Vasant Honavar

Huck Chair in Biomedical Data Sciences and AI; 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

Links

Most Recent Publications

Checking Consistency of CP-Theory Preferences in Polynomial Time

Erik Rauer, Samik Basu, Vasant Honavar, 2025, on p. 15126-15133

Hyperdimensional Representation Learning for Node Classification and Link Prediction

Abhishek Dalvi, Vasant Honavar, 2025, on p. 88-97

A practical guide to machine learning interatomic potentials – Status and future

Ryan Jacobs, Dane Morgan, Siamak Attarian, Jun Meng, Chen Shen, Zhenghao Wu, Clare Yijia Xie, Julia H. Yang, Nongnuch Artrith, Ben Blaiszik, Gerbrand Ceder, Kamal Choudhary, Gabor Csanyi, Ekin Dogus Cubuk, Bowen Deng, Ralf Drautz, Xiang Fu, Jonathan Godwin, Vasant Honavar, Olexandr Isayev, Anders Johansson, Stefano Martiniani, Shyue Ping Ong, Igor Poltavsky, K. J. Schmidt, So Takamoto, Aidan P. Thompson, Julia Westermayr, Brandon M. Wood, Boris Kozinsky, 2025, Current Opinion in Solid State and Materials Science

Class Incremental Learning from First Principles: A Review

Neil Ashtekar, Jingxi Zhu, Vasant G. Honavar, 2025, Transactions on Machine Learning Research

Efficient Contrastive Learning for Fast andAccurate Inference on Graphs

Teng Xiao, Huaisheng Zhu, Zhiwei Zhang, Zhimeng Guo, Charu Aggarwal, Suhang Wang, V Honavar, 2024, on p. 54363 - 54381

Inducing Clusters Deep Kernel Gaussian Process for Longitudinal Data

Junjie Liang, Weijieying Ren, Hanifi Sahar, Vasant Honavar, 2024, Proceedings of the AAAI Conference on Artificial Intelligence on p. 13736-13743

Inducing Clusters Deep Kernel Gaussian Process for Longitudinal Data

Junjie Liang, Weijieying Ren, Sahar Hanifi, Vasant Honavar, 2024, Proceedings of the AAAI Conference on Artificial Intelligence on p. 13736-13743

Cal-DPO: Calibrated Direct Preference Optimization for Language Model Alignment

Teng Xiao, Yige Yuan, Huaisheng Zhu, Mingxiao Li, Vasant Honavar, 2024,

3M-Diffusion: Latent Multi-Modal Diffusion for Language-Guided Molecular Structure Generation

Huaisheng Zhu, Teng Xiao, Vasant Honavar, 2024,

How to Leverage Demonstration Data in Alignment for Large Language Model? A Self-Imitation Learning Perspective

Teng Xiao, Mingxiao Li, Yige Yuan, Huaisheng Zhu, Chao Cui, Vasant Honavar, 2024, on p. 13413--13426

Most-Cited Papers

Adversarial Attacks on Graph Neural Networks via Node Injections: A Hierarchical Reinforcement Learning Approach

Yiwei Sun, Suhang Wang, Xianfeng Tang, Tsung-Yu Hsieh, Vasant Honavar, 2020, on p. 673--683

Computational prediction of protein interfaces: A review of data driven methods

Li C. Xue, Drena Dobbs, Alexandre M J J Bonvin, Vasant Honavar, 2015, FEBS Letters on p. 3516-3526

Fairness in algorithmic decision making: An excursion through the lens of causality

Aria Khademi, David Foley, Sanghack Lee, Vasant Honavar, 2019, on p. 2907-2914

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 Time Intervals

Tsung Yu Hsieh, Suhang Wang, Yiwei Sun, Vasant Honavar, 2021, on p. 607-615

Min-redundancy and max-relevance multi-view feature selection for predicting ovarian cancer survival using multi-omics data 06 Biological Sciences 0604 Genetics

Yasser El-Manzalawy, Tsung Yu Hsieh, Manu Shivakumar, Dokyoon Kim, Vasant Honavar, 2018, BMC Medical Genomics on p. 71

Improving image captioning by leveraging knowledge graphs

Yimin Zhou, Yiwei Sun, Vasant Honavar, 2019, on p. 283-293

In silico prediction of linear B-cell epitopes on proteins

Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar, 2017, on p. 255-264

Megan: A generative adversarial network for multi-view network embedding

Yiwei Sun, Suhang Wang, Tsung Yu Hsieh, Xianfeng Tang, Vasant Honavar, 2019, on p. 3527-3533

Personalized sleep parameters estimation from actigraphy: A machine learning approach

Aria Khademi, Yasser El-Manzalawy, EL-Manzalawy Yasser, Lindsay Master, Orfeu M. Buxton, Vasant Honavar, 2019, Nature and Science of Sleep on p. 387-391

News Articles Featuring Vasant Honavar

Apr 28, 2025

Penn State adds artificial intelligence major, with a focus on ethics

Starting this fall, Penn State students will be able to major in artificial intelligence, focusing on the development, application and ethical considerations of AI.

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Apr 09, 2025

NCEMS working groups to answer molecular and cellular bioscience questions

The U.S. National Science Foundation National Synthesis Center for Emergence in the Molecular and Cellular Sciences at Penn State aims to drive multidisciplinary collaboration utilizing publicly available research data.

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Oct 31, 2024

Huck researchers reflect on the 2024 Nobel Prize in Chemistry

This month, the Nobel Prize in Chemistry was awarded to three scientists credited with historic breakthroughs surrounding proteins and their structures. Three Huck researchers working on similar challenges chime in with their thoughts.

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Oct 03, 2024

ICDS Day seeks to amplify synergy for interdisciplinary research opportunities

Oct. 23 event aims to bring together faculty, students and industry professionals to foster innovation and interdisciplinary collaboration.

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Jun 27, 2024

ICDS associate director's work driven by unanswered fundamental questions in AI

The work of Vasant Honavar, the Dorothy Foehr Huck and J. Lloyd Huck Chair in biomedical data sciences and artificial intelligence (AI) and a professor of data science in the College of Information Sciences and Technology professor of data science, is driven by answering fundamental questions using machine learning.

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Apr 25, 2024

$20M NSF grant to support center to study how complex biological processes arise

A $20 million grant from the U.S. National Science Foundation (NSF) will support the establishment and operation of the National Synthesis Center for Emergence in the Molecular and Cellular Sciences (NCEMS) at Penn State.

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Sep 16, 2022

Millennium Café series to feature special editions in October, November

The Millennium Café, held every Tuesday by the Materials Research Institute (MRI) featuring two talks by Penn State researchers that serve as an exchange of ideas and solutions, will hold three special sessions in October and November.

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Oct 04, 2021

Vasant Honavar named Huck Chair in Biomedical Data Sciences and AI

Vasant Honavar, professor in the College of Information Sciences and Technology, has been named the Dorothy Foehr Huck and J. Lloyd Huck Chair in Biomedical Data Sciences and Artificial Intelligence by the University’s Huck Institutes of the Life Sciences.

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Jul 17, 2019

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.

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Jul 17, 2019

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?

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Jul 15, 2019

AI to fight unfair discrimination

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

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Jul 12, 2019

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.

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Jul 12, 2019

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.

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Jul 11, 2019

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.

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Jul 11, 2019

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.

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Apr 02, 2019

'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.​

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Feb 20, 2019

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.

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