S. Joshua Swamidass

Publication Activity (10 Years)

Years Active: 2007-2024
Publications (10 Years): 17

Top Topics

Gene Expression Analysis

Adverse Drug Reaction

Top Venues

J. Chem. Inf. Model.

Publications

Michael R. Waters, Matthew Inkman, Kay Jayachandran, Roman M. Kowalchuk, Clifford Robinson, Julie K. Schwarz, S. Joshua Swamidass, Obi L. Griffith, Jeffrey J. Szymanski, Jin Zhang
GAiN: An integrative tool utilizing generative adversarial neural networks for augmented gene expression analysis. Patterns 5 (2) (2024)
Noah R. Flynn, S. Joshua Swamidass
Message Passing Neural Networks Improve Prediction of Metabolite Authenticity. J. Chem. Inf. Model. 63 (6) (2023)
Arghya Datta, S. Joshua Swamidass
Fair-Net: A Network Architecture for Reducing Performance Disparity between Identifiable Sub-populations. ICAART (3) (2022)
Arghya Datta, S. Joshua Swamidass
Fair-Net: A Network Architecture For Reducing Performance Disparity Between Identifiable Sub-Populations. CoRR (2021)
Arghya Datta, Noah R. Flynn, S. Joshua Swamidass
Cal-Net: Jointly Learning Classification and Calibration On Imbalanced Binary Classification Tasks. IJCNN (2021)
Arghya Datta, Noah R. Flynn, Dustyn A. Barnette, Keith F. Woeltje, Grover P. Miller, S. Joshua Swamidass
Machine learning liver-injuring drug interactions with non-steroidal anti-inflammatory drugs (NSAIDs) from a retrospective electronic health record (EHR) cohort. PLoS Comput. Biol. 17 (7) (2021)
Na Le Dang, Matthew K. Matlock, Tyler B. Hughes, S. Joshua Swamidass
The Metabolic Rainbow: Deep Learning Phase I Metabolism in Five Colors. J. Chem. Inf. Model. 60 (3) (2020)
Noah R. Flynn, Na Le Dang, Michael D. Ward, S. Joshua Swamidass
XenoNet: Inference and Likelihood of Intermediate Metabolite Formation. J. Chem. Inf. Model. 60 (7) (2020)
Tyler B. Hughes, Na Le Dang, Ayush Kumar, Noah R. Flynn, S. Joshua Swamidass
Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites. J. Chem. Inf. Model. 60 (10) (2020)
Matthew K. Matlock, Arghya Datta, Na Le Dang, Kevin Jiang, S. Joshua Swamidass
Deep learning long-range information in undirected graphs with wave networks. IJCNN (2019)
Matthew K. Matlock, Tyler B. Hughes, Jayme L. Dahlin, S. Joshua Swamidass
Modeling Small-Molecule Reactivity Identifies Promiscuous Bioactive Compounds. J. Chem. Inf. Model. 58 (8) (2018)
Jon N. Marsh, Matthew K. Matlock, Satoru Kudose, Ta-Chiang Liu, Thaddeus S. Stappenbeck, Joseph P. Gaut, S. Joshua Swamidass
Deep Learning Global Glomerulosclerosis in Transplant Kidney Frozen Sections. IEEE Trans. Medical Imaging 37 (12) (2018)
Matthew K. Matlock, Arghya Datta, Na Le Dang, Kevin Jiang, S. Joshua Swamidass
Deep learning long-range information in undirected graphs with wave networks. CoRR (2018)
William M. Southerland, S. Joshua Swamidass, Philip R. O. Payne, Laura K. Wiley, ClarLynda R. Williams-DeVane
The diversity and disparity in biomedical informatics (DDBI) workshop. PSB (2018)
Shuxiang Ruan, S. Joshua Swamidass, Gary D. Stormo
BEESEM: estimation of binding energy models using HT-SELEX data. Bioinform. 33 (15) (2017)
Jiao Li, Si Zheng, Bin Chen, Atul J. Butte, S. Joshua Swamidass, Zhiyong Lu
A survey of current trends in computational drug repositioning. Briefings Bioinform. 17 (1) (2016)
Na Le Dang, Tyler B. Hughes, Varun Krishnamurthy, S. Joshua Swamidass
A simple model predicts UGT-mediated metabolism. Bioinform. 32 (20) (2016)
Runjun D. Kumar, Adam C. Searleman, S. Joshua Swamidass, Obi L. Griffith, Ron Bose
Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data. Bioinform. 31 (22) (2015)
Jed M. Zaretzki, Michael R. Browning, Tyler B. Hughes, S. Joshua Swamidass
Extending P450 site-of-metabolism models with region-resolution data. Bioinform. 31 (12) (2015)
Alessandro Lusci, Michael R. Browning, David Fooshee, S. Joshua Swamidass, Pierre Baldi
Accurate and efficient target prediction using a potency-sensitive influence-relevance voter. J. Cheminformatics 7 (2015)
Sean Ekins, Alex M. Clark, S. Joshua Swamidass, Nadia K. Litterman, Antony J. Williams
Bigger data, collaborative tools and the future of predictive drug discovery. J. Comput. Aided Mol. Des. 28 (10) (2014)
S. Joshua Swamidass, Zhiyong Lu, Pankaj Agarwal, Atul J. Butte
Session Introduction. Pacific Symposium on Biocomputing (2014)
Matthew K. Matlock, S. Joshua Swamidass
Sharing Chemical Relationships Does Not Reveal Structures. J. Chem. Inf. Model. 54 (1) (2014)
Matthew K. Matlock, Jed Zaretzki, S. Joshua Swamidass
Scaffold network generator: a tool for mining molecular structures. Bioinform. 29 (20) (2013)
Roman Sloutsky, Nicolas Jimenez, S. Joshua Swamidass, Kristen M. Naegle
Accounting for noise when clustering biological data. Briefings Bioinform. 14 (4) (2013)
Jed Zaretzki, Charles Bergeron, Tao-wei Huang, Patrik Rydberg, S. Joshua Swamidass, Curt M. Breneman
RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules. Bioinform. 29 (4) (2013)
Jed Zaretzki, Matthew K. Matlock, S. Joshua Swamidass
XenoSite: Accurately Predicting CYP-Mediated Sites of Metabolism with Neural Networks. J. Chem. Inf. Model. 53 (12) (2013)
S. Joshua Swamidass, Bradley T. Calhoun, Joshua A. Bittker, Nicole E. Bodycombe, Paul A. Clemons
Utility-Aware Screening with Clique-Oriented Prioritization. J. Chem. Inf. Model. 52 (1) (2012)
S. Joshua Swamidass, Chloé-Agathe Azencott, Ting-Wan Lin, Hugo Gramajo, Shiou-Chuan Tsai, Pierre Baldi
Influence Relevance Voting: An Accurate And Interpretable Virtual High Throughput Screening Method. J. Chem. Inf. Model. 49 (4) (2009)
Ryan W. Benz, S. Joshua Swamidass, Pierre Baldi
Discovery of Power-Laws in Chemical Space. J. Chem. Inf. Model. 48 (6) (2008)
Pierre Baldi, Ryan W. Benz, Daniel S. Hirschberg, S. Joshua Swamidass
Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval. J. Chem. Inf. Model. 47 (6) (2007)
S. Joshua Swamidass, Pierre Baldi
Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time. J. Chem. Inf. Model. 47 (2) (2007)
S. Joshua Swamidass, Pierre Baldi
Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval. J. Chem. Inf. Model. 47 (3) (2007)
Chloé-Agathe Azencott, Alexandre Ksikes, S. Joshua Swamidass, Jonathan H. Chen, Liva Ralaivola, Pierre Baldi
One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties. J. Chem. Inf. Model. 47 (3) (2007)