Papers

@misc{yazdanijahromi2026mirage,
  title = {MIRAGE: Measuring Interpolation and Redundancy in Affinity GEneralization},
  author = {Mehdi Yazdani-Jahromi and Sanjay Padhi and Ivan Garibay},
  year = {2026},
  eprint = {2609.14491},
  archivePrefix = {arXiv},
  primaryClass = {q-bio.QM},
  url = {https://arxiv.org/abs/2609.14491}
}

@misc{yazdanijahromi2025advancing,
  title = {Advancing Drug Discovery with Structural and Representation Learning of Biological Systems},
  author = {Mehdi Yazdani-Jahromi},
  year = {2025},
  howpublished = {PhD Dissertation, University of Central Florida}
}

@article{Khodabandeh_Yalabadi_2024, title={BoKDiff: best-of-K diffusion alignment for target-specific 3D molecule generation}, volume={5}, ISSN={2635-0041}, url={http://dx.doi.org/10.1093/bioadv/vbaf137}, DOI={10.1093/bioadv/vbaf137}, number={1}, journal={Bioinformatics Advances}, publisher={Oxford University Press (OUP)}, author={Khodabandeh Yalabadi, Ali and Yazdani-Jahromi, Mehdi and Garibay, Ozlem Ozmen}, editor={Lengauer, Thomas}, year={2024}, month=Dec }

@inproceedings{Yazdani_Jahromi_2025, series={NeurIPS 2025}, title={Equi-mRNA: Protein Translation Equivariant Encoding for mRNA Language Models}, url={http://dx.doi.org/10.52202/085713-0904}, DOI={10.52202/085713-0904}, booktitle={Advances in Neural Information Processing Systems 38}, publisher={Neural Information Processing Systems Foundation, Inc. (NeurIPS)}, author={Yazdani-Jahromi, Mehdi and Khodabandeh Yalabadi, Ali and Garibay, Ozlem}, year={2025}, pages={30416–30456}, collection={NeurIPS 2025} }

@misc{tayebi2025faircontrast,
  title = {FairContrast: Enhancing Fairness through Contrastive learning and Customized Augmenting Methods on Tabular Data},
  author = {Aida Tayebi and Ali Khodabandeh Yalabadi and Mehdi Yazdani-Jahromi and Ozlem Ozmen Garibay},
  year = {2025},
  eprint = {2510.02017},
  archivePrefix = {arXiv},
  primaryClass = {cs.LG},
  url = {https://arxiv.org/abs/2510.02017}
}

@article{yazdani2024helm,
  title={HELM: Hierarchical Encoding for mRNA Language Modeling},
  author={Yazdani-Jahromi, Mehdi and Prakash, Mangal and Mansi, Tommaso and Moskalev, Artem and Liao, Rui},
  journal={ICLR 2025},
  url={https://arxiv.org/abs/2410.12459},
  year={2024}
}

@inproceedings{Yazdani_Jahromi_2024, series={NeurIPS 2024}, title={Fair Bilevel Neural Network (FairBiNN): On Balancing fairness and accuracy via Stackelberg Equilibrium}, url={http://dx.doi.org/10.52202/079017-3355}, DOI={10.52202/079017-3355}, booktitle={Advances in Neural Information Processing Systems 37}, publisher={Neural Information Processing Systems Foundation, Inc. (NeurIPS)}, author={Yazdani-Jahromi, Mehdi and Yalabadi, Ali and Rajabi, Amirarsalan and Tayebi, Aida and Garibay, Ivan and Garibay, Ozlem}, year={2024}, pages={105780–105818}, collection={NeurIPS 2024} }

@inproceedings{khodabandeh2024fragxsitedti,
  title={FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation},
  author={Khodabandeh Yalabadi, Ali and Yazdani-Jahromi, Mehdi and Yousefi, Niloofar and Tayebi, Aida and Abdidizaji, Sina and Garibay, Ozlem Ozmen},
  booktitle={International Conference on Research in Computational Molecular Biology},
  url={https://arxiv.org/abs/2311.02326},
  pages={68--85},
  year={2024},
  organization={Springer}
}

@inproceedings{tayebi2024learning,
  title={Learning Fair Representations: Mitigating Statistical Dependencies},
  author={Tayebi, Aida and Yazdani-Jahromi, Mehdi and Yalabadi, Ali Khodabandeh and Yousefi, Niloofar and Garibay, Ozlem Ozmen},
  booktitle={International Conference on Human-Computer Interaction},
  url={https://link.springer.com/chapter/10.1007/978-3-031-60611-3_8},
  pages={105--115},
  year={2024},
  organization={Springer}
}

@inbook{Abdidizaji_2024, title={Agent-Based Modeling of C. Difficile Spread in Hospitals: Assessing Contribution of High-Touch vs. Low-Touch Surfaces and Inoculations’ Containment Impact}, ISBN={9783031641930}, ISSN={2213-8692}, url={http://dx.doi.org/10.1007/978-3-031-64193-0_11}, DOI={10.1007/978-3-031-64193-0_11}, booktitle={Proceedings of the 2023 International Conference of The Computational Social Science Society of the Americas}, publisher={Springer Nature Switzerland}, author={Abdidizaji, Sina and Yalabadi, Ali Khodabandeh and Yazdani-Jahromi, Mehdi and Garibay, Ozlem Ozmen and Garibay, Ivan}, year={2024}, pages={173–188} }

@article{Yousefi_2023, title={BindingSite-AugmentedDTA: enabling a next-generation pipeline for interpretable prediction models in drug repurposing}, volume={24}, ISSN={1477-4054}, url={http://dx.doi.org/10.1093/bib/bbad136}, DOI={10.1093/bib/bbad136}, number={3}, journal={Briefings in Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Yousefi, Niloofar and Yazdani-Jahromi, Mehdi and Tayebi, Aida and Kolanthai, Elayaraja and Neal, Craig J and Banerjee, Tanumoy and Gosai, Agnivo and Balasubramanian, Ganesh and Seal, Sudipta and Ozmen Garibay, Ozlem}, year={2023}, month=Apr }

@inbook{Yalabadi_2024, title={Controlling the Misinformation Diffusion in Social Media by the Effect of Different Classes of Agents}, ISBN={9783031641930}, ISSN={2213-8692}, url={http://dx.doi.org/10.1007/978-3-031-64193-0_9}, DOI={10.1007/978-3-031-64193-0_9}, booktitle={Proceedings of the 2023 International Conference of The Computational Social Science Society of the Americas}, publisher={Springer Nature Switzerland}, author={Yalabadi, Ali Khodabandeh and Yazdani-Jahromi, Mehdi and Abdidizaji, Sina and Garibay, Ivan and Garibay, Ozlem Ozmen}, year={2024}, pages={143–157} }

@inproceedings{rajabi2023through,
  title={Through a fair looking-glass: mitigating bias in image datasets},
  author={Rajabi, Amirarsalan and Yazdani-Jahromi, Mehdi and Garibay, Ozlem Ozmen and Sukthankar, Gita},
  booktitle={International Conference on Human-Computer Interaction},
  pages={446--459},
  year={2023},
  organization={Springer},
  url={https://link.springer.com/chapter/10.1007/978-3-031-35891-3_27}
}

@article{Yazdani_Jahromi_2022, title={AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification}, volume={23}, ISSN={1477-4054}, url={http://dx.doi.org/10.1093/bib/bbac272}, DOI={10.1093/bib/bbac272}, number={4}, journal={Briefings in Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Yazdani-Jahromi, Mehdi and Yousefi, Niloofar and Tayebi, Aida and Kolanthai, Elayaraja and Neal, Craig J and Seal, Sudipta and Garibay, Ozlem Ozmen}, year={2022}, month=July }

@article{Tayebi_2022, title={UnbiasedDTI: Mitigating Real-World Bias of Drug-Target Interaction Prediction by Using Deep Ensemble-Balanced Learning}, volume={27}, ISSN={1420-3049}, url={http://dx.doi.org/10.3390/molecules27092980}, DOI={10.3390/molecules27092980}, number={9}, journal={Molecules}, publisher={MDPI AG}, author={Tayebi, Aida and Yousefi, Niloofar and Yazdani-Jahromi, Mehdi and Kolanthai, Elayaraja and Neal, Craig and Seal, Sudipta and Garibay, Ozlem}, year={2022}, month=May, pages={2980} }