相关论文: MedMentions: A Large Biomedical Corpus Annotated w…
Biomedical named entities often play important roles in many biomedical text mining tools. However, due to the incompleteness of provided synonyms and numerous variations in their surface forms, normalization of biomedical entities is very…
This paper shines a light on the potential of definition-based semantic models for detecting idiomatic and semi-idiomatic multiword expressions (MWEs) in clinical terminology. Our study focuses on biomedical entities defined in the UMLS…
The wide adoption of electronic health records (EHRs) has enabled a wide range of applications leveraging EHR data. However, the meaningful use of EHR data largely depends on our ability to efficiently extract and consolidate information…
The unstructured nature of clinical notes within electronic health records often conceals vital patient-related information, making it challenging to access or interpret. To uncover this hidden information, specialized Natural Language…
Objective: Our study aimed to construct an exhaustive Complementary and Integrative Health (CIH) Lexicon (CIHLex) to better represent the often underrepresented physical and psychological CIH approaches in standard terminologies. We also…
Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations…
Recent advances in large language models (LLMs) and biomedical foundation models (BioFMs) have achieved strong results in biological text reasoning, molecular modeling, and single-cell analysis, yet they remain siloed in disjoint embedding…
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) have fundamentally transformed approaches to Natural Language Processing (NLP) tasks across diverse domains. In healthcare, accurate and cost-efficient text classification is crucial, whether for clinical notes…
Large Language Models (LLMs) demonstrate remarkable versatility in various NLP tasks but encounter distinct challenges in biomedical due to the complexities of language and data scarcity. This paper investigates LLMs application in the…
Named entity recognition (NER) is the very first step in the linguistic processing of any new domain. It is currently a common process in BioNLP on English clinical text. However, it is still in its infancy in other major languages, as it…
We introduce ChemDisGene, a new dataset for training and evaluating multi-class multi-label document-level biomedical relation extraction models. Our dataset contains 80k biomedical research abstracts labeled with mentions of chemicals,…
Linking (aligning) biomedical concepts across diverse data sources enables various integrative analyses, but it is challenging due to the discrepancies in concept naming conventions. Various strategies have been developed to overcome this…
Can language models read biomedical texts and explain the biomedical mechanisms discussed? In this work we introduce a biomedical mechanism summarization task. Biomedical studies often investigate the mechanisms behind how one entity (e.g.,…
Biomedical data is inherently multimodal, consisting of electronic health records, medical imaging, digital pathology, genome sequencing, wearable sensors, and more. The application of artificial intelligence tools to these multifaceted…
Bioinformatics workflows are essential for complex biological data analyses and are often described in scientific articles with source code in public repositories. Extracting detailed workflow information from articles can improve…
In this work, we propose a method for the automated refinement of subject annotations in biomedical literature at the level of concepts. Semantic indexing and search of biomedical articles in MEDLINE/PubMed are based on semantic subject…
Despite the excitement behind biomedical artificial intelligence (AI), access to high-quality, diverse, and large-scale data - the foundation for modern AI systems - is still a bottleneck to unlocking its full potential. To address this…
The paper introduces a framework for the evaluation of the encoding of factual scientific knowledge, designed to streamline the manual evaluation process typically conducted by domain experts. Inferring over and extracting information from…
The exponential growth of biomedical texts such as biomedical literature and electronic health records (EHRs), poses a significant challenge for clinicians and researchers to access clinical information efficiently. To tackle this…