Computational Biology & Machine Learning
👋 Welcome! I’m Mahbuba Tasmin, a Ph.D. candidate in Computer Science at the University of Massachusetts Amherst, advised by Prof. Anna Green. I work in the SAGE Lab (Statistical and Genomic Evidence Lab), where my research bridges machine learning, computational biology, and antibiotic resistance genomics.
My current focus is on building interpretable, biology-grounded models for predicting drug resistance in Mycobacterium tuberculosis — combining sequence-based deep learning, evolutionary augmentation, and causal variant discovery.
I’m particularly interested in:
- Genomic and protein-based ML for resistance prediction
- Causal interpretability and structural biology
- Cross-species learning and data augmentation
- Benchmark dataset design for biological ML models
🔬 Research Highlights
- BIG-TB Benchmark (17K isolates, 11 drugs): Developing a unified dataset and evaluation framework for resistance prediction across modalities.
- Resistance Forecast Project: Integrating structural, evolutionary, and machine-learning features to predict variant impact.
- Evolutionary Augmentation: Leveraging multi-species homologs to enhance sparse training data for protein-level models.
You can read more about these in my publications and projects.
Year in Review (2025)
This year marked a series of important academic and research milestones:
- Published a research article in eLife on predicting antibiotic resistance using protein structural context
- Presented work at ICLR (MLGenX Workshop) on structure-aware machine learning models
- Delivered a lightning/spotlight talk at the Machine Learning for Computational Biology (MLCB) workshop
- Completed my M.S. in Computer Science, with thesis research aligned with my PhD work
- Advanced to PhD candidacy
- Currently preparing two journal manuscripts focused on resistance forecasting and interpretable biological ML
Overall, this year represented a transition from exploratory experimentation to defining a focused research agenda at the intersection of machine learning, structural bioinformatics, and infectious disease genomics.
📚 Teaching & Mentorship
I serve as a Teaching Assistant for CS520 (Software Testing) at UMass, where I help students design and evaluate test coverage, mutation analysis, and automated testing frameworks in Java. I also mentor undergraduate and master’s students in research on ML for biological sequences.
Beyond Research
Outside the lab, I enjoy clay crafts, photography, and event organization— from handmade air-dry clay bowls to campus community events. I also contribute to graduate student initiatives at UMass through organizing academic and social programs.
📄 Quick Links
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