Mehdi Yazdani-Jahromi

AI Research Scientist · Computational Biology

DeepBio Scientific
Microsoft
Johnson & Johnson
University of Central Florida

Representation learning for biological systems, from mRNA language models to drug–target interaction.

I’m a Senior Research Scientist at DeepBio Scientific, where I lead research on machine learning for biomedical data and agentic systems for retrieval and reasoning. Previously I was at Microsoft and Johnson & Johnson, and earned my PhD in Computer Science at UCF.

View publications Curriculum vitae →

Line drawing of a protein binding-site graph with highlighted attention nodes — **Fig. 1.** Attention concentrates on a few residues of a protein binding-site graph, the idea behind AttentionSiteDTI.

Selected papers

All 14 publications →

HELM: Hierarchical Encoding for mRNA Language Modeling Mehdi Yazdani-Jahromi, Mangal Prakash, Tommaso Mansi, Artem Moskalev, Rui Liao

International Conference on Learning Representations (ICLR 2025)

Cite

@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}
}

Equi-mRNA: Protein Translation Equivariant Encoding for mRNA Language Models Mehdi Yazdani-Jahromi, Ali Khodabandeh Yalabadi, Ozlem Ozmen Garibay

Advances in Neural Information Processing Systems (NeurIPS 2025)

Cite

@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}
}

Fair Bilevel Neural Network (FairBiNN): On Balancing fairness and accuracy via Stackelberg Equilibrium Mehdi Yazdani-Jahromi, Ali Khodabandeh Yalabadi, AmirArsalan Rajabi, Aida Tayebi, Ivan Garibay, Ozlem Garibay

Advances in Neural Information Processing Systems (NeurIPS 2024)Code

Cite

@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}
}

AttentionSiteDTI: an interpretable graph-based model for drug-target interaction prediction using NLP sentence-level relation classification Mehdi Yazdani-Jahromi, Niloofar Yousefi, Aida Tayebi, Elayaraja Kolanthai, Craig J Neal, Sudipta Seal, Ozlem Ozmen Garibay

Briefings in Bioinformatics, 2022Code

Cite

@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}
}

Research

Research overview →

Language models for mRNA
Encodings that reflect codon hierarchy and protein translation, improving property prediction and sequence design.
Drug–target interaction & molecule design
Interpretable models over 3D binding sites and fragments, and diffusion-based generation of target-specific molecules.
Trustworthy & agentic ML
Fair representation learning with bilevel formulations, and agents that retrieve, reason and cite over biomedical data.