Daily Papers

Efficiently serving Large Language Models (LLMs) requires selecting an optimal parallel execution plan, balancing computation, memory, and communication overhead. However, determining the best strategy is challenging due to varying parallelism techniques (data, pipeline, tensor) and workload characteristics (e.g., compute-intensive tasks with long prompts vs. memory-intensive tasks with long generation). We propose APEX, an LLM serving system simulator that efficiently identifies optimal parallel execution plans by considering key factors of LLM serving systems, such as memory usage, batching behavior, etc. APEX performs dynamism-aware simulation to model iteration-level batching, and leverages LLMs' repetitive structure to reduce design space, scaling efficiently to trillion-scale models. APEX abstracts the key components of LLM serving systems, including the model, batching module, quantization formats, and device clusters, enabling the simulator to be general and extensible. Simulating on a CPU, APEX evaluates execution plans for various device clusters, covering diverse LLMs and workloads. APEX finds plans up to 3.37x faster than heuristics, and also plans that reduce energy consumption by up to 45% compared to latency-optimal plans. APEX performs comprehensive evaluations, reporting key system metrics like time per output token and time to first token, which can help service providers meet SLOs. APEX identifies an optimal plan within 15 minutes on a CPU, making it 71x faster and 1234x more cost-effective than cloud-based GPU deployment. APEX can be accessed at https://github.com/microsoft/apex_plus

Antimicrobial resistance (AMR) is escalating and outpacing current antibiotic development. Thus, discovering antibiotics effective against emerging pathogens is becoming increasingly critical. However, existing approaches cannot rapidly identify effective molecules against novel pathogens or emerging drug-resistant strains. Here, we introduce ApexOracle, an artificial intelligence (AI) model that both predicts the antibacterial potency of existing compounds and designs de novo molecules active against strains it has never encountered. Departing from models that rely solely on molecular features, ApexOracle incorporates pathogen-specific context through the integration of molecular features captured via a foundational discrete diffusion language model and a dual-embedding framework that combines genomic- and literature-derived strain representations. Across diverse bacterial species and chemical modalities, ApexOracle consistently outperformed state-of-the-art approaches in activity prediction and demonstrated reliable transferability to novel pathogens with little or no antimicrobial data. Its unified representation-generation architecture further enables the in silico creation of "new-to-nature" molecules with high predicted efficacy against priority threats. By pairing rapid activity prediction with targeted molecular generation, ApexOracle offers a scalable strategy for countering AMR and preparing for future infectious-disease outbreaks.

In this paper we present APEX-Embedding-7B (Advanced Processing for Epistemic eXtraction), a 7-billion parameter decoder-only text Feature Extraction Model, specifically designed for Document Retrieval-Augmented Generation (RAG) tasks. Our approach employs two training techniques that yield an emergent improvement in factual focus: (1) Pre-convergence interrupted fine-tuning using Structured Entity Relationship Maps as training data input: designed to shift the model's attention and create a bias towards factual content rather than semantic style - this enhances plain text performance despite not being directly trained for it; and (2) Model-Aware Contrastive Sampling, creating a balanced and evenly distributed collation map of hard and soft negatives directly informed by the base model's competency. This combined methodology yields significant improvements, enhancing plain text query/document pair retrieval to achieve an absolute rank@1 accuracy of 90.86% (an increase of 6.26% compared to the next leading model) in our evaluation, and reducing training data input context size by an average of 37.71% compared to plain text for both queries and document texts. Based on our evaluations, our model establishes a new state-of-the-art standard in text feature extraction for longer context document retrieval tasks.

Assessing the capabilities of large multimodal models (LMMs) often requires the creation of ad-hoc evaluations. Currently, building new benchmarks requires tremendous amounts of manual work for each specific analysis. This makes the evaluation process tedious and costly. In this paper, we present APEx, Automatic Programming of Experiments, the first framework for automatic benchmarking of LMMs. Given a research question expressed in natural language, APEx leverages a large language model (LLM) and a library of pre-specified tools to generate a set of experiments for the model at hand, and progressively compile a scientific report. The report drives the testing procedure: based on the current status of the investigation, APEx chooses which experiments to perform and whether the results are sufficient to draw conclusions. Finally, the LLM refines the report, presenting the results to the user in natural language. Thanks to its modularity, our framework is flexible and extensible as new tools become available. Empirically, APEx reproduces the findings of existing studies while allowing for arbitrary analyses and hypothesis testing.

Using a set of LambdaCDM simulations of cosmic structure formation, we study the evolving connectivity and changing topological structure of the cosmic web using state-of-the-art tools of multiscale topological data analysis (TDA). We follow the development of the cosmic web topology in terms of the evolution of Betti number curves and feature persistence diagrams of the three (topological) classes of structural features: matter concentrations, filaments and tunnels, and voids. The Betti curves specify the prominence of features as a function of density level, and their evolution with cosmic epoch reflects the changing network connections between these structural features. The persistence diagrams quantify the longevity and stability of topological features. In this study we establish, for the first time, the link between persistence diagrams, the features they show, and the gravitationally driven cosmic structure formation process. By following the diagrams' development over cosmic time, the link between the multiscale topology of the cosmic web and the hierarchical buildup of cosmic structure is established. The sharp apexes in the diagrams are intimately related to key transitions in the structure formation process. The apex in the matter concentration diagrams coincides with the density level at which, typically, they detach from the Hubble expansion and begin to collapse. At that level many individual islands merge to form the network of the cosmic web and a large number of filaments and tunnels emerge to establish its connecting bridges. The location trends of the apex possess a self-similar character that can be related to the cosmic web's hierarchical buildup. We find that persistence diagrams provide a significantly higher and more profound level of information on the structure formation process than more global summary statistics like Euler characteristic or Betti numbers.