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.
no code implementations • 8 Nov 2023 • Oluwamayowa O. Amusat, Harshad Hegde, Christopher J. Mungall, Anna Giannakou, Neil P. Byers, Dan Gunter, Kjiersten Fagnan, Lavanya Ramakrishnan
In this paper, we present two novel automated text labeling approaches for the validation of ML-generated metadata for unlabeled texts, with specific applications in environmental genomics.
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 • 11 Jul 2023 • Tiffany J. Callahan, Ignacio J. Tripodi, Adrianne L. Stefanski, Luca Cappelletti, Sanya B. Taneja, Jordan M. Wyrwa, Elena Casiraghi, Nicolas A. Matentzoglu, Justin Reese, Jonathan C. Silverstein, Charles Tapley Hoyt, Richard D. Boyce, Scott A. Malec, Deepak R. Unni, Marcin P. Joachimiak, Peter N. Robinson, Christopher J. Mungall, Emanuele Cavalleri, Tommaso Fontana, Giorgio Valentini, Marco Mesiti, Lucas A. Gillenwater, Brook Santangelo, Nicole A. Vasilevsky, Robert Hoehndorf, Tellen D. Bennett, Patrick B. Ryan, George Hripcsak, Michael G. Kahn, Michael Bada, William A. Baumgartner Jr, Lawrence E. Hunter
Translational research requires data at multiple scales of biological organization.
no code implementations • 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 • 14 Oct 2022 • Hector Garcia Martin, Tijana Radivojevic, Jeremy Zucker, Kristofer Bouchard, Jess Sustarich, Sean Peisert, Dan Arnold, Nathan Hillson, Gyorgy Babnigg, Jose Manuel Marti, Christopher J. Mungall, Gregg T. Beckham, Lucas Waldburger, James Carothers, Shivshankar Sundaram, Deb Agarwal, Blake A. Simmons, Tyler Backman, Deepanwita Banerjee, Deepti Tanjore, Lavanya Ramakrishnan, Anup Singh
Self-driving labs (SDLs) combine fully automated experiments with artificial intelligence (AI) that decides the next set of experiments.
no code implementations • 24 Jun 2022 • Anne Niknejad, Christopher J. Mungall, David Osumi-Sutherland, Marc Robinson-Rechavi, Frederic B. Bastian
With the new era of genomics, an increasing number of animal species are amenable to large-scale data generation.
1 code implementation • 18 Apr 2022 • Tiago Lubiana, Paola Roncaglia, Christopher J. Mungall, Ellen M. Quardokus, Joshua D. Fortriede, David Osumi-Sutherland, Alexander D. Diehl
Cell types are at the root of modern biology, and describing them is a core task of the Human Cell Atlas project.
2 code implementations • 12 Oct 2021 • Luca Cappelletti, Tommaso Fontana, Elena Casiraghi, Vida Ravanmehr, Tiffany J. Callahan, Carlos Cano, Marcin P. Joachimiak, Christopher J. Mungall, Peter N. Robinson, Justin Reese, Giorgio Valentini
Graph Representation Learning (GRL) methods opened new avenues for addressing complex, real-world problems represented by graphs.