Related papers: BioCoref: Benchmarking Biomedical Coreference Reso…

Recent advancements in Large Language Models (LLMs) have shown that it is promising to utilize Process Reward Models (PRMs) as verifiers to enhance the performance of LLMs. However, current PRMs face three key challenges: (1) limited…

Language Models (LMs) have performed well on biomedical natural language processing applications. In this study, we conducted some experiments to use prompt methods to extract knowledge from LMs as new knowledge Bases (LMs as KBs). However,…

We study allowing large language models (LLMs) to process arbitrarily long prompts through the lens of inference-time scaling. We propose Recursive Language Models (RLMs), a general inference paradigm that treats long prompts as part of an…

Manual relevance judgements in Information Retrieval are costly and require expertise, driving interest in using Large Language Models (LLMs) for automatic assessment. While LLMs have shown promise in general web search scenarios, their…

Aligning terminological resources, including ontologies, controlled vocabularies, taxonomies, and value sets is a critical part of data integration in many domains such as healthcare, chemistry, and biomedical research. Entity mapping is…

Models such as GPT-4 and Med-PaLM 2 have demonstrated impressive performance on a wide variety of biomedical NLP tasks. However, these models have hundreds of billions of parameters, are computationally expensive to run, require users to…

Large Language Models (LLMs) were used to assist four Commonwealth Scientific and Industrial Research Organisation (CSIRO) researchers to perform systematic literature reviews (SLR). We evaluate the performance of LLMs for SLR tasks in…

Objective: To develop a high-throughput biomedical relation extraction system that takes advantage of the large language models'(LLMs) reading comprehension ability and biomedical world knowledge in a scalable and evidential manner.…

One of the major barriers to using large language models (LLMs) in medicine is the perception they use uninterpretable methods to make clinical decisions that are inherently different from the cognitive processes of clinicians. In this…

Large Language Models (LLMs) have recently gained attention in the life sciences due to their capacity to model, extract, and apply complex biological information. Beyond their classical use as chatbots, these systems are increasingly used…

In practice, clinicians achieve a diagnosis by following a sequence of steps, such as laboratory exams, observations, or imaging. The pathways to reach diagnosis decisions are documented by guidelines authored by expert organizations, which…

Large language models (LLMs) show increasing promise in medical applications, but their ability to detect and correct errors in clinical texts -- a prerequisite for safe deployment -- remains under-evaluated, particularly beyond English. We…

Georeferencing text documents has typically relied on either gazetteer-based methods to assign geographic coordinates to place names, or on language modelling approaches that associate textual terms with geographic locations. However, many…

Document-Level Biomedical Relation Extraction (Bio-RE) aims to identify relations between biomedical entities within extensive texts, serving as a crucial subfield of biomedical text mining. Existing Bio-RE methods struggle with…

In recent years, Large Language Models (LLMs) have become widely used in medical applications, such as clinical decision support, medical education, and medical question answering. Yet, these models are often English-centric, limiting their…

Objective: Biomedical Knowledge Graphs play a pivotal role in various biomedical research domains. Concurrently, term clustering emerges as a crucial step in constructing these knowledge graphs, aiming to identify synonymous terms. Due to a…

Biomedical queries have become increasingly prevalent in web searches, reflecting the growing interest in accessing biomedical literature. Despite recent research on large-language models (LLMs) motivated by endeavours to attain generalized…

Effective Question Answering (QA) on large biomedical document collections requires effective document retrieval techniques. The latter remains a challenging task due to the domain-specific vocabulary and semantic ambiguity in user queries.…

Large language models (LLMs) typically utilize the top-k contexts from a retriever in retrieval-augmented generation (RAG). In this work, we propose a novel instruction fine-tuning framework RankRAG, which instruction-tunes a single LLM for…

Evaluating Information Retrieval (IR) systems relies on high-quality manual relevance judgments (qrels), which are costly and time-consuming to obtain. While pooling reduces the annotation effort, it results in only partially labeled…