Related papers: Biomedical Interpretable Entity Representations
Entity linking is the task of linking mentions of named entities in natural language text, to entities in a curated knowledge-base. This is of significant importance in the biomedical domain, where it could be used to semantically annotate…
Named entity recognition (NER) models generally perform poorly when large training datasets are unavailable for low-resource domains. Recently, pre-training a large-scale language model has become a promising direction for coping with the…
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…
The surging amount of biomedical literature & digital clinical records presents a growing need for text mining techniques that can not only identify but also semantically relate entities in unstructured data. In this paper we propose a text…
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…
Electronic health records (EHR) contain narrative notes that provide extensive details on the medical condition and management of patients. Natural language processing (NLP) of clinical notes can use observed frequencies of clinical terms…
Named Entity Recognition (NER) or the extraction of concepts from clinical text is the task of identifying entities in text and slotting them into categories such as problems, treatments, tests, clinical departments, occurrences (such as…
The advancement of Large Language Models (LLMs) has significantly impacted biomedical Natural Language Processing (NLP), enhancing tasks such as named entity recognition, relation extraction, event extraction, and text classification. In…
Progress in biomedical Named Entity Recognition (NER) and Entity Linking (EL) is currently hindered by a fragmented data landscape, a lack of resources for building explainable models, and the limitations of semantically-blind evaluation…
There is an increasing interest in the use of Deep Learning (DL) based methods as a supporting analytical framework in oncology. However, most direct applications of DL will deliver models with limited transparency and explainability, which…
Extracting clinically relevant information from unstructured medical narratives such as admission notes, discharge summaries, and emergency case histories remains a challenge in clinical natural language processing (NLP). Medical Entity…
Named entity recognition (NER) is a vital task in spoken language understanding, which aims to identify mentions of named entities in text e.g., from transcribed speech. Existing neural models for NER rely mostly on dedicated word-level…
Due to large number of entities in biomedical knowledge bases, only a small fraction of entities have corresponding labelled training data. This necessitates entity linking models which are able to link mentions of unseen entities using…
Biomedical entity linking is the task of linking entity mentions in a biomedical document to referent entities in a knowledge base. Recently, many BERT-based models have been introduced for the task. While these models have achieved…
The clinical named entity recognition (CNER) task seeks to locate and classify clinical terminologies into predefined categories, such as diagnostic procedure, disease disorder, severity, medication, medication dosage, and sign symptom.…
In this paper, we present our approach to extracting structured information from unstructured Electronic Health Records (EHR) [2] which can be used to, for example, study adverse drug reactions in patients due to chemicals in their…
We present iBERT (interpretable-BERT), an encoder to produce inherently interpretable and controllable embeddings - designed to modularize and expose the discriminative cues present in language, such as semantic or stylistic structure. Each…
Injecting external domain-specific knowledge (e.g., UMLS) into pretrained language models (LMs) advances their capability to handle specialised in-domain tasks such as biomedical entity linking (BEL). However, such abundant expert knowledge…
Hierarchical knowledge structures are ubiquitous across real-world domains and play a vital role in organizing information from coarse to fine semantic levels. While such structures have been widely used in taxonomy systems, biomedical…
Concept normalization in free-form texts is a crucial step in every text-mining pipeline. Neural architectures based on Bidirectional Encoder Representations from Transformers (BERT) have achieved state-of-the-art results in the biomedical…