Machine Learning Scientist - Small Molecule Drug Design

Roche seeks a Senior Machine Learning Scientist in Basel to develop ML models for small-molecule drug design, collaborating with computational and medicinal chemists to accelerate discovery.

This role sits within the small-molecule team of AI for Drug Discovery (AI4DD) at Roche and Genentech’s Computational Sciences Center of Excellence. The position focuses on creating and deploying machine learning techniques to speed up the design of small-molecule drugs, particularly through structure-driven methods, in close partnership with expert computational and medicinal chemists and structural biologists.

Responsibilities

• Create and implement advanced machine learning models tailored for small-molecule drug design, emphasizing protein–ligand interactions, binding affinity, and essential molecular properties.
• Train and adjust foundation models for structure prediction, utilizing both proprietary and open-source tools on internal data.
• Test and improve machine learning-generated hypotheses in collaboration with computational and medicinal chemists and structural biologists.
• Generate scientific impact via publications, open-source contributions, and conference presentations.
• Work closely with computational and experimental researchers at Roche as well as academic collaborators.

Requirements

• Strong background in machine learning, including linear algebra, probability, and optimization, plus practical experience with graph neural networks, sequence models, and reinforcement learning.
• Experience in structure-driven modeling, including co-folding methods, binding-affinity prediction, and working with structural-biology datasets.
• Proficiency in Python and cheminformatics, using toolkits like RDKit and OpenEye, along with modern ML frameworks such as PyTorch or JAX.
• A PhD or equivalent research depth in machine learning, computational chemistry, chemical engineering, or a related quantitative field like physics or statistics.
• A track record of scientific excellence demonstrated through journal and conference publications or a public portfolio of relevant projects (e.g., on GitHub/GitLab).

Nice to have

• Practical experience in building structure-prediction foundation models.
• Experience working directly with medicinal chemists and structural biologists.

About the company

Roche fosters a culture that values personal expression, open dialogue, and genuine connections, ensuring employees feel respected and supported both personally and professionally. The company is driven by a mission to innovate and deliver life-changing healthcare solutions, aiming to prevent, stop, and cure diseases while ensuring global access to healthcare for current and future generations. With over 100,000 employees worldwide, Roche encourages creativity and high ambitions to advance science and make a global impact.

• Encourages personal expression, open dialogue, and genuine connections.
• Values employees, fostering an environment where they are accepted and respected.
• Aims to prevent, stop, and cure diseases while ensuring healthcare access for all.
• Drives innovation to deliver life-changing healthcare solutions with a global impact.
• Empowers employees to explore new possibilities and maintain high ambitions.