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Aug 19

Extraction of Medication and Temporal Relation from Clinical Text using Neural Language Models

Clinical texts, represented in electronic medical records (EMRs), contain rich medical information and are essential for disease prediction, personalised information recommendation, clinical decision support, and medication pattern mining and measurement. Relation extractions between medication mentions and temporal information can further help clinicians better understand the patients' treatment history. To evaluate the performances of deep learning (DL) and large language models (LLMs) in medication extraction and temporal relations classification, we carry out an empirical investigation of MedTem project using several advanced learning structures including BiLSTM-CRF and CNN-BiLSTM for a clinical domain named entity recognition (NER), and BERT-CNN for temporal relation extraction (RE), in addition to the exploration of different word embedding techniques. Furthermore, we also designed a set of post-processing roles to generate structured output on medications and the temporal relation. Our experiments show that CNN-BiLSTM slightly wins the BiLSTM-CRF model on the i2b2-2009 clinical NER task yielding 75.67, 77.83, and 78.17 for precision, recall, and F1 scores using Macro Average. BERT-CNN model also produced reasonable evaluation scores 64.48, 67.17, and 65.03 for P/R/F1 using Macro Avg on the temporal relation extraction test set from i2b2-2012 challenges. Code and Tools from MedTem will be hosted at https://github.com/HECTA-UoM/MedTem

arXivEdits: Understanding the Human Revision Process in Scientific Writing

Scientific publications are the primary means to communicate research discoveries, where the writing quality is of crucial importance. However, prior work studying the human editing process in this domain mainly focused on the abstract or introduction sections, resulting in an incomplete picture. In this work, we provide a complete computational framework for studying text revision in scientific writing. We first introduce arXivEdits, a new annotated corpus of 751 full papers from arXiv with gold sentence alignment across their multiple versions of revision, as well as fine-grained span-level edits and their underlying intentions for 1,000 sentence pairs. It supports our data-driven analysis to unveil the common strategies practiced by researchers for revising their papers. To scale up the analysis, we also develop automatic methods to extract revision at document-, sentence-, and word-levels. A neural CRF sentence alignment model trained on our corpus achieves 93.8 F1, enabling the reliable matching of sentences between different versions. We formulate the edit extraction task as a span alignment problem, and our proposed method extracts more fine-grained and explainable edits, compared to the commonly used diff algorithm. An intention classifier trained on our dataset achieves 78.9 F1 on the fine-grained intent classification task. Our data and system are released at tiny.one/arxivedits.

EmotionIC: Emotional Inertia and Contagion-driven Dependency Modelling for Emotion Recognition in Conversation

Emotion Recognition in Conversation (ERC) has attracted growing attention in recent years as a result of the advancement and implementation of human-computer interface technologies. However, previous approaches to modeling global and local context dependencies lost the diversity of dependency information and do not take the context dependency into account at the classification level. In this paper, we propose a novel approach to dependency modeling driven by Emotional Inertia and Contagion (EmotionIC) for conversational emotion recognition at the feature extraction and classification levels. At the feature extraction level, our designed Identity Masked Multi-head Attention (IM-MHA) captures the identity-based long-distant context in the dialogue to contain the diverse influence of different participants and construct the global emotional atmosphere, while the devised Dialogue-based Gate Recurrent Unit (DialogGRU) that aggregates the emotional tendencies of dyadic dialogue is applied to refine the contextual features with inter- and intra-speaker dependencies. At the classification level, by introducing skip connections in Conditional Random Field (CRF), we elaborate the Skip-chain CRF (SkipCRF) to capture the high-order dependencies within and between speakers, and to emulate the emotional flow of distant participants. Experimental results show that our method can significantly outperform the state-of-the-art models on four benchmark datasets. The ablation studies confirm that our modules can effectively model emotional inertia and contagion.

Identity Preserving Loss for Learned Image Compression

Deep learning model inference on embedded devices is challenging due to the limited availability of computation resources. A popular alternative is to perform model inference on the cloud, which requires transmitting images from the embedded device to the cloud. Image compression techniques are commonly employed in such cloud-based architectures to reduce transmission latency over low bandwidth networks. This work proposes an end-to-end image compression framework that learns domain-specific features to achieve higher compression ratios than standard HEVC/JPEG compression techniques while maintaining accuracy on downstream tasks (e.g., recognition). Our framework does not require fine-tuning of the downstream task, which allows us to drop-in any off-the-shelf downstream task model without retraining. We choose faces as an application domain due to the ready availability of datasets and off-the-shelf recognition models as representative downstream tasks. We present a novel Identity Preserving Reconstruction (IPR) loss function which achieves Bits-Per-Pixel (BPP) values that are ~38% and ~42% of CRF-23 HEVC compression for LFW (low-resolution) and CelebA-HQ (high-resolution) datasets, respectively, while maintaining parity in recognition accuracy. The superior compression ratio is achieved as the model learns to retain the domain-specific features (e.g., facial features) while sacrificing details in the background. Furthermore, images reconstructed by our proposed compression model are robust to changes in downstream model architectures. We show at-par recognition performance on the LFW dataset with an unseen recognition model while retaining a lower BPP value of ~38% of CRF-23 HEVC compression.

An Automatic SOAP Classification System Using Weakly Supervision And Transfer Learning

In this paper, we introduce a comprehensive framework for developing a machine learning-based SOAP (Subjective, Objective, Assessment, and Plan) classification system without manually SOAP annotated training data or with less manually SOAP annotated training data. The system is composed of the following two parts: 1) Data construction, 2) A neural network-based SOAP classifier, and 3) Transfer learning framework. In data construction, since a manual construction of a large size training dataset is expensive, we propose a rule-based weak labeling method utilizing the structured information of an EHR note. Then, we present a SOAP classifier composed of a pre-trained language model and bi-directional long-short term memory with conditional random field (Bi-LSTM-CRF). Finally, we propose a transfer learning framework that re-uses the trained parameters of the SOAP classifier trained with the weakly labeled dataset for datasets collected from another hospital. The proposed weakly label-based learning model successfully performed SOAP classification (89.99 F1-score) on the notes collected from the target hospital. Otherwise, in the notes collected from other hospitals and departments, the performance dramatically decreased. Meanwhile, we verified that the transfer learning framework is advantageous for inter-hospital adaptation of the model increasing the models' performance in every cases. In particular, the transfer learning approach was more efficient when the manually annotated data size was smaller. We showed that SOAP classification models trained with our weakly labeling algorithm can perform SOAP classification without manually annotated data on the EHR notes from the same hospital. The transfer learning framework helps SOAP classification model's inter-hospital migration with a minimal size of the manually annotated dataset.

A Natural Language Processing Pipeline of Chinese Free-text Radiology Reports for Liver Cancer Diagnosis

Despite the rapid development of natural language processing (NLP) implementation in electronic medical records (EMRs), Chinese EMRs processing remains challenging due to the limited corpus and specific grammatical characteristics, especially for radiology reports. In this study, we designed an NLP pipeline for the direct extraction of clinically relevant features from Chinese radiology reports, which is the first key step in computer-aided radiologic diagnosis. The pipeline was comprised of named entity recognition, synonyms normalization, and relationship extraction to finally derive the radiological features composed of one or more terms. In named entity recognition, we incorporated lexicon into deep learning model bidirectional long short-term memory-conditional random field (BiLSTM-CRF), and the model finally achieved an F1 score of 93.00%. With the extracted radiological features, least absolute shrinkage and selection operator and machine learning methods (support vector machine, random forest, decision tree, and logistic regression) were used to build the classifiers for liver cancer prediction. For liver cancer diagnosis, random forest had the highest predictive performance in liver cancer diagnosis (F1 score 86.97%, precision 87.71%, and recall 86.25%). This work was a comprehensive NLP study focusing on Chinese radiology reports and the application of NLP in cancer risk prediction. The proposed NLP pipeline for the radiological feature extraction could be easily implemented in other kinds of Chinese clinical texts and other disease predictive tasks.