Related papers: Biomedical Information Extraction for Disease Gene…

Joint medical relation extraction refers to extracting triples, composed of entities and relations, from the medical text with a single model. One of the solutions is to convert this task into a sequential tagging task. However, in the…

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…

This report argues that, even in the simplest cases, IE is an ontology-driven process. It is not a mere text filtering method based on simple pattern matching and keywords, because the extracted pieces of texts are interpreted with respect…

Motivation: Protein-protein interactions (PPI) are critical to the function of proteins in both normal and diseased cells, and many critical protein functions are mediated by interactions.Knowledge of the nature of these interactions is…

Automatically extracting organization names from the affiliation sentences of articles related to biomedicine is of great interest to the pharmaceutical marketing industry, health care funding agencies and public health officials. It will…

Current research on the advantages and trade-offs of using characters, instead of tokenized text, as input for deep learning models, has evolved substantially. New token-free models remove the traditional tokenization step; however, their…

Open information extraction (IE) is the task of extracting open-domain assertions from natural language sentences. A key step in open IE is confidence modeling, ranking the extractions based on their estimated quality to adjust precision…

We propose an approach for biomedical information extraction that marries the advantages of machine learning models, e.g., learning directly from data, with the benefits of rule-based approaches, e.g., interpretability. Our approach starts…

Understanding the meaning of text often involves reasoning about entities and their relationships. This requires identifying textual mentions of entities, linking them to a canonical concept, and discerning their relationships. These tasks…

We propose a knowledge-based approach for extraction of Cause-Effect (CE) relations from biomedical text. Our approach is a combination of an unsupervised machine learning technique to discover causal triggers and a set of high-precision…

We present an open-access natural language processing toolkit for Japanese medical information extraction. We first propose a novel relation annotation schema for investigating the medical and temporal relations between medical entities in…

Document-level biomedical concept extraction is the task of identifying biomedical concepts mentioned in a given document. Recent advancements have adapted pre-trained language models for this task. However, the scarcity of domain-specific…

The Interaction between Drugs and Targets (DTI) in human body plays a crucial role in biomedical science and applications. As millions of papers come out every year in the biomedical domain, automatically discovering DTI knowledge from…

Typically, information extraction (IE) requires a pipeline approach: first, a sequence labeling model is trained on manually annotated documents to extract relevant spans; then, when a new document arrives, a model predicts spans which are…

The task of Information Extraction (IE) involves automatically converting unstructured textual content into structured data. Most research in this field concentrates on extracting all facts or a specific set of relationships from documents.…

This paper describes a machine learning and data science pipeline for structured information extraction from documents, implemented as a suite of open-source tools and extensions to existing tools. It centers around a methodology for…

Drug-drug interaction (DDI) is a major cause of morbidity and mortality and a subject of intense scientific interest. Biomedical literature mining can aid DDI research by extracting evidence for large numbers of potential interactions from…

Protein-protein interactions (PPIs) are crucial in regulating numerous cellular functions, including signal transduction, transportation, and immune defense. As the accuracy of multi-chain protein complex structure prediction improves, the…

Automated entity relation extraction (RE) from literature provides an important source for constructing biomedical database, which is more efficient and extensible than manual curation. However, existing RE models usually ignore the…

Biomedical events describe complex interactions between various biomedical entities. Event trigger is a word or a phrase which typically signifies the occurrence of an event. Event trigger identification is an important first step in all…