Related papers: Clustering-based Inference for Biomedical Entity L…

Entity linking is the task of identifying mentions of entities in text, and linking them to entries in a knowledge base. This task is especially difficult in microblogs, as there is little additional text to provide disambiguating context;…

Despite recent progress, Biomedical Entity Linking (BEL) with large language models (LLMs) remains computationally inefficient and challenging to deploy in practical settings. In this work, we demonstrate that instruction-tuning of…

Traditional learning-based coreference resolvers operate by training the mention-pair model for determining whether two mentions are coreferent or not. Though conceptually simple and easy to understand, the mention-pair model is…

The metadata about scientific experiments published in online repositories have been shown to suffer from a high degree of representational heterogeneity---there are often many ways to represent the same type of information, such as a…

Pretrained language models have shown success in many natural language processing tasks. Many works explore incorporating knowledge into language models. In the biomedical domain, experts have taken decades of effort on building large-scale…

We introduce a novel profile-based patient clustering model designed for clinical data in healthcare. By utilizing a method grounded on constrained low-rank approximation, our model takes advantage of patients' clinical data and digital…

Entity linking is an indispensable operation of populating knowledge repositories for information extraction. It studies on aligning a textual entity mention to its corresponding disambiguated entry in a knowledge repository. In this paper,…

Accurate entity linkers have been produced for domains and languages where annotated data (i.e., texts linked to a knowledge base) is available. However, little progress has been made for the settings where no or very limited amounts of…

Statements about entities occur everywhere, from newspapers and web pages to structured databases. Correlating references to entities across systems that use different identifiers or names for them is a widespread problem. In this paper, we…

Many fundamental problems in natural language processing rely on determining what entities appear in a given text. Commonly referenced as entity linking, this step is a fundamental component of many NLP tasks such as text understanding,…

Model-based clustering is a powerful tool that is often used to discover hidden structure in data by grouping observational units that exhibit similar response values. Recently, clustering methods have been developed that permit…

We introduce BioCoM, a contrastive learning framework for biomedical entity linking that uses only two resources: a small-sized dictionary and a large number of raw biomedical articles. Specifically, we build the training instances from raw…

Classification model selection is a process of identifying a suitable model class for a given classification task on a dataset. Traditionally, model selection is based on cross-validation, meta-learning, and user preferences, which are…

Compared to the general news domain, information extraction (IE) from biomedical text requires much broader domain knowledge. However, many previous IE methods do not utilize any external knowledge during inference. Due to the exponential…

We propose a triad-based neural network system that generates affinity scores between entity mentions for coreference resolution. The system simultaneously accepts three mentions as input, taking mutual dependency and logical constraints of…

Background: Finding biomedical named entities is one of the most essential tasks in biomedical text mining. Recently, deep learning-based approaches have been applied to biomedical named entity recognition (BioNER) and showed promising…

Biomedical question answering often requires decisions from retrieved literature whose relevance, quality, and support for candidate answers are uneven. Most retrieval-augmented large language model (LLM) methods feed this literature to the…

Clustering methods are applied regularly in the bibliometric literature to identify research areas or scientific fields. These methods are for instance used to group publications into clusters based on their relations in a citation network.…

Entity linking (EL) is the computational process of connecting textual mentions to corresponding entities. Like many areas of natural language processing, the EL field has greatly benefited from deep learning, leading to significant…

In entity linking, mentions of named entities in raw text are disambiguated against a knowledge base (KB). This work focuses on linking to unseen KBs that do not have training data and whose schema is unknown during training. Our approach…