Ali Khodabandeh Yalabadi

Hello, I’m Ali Khodabandeh Yalabadi, a Ph.D. candidate and AI researcher with a strong focus on computational drug discovery, machine learning, and data science. Experienced in developing advanced AI models for drug-target interaction prediction, generative molecular design, and algorithmic fairness. Proficient in statistics, data analysis, and predictive modeling, with publications in top-tier venues. Adept at leading projects and managing cross-functional collaborations, combining technical expertise with business acumen. Background in industrial engineering, applying optimization and data-driven strategies to real-world AI challenges.

News

Sep 25, 2025	Our paper, “Equi-mRNA: Protein Translation Equivariant Encoding for mRNA Language Models,” has been accepted to NeurIPS 2025. We present a codon-level equivariant architecture that models synonymous codon symmetries through group-theoretic priors, achieving up to 10% higher accuracy and more biologically realistic mRNA generation that better preserves functional properties.
Aug 10, 2025	I’m excited to share that I’ve joined BioTrillion as an AI Engineer Intern (Aug–Dec 2025). At BioTrillion, I’m developing and optimizing AI models for digital biomarker detection using multi-modal health data, including signal and depth information captured from iOS devices. My work focuses on real-world health analytics, combining computer vision, signal processing, and AI to advance personalized digital health solutions.
Sep 25, 2024	Our paper, “Fair Bilevel Neural Network (FairBiNN): On Balancing Fairness and Accuracy via Stackelberg Equilibrium,” has been accepted to NeurIPS 2024. We introduce a novel bilevel optimization approach to enhance fairness in machine learning, achieving superior results on key datasets.
Dec 22, 2023	Thrilled to announce that our paper (FragXsiteDTI) has been accepted at RECOMB 2024, following its acceptance at the NeurIPS 2023 AI for Drug Discovery and Development Workshop!

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Selected Publications

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}
}

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},
}

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}
}

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}
}