Portrait of Asif Khan

Asif Khan

Machine Learning & AI for Medicine Postdoctoral Fellow · Harvard Medical School

I am a Postdoctoral Fellow at Harvard Medical School, working with Chris Sander. Before Harvard, I completed my PhD with Amos Storkey in the Bayesian and Neural Systems Group at the University of Edinburgh. My doctoral thesis was on the geometry for deep representation learning.

My research lies at the intersection of machine learning and biomedicine, addressing two critical challenges in cancer biology: early detection using longitudinal patient records and optimization of combination therapies through mechanistic models of drug response. Late-stage diagnosis remains the primary cause of cancer mortality, as many patients present when curative treatment is no longer possible. By training AI on large-scale clinical data, our work aims to identify high-risk individuals who can benefit from earlier intervention and effective treatment strategies. My current work is centered around following topics:

  • Representation learning from longitudinal EHRs: Developing foundation models that encode patient histories into continuous representation spaces of patient health states for downstream survival and risk assessments.
  • Uncertainty-aware cancer risk prediction: Building well-calibrated, robust, and generalizable models that capture distribution shifts across hospitals and populations.
  • AI-guided therapy design: Learning differential equation models that capture molecular dynamics under drug perturbations to inform combination therapies.

Interests

  • Representation learning
  • Geometry for deep learning
  • Computational biology
  • Cancer risk stratification

Education

  • PhD in Machine Learning, University of Edinburgh2018–2023
    Bayesian and Neural Systems Group (Prof. Amos Storkey)
  • MSc in Computer Science, University of Bonn2016–2018
    Focus on machine learning and knowledge graphs

Research Overview

Representation learning from large-scale real-world EHR data

Diagram showing patient trajectories, token embeddings, and downstream prediction.

Transforming longitudinal patient trajectories into structured embeddings that capture the evolving health state of patients and support downstream clinical decision-making tasks.

Multi-cancer risk prediction

Transformer architecture for multi-cancer risk pooled trajectory modelling.

Developing well-calibrated deep learning event models that predict cancer risk across horizons while quantifying uncertainty at the patient level.

Machine learning models for combination therapy (Perturb • Measure • Model • Predict • Test)

Illustration of cellular perturbations, modelling, and therapeutic design.

Modeling cellular dynamics with machine-learning driven differential equation models trained on drug and CRISPR perturbation data.