1 code implementation • 3 Apr 2024 • Marcin P. Joachimiak, Mark A. Miller, J. Harry Caufield, Ryan Ly, Nomi L. Harris, Andrew Tritt, Christopher J. Mungall, Kristofer E. Bouchard
This approach not only ensures the ontology's relevance amidst the fast-paced advancements in AI but also significantly enhances its utility for researchers, developers, and educators by simplifying the integration of new AI concepts and methodologies.
1 code implementation • 5 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.
1 code implementation • 21 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).
1 code implementation • 5 Apr 2023 • J. Harry Caufield, Harshad Hegde, Vincent Emonet, Nomi L. Harris, Marcin P. Joachimiak, Nicolas Matentzoglu, HyeongSik Kim, Sierra A. T. Moxon, Justin T. Reese, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall
Creating knowledge bases and ontologies is a time consuming task that relies on a manual curation.
no code implementations • 23 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.
no code implementations • 28 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.
2 code implementations • 16 Dec 2020 • Yichao Zhou, Yu Yan, Rujun Han, J. Harry Caufield, Kai-Wei Chang, Yizhou Sun, Peipei Ping, Wei Wang
There has been a steady need in the medical community to precisely extract the temporal relations between clinical events.