Machine Learning Scientist – Digital Pathology & Multimodal AI

Position Summary: We are seeking a Machine Learning Scientist to join our Digital Pathology Data Science team. This role will focus on developing and deploying AI models for whole-slide images (WSIs), and integrating these insights with molecular and clinical data. You will work closely with a multidisciplinary team to advance biomarker discovery, therapeutic development, and real-world clinical applications.

Key Responsibilities: Model Development: Design, train, and validate deep learning models for pathology image analysis, including tasks such as tissue classification, cellular segmentation, and spatial biomarker prediction. Multimodal Integration: Collaborate on AI models that fuse digital pathology data with genomic, transcriptomic, and clinical modalities. Algorithm Validation & Deployment: Conduct analytical and clinical validation of models and deploy them in research and production environments. Data Management & Curation: Work with large-scale histopathology datasets, including WSI annotation, image preprocessing, and data quality assurance. Collaborative Research: Partner with pathologists, computational biologists, immunologists, and software engineers to ensure model outputs are biologically and clinically meaningful. Innovation & Publication: Contribute to internal R&D initiatives, stay up to date with the latest ML research in medical imaging, and support scientific publications and presentations. Biomarker Discovery: Help identify spatial and morphological features associated with patient outcomes and therapeutic responses.

Required Qualifications: PhD (or MS with 2+ years experience) in Computer Science, Artificial Intelligence, Computational Biology, or related field. Strong experience with deep learning architectures (CNNs, ViTs, UNet, etc.) for image classification, segmentation, or detection. Solid understanding of machine learning principles including self-supervised and weakly supervised learning. Proficiency in Python and deep learning frameworks such as PyTorch or TensorFlow. Experience working with whole-slide images and digital pathology datasets. Strong problem-solving and communication skills; ability to work in cross-functional teams. Demonstrated contributions through publications, patents, or production-level ML applications.

Preferred Qualifications: Experience with pretraining or fine-tuning of foundational or multimodal models. Familiarity with spatial omics, RNA/DNA sequencing, or clinical datasets. Background in oncology, immunology, or precision diagnostics. Industry experience in biotech, healthcare, or regulated environments.

What We Offer: Opportunity to shape foundational AI models that impact patient care Access to rich multimodal datasets and clinical collaborations A collaborative, mission-driven culture focused on innovation Competitive salary, stock options, and comprehensive benefits Seniority levelSeniority level Mid-Senior level Employment typeEmployment type Full-time Job functionJob function Science and Information Technology Industries Biotechnology, Biotechnology Research, and Pharmaceutical Manufacturing Referrals increase your chances of interviewing at BostonGene by 2x Inferred from the description for this jobMedical insurance Vision insurance 401(k) Paid maternity leave Paid paternity leave Tuition assistance Disability insurance Get notified about new Machine Learning Researcher jobs inWaltham, MA. Research Scientist, Responsible AI PracticePrincipal Machine Learning: Generative AIMassachusetts, United States 21 hours ago Sr. Bioinformatics Scientist – AI/ML for Multimodal Precision MedicinePrincipal Machine Learning: Generative AIAdvisor - Data Science / Machine LearningBoston, MA $180,000.00-$220,000.00 2 months ago Chief of Staff to the CTO (Machine Learning) Part-time Professors, School of Information Technology -Artificial Intelligence and Machine LearningPost Doctoral Fellow - Computational Modeling and Machine LearningAdvisor - Data Science / Machine LearningChief of Staff to the CTO (Machine Learning) Senior Data Scientist, Real World EvidenceMachine Learning Engineer, Data AcquisitionPrincipal Data Scientist - Simulation, Amazon RoboticsmRNA - Computational Biology - Principal Data Scientist- VaccinesPostdoctoral Researcher, Fundamental AI Research (PhD) Sr. Machine Learning Engineer, Amazon General Intelligence (AGI) We’re unlocking community knowledge in a new way. Experts add insights directly into each article, started with the help of AI.