Publications

2025

1. 

   Equi-mRNA: Protein Translation Equivariant Encoding for mRNA Language Models

   Mehdi Yazdani-Jahromi ,  Ali Khodabandeh Yalabadi ,  and  Ozlem Ozmen Garibay

   Neurips 2025, 2025

   Bib

   @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://doi.org/10.48550/arXiv.2508.15103},
     year = {2025}
   }

2. 

   FairContrast: Enhancing Fairness through Contrastive learning and Customized Augmenting Methods on Tabular Data

   Aida Tayebi ,  Ali Khodabandeh Yalabadi ,  Mehdi Yazdani-Jahromi , and 1 more author

   Neurips 2025 - Reliable ML Workshop, 2025

   Bib

   @article{tayebi2025faircontrast,
     title = {FairContrast: Enhancing Fairness through Contrastive learning and Customized Augmenting Methods on Tabular Data},
     author = {Tayebi, Aida and Yalabadi, Ali Khodabandeh and Yazdani-Jahromi, Mehdi and Garibay, Ozlem Ozmen},
     journal = {Neurips 2025 - Reliable ML Workshop},
     url = {https://doi.org/10.48550/arXiv.2510.02017},
     year = {2025}
   }

3. 

   BoKDiff: Best-of-K Diffusion Alignment for Target-Specific 3D Molecule Generation

   Ali Khodabandeh Yalabadi ,  Mehdi Yazdani-Jahromi ,  and  Ozlem Ozmen Garibay

   Bioinformatics Advances, 2025

   Bib

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

2024

1. 

   Fair Bilevel Neural Network (FairBiNN): On Balancing fairness and accuracy via Stackelberg Equilibrium

   Mehdi Yazdani-Jahromi ,  Ali Khodabandeh Yalabadi ,  AmirArsalan Rajabi , and 3 more authors

   Neurips 2024, 2024

   Bib

   @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}
   }

2. 

   Enhancing supply chain resilience under disruption: analysis of the farmed data by Monte Carlo simulation

   Ali Khodabandeh-Yalabadi ,  Mohammad Sheikhalishahi ,  Seyed Ali Torabi , and 2 more authors

   International Journal of Systems Science: Operations & Logistics, 2024

3. 

   FragXsiteDTI: Revealing Responsible Segments in Drug-Target Interaction with Transformer-Driven Interpretation

   Ali Khodabandeh Yalabadi ,  Mehdi Yazdani-Jahromi ,  Niloofar Yousefi , and 3 more authors

   In International Conference on Research in Computational Molecular Biology , 2024

   Bib

   @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}
   }

4. HCII

   Learning Fair Representations: Mitigating Statistical Dependencies

   Aida Tayebi ,  Mehdi Yazdani-Jahromi ,  Ali Khodabandeh Yalabadi , and 2 more authors

   In International Conference on Human-Computer Interaction , 2024

   Bib

   @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}
   }

2023

1. 

   Controlling the Misinformation Diffusion in Social Media by the Effect of Different Classes of Agents

   Ali Khodabandeh Yalabadi ,  Mehdi Yazdani-Jahromi ,  Sina Abdidizaji , and 2 more authors

   In Conference of the Computational Social Science Society of the Americas , 2023

2. 

   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 , and 2 more authors

   In Conference of the Computational Social Science Society of the Americas , 2023