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Machine Learning Engineer (pharmaceutical, large molecules)

Apex Systems

Salary not specified
Sep 10, 2025
South San Francisco, CA, US
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Developing structural and machine learning based methods for molecular design within the Research and Early Development organization.

Requirements

  • Demonstrated experience with machine learning libraries in production-ready workflows (e.g., PyTorch + Lightning + Weights and Biases)
  • Experience with physical modeling methods (e.g., molecular dynamics) and cheminformatics toolkits (e.g., rdkit)
  • Previous focus on one or more of these areas: molecular property prediction, computational chemistry, de novo drug design, medicinal chemistry, small molecule design, self-supervised learning, geometric deep learning, Bayesian optimization, probabilistic modeling, statistical methods.
  • Public portfolio of computational projects (available on e.g. GitHub).

Responsibilities

  • Manage projects deploying new techniques for machine learning based molecular optimization for the analysis and design of small and large molecule drugs within target-driven design campaigns.
  • Engineering pipelines for probabilistic molecular property prediction and Bayesian acquisition for active learning based drug discovery.
  • Engineering pipelines for molecular generative modeling.
  • Develop machine learning and Bayesian optimization workflows to analyze existing, and design new, small and large molecules.
  • Work on existing projects and generate new project ideas.

Other

  • PhD degree in a quantitative field (e.g., Computer Science, Chemistry, Chemical Engineering, Computational Biology, Physics), or MS degree and 3+ years of industry experience.
  • Record of achievement, including at least one high-impact first author publication or equivalent.
  • Excellent written, visual, and oral communication and collaboration skills.
  • You will closely collaborate with scientists across the organization
  • You will be expected to form close working relationships with small molecule and protein therapeutic development efforts across the organization.