DKE-Research at SemEval-2024 Task 2: Incorporating Data Augmentation with Generative Models and Biomedical Knowledge to Enhance Inference Robustness

Safe and reliable natural language inference is critical for extracting insights from clinical trial reports but poses challenges due to biases in large pre-trained language models. This paper presents a novel data augmentation technique to improve model robustness for biomedical natural language inference in clinical trials. By generating synthetic examples through semantic perturbations and domain-specific vocabulary replacement and adding a new task for numerical and quantitative reasoning, we introduce greater diversity and reduce shortcut learning. Our approach, combined with multi-task learning and the DeBERTa architecture, achieved significant performance gains on the NLI4CT 2024 benchmark compared to the original language models. Ablation studies validate the contribution of each augmentation method in improving robustness. Our best-performing model ranked 12th in terms of faithfulness and 8th in terms of consistency, respectively, out of the 32 participants.

Zero-Shot Medical Information Retrieval via Knowledge Graph Embedding

In the era of the Internet of Things (IoT), the retrieval of relevant medical information has become essential for efficient clinical decision-making. This paper introduces MedFusionRank, a novel approach to zero-shot medical information retrieval (MIR) that combines the strengths of pre-trained language models and statistical methods while addressing their limitations. The proposed approach leverages a pre-trained BERT-style model to extract compact yet informative keywords. These keywords are then enriched with domain knowledge by linking them to conceptual entities within a medical knowledge graph. Experimental evaluations on medical datasets demonstrate MedFusion Rank's superior performance over existing methods, with promising results with a variety of evaluation metrics. MedFusionRank demonstrates efficacy in retrieving relevant information, even from short or single-term queries.

YATO: Yet Another deep learning based Text analysis Open toolkit

We introduce YATO, an open-source toolkit for text analysis with deep learning. It focuses on fundamental sequence labeling and sequence classification tasks on text. Designed in a hierarchical structure, YATO supports free combinations of three types of features including 1) traditional neural networks (CNN, RNN, etc.); 2) pre-trained language models (BERT, RoBERTa, ELECTRA, etc.); and 3) user-customed neural features via a simple configurable file. Benefiting from the advantages of flexibility and ease of use, YATO can facilitate reproducing and refinement of state-of-the-art NLP models, and promote the cross-disciplinary applications of NLP techniques. Source code, examples, and documentation are publicly available at https://github.com/jiesutd/YATO.

METS-CoV: A Dataset of Medical Entity and Targeted Sentiment on COVID-19 Related Tweets

The COVID-19 pandemic continues to bring up various topics discussed or debated on social media. In order to explore the impact of pandemics on people's lives, it is crucial to understand the public's concerns and attitudes towards pandemic-related entities (e.g., drugs, vaccines) on social media. However, models trained on existing named entity recognition (NER) or targeted sentiment analysis (TSA) datasets have limited ability to understand COVID-19-related social media texts because these datasets are not designed or annotated from a medical perspective. This paper releases METS-CoV, a dataset containing medical entities and targeted sentiments from COVID-19-related tweets. METS-CoV contains 10,000 tweets with 7 types of entities, including 4 medical entity types (Disease, Drug, Symptom, and Vaccine) and 3 general entity types (Person, Location, and Organization). To further investigate tweet users' attitudes toward specific entities, 4 types of entities (Person, Organization, Drug, and Vaccine) are selected and annotated with user sentiments, resulting in a targeted sentiment dataset with 9,101 entities (in 5,278 tweets). To the best of our knowledge, METS-CoV is the first dataset to collect medical entities and corresponding sentiments of COVID-19-related tweets. We benchmark the performance of classical machine learning models and state-of-the-art deep learning models on NER and TSA tasks with extensive experiments. Results show that the dataset has vast room for improvement for both NER and TSA tasks. METS-CoV is an important resource for developing better medical social media tools and facilitating computational social science research, especially in epidemiology. Our data, annotation guidelines, benchmark models, and source code are publicly available (https://github.com/YLab-Open/METS-CoV) to ensure reproducibility.