Publications
Browse my research publications. Use the filters below to search by keyword, year, or type.
BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation
Ali Khodabandeh Yalabadi, Mehdi Yazdani-Jahromi, Ozlem Ozmen Garibay
arXiv preprint arXiv:2501.15631, 2025
Equi-mRNA: Protein Translation Equivariant Encoding for mRNA Language Models
Mehdi Yazdani-Jahromi, Ali Khodabandeh Yalabadi, Ozlem Ozmen Garibay
Neurips 2025, 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
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 Ozmen Garibay
Neurips 2024, 2024
HELM: Hierarchical Encoding for mRNA Language Modeling
Mehdi Yazdani-Jahromi, Mangal Prakash, Tommaso Mansi, Artem Moskalev, Rui Liao
ICLR 2025, 2024
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
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