| MSA-regularized protein sequence transformer toward predicting genome-wide chemical-protein interactions: application to GPCRome deorphanization T Cai, H Lim, KA Abbu, Y Qiu, R Nussinov, L Xie Journal of chemical information and modeling 61 (4), 1570-1582, 2021 | 26 | 2021 |
| End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins T Cai, L Xie, S Zhang, M Chen, D He, A Badkul, Y Liu, HK Namballa, ... PLOS Computational Biology 19 (1), e1010851, 2023 | 8 | 2023 |
| DeepREAL: a deep learning powered multi-scale modeling framework for predicting out-of-distribution ligand-induced GPCR activity T Cai, KA Abbu, Y Liu, L Xie Bioinformatics 38 (9), 2561-2570, 2022 | 6 | 2022 |
| Music autotagging as captioning T Cai, MI Mandel, D He Proceedings of the 1st Workshop on NLP for Music and Audio (NLP4MusA), 67-72, 2020 | 5 | 2020 |
| Exploration of dark chemical genomics space via portal learning: applied to targeting the undruggable genome and covid-19 anti-infective polypharmacology T Cai, L Xie, M Chen, Y Liu, D He, S Zhang, C Mura, PE Bourne, L Xie Research Square, 2021 | 4 | 2021 |
| A deep learning framework for elucidating whole-genome chemical interaction space T Cai, H Lim, KA Abbu, Y Qiu, R Nussinov, L Xie bioRxiv, 2020.10. 08.332346, 2020 | 3 | 2020 |
| Interpretable classification of categorical time series using the spectral envelope and optimal scalings Z Li, SA Bruce, T Cai Journal of Machine Learning Research 23 (299), 1-31, 2022 | 1 | 2022 |
| DeepREAL: A Deep Learning Powered Multi-scale Modeling Framework Towards Predicting Out-of-distribution Receptor Activity of Ligand Binding T Cai, KA Abbu, Y Liu, L Xie bioRxiv, 2021.09. 12.460001, 2021 | 1 | 2021 |
| Genome-wide prediction of small molecule binding to remote orphan proteins using distilled sequence alignment embedding T Cai, H Lim, KA Abbu, Y Qiu, R Nussinov, L Xie bioRxiv, 2020.08. 04.236729, 2020 | 1 | 2020 |
| Out-of-Distribution Generalization of Deep Learning to Illuminate Dark Protein Functional Space T Cai City University of New York, 2023 | | 2023 |
| Binding Site-enhanced Sequence Pretraining and Out-of-cluster Meta-learning Predict Genome-Wide Chemical-Protein Interactions for Dark Proteins T Cai, L Xie, S Zhang, M Chen, D He, A Badkul, Y Liu, HK Namballa, ... bioRxiv, 2022.11. 15.516682, 2022 | | 2022 |
