EMBER: multi-label prediction of kinase-substrate phosphorylation events through deep learning. - Kathryn E. Kirchoff; Shawn M. Gomez (Bioinform., 2022)

SALSA: Semantically-Aware Latent Space Autoencoder. - Kathryn E. Kirchoff; Travis Maxfield; Alexander Tropsha; Shawn M. Gomez (AAAI, 2024)

Utilizing Low-Dimensional Molecular Embeddings for Rapid Chemical Similarity Search. - Kathryn E. Kirchoff; James Wellnitz; Joshua E. Hochuli; Travis Maxfield; Konstantin I. Popov; Shawn M. Gomez; Alexander Tropsha (ECIR (2), 2024)

Learning Improved Representations Through Informed Self-Supervision: Applications to Drug Discovery. - Kathryn E. Kirchoff (2024)