Lay summarization of biomedical research articles is a challenging problem due to their use of technical terms and background knowledge requirements, despite the potential benefits of these research articles to the public. We worked on this problem as participating in BioLaySumm 2024. We experimented with various fine-tuning approaches to generate better lay summaries for biomedical research articles. After several experiments, we built a LoRA model with unsupervised fine-tuning based on the abstracts of the given articles, followed by a post-processing unit to take off repeated sentences. Our model was ranked 3rd overall in the BioLaySumm 2024 leaderboard. We analyzed the different approaches we experimented with and suggested several ideas to improve our model further.

Participating in SemEval 2024 Task 2, we built a three-module system to predict entailment labels for NLI4CT, which consists of a sequence of the query generation module, the query answering module, and the aggregation module. We fine-tuned or prompted each module with the intermediate labels we generated with LLMs, and we optimized the combinations of different modules through experiments. Our system is ranked 19th ~ 24th in the SemEval 2024 Task 2 leaderboard in different metrics. We made several interesting observations regarding the correlation between different metrics and the sensitivity of our system on the aggregation module. We performed the error analysis on our system which can potentially help to improve our system further.

The goal of the NLI4CT task is to build a Natural Language Inference system for Clinical Trial Reports that will be used for evidence interpretation and retrieval. Large Language models have demonstrated state-of-the-art performance in various natural language processing tasks across multiple domains. We suggest using an instruction-finetuned Large Language Models (LLMs) to take on this particular task in light of these developments. We have evaluated the publicly available LLMs under zeroshot setting, and finetuned the best performing Flan-T5 model for this task. On the leaderboard, our system ranked second, with an F1 Score of 0.834 on the official test set.

Sentence embeddings in the form of fixed-size vectors that capture the information in the sentence as well as the context are critical components of Natural Language Processing systems. With transformer model based sentence encoders outperforming the other sentence embedding methods in the general domain, we explore the transformer based architectures to generate dense sentence embeddings in the biomedical domain. In this work, we present BioSimCSE, where we train sentence embeddings with domain specific transformer based models with biomedical texts. We assess our model’s performance with zero-shot and fine-tuned settings on Semantic Textual Similarity (STS) and Recognizing Question Entailment (RQE) tasks. Our BioSimCSE model using BioLinkBERT achieves state of the art (SOTA) performance on both tasks.

Recent advancements in pretraining strategies in NLP have shown a significant improvement in the performance of models on various text mining tasks. We apply ‘replaced token detection’ pretraining technique proposed by ELECTRA and pretrain a biomedical language model from scratch using biomedical text and vocabulary. We introduce BioELECTRA, a biomedical domain-specific language encoder model that adapts ELECTRA for the Biomedical domain. WE evaluate our model on the BLURB and BLUE biomedical NLP benchmarks. BioELECTRA outperforms the previous models and achieves state of the art (SOTA) on all the 13 datasets in BLURB benchmark and on all the 4 Clinical datasets from BLUE Benchmark across 7 different NLP tasks. BioELECTRA pretrained on PubMed and PMC full text articles performs very well on Clinical datasets as well. BioELECTRA achieves new SOTA 86.34%(1.39% accuracy improvement) on MedNLI and 64% (2.98% accuracy improvement) on PubMedQA dataset.

Natural Language inference is the task of identifying relation between two sentences as entailment, contradiction or neutrality. MedNLI is a biomedical flavour of NLI for clinical domain. This paper explores the use of Bidirectional Encoder Representation from Transformer (BERT) for solving MedNLI. The proposed model, BERT pre-trained on PMC, PubMed and fine-tuned on MIMICIII v1.4, achieves state of the art results on MedNLI (83.45%) and an accuracy of 78.5% in MEDIQA challenge. The authors present an analysis of the attention patterns that emerged as a result of training BERT on MedNLI using a visualization tool, bertviz.