Vasant Honavar

Professor and Edward Frymoyer Chair of Information Sciences and Technology

Vasant Honavar

Research Summary

Statistical machine learning algorithms for predictive modeling; modeling and inference of biological networks; characterization and prediction of protein-protein, protein-RNA, and protein-DNA interactions.

Huck Affiliations


Publication Tags

Proteins Rna Machine Learning Protein Biomarkers Peptides Prediction Conformations Amino Acid Sequence Homology Sequence Homology Learning Systems Class Artifact Science Support Vector Machines Classifiers Interaction Datasets Scoring Methodology Nucleic Acid Databases Rna Binding Proteins Artificial Intelligence Inflammatory Bowel Diseases Model

Most Recent Papers

The Virtual Data Collaboratory

Manish Parashar, Anthony Simonet, Ivan Rodero, Forough Ghahramani, Grace Agnew, Ron Jantz, Vasant Honavar, 2020, Computing in Science and Engineering on p. 79-92

IScore: A novel graph kernel-based function for scoring protein-protein docking models

Cunliang Geng, Yong Jung, Nicolas Renaud, Vasant Honavar, Alexandre M.J.J. Bonvin, Li C. Xue, 2020, Bioinformatics on p. 112-121

Explainable Multivariate Time Series Classification: A Deep Neural Network Which Learns To Attend To Important Variables As Well As Informative Time Intervals

Tsung-Yu Hsieh, Suhang Wang, Yiwei Sun, Vasant Honavar, 2020, arXiv preprint arXiv:2011.11631

Two-dimensional hybrid organic--inorganic perovskites as emergent ferroelectric materials

Yuchen Hou, Congcong Wu, Dong Yang, Tao Ye, Vasant Honavar, Adri Van Duin, Kai Wang, Shashank Priya, 2020, Journal of Applied Physics on p. 060906

A Causal Lens for Peeking into Black Box Predictive Models: Predictive Model Interpretation via Causal Attribution

Aria Khademi, Vasant Honavar, 2020, arXiv preprint arXiv:2008.00357

Longitudinal Deep Kernel Gaussian Process Regression

Junjie Liang, Yanting Wu, Dongkuan Xu, Vasant Honavar, 2020, arXiv preprint arXiv:2005.11770

Commuting Network Spillovers and COVID-19 Deaths Across US Counties

Christopher Seto, Aria Khademi, Corina Graif, Vasant Honavar, 2020, arXiv preprint arXiv:2010.01101

iScore: An MPI supported software for ranking protein–protein docking models based on a random walk graph kernel and support vector machines

Nicolas Renaud, Yong Jung, Vasant Honavar, Cunliang Geng, Alexandre M.J.J. Bonvin, Li C. Xue, 2020, SoftwareX

Biomarker discovery in inflammatory bowel diseases using network-based feature selection

Mostafa Abbas, John Matta, Thanh Le, Halima Bensmail, Tayo Obafemi-Ajayi, Vasant Honavar, Yasser EL-Manzalawy, 2019, PLoS One

Personalized sleep parameters estimation from actigraphy

Aria Khademi, Yasser El-Manzalawy, Lindsay Master, Orfeu M. Buxton, Vasant G. Honavar, 2019, Nature and Science of Sleep on p. 387-399

Most-Cited Papers

Mobile health technology evaluation

Santosh Kumar, Wendy J. Nilsen, Amy Abernethy, Audie Atienza, Kevin Patrick, Misha Pavel, William T. Riley, Albert Shar, Bonnie Spring, Donna Spruijt-Metz, Donald Hedeker, Vasant Honavar, Richard Kravitz, R. Craig Lefebvre, David C. Mohr, Susan A. Murphy, Charlene Quinn, Vladimir Shusterman, Dallas Swendeman, 2013, American Journal of Preventive Medicine on p. 228-236

Predicting RNA-Protein Interactions Using Only Sequence Information

Usha K. Muppirala, Vasant G. Honavar, Drena Dobbs, 2011, BMC Bioinformatics


Benjamin A. Lewis, Rasna R. Walia, Michael Terribilini, Jeff Ferguson, Charles Zheng, Vasant Honavar, Drena Dobbs, 2011, Nucleic Acids Research on p. D277-D282


Li C. Xue, Drena Dobbs, Vasant Honavar, 2011, BMC Bioinformatics

RNABindRPlus: a predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins.

R Walia, Lingzhou Xue, K Wilkins, Yasser Elmanzalawi, D Dobbs, Vasant Honavar, 2014, PLoS One on p. e97725

Predicting protein-protein interface residues using local surface structural similarity

Rafael A. Jordan, Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar, 2012, BMC Bioinformatics

Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art

Rasna R. Walia, Cornelia Caragea, Benjamin A. Lewis, Fadi Towfic, Michael Terribilini, Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar, 2012, BMC Bioinformatics


Li C. Xue, Rafael A. Jordan, El Manzalawy Yasser, Drena Dobbs, Vasant Honavar, 2014, Proteins: Structure, Function and Genetics on p. 250-267

Predicting MHC-II binding affinity using multiple instance regression

Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar, 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics on p. 1067-1079

The promise and potential of big data

Vasant G. Honavar, 2014, Review of Policy Research on p. 326-330

News Articles Featuring Vasant Honavar

Researchers deploy AI to detect bias in AI and humans

Researchers have developed a tool using artificial intelligence (AI) to detect unfair bias in protected areas such as race or gender. The tool could be used in finding bias in AI systems or even bias by human decisions makers, according to the researchers at Penn State and Columbia University.

What is bias in AI really, and why can’t AI neutralize it?

Selection algorithms everywhere are exhibiting traits that appear to be racist, sexist, and otherwise discriminatory. Have neural networks already developed their own neuropathy? Or are people somehow the problem?

AI to fight unfair discrimination

Researchers developed a new artificial intelligence (AI) tool for detecting unfair discrimination such as race or gender.

Penn State researchers develop bias-detecting technology

Researchers at Penn State and Columbia University have developed artificial intelligence technology that can detect unfair discrimination within specific demographics.

Artificial intelligence tool can identify gender and racial bias

Scientists have developed a new artificial intelligence (AI) tool for detecting unfair discrimination—such as on the basis of race or gender.

Researchers Create New AI Tool for Detecting Unfair Discrimination

Penn State and Columbia University researchers have created a new artificial intelligence tool to detect unfair discrimination based on gender and race. For example, a long-standing concern of civilized societies has been preventing unfair treatment of individuals based on gender, race, or ethnicity.

US researchers create AI tool that can detect discrimination on basis of race, gender

A team of researchers at Pennsylvania State and Columbia University created an artificial intelligence (AI) tool for detecting discrimination with respect to a protected attribute, such as race or gender.

'AI will see you now': Panel to discuss the AI revolution in health and medicine

​This month’s CyberScience Seminar, organized by the Institute for CyberScience (ICS), will be held from 1:30–3 p.m. on Thursday, April 11, in 233B HUB-Robeson Center and will feature a panel of Penn State experts who will discuss the benefits — and the risks — of using AI in the healthcare industry.​

Is artificial intelligence affecting the job market?

The term Artificial Intelligence elicits images of cyborgs and terminators; human-like robots intent on pursuing death and destruction. Hollywood representations distort what AI really is and the technological achievements that scientists are making.