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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…

Over the past decade, low-resource natural language processing (NLP) has experienced explosive growth, propelled by cross-lingual transfer, massively multilingual models, and the rapid proliferation of benchmarks. Yet this apparent progress…

Large Language Models (LLMs) have swiftly emerged as vital resources for different applications in the biomedical and healthcare domains; however, these models encounter issues such as generating inaccurate information or hallucinations.…

The recent growth in the popularity and success of deep learning models on NLP classification tasks has accompanied the need for generating some form of natural language explanation of the predicted labels. Such generated natural language…

Distantly-supervised relation extraction (RE) is an effective method to scale RE to large corpora but suffers from noisy labels. Existing approaches try to alleviate noise through multi-instance learning and by providing additional…

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…

Neural network representation learning frameworks have recently shown to be highly effective at a wide range of tasks ranging from radiography interpretation via data-driven diagnostics to clinical decision support. This often superior…

We introduce random adversarial training (RAT), a novel framework successfully applied to biomedical information extraction (BioIE) tasks. Building on PubMedBERT as the foundational architecture, our study first validates the effectiveness…

Relation extraction is a core problem for natural language processing in the biomedical domain. Recent research on relation extraction showed that prompt-based learning improves the performance on both fine-tuning on full training set and…

During the past decade, neural networks have become prominent in Natural Language Processing (NLP), notably for their capacity to learn relevant word representations from large unlabeled corpora. These word embeddings can then be…

Due to the exponential growth of biomedical literature, event and relation extraction are important tasks in biomedical text mining. Most work only focus on relation extraction, and detect a single entity pair mention on a short span of…

Unsupervised Relation Extraction (RE) aims to identify relations between entities in text, without having access to labeled data during training. This setting is particularly relevant for domain specific RE where no annotated dataset is…

Natural language processing (NLP) techniques have been widely applied in the requirements engineering (RE) field to support tasks such as classification and ambiguity detection. Although RE research is rooted in empirical investigation, it…

This paper presents our participation in the AGAC Track from the 2019 BioNLP Open Shared Tasks. We provide a solution for Task 3, which aims to extract "gene - function change - disease" triples, where "gene" and "disease" are mentions of…

Information Extraction (IE), encompassing Named Entity Recognition (NER), Named Entity Linking (NEL), and Relation Extraction (RE), is critical for transforming the rapidly growing volume of scientific publications into structured,…

Relation extraction (RE) is a crucial task in natural language processing (NLP) that aims to identify and classify relationships between entities mentioned in text. In the financial domain, relation extraction plays a vital role in…

Backgrounds: Information extraction (IE) is critical in clinical natural language processing (NLP). While large language models (LLMs) excel on generative tasks, their performance on extractive tasks remains debated. Methods: We…

The abductive natural language inference task ($\alpha$NLI) is proposed to evaluate the abductive reasoning ability of a learning system. In the $\alpha$NLI task, two observations are given and the most plausible hypothesis is asked to pick…

In rural regions of several developing countries, access to quality healthcare, medical infrastructure, and professional diagnosis is largely unavailable. Many of these regions are gradually gaining access to internet infrastructure,…

The state-of-the-art named entity recognition (NER) systems are supervised machine learning models that require large amounts of manually annotated data to achieve high accuracy. However, annotating NER data by human is expensive and…