J. Harry Caufield

Publication Activity (10 Years)

Years Active: 2015-2024
Publications (10 Years): 15

Top Topics

Dependency Trees

Protein Complexes

Named Entity Recognition

Relation Extraction

Top Venues

BMC Medical Informatics Decis. Mak.

Publications

Tudor Groza, J. Harry Caufield, Dylan Gration, Gareth Baynam, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall, Justin T. Reese
An evaluation of GPT models for phenotype concept recognition. BMC Medical Informatics Decis. Mak. 24 (1) (2024)
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
Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning. Bioinform. 40 (3) (2024)
Marcin P. Joachimiak, Mark A. Miller, J. Harry Caufield, Ryan Ly, Nomi L. Harris, Andrew J. Tritt, Christopher J. Mungall, Kristofer E. Bouchard
The Artificial Intelligence Ontology: LLM-assisted construction of AI concept hierarchies. CoRR (2024)
Emanuele Cavalleri, Mauricio Soto Gomez, Ali Pashaeibarough, Dario Malchiodi, J. Harry Caufield, Justin T. Reese, Christopher J. Mungall, Peter N. Robinson, Elena Casiraghi, Giorgio Valentini, Marco Mesiti
Initial achievements in relation extraction from RNA-focused scientific papers. SEBD (2024)
J. Harry Caufield, Tim E. Putman, Kevin Schaper, Deepak R. Unni, Harshad Hegde, Tiffany J. Callahan, Luca Cappelletti, Sierra A. T. Moxon, Vida Ravanmehr, Seth Carbon, Lauren E. Chan, Katherina Cortes, Kent A. Shefchek, Glass Elsarboukh, James P. Balhoff, Tommaso Fontana, Nicolas Matentzoglu, Richard M. Bruskiewich, Anne E. Thessen, Nomi L. Harris, Monica C. Munoz-Torres, Melissa A. Haendel, Peter N. Robinson, Marcin P. Joachimiak, Christopher J. Mungall, Justin T. Reese
KG-Hub - Building and Exchanging Biological Knowledge Graphs. CoRR (2023)
Nicolas Matentzoglu, J. Harry Caufield, Harshad B. Hegde, Justin T. Reese, Sierra A. T. Moxon, Hyeongsik Kim, Nomi L. Harris, Melissa A. Haendel, Christopher J. Mungall
MapperGPT: Large Language Models for Linking and Mapping Entities. CoRR (2023)
Marcin P. Joachimiak, J. Harry Caufield, Nomi L. Harris, Christopher J. Mungall
Gene Set Summarization using Large Language Models. CoRR (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
Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning. CoRR (2023)
Tudor Groza, J. Harry Caufield, Dylan Gration, Gareth Baynam, Melissa A. Haendel, Peter N. Robinson, Chris Mungall, Justin T. Reese
An evaluation of GPT models for phenotype concept recognition. CoRR (2023)
Yichao Zhou, Wei-Ting Chen, Bowen Zhang, David Lee, J. Harry Caufield, Kai-Wei Chang, Yizhou Sun, Peipei Ping, Wei Wang
CREATe: Clinical Report Extraction and Annotation Technology. ICDE (2021)
Yichao Zhou, Yu Yan, Rujun Han, J. Harry Caufield, Kai-Wei Chang, Yizhou Sun, Peipei Ping, Wei Wang
Clinical Temporal Relation Extraction with Probabilistic Soft Logic Regularization and Global Inference. AAAI (2021)
Yichao Zhou, Wei-Ting Chen, Bowen Zhang, David Lee, J. Harry Caufield, Kai-Wei Chang, Yizhou Sun, Peipei Ping, Wei Wang
CREATe: Clinical Report Extraction and Annotation Technology. CoRR (2021)
Yichao Zhou, Chelsea Ju, J. Harry Caufield, Kevin Shih, Calvin Yu-Chian Chen, Yizhou Sun, Kai-Wei Chang, Peipei Ping, Wei Wang
Clinical Named Entity Recognition using Contextualized Token Representations. CoRR (2021)
Yichao Zhou, Yu Yan, Rujun Han, J. Harry Caufield, Kai-Wei Chang, Yizhou Sun, Peipei Ping, Wei Wang
Clinical Temporal Relation Extraction with Probabilistic Soft Logic Regularization and Global Inference. CoRR (2020)
J. Harry Caufield, Christopher Wimble, Shary Semarjit, Stefan Wuchty, Peter Uetz
Bacterial protein meta-interactomes predict cross-species interactions and protein function. BMC Bioinform. 18 (1) (2017)
J. Harry Caufield, Marco Abreu, Christopher Wimble, Peter Uetz
Protein Complexes in Bacteria. PLoS Comput. Biol. 11 (2) (2015)