Related papers: Do LLMs Surpass Encoders for Biomedical NER?

This paper presents a comprehensive evaluation of cost-efficient Large Language Models (LLMs) for diverse biomedical tasks spanning both text and image modalities. We evaluated a range of closed-source and open-source LLMs on tasks such as…

In this study, we uncover the unexpected efficacy of residual-based large language models (LLMs) as part of encoders for biomedical imaging tasks, a domain traditionally devoid of language or textual data. The approach diverges from…

Tools to explore scientific literature are essential for scientists, especially in biomedicine, where about a million new papers are published every year. Many such tools provide users the ability to search for specific entities (e.g.…

Biomedical entity linking (EL) consists of named entity recognition (NER) and named entity disambiguation (NED). EL models are trained on corpora labeled by a predefined KB. However, it is a common scenario that only entities within a…

This pilot study presents a small-scale but carefully annotated benchmark of Named Entity Recognition (NER) performance across six systems: three non-LLM NLP tools (NLTK, spaCy, Stanza) and three general-purpose large language models (LLMs:…

Motivation: Biomedical named-entity normalization involves connecting biomedical entities with distinct database identifiers in order to facilitate data integration across various fields of biology. Existing systems for biomedical named…

While humans process language incrementally, the best language encoders currently used in NLP do not. Both bidirectional LSTMs and Transformers assume that the sequence that is to be encoded is available in full, to be processed either…

Enhancement reports (ERs) serve as a critical communication channel between users and developers, capturing valuable suggestions for software improvement. However, manually processing these reports is resource-intensive, leading to delays…

Generative LLMs typically improve Named Entity Recognition (NER) performance through instruction tuning. They excel at generating entities by semantic pattern matching but lack an explicit, verifiable reasoning mechanism. This "cognitive…

Large language models (LLMs) have ushered in a new era for processing complex information in various fields, including science. The increasing amount of scientific literature allows these models to acquire and understand scientific…

Contextual word embedding models such as ELMo (Peters et al., 2018) and BERT (Devlin et al., 2018) have dramatically improved performance for many natural language processing (NLP) tasks in recent months. However, these models have been…

Named Entity Recognition (NER) is a machine learning task that traditionally relies on supervised learning and annotated data. Acquiring such data is often a challenge, particularly in specialized fields like medical, legal, and financial…

Biomedical entity linking aims to map biomedical mentions, such as diseases and drugs, to standard entities in a given knowledge base. The specific challenge in this context is that the same biomedical entity can have a wide range of names,…

The availability of biomedical text data and advances in natural language processing (NLP) have made new applications in biomedical NLP possible. Language models trained or fine tuned using domain specific corpora can outperform general…

Detecting music entities such as song titles or artist names is a useful application to help use cases like processing music search queries or analyzing music consumption on the web. Recent approaches incorporate smaller language models…

There are a few challenges related to the task of biomedical named entity recognition, which are: the existing methods consider a fewer number of biomedical entities (e.g., disease, symptom, proteins, genes); and these methods do not…

Vision-language pretraining has advanced image-text alignment, yet progress in radiology remains constrained by the heterogeneity of clinical reports, including abbreviations, impression-only notes, and stylistic variability. Unlike…

Electronic Health Records (EHRs) are digital records of patient information, often containing unstructured clinical text. Named Entity Recognition (NER) is essential in EHRs for extracting key medical entities like problems, tests, and…

Coreference resolution in biomedical texts presents unique challenges due to complex domain-specific terminology, high ambiguity in mention forms, and long-distance dependencies between coreferring expressions. In this work, we present a…

Natural language processing (NLP) is a key technology to extract important patient information from clinical narratives to support healthcare applications. The rapid development of large language models (LLMs) has revolutionized many NLP…