Publications

Full, current list: Google Scholar. Papers are grouped by research thread.

Graph machine learning for drug repositioning

Drug repositioning looks for new uses of existing drugs. My work models drugs, diseases, genes, and targets as heterogeneous graphs and learns from them to rank candidate drug–disease and drug–target associations.

• Jaswanth K. Yella, Anil G. Jegga. MGATRx: Discovering Drug Repositioning Candidates Using Multi-View Graph Attention. IEEE/ACM Transactions on Computational Biology and Bioinformatics 19(5), 2022. doi:10.1109/TCBB.2021.3082466
• Jaswanth K. Yella, Sudhir K. Ghandikota, Anil G. Jegga. GraMDTA: Multimodal Graph Neural Networks for Predicting Drug-Target Associations. IEEE BIBM 2022. doi:10.1109/BIBM55620.2022.9995245
• Jaswanth K. Yella, S. Yaddanapudi, Yunguan Wang, Anil G. Jegga. Changing Trends in Computational Drug Repositioning. Pharmaceuticals 11(2):57, 2018. doi:10.3390/ph11020057
• Jaswanth K. Yella, Anil G. Jegga. Magic Bullets: Drug Repositioning and Drug Combinations. In Comprehensive Pharmacology, Elsevier, 2022 (book chapter). doi:10.1016/B978-0-12-820472-6.00116-X
• Yizong Cheng, Jaswanth K. Yella, Anil G. Jegga. Triangle-Based Tripartite Graph Clustering. IEEE BIBM 2020 (workshop). doi:10.1109/BIBM49941.2020.9313324

Biomedical networks and transcriptomics

Integrating gene expression and biological networks to prioritize disease genes, biomarkers, and candidate therapeutics, with much of the applied work on idiopathic pulmonary fibrosis.

• Sudhir Ghandikota, Jaswanth K. Yella, Anil G. Jegga. Multimodal Feature Learning Framework for Disease Biomarker Discovery. IEEE BIBM 2022. doi:10.1109/BIBM55620.2022.9995233
• Yunguan Wang, Jaswanth K. Yella, Sudhir Ghandikota, et al. Pan-transcriptome-based Candidate Therapeutic Discovery for Idiopathic Pulmonary Fibrosis. Therapeutic Advances in Respiratory Disease 14, 2020. doi:10.1177/1753466620971143
• Yunguan Wang, Jaswanth Yella, Anil G. Jegga. Transcriptomic Data Mining and Repurposing for Computational Drug Discovery. In Computational Methods for Drug Repurposing, Methods in Molecular Biology 1903, Springer, 2019 (book chapter). doi:10.1007/978-1-4939-8955-3_5
• Yunguan Wang, Jaswanth Yella, J. Chen, F. X. McCormack, Satish K. Madala, Anil G. Jegga. Unsupervised Gene Expression Analyses Identify IPF-Severity Correlated Signatures, Associated Genes and Biomarkers. BMC Pulmonary Medicine 17:133, 2017. doi:10.1186/s12890-017-0472-9

Machine learning for industrial sensor data

Work done at Seagate: classifying multivariate time series from semiconductor manufacturing sensors, where labels are sparse and heavily imbalanced.

• Jaswanth Yella, Chao Zhang, Sergei Petrov, Yu Huang, Xiaoye Qian, Ali A. Minai, Sthitie Bom. Soft-Sensing ConFormer: A Curriculum Learning-based Convolutional Transformer. IEEE BigData 2021. doi:10.1109/BigData52589.2021.9671991
• Chao Zhang, Jaswanth Yella, Yu Huang, Xiaoye Qian, Sergei Petrov, Andrey Rzhetsky, Sthitie Bom. Soft Sensing Transformer: Hundreds of Sensors are Worth a Single Word. IEEE BigData 2021. doi:10.1109/BigData52589.2021.9671925
• Yu Huang, Chao Zhang, Jaswanth Yella, et al. GraSSNet: Graph Soft Sensing Neural Networks. IEEE BigData 2021. doi:10.1109/BigData52589.2021.9671903
• Xiaoye Qian, Chao Zhang, Jaswanth Yella, et al. Soft Sensing Model Visualization: Fine-tuning Neural Network from What Model Learned. IEEE BigData 2021. doi:10.1109/BigData52589.2021.9671850
• Sergei Petrov, Chao Zhang, Jaswanth Yella, et al. IEEE BigData 2021 Cup: Soft Sensing at Scale. IEEE BigData 2021. doi:10.1109/BigData52589.2021.9671769
• Chao Zhang, Jaswanth Yella, Yu Huang, Sthitie Bom. Learning from Failures in Large Scale Soft Sensing. IEEE BigData 2021. doi:10.1109/BigData52589.2021.9671366

Theses

• Modeling Complex Networks via Graph Neural Networks. PhD dissertation, University of Cincinnati, 2023. PDF
• Machine Learning-based Prediction and Characterization of Drug-Drug Interactions. MS thesis, University of Cincinnati, 2018. PDF

Conference abstracts

• Y. Wang, S. Yaddanapudi, J. Yella, et al. Integrative Omics to Discover Drug Repurposing Candidates for Idiopathic Pulmonary Fibrosis. ATS 2018, Am J Respir Crit Care Med 197:A1637 (abstract).
• Y. Wang, J. Yella, S. K. Madala, A. Jegga. Prioritizing Idiopathic Pulmonary Fibrosis Candidate Genes Based on “Guilt by Association” Analysis. ATS 2018, Am J Respir Crit Care Med 197:A2228 (abstract).