AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification. - Mehdi Yazdani-Jahromi; Niloofar Yousefi 001; Aida Tayebi; Elayaraja Kolanthai; Craig J. Neal; Sudipta Seal; Özlem Özmen Garibay (Briefings Bioinform., 2022)

Distraction is All You Need for Fairness. - Mehdi Yazdani-Jahromi; Amirarsalan Rajabi; Aida Tayebi; Özlem Özmen Garibay (CoRR, 2022)

Through a Fair Looking-Glass: Mitigating Bias in Image Datasets. - Amirarsalan Rajabi; Mehdi Yazdani-Jahromi; Özlem Özmen Garibay; Gita Sukthankar (HCI (40), 2023)

BindingSite-AugmentedDTA: enabling a next-generation pipeline for interpretable prediction models in drug repurposing. - Niloofar Yousefi 001; Mehdi Yazdani-Jahromi; Aida Tayebi; Elayaraja Kolanthai; Craig J. Neal; Tanumoy Banerjee; Agnivo Gosai; Ganesh Balasubramanian; Sudipta Seal; Özlem Özmen Garibay (Briefings Bioinform., 2023)

Learning Fair Representations: Mitigating Statistical Dependencies. - Aida Tayebi; Mehdi Yazdani-Jahromi; Ali Khodabandeh Yalabadi; Niloofar Yousefi 001; Özlem Özmen Garibay (HCI (52), 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 O. Garibay (NeurIPS, 2024)

FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation. - Ali Khodabandeh Yalabadi; Mehdi Yazdani-Jahromi; Niloofar Yousefi 001; Aida Tayebi; Sina Abdidizaji; Özlem Özmen Garibay (RECOMB, 2024)

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; Özlem Özmen Garibay (CoRR, 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; Özlem Özmen Garibay; Ivan Garibay (CoRR, 2024)

HELM: Hierarchical Encoding for mRNA Language Modeling. - Mehdi Yazdani-Jahromi; Mangal Prakash; Tommaso Mansi; Artem Moskalev; Rui Liao (ICLR, 2025)

BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation. - Ali Khodabandeh Yalabadi; Mehdi Yazdani-Jahromi; Özlem Özmen Garibay (CoRR, 2025)