Publications

2025

1. 

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

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

   arXiv preprint arXiv:2501.15631, 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 = {arXiv preprint arXiv:2501.15631},
     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. 

   HELM: Hierarchical Encoding for mRNA Language Modeling

   Mehdi Yazdani-Jahromi ,  Mangal Prakash ,  Tommaso Mansi , and 2 more authors

   ICLR 2025, 2024

   Bib

   @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}
   }

3. 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}
   }

4. 

   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}
   }

2023

1. 

   BindingSite-AugmentedDTA: enabling a next-generation pipeline for interpretable prediction models in drug repurposing

   Niloofar Yousefi ,  Mehdi Yazdani-Jahromi ,  Aida Tayebi , and 7 more authors

   Briefings in Bioinformatics, 2023
2. HCII, AAAI

   Through a fair looking-glass: mitigating bias in image datasets

   Amirarsalan Rajabi ,  Mehdi Yazdani-Jahromi ,  Ozlem Ozmen Garibay , and 1 more author

   In International Conference on Human-Computer Interaction , 2023

2022

1. 

   AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification

   Mehdi Yazdani-Jahromi ,  Niloofar Yousefi ,  Aida Tayebi , and 4 more authors

   Briefings in Bioinformatics, 2022
2. Molecules

   UnbiasedDTI: Mitigating real-world bias of drug-target interaction prediction by using deep ensemble-balanced learning

   Aida Tayebi ,  Niloofar Yousefi ,  Mehdi Yazdani-Jahromi , and 4 more authors

   Molecules, 2022