approaching the problem by generative translation, i.e., by training a language model to generate fixed-schema assertions from open ones. Experiments show that this approach occupies a sweet spot between traditional manual, rule-based, or classification-based canonicalization and purely generative KB construction like COMET. Moreover, it produces higher mapping accuracy than the former while avoiding the association-based noise of the latter.

Enterprises often own large collections of structured data in the form of large databases or an enterprise data lake. Such data collections come with limited metadata and strict access policies that could limit access to the data contents and, therefore, limit the application of classic retrieval and analysis solutions. As a result, there is a need for solutions that can effectively utilize the available metadata. In this paper, we study the problem of matching table metadata to a business glossary containing data labels and descriptions. The resulting matching enables the use of an available or curated business glossary for retrieval and analysis without or before requesting access to the data contents. One solution to this problem is to use manually-defined rules or similarity measures on column names and glossary descriptions (or their vector embeddings) to find the closest match. However, such approaches need to be tuned through manual labeling and cannot handle many business glossaries that contain a combination of simple as well as complex and long descriptions. In this work, we leverage the power of large language models (LLMs) to design generic matching methods that do not require manual tuning and can identify complex relations between column names and glossaries. We propose methods that utilize LLMs in two ways: a) by generating additional context for column names that can aid with matching b) by using LLMs to directly infer if there is a relation between column names and glossary descriptions. Our preliminary experimental results show the effectiveness of our proposed methods.

This paper explores the use of large language models (LLMs) as research tools in the history, philosophy, and sociology of science (HPSS). LLMs are remarkably effective at processing unstructured text and inferring meaning from context, offering new affordances that challenge long-standing divides between computational and interpretive methods. This raises both opportunities and challenges for HPSS, which emphasizes interpretive methodologies and understands meaning as context-dependent, ambiguous, and historically situated. We argue that HPSS is uniquely positioned not only to benefit from LLMs' capabilities but also to interrogate their epistemic assumptions and infrastructural implications. To this end, we first offer a concise primer on LLM architectures and training paradigms tailored to non-technical readers. We frame LLMs not as neutral tools but as epistemic infrastructures that encode assumptions about meaning, context, and similarity, conditioned by their training data, architecture, and patterns of use. We then examine how computational techniques enhanced by LLMs, such as structuring data, detecting patterns, and modeling dynamic processes, can be applied to support interpretive research in HPSS. Our analysis compares full-context and generative models, outlines strategies for domain and task adaptation (e.g., continued pretraining, fine-tuning, and retrieval-augmented generation), and evaluates their respective strengths and limitations for interpretive inquiry in HPSS. We conclude with four lessons for integrating LLMs into HPSS: (1) model selection involves interpretive trade-offs; (2) LLM literacy is foundational; (3) HPSS must define its own benchmarks and corpora; and (4) LLMs should enhance, not replace, interpretive methods.

We describe a dataset developed for Named Entity Recognition in German federal court decisions. It consists of approx. 67,000 sentences with over 2 million tokens. The resource contains 54,000 manually annotated entities, mapped to 19 fine-grained semantic classes: person, judge, lawyer, country, city, street, landscape, organization, company, institution, court, brand, law, ordinance, European legal norm, regulation, contract, court decision, and legal literature. The legal documents were, furthermore, automatically annotated with more than 35,000 TimeML-based time expressions. The dataset, which is available under a CC-BY 4.0 license in the CoNNL-2002 format, was developed for training an NER service for German legal documents in the EU project Lynx.

Machine learning about language can be improved by supplying it with specific knowledge and sources of external information. We present here a new version of the linked open data resource ConceptNet that is particularly well suited to be used with modern NLP techniques such as word embeddings. ConceptNet is a knowledge graph that connects words and phrases of natural language with labeled edges. Its knowledge is collected from many sources that include expert-created resources, crowd-sourcing, and games with a purpose. It is designed to represent the general knowledge involved in understanding language, improving natural language applications by allowing the application to better understand the meanings behind the words people use. When ConceptNet is combined with word embeddings acquired from distributional semantics (such as word2vec), it provides applications with understanding that they would not acquire from distributional semantics alone, nor from narrower resources such as WordNet or DBPedia. We demonstrate this with state-of-the-art results on intrinsic evaluations of word relatedness that translate into improvements on applications of word vectors, including solving SAT-style analogies.

We present a new resource for the NLP community, namely a large (3.5M+ sentence) knowledge base of *generic statements*, e.g., "Trees remove carbon dioxide from the atmosphere", collected from multiple corpora. This is the first large resource to contain *naturally occurring* generic sentences, as opposed to extracted or crowdsourced triples, and thus is rich in high-quality, general, semantically complete statements. All GenericsKB sentences are annotated with their topical term, surrounding context (sentences), and a (learned) confidence. We also release GenericsKB-Best (1M+ sentences), containing the best-quality generics in GenericsKB augmented with selected, synthesized generics from WordNet and ConceptNet. In tests on two existing datasets requiring multihop reasoning (OBQA and QASC), we find using GenericsKB can result in higher scores and better explanations than using a much larger corpus. This demonstrates that GenericsKB can be a useful resource for NLP applications, as well as providing data for linguistic studies of generics and their semantics. GenericsKB is available at https://allenai.org/data/genericskb.

Data plays the most prominent role in how language models acquire skills and knowledge. The lack of massive, well-organized pre-training datasets results in costly and inaccessible data pipelines. We present Essential-Web v1.0, a 24-trillion-token dataset in which every document is annotated with a twelve-category taxonomy covering topic, format, content complexity, and quality. Taxonomy labels are produced by EAI-Distill-0.5b, a fine-tuned 0.5b-parameter model that achieves an annotator agreement within 3% of Qwen2.5-32B-Instruct. With nothing more than SQL-style filters, we obtain competitive web-curated datasets in math (-8.0% relative to SOTA), web code (+14.3%), STEM (+24.5%) and medical (+8.6%). Essential-Web v1.0 is available on HuggingFace: https://huggingface.co/datasets/EssentialAI/essential-web-v1.0

In this paper, we propose a robot oriented knowledge management system based on the use of the Prolog language. Our framework hinges on a special organisation of knowledge base that enables: 1. its efficient population from natural language texts using semi-automated procedures based on Large Language Models, 2. the bumpless generation of temporal parallel plans for multi-robot systems through a sequence of transformations, 3. the automated translation of the plan into an executable formalism (the behaviour trees). The framework is supported by a set of open source tools and is shown on a realistic application.

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph, FAIR Jupyter, that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph's content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness, i.e., their findability, accessibility, interoperability, and reusability, and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

In this paper, we present our approaches for the FinSim-3 Shared Task 2021: Learning Semantic Similarities for the Financial Domain. The aim of this shared task is to correctly classify a list of given terms from the financial domain into the most relevant hypernym (or top-level) concept in an external ontology. For our system submission, we evaluate two methods: a Sentence-RoBERTa (SRoBERTa) embeddings model pre-trained on a custom corpus, and a dual word-sentence embeddings model that builds on the first method by improving the proposed baseline word embeddings construction using the FastText model to boost the classification performance. Our system ranks 2nd overall on both metrics, scoring 0.917 on Average Accuracy and 1.141 on Mean Rank.

Traditionally, a debate usually requires a manual preparation process, including reading plenty of articles, selecting the claims, identifying the stances of the claims, seeking the evidence for the claims, etc. As the AI debate attracts more attention these years, it is worth exploring the methods to automate the tedious process involved in the debating system. In this work, we introduce a comprehensive and large dataset named IAM, which can be applied to a series of argument mining tasks, including claim extraction, stance classification, evidence extraction, etc. Our dataset is collected from over 1k articles related to 123 topics. Near 70k sentences in the dataset are fully annotated based on their argument properties (e.g., claims, stances, evidence, etc.). We further propose two new integrated argument mining tasks associated with the debate preparation process: (1) claim extraction with stance classification (CESC) and (2) claim-evidence pair extraction (CEPE). We adopt a pipeline approach and an end-to-end method for each integrated task separately. Promising experimental results are reported to show the values and challenges of our proposed tasks, and motivate future research on argument mining.

This paper explores the potential of contextualized word embeddings (CWEs) as a new tool in the history, philosophy, and sociology of science (HPSS) for studying contextual and evolving meanings of scientific concepts. Using the term "Planck" as a test case, I evaluate five BERT-based models with varying degrees of domain-specific pretraining, including my custom model Astro-HEP-BERT, trained on the Astro-HEP Corpus, a dataset containing 21.84 million paragraphs from 600,000 articles in astrophysics and high-energy physics. For this analysis, I compiled two labeled datasets: (1) the Astro-HEP-Planck Corpus, consisting of 2,900 labeled occurrences of "Planck" sampled from 1,500 paragraphs in the Astro-HEP Corpus, and (2) a physics-related Wikipedia dataset comprising 1,186 labeled occurrences of "Planck" across 885 paragraphs. Results demonstrate that the domain-adapted models outperform the general-purpose ones in disambiguating the target term, predicting its known meanings, and generating high-quality sense clusters, as measured by a novel purity indicator I developed. Additionally, this approach reveals semantic shifts in the target term over three decades in the unlabeled Astro-HEP Corpus, highlighting the emergence of the Planck space mission as a dominant sense. The study underscores the importance of domain-specific pretraining for analyzing scientific language and demonstrates the cost-effectiveness of adapting pretrained models for HPSS research. By offering a scalable and transferable method for modeling the meanings of scientific concepts, CWEs open up new avenues for investigating the socio-historical dynamics of scientific discourses.

A key component of deep learning (DL) for natural language processing (NLP) is word embeddings. Word embeddings that effectively capture the meaning and context of the word that they represent can significantly improve the performance of downstream DL models for various NLP tasks. Many existing word embeddings techniques capture the context of words based on word co-occurrence in documents and text; however, they often cannot capture broader domain-specific relationships between concepts that may be crucial for the NLP task at hand. In this paper, we propose a method to integrate external knowledge from medical terminology ontologies into the context captured by word embeddings. Specifically, we use a medical knowledge graph, such as the unified medical language system (UMLS), to find connections between clinical terms in cancer pathology reports. This approach aims to minimize the distance between connected clinical concepts. We evaluate the proposed approach using a Multitask Convolutional Neural Network (MT-CNN) to extract six cancer characteristics -- site, subsite, laterality, behavior, histology, and grade -- from a dataset of ~900K cancer pathology reports. The results show that the MT-CNN model which uses our domain informed embeddings outperforms the same MT-CNN using standard word2vec embeddings across all tasks, with an improvement in the overall micro- and macro-F1 scores by 4.97\%and 22.5\%, respectively.

Large Language Models (LLMs) have demonstrated unprecedented capabilities across various natural language processing tasks. Their ability to process and generate viable text and code has made them ubiquitous in many fields, while their deployment as knowledge bases and "reasoning" tools remains an area of ongoing research. In geography, a growing body of literature has been focusing on evaluating LLMs' geographical knowledge and their ability to perform spatial reasoning. However, very little is still known about the internal functioning of these models, especially about how they process geographical information. In this chapter, we establish a novel framework for the study of geospatial mechanistic interpretability - using spatial analysis to reverse engineer how LLMs handle geographical information. Our aim is to advance our understanding of the internal representations that these complex models generate while processing geographical information - what one might call "how LLMs think about geographic information" if such phrasing was not an undue anthropomorphism. We first outline the use of probing in revealing internal structures within LLMs. We then introduce the field of mechanistic interpretability, discussing the superposition hypothesis and the role of sparse autoencoders in disentangling polysemantic internal representations of LLMs into more interpretable, monosemantic features. In our experiments, we use spatial autocorrelation to show how features obtained for placenames display spatial patterns related to their geographic location and can thus be interpreted geospatially, providing insights into how these models process geographical information. We conclude by discussing how our framework can help shape the study and use of foundation models in geography.