J. Harry Caufield

According to our database, J. Harry Caufield authored at least 15 papers between 2015 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

An evaluation of GPT models for phenotype concept recognition.

Tudor Groza, J. Harry Caufield, Dylan Gration, Gareth Baynam, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall, Justin T. Reese

BMC Medical Informatics Decis. Mak., December, 2024

Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning.

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

Bioinform., March, 2024

CurateGPT: A flexible language-model assisted biocuration tool.

J. Harry Caufield, Carlo Kroll, Shawn T. O'Neil, Justin T. Reese, Marcin P. Joachimiak, Harshad Hegde, Nomi L. Harris, Madan Krishnamurthy, James A McLaughlin, Damian Smedley, Melissa A. Haendel, Peter N. Robinson, Christopher J. Mungall

CoRR, 2024

A Change Language for Ontologies and Knowledge Graphs.

Harshad Hegde, Jennifer Vendetti, Damien Goutte-Gattat, J. Harry Caufield, John Graybeal, Nomi L. Harris, Naouel Karam, Christian Kindermann, Nicolas Matentzoglu, James A. Overton, Mark A. Musen, Christopher J. Mungall

CoRR, 2024

The Artificial Intelligence Ontology: LLM-assisted construction of AI concept hierarchies.

Marcin P. Joachimiak, Mark A. Miller, J. Harry Caufield, Ryan Ly, Nomi L. Harris, Andrew J. Tritt, Christopher J. Mungall, Kristofer E. Bouchard

CoRR, 2024

SPIREX: Improving LLM-based relation extraction from RNA-focused scientific literature using graph machine learning.

Emanuele Cavalleri, Mauricio Soto Gomez, Ali Pashaeibarough, Dario Malchiodi, J. Harry Caufield, Justin T. Reese, Chris Mungall, Peter N. Robinson, Elena Casiraghi, Giorgio Valentini, Marco Mesiti

Proceedings of Workshops at the 50th International Conference on Very Large Data Bases, 2024

Initial achievements in relation extraction from RNA-focused scientific papers.

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

Proceedings of the 32nd Symposium of Advanced Database Systems, 2024

2023

MapperGPT: Large Language Models for Linking and Mapping Entities.

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

CoRR, 2023

Gene Set Summarization using Large Language Models.

Marcin P. Joachimiak, J. Harry Caufield, Nomi L. Harris, Hyeongsik Kim, Christopher J. Mungall

CoRR, 2023

KG-Hub - Building and Exchanging Biological Knowledge Graphs.

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

CoRR, 2023

2021

Clinical Named Entity Recognition using Contextualized Token Representations.

Yichao Zhou, Chelsea Ju, J. Harry Caufield, Kevin Shih, Calvin Yu-Chian Chen, Yizhou Sun, Kai-Wei Chang, Peipei Ping, Wei Wang

CoRR, 2021

CREATe: Clinical Report Extraction and Annotation Technology.

Yichao Zhou, Wei-Ting Chen, Bowen Zhang, David Lee, J. Harry Caufield, Kai-Wei Chang, Yizhou Sun, Peipei Ping, Wei Wang

Proceedings of the 37th IEEE International Conference on Data Engineering, 2021

Clinical Temporal Relation Extraction with Probabilistic Soft Logic Regularization and Global Inference.

Yichao Zhou, Yu Yan, Rujun Han, J. Harry Caufield, Kai-Wei Chang, Yizhou Sun, Peipei Ping, Wei Wang

Proceedings of the Thirty-Fifth AAAI Conference on Artificial Intelligence, 2021

2017

Bacterial protein meta-interactomes predict cross-species interactions and protein function.

J. Harry Caufield, Christopher Wimble, Shary Semarjit, Stefan Wuchty, Peter Uetz

BMC Bioinform., 2017

2015

Protein Complexes in Bacteria.

J. Harry Caufield, Marco Abreu, Christopher Wimble, Peter Uetz

PLoS Comput. Biol., 2015