1 code implementation • 24 Sep 2024 • Lucie Dvorackova, Marcin P. Joachimiak, Michal Cerny, Adriana Kubecova, Vilem Sklenak, Tomas Kliegr
Best performing approaches for scholarly document quality prediction are based on embedding models, which do not allow direct explanation of classifiers as distinct words no longer correspond to the input features for model training.
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 • 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.
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.
1 code implementation • 24 Sep 2022 • Sanya B. Taneja, Tiffany J. Callahan, Mary F. Paine, Sandra L. Kane-Gill, Halil Kilicoglu, Marcin P. Joachimiak, Richard D. Boyce
NP-KG is a heterogeneous KG with biomedical ontologies, linked data, and full texts of the scientific literature, constructed with the Phenotype Knowledge Translator framework and the semantic relation extraction systems, SemRep and Integrated Network and Dynamic Reasoning Assembler.
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.