Search Results for author: J. Harry Caufield

Found 6 papers, 3 papers with code

MapperGPT: Large Language Models for Linking and Mapping Entities

no code implementations5 Oct 2023 Nicolas Matentzoglu, J. Harry Caufield, Harshad B. Hegde, Justin T. Reese, Sierra Moxon, HyeongSik Kim, Nomi L. Harris, Melissa A Haendel, Christopher J. Mungall

Here we present MapperGPT, an approach that uses LLMs to review and refine mapping relationships as a post-processing step, in concert with existing high-recall methods that are based on lexical and structural heuristics.

Anatomy Data Integration +1

Gene Set Summarization using Large Language Models

1 code implementation21 May 2023 Marcin P. Joachimiak, J. Harry Caufield, Nomi L. Harris, HyeongSik Kim, Christopher J. Mungall

This is typically done as a statistical enrichment analysis that measures the over- or under-representation of biological function terms associated with genes or their properties, based on curated assertions from a knowledge base (KB) such as the Gene Ontology (GO).

Clinical Named Entity Recognition using Contextualized Token Representations

no code implementations23 Jun 2021 Yichao Zhou, Chelsea Ju, J. Harry Caufield, Kevin Shih, Calvin Chen, Yizhou Sun, Kai-Wei Chang, Peipei Ping, Wei Wang

To facilitate various downstream applications using clinical case reports (CCRs), we pre-train two deep contextualized language models, Clinical Embeddings from Language Model (C-ELMo) and Clinical Contextual String Embeddings (C-Flair) using the clinical-related corpus from the PubMed Central.

Language Modelling named-entity-recognition +3

CREATe: Clinical Report Extraction and Annotation Technology

no code implementations28 Feb 2021 Yichao Zhou, Wei-Ting Chen, BoWen Zhang, David Lee, J. Harry Caufield, Kai-Wei Chang, Yizhou Sun, Peipei Ping, Wei Wang

Clinical case reports are written descriptions of the unique aspects of a particular clinical case, playing an essential role in sharing clinical experiences about atypical disease phenotypes and new therapies.

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