Papers

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

@article{yalabadi2025bokdiffbestofkdiffusionalignment,
      title={BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation}, 
      author={Ali Khodabandeh Yalabadi and Mehdi Yazdani-Jahromi and Ozlem Ozmen Garibay},
      year={2025},
      journal={arXiv preprint arXiv:2501.15631},
      url={https://arxiv.org/abs/2501.15631}
}

@article{yazdani2025equi, 
      title={Equi-mRNA: Protein Translation Equivariant Encoding for mRNA Language Models},
      author={Yazdani-Jahromi, Mehdi and Yalabadi, Ali Khodabandeh and Garibay, Ozlem Ozmen},
      journal={Neurips 2025},
      url={https://arxiv.org/abs/2508.15103},
      year={2025}
}

@article{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},
  journal = {arXiv preprint arXiv:2510.02017},
  year = {2025}
}

@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}
}

@article{yazdani2024fair,
  title={Fair Bilevel Neural Network (FairBiNN): On Balancing fairness and accuracy via Stackelberg Equilibrium},
  author={Yazdani-Jahromi, Mehdi and Yalabadi, Ali Khodabandeh and Rajabi, AmirArsalan and Tayebi, Aida and Garibay, Ivan and Garibay, Ozlem Ozmen},
  journal={Neurips 2024},
  url={https://arxiv.org/abs/2410.16432},
  year={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}
}

@inproceedings{abdidizaji2023agentbased,
  title = {Agent-based modeling of C. difficile spread in hospitals: assessing contribution of high-touch vs. Low-touch surfaces and inoculations’ containment Impact},
  author = {Sina Abdidizaji and Ali Khodabandeh Yalabadi and Mehdi Yazdani-Jahromi and Ozlem Ozmen Garibay and Ivan Garibay},
  booktitle = {Computational Social Science Society of the Americas (CSSSA) Annual Conference},
  year = {2023}
}

@article{yousefi2023bindingsite,
  title={BindingSite-AugmentedDTA: enabling a next-generation pipeline for interpretable prediction models in drug repurposing},
  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},
  journal={Briefings in Bioinformatics},
  volume={24},
  number={3},
  pages={bbad136},
  year={2023},
  publisher={Oxford University Press},
  url={https://academic.oup.com/bib/article/24/3/bbad136/7140297}
}

@inproceedings{yalabadi2023controlling,
  title = {Controlling the misinformation diffusion in social media by the effect of different classes of agents},
  author = {Ali Khodabandeh Yalabadi and Mehdi Yazdani-Jahromi and Sina Abdidizaji and Ivan Garibay and Ozlem Ozmen Garibay},
  booktitle = {Computational Social Science Society of the Americas (CSSSA) Annual Conference},
  year = {2023}
}

@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{yazdani2022attentionsitedti,
  title={AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification},
  author={Yazdani-Jahromi, Mehdi and Yousefi, Niloofar and Tayebi, Aida and Kolanthai, Elayaraja and Neal, Craig J and Seal, Sudipta and Garibay, Ozlem Ozmen},
  journal={Briefings in Bioinformatics},
  volume={23},
  number={4},
  pages={bbac272},
  year={2022},
  publisher={Oxford University Press},
  doi={10.1093/bib/bbac272},
  url={https://academic.oup.com/bib/article/23/4/bbac272/6640006?login=false}
}

@article{tayebi2022unbiaseddti,
  title={UnbiasedDTI: Mitigating real-world bias of drug-target interaction prediction by using deep ensemble-balanced learning},
  author={Tayebi, Aida and Yousefi, Niloofar and Yazdani-Jahromi, Mehdi and Kolanthai, Elayaraja and Neal, Craig J and Seal, Sudipta and Garibay, Ozlem Ozmen},
  journal={Molecules},
  volume={27},
  number={9},
  pages={2980},
  year={2022},
  publisher={MDPI},
  url={https://www.mdpi.com/1420-3049/27/9/2980}
}