Seyednami Niyakan

Seyednami Niyakan

Ph.D. candidate

Texas A&M University

Biography

I’m a Ph.D. candidate in the Genomic Signal Processing Lab at the Department of Electrical and Computer Engineering, Texas A&M University, advised by Prof. Xiaoning Qian. My research bridges Bayesian machine learning, generative models, and multi-modal data integration, with a focus on designing interpretable and scalable AI systems for complex, high-dimensional datasets. While much of my work is grounded in biomedical data (e.g., transcriptomics, proteomics), the core techniques extend broadly to any domain involving noisy, structured, and heterogeneous data.

I’ve developed and published several open-source ML tools and models, including:

  • Phenograph: LLM-based multi-agent system for spatial phenotype discovery augmented with knowledge graphs [Paper]
  • EXPORT: An Interpretable, dual decoder variational autoencoder (VAE) for modeling ordinal perturbations in transcriptomic data [Github] [Paper]
  • MUSTANG: A Bayesian hierachical model for analyzing multi-sample spatial transcriptomics data [Github] [Paper]
  • SimCD: A probabilistic model for simultaneous clustering and differential expression in single-cell RNA-seq data [Github] [Paper]
  • Pathway-based analyses of radiated bulk RNA-seq data [Paper]
  • Joint Metabolomics and RNA-seq transcriptomics data analysis pipeline [Paper]
  • As of having interest in solving challenges in scRNA-seq data analysis, I participated in IEEE COVID-19 Single-cell transcriptomics Data Hackathon where I won first place by presenting Biomarker identification for COVID-19 severity based on BALF scRNA-seq data. To learn more about this work you can check on this Github page.

    Outside academia, I’ve collaborated in fast-paced research environments at Genentech and Mayo Clinic, where I built scalable pipelines for large-scale single-cell and gene-drug relationship analyses. I thrive in cross-functional teams and enjoy translating cutting-edge ML research into real-world tools for discovery, diagnostics, and decision-making.

    Interests

    • Bayesian Deep Learning
    • LLM-based Agents Design
    • Foundation Models
    • Multi-Modal Data Analysis
    • Model Interpretability
    • Statistical Machine Learning
    • Computational Biology
    • Multi-Omics Data Analysis

    Education

    • Ph.D. in Electrical & Computer Engineering, 2019 - present

      Texas A&M University

    • M.Sc. in Electrical & Computer Engineering, 2018 - 2021

      Texas A&M University

    • B.Sc. in Electrical Engineering, 2013 - 2018

      Sharif University of Technology

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