Related papers: Zero-shot Medical Entity Retrieval without Annotat…

The extraction of relevant data from Electronic Health Records (EHRs) is crucial to identifying symptoms and automating epidemiological surveillance processes. By harnessing the vast amount of unstructured text in EHRs, we can detect…

Structured and unstructured data and facts about drugs, genes, protein, viruses, and their mechanism are spread across a huge number of scientific articles. These articles are a large-scale knowledge source and can have a huge impact on…

The most common Named Entity Recognizers are usually sequence taggers trained on fully annotated corpora, i.e. the class of all words for all entities is known. Partially annotated corpora, i.e. some but not all entities of some types are…

Retrieval-Augmented Generation (RAG) enhances language models by incorporating external knowledge at inference time. However, graph-based RAG systems often suffer from structural overhead and imprecise retrieval: they require costly…

Accurate recognition of biomedical named entities is critical for medical information extraction and knowledge discovery. However, existing methods often struggle with nested entities, entity boundary ambiguity, and cross-lingual…

Named entity recognition often fails in idiosyncratic domains. That causes a problem for depending tasks, such as entity linking and relation extraction. We propose a generic and robust approach for high-recall named entity recognition. Our…

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…

Machine learning has been widely adopted for medical image analysis in recent years given its promising performance in image segmentation and classification tasks. As a data-driven science, the success of machine learning, in particular…

Recent developments in pre-trained neural language modeling have led to leaps in accuracy on commonsense question-answering benchmarks. However, there is increasing concern that models overfit to specific tasks, without learning to utilize…

Large Language Models (LLMs) have demonstrated impressive capabilities for generalizing in unseen tasks. In the Named Entity Recognition (NER) task, recent advancements have seen the remarkable improvement of LLMs in a broad range of entity…

Electronic Health Records (EHR) are high-dimensional data with implicit connections among thousands of medical concepts. These connections, for instance, the co-occurrence of diseases and lab-disease correlations can be informative when…

Knowledge graphs (KGs) are valuable for representing structured, interconnected information across domains, enabling tasks like semantic search, recommendation systems and inference. A pertinent challenge with KGs, however, is that many…

Retrieval-augmented generation (RAG) is a well-suited technique for retrieving privacy-sensitive Electronic Health Records (EHR). It can serve as a key module of the healthcare copilot, helping reduce misdiagnosis for healthcare…

Electronic Health Records are large repositories of valuable clinical data, with a significant portion stored in unstructured text format. This textual data includes clinical events (e.g., disorders, symptoms, findings, medications and…

Off-the-shelf biomedical embeddings obtained from the recently released various pre-trained language models (such as BERT, XLNET) have demonstrated state-of-the-art results (in terms of accuracy) for the various natural language…

Human-annotated attributes serve as powerful semantic embeddings in zero-shot learning. However, their annotation process is labor-intensive and needs expert supervision. Current unsupervised semantic embeddings, i.e., word embeddings,…

Exploring the application of powerful large language models (LLMs) on the named entity recognition (NER) task has drawn much attention recently. This work pushes the performance boundary of zero-shot NER with LLMs by proposing a…

Entity recognition is a fundamental task in understanding document images. Traditional sequence labeling frameworks treat the entity types as class IDs and rely on extensive data and high-quality annotations to learn semantics which are…

In electronic health record (EHR) mining, learning high-quality representations of medical concepts (e.g., standardized diagnosis, medication, and procedure codes) is fundamental for downstream clinical prediction. However, ro bust concept…

Named entity recognition (NER) is a widely applicable natural language processing task and building block of question answering, topic modeling, information retrieval, etc. In the medical domain, NER plays a crucial role by extracting…