Sihyeon Park

Chanhwi Kim, Hyunjae Kim, Sihyeon Park et al.

Generative models have become widely used in biomedical entity linking (BioEL) due to their excellent performance and efficient memory usage. However, these models are usually trained only with positive samples, i.e., entities that match the input mention's identifier, and do not explicitly learn from hard negative samples, which are entities that look similar but have different meanings. To address this limitation, we introduce ANGEL (Learning from Negative Samples in Biomedical Generative Entity Linking), the first framework that trains generative BioEL models using negative samples. Specifically, a generative model is initially trained to generate positive entity names from the knowledge base for given input entities. Subsequently, both correct and incorrect outputs are gathered from the model's top-k predictions. Finally, the model is updated to prioritize the correct predictions through preference optimization. Our models outperform the previous best baseline models by up to an average top-1 accuracy of 1.4% on five benchmarks. When incorporating our framework into pre-training, the performance improvement increases further to 1.7%, demonstrating its effectiveness in both the pre-training and fine-tuning stages. The code and model weights are available at https://github.com/dmis-lab/ANGEL.

Hyunjae Kim, Hyeon Hwang, Jiwoo Lee et al.

While recent advancements in commercial large language models (LM) have shown promising results in medical tasks, their closed-source nature poses significant privacy and security concerns, hindering their widespread use in the medical field. Despite efforts to create open-source models, their limited parameters often result in insufficient multi-step reasoning capabilities required for solving complex medical problems. To address this, we introduce Meerkat, a new family of medical AI systems ranging from 7 to 70 billion parameters. The models were trained using our new synthetic dataset consisting of high-quality chain-of-thought reasoning paths sourced from 18 medical textbooks, along with diverse instruction-following datasets. Our systems achieved remarkable accuracy across six medical benchmarks, surpassing the previous best models such as MediTron and BioMistral, and GPT-3.5 by a large margin. Notably, Meerkat-7B surpassed the passing threshold of the United States Medical Licensing Examination (USMLE) for the first time for a 7B-parameter model, while Meerkat-70B outperformed GPT-4 by an average of 1.3%. Additionally, Meerkat-70B correctly diagnosed 21 out of 38 complex clinical cases, outperforming humans' 13.8 and closely matching GPT-4's 21.8. Our systems offered more detailed free-form responses to clinical queries compared to existing small models, approaching the performance level of large commercial models. This significantly narrows the performance gap with large LMs, showcasing its effectiveness in addressing complex medical challenges.

Jiwoong Sohn, Yein Park, Chanwoong Yoon et al.

Large language models (LLM) hold significant potential for applications in biomedicine, but they struggle with hallucinations and outdated knowledge. While retrieval-augmented generation (RAG) is generally employed to address these issues, it also has its own set of challenges: (1) LLMs are vulnerable to irrelevant or incorrect context, (2) medical queries are often not well-targeted for helpful information, and (3) retrievers are prone to bias toward the specific source corpus they were trained on. In this study, we present RAG$^2$ (RAtionale-Guided RAG), a new framework for enhancing the reliability of RAG in biomedical contexts. RAG$^2$ incorporates three key innovations: a small filtering model trained on perplexity-based labels of rationales, which selectively augments informative snippets of documents while filtering out distractors; LLM-generated rationales as queries to improve the utility of retrieved snippets; a structure designed to retrieve snippets evenly from a comprehensive set of four biomedical corpora, effectively mitigating retriever bias. Our experiments demonstrate that RAG$^2$ improves the state-of-the-art LLMs of varying sizes, with improvements of up to 6.1\%, and it outperforms the previous best medical RAG model by up to 5.6\% across three medical question-answering benchmarks. Our code is available at https://github.com/dmis-lab/RAG2.