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Ahmed Khan

Senior Research Scientist and ML Engineer specializing in computational biology

Icahn School of Medicine at Mount SinaiMcGill UniversityNew York, NY12 Years ExperienceSenior Level

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About

Postdoctoral/PhD researcher focused on Alzheimer's disease who has built scalable end-to-end AI systems across pathology imaging, transcriptomics, and longitudinal neuroimaging. Particularly strong in turning novel research ideas into robust Python pipelines on GPU/HPC infrastructure, with pathologist-facing impact and scientifically novel findings such as image-derived disease severity trajectories and subtype discovery.

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Key Strengths

  • End-to-end ML pipeline ownership from raw biomedical data to deployed scoring outputs
  • Deep expertise in Alzheimer's disease modeling and neuropathology imaging
  • Strong handling of batch effects and domain shift across sites/datasets
  • Scalable ML systems on GPU/HPC for terabyte-scale image workloads
  • Novel representation learning and pooling method development
  • Cross-modal alignment of pathology images with transcriptomics data
  • Robust evaluation under weak ground truth using clinical correlation, resampling, and permutation tests
  • Translation of research methods into reusable production-grade Python pipelines
  • Improved lab productivity through standardized preprocessing libraries
  • Scientifically impactful work that identified distinct Alzheimer's disease sub-trajectories

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Experience

Postdoctoral Fellow in Computational Biology, Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount Sinai · Sep 2024 – Present
PhD Student, Neuroinformatics for Personalized Medicine LabMcGill University · Sep 2018 – Jul 2024
Master’s Student, Computer ScienceUniversity of Waterloo · Sep 2016 – Aug 2018
EngineerXLV Diagnostics Inc. · May 2016 – Aug 2016
Engineering InternXLV Diagnostics Inc. · May 2014 – May 2015internship
Research Intern, AI LabSoftBank Robotics · May 2015 – Sep 2015internship
Undergraduate Research Assistant, Learning Systems and Robotics LabUniversity of Toronto · May 2013 – Aug 2013part-time

Education

McGill Universitydoctorate, Neuroscience (2024)
University of Waterloomaster, Computer Science (2018)
University of Torontobachelor, Engineering Science (2016)

Awards

  • Hay Foundation Travel Award
  • Graduate Research Enhancement and Travel Award
  • OHBM Merit Abstract Award
  • Parkinson Canada Graduate Student Award
  • Integrated Program in Neuroscience Internal Award
  • Orbis Den Prize
  • Engineering Science International Opportunities Award
  • NSERC Student Research Award
  • Dean’s Honours List - University of Toronto

Skills

Machine LearningUnsupervised LearningAlgorithmsPrototypingReinforcement LearningComputer VisionPythonRMATLABPandasNumPySciPyScikit-learnPyTorchTensorFlow

Languages

EnglishKashmiriHindi/UrduGermanFrench

Publications

11 publications

Computational BiologyMachine LearningNeuroinformaticsNeurodegenerative DiseaseAlzheimer’s DiseaseParkinson’s DiseaseMultimodal NeuroimagingTranscriptomicsProteomicsSingle-cell GenomicsBrain ModelingNeuroscienceRoboticsArtificial Intelligence

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EducationEducation in NYC MetroMachine LearningUnsupervised LearningAlgorithmsPrototyping

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Ahmed KhanSenior Research Scientist and ML Engineer specializing in computational biology