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mattscicluna/README.md

Hi there 👋

  • 🎓 Ph.D. Candidate in Bioinformatics at Université de Montréal
    Affiliations: Mila – Quebec AI Institute, Montreal Heart Institute (MHI), and IRIC
    Thesis: On the Visualization of Genetic Data
  • 🧠 Research Interests: population genetics, manifold learning, causal inference, deep learning for genomics
  • 🧳 Experience: Machine Learning Engineer (insitro, Huawei Noah’s Ark Lab), Research Assistant (MHI), Visiting Scholar (Yale, Dept. of Genetics)
  • 📚 Publications: Bioinformatics Advances (2023), CSBJ (2025), Behavior Research Methods (2018)
  • 🎤 Talks: How to Visualize a Biobank, Lessons from the All of Us UMAP Scandal (MHI, 2024–25), What Every Biologist Should Know About Manifold Learning (IRIC, 2023)
  • 🏆 Awards: NSERC CGS-D, Michael Smith Foreign Study Supplement, Canadian Bioinformatics Hub Training Award, Ontario Graduate Scholarship
  • 💻 Skills: Python, Bash, LaTeX, SLURM, Nextflow, PLINK, Git, AWS
  • 🌐 Links: LinkedIn · Google Scholar
  • 🙂 Pronouns: he/him

📝 Selected Publications (and Pre-Prints)

  • A Transparent and Generalizable Deep Learning Framework for Genomic Ancestry Prediction bioRxiv (2025) doi
  • Predicting pathogen evolution and immune evasion in the age of AI, CSBJ (2025) doi
  • Towards computing attributions for dimensionality reduction techniques, Bioinformatics Advances (2023) doi
  • A modern take on the bias-variance tradeoff in neural networks ArXiv (2018) doi
  • Argus: Automated quantification of zebrafish behavior, Behavior Research Methods (2018) doi

✨ Maintainer & contributor to: PHATE, scprep, graphtools
📢 (Previously) Organizer: Bio+AI Reading Group at Mila, Machine Learning on Molecules (MoML 2023) conference

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  1. interpretable_tsne interpretable_tsne Public

    Implementation of the gradient-based t-SNE sttribution method described in our GLBIO oral presentation: 'Towards Computing Attributions for Dimensionality Reduction Techniques'

    Python 1 1

  2. CourseWork-UofT CourseWork-UofT Public

    A repo consisting of the coursework I did as a student at UofT.

    Java 2 2