Publications
Browse my research publications. Use the filters below to search by keyword, year, or type.
FairContrast: Enhancing Fairness through Contrastive learning and Customized Augmenting Methods on Tabular Data
Aida Tayebi, Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Ozlem Ozmen Garibay
arXiv preprint arXiv:2510.02017, 2025
BoKDiff: best-of-K diffusion alignment for target-specific 3D molecule generation
Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Ozlem Ozmen Garibay
Bioinformatics Advances, 2025
Fair Bilevel Neural Network (FairBiNN): On Balancing fairness and accuracy via Stackelberg Equilibrium
Mehdi Yazdani-Jahromi, Ali Khodabandeh Yalabadi, AmirArsalan Rajabi, Aida Tayebi, Ivan Garibay, Ozlem Garibay
Advances in Neural Information Processing Systems, 2025
Equi-mRNA: Protein Translation Equivariant Encoding for mRNA Language Models
Mehdi Yazdani-Jahromi, Ali Khodabandeh Yalabadi, Ozlem Ozmen Garibay
arXiv preprint arXiv:2508.15103, 2025
Advancing Drug Discovery with Structural and Representation Learning of Biological Systems
Mehdi Yazdani-Jahromi
, 2025
FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation
Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Niloofar Yousefi, Aida Tayebi, Sina Abdidizaji, Ozlem Ozmen Garibay
International Conference on Research in Computational Molecular Biology, 2024
Learning fair representations: Mitigating statistical dependencies
Aida Tayebi, Mehdi Yazdani-Jahromi, Ali Khodabandeh Yalabadi, Niloofar Yousefi, Ozlem Ozmen Garibay
International Conference on Human-Computer Interaction, 2024
HELM: Hierarchical Encoding for mRNA Language Modeling
Mehdi Yazdani-Jahromi, Mangal Prakash, Tommaso Mansi, Artem Moskalev, Rui Liao
ICLR 2025; also Neurips 2024 Workshop on AI for New Drug Modalities, 2024
Agent-based modeling of C. difficile spread in hospitals: assessing contribution of high-touch vs. Low-touch surfaces and inoculations’ containment Impact
Sina Abdidizaji, Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Ozlem Ozmen Garibay, Ivan Garibay
, 2023
Through a fair looking-glass: mitigating bias in image datasets
Amirarsalan Rajabi, Mehdi Yazdani-Jahromi, Ozlem Ozmen Garibay, Gita Sukthankar
International Conference on Human-Computer Interaction, 2023
Controlling the misinformation diffusion in social media by the effect of different classes of agents
Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Sina Abdidizaji, Ivan Garibay, Ozlem Ozmen Garibay
, 2023
BindingSite-AugmentedDTA: enabling a next-generation pipeline for interpretable prediction models in drug repurposing
Niloofar Yousefi, Mehdi Yazdani-Jahromi, Aida Tayebi, Elayaraja Kolanthai, Craig J Neal, Tanumoy Banerjee, Agnivo Gosai, Ganesh Balasubramanian, Sudipta Seal, Ozlem Ozmen Garibay
Briefings in Bioinformatics, 2023
Unbiaseddti: Mitigating real-world bias of drug-target interaction prediction by using deep ensemble-balanced learning
Aida Tayebi, Niloofar Yousefi, Mehdi Yazdani-Jahromi, Elayaraja Kolanthai, Craig J Neal, Sudipta Seal, Ozlem Ozmen Garibay
Molecules, 2022
AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification
Mehdi Yazdani-Jahromi, Niloofar Yousefi, Aida Tayebi, Elayaraja Kolanthai, Craig J Neal, Sudipta Seal, Ozlem Ozmen Garibay
Briefings in Bioinformatics, 2022