Principal Machine Learning Engineer

Roche; South San Francisco (CA); On-site; USD 193,000 - 358,000; Full time

Job summary

Roche’s AI for Drug Discovery group seeks a Principal Machine Learning Engineer to advance autonomous agents and foundation models in drug discovery. You will work across engineering and research, building scalable ML systems and robust production pipelines, partnering with Genentech scientists to translate complex problems into efficient, end-to-end workflows.

You will lead the MLOps/AgentOps stack, define the engineering roadmap, and guide cross-functional platforms while applying frontier AI

Qualifications

• PhD/MS/BS with extensive ML infra leadership and track record.
• Strong Python programming and software engineering fundamentals.
• Hands-on experience with PyTorch/JAX and distributed training on AWS or HPC.
• Experience designing agent orchestration frameworks and persistent memory.
• Interest in AI for Drug Discovery and biology/chemistry.

Responsibilities

• Architect and deploy autonomous agents for drug discovery workflows.
• Design scalable ML systems and productionize foundation models.
• Own MLOps/AgentOps stack: tracking, observability, evaluation, CI/CD.
• Define long-term engineering roadmap for AI4DD; collaborate with Genentech leadership.
• Translate scientific problems into scalable, efficient systems.

Skills

Python programming

Git

CI/CD

Software engineering fundamentals

Distributed systems

Education

PhD in CS/ML/Engineering

MS in CS/ML/Engineering

BS in CS/Eng

Tools

LangGraph

MCP-based tool integration

PyTorch

JAX

AWS

HPC environments

Job description

A healthier future. It’s what drives us to innovate. To continuously advance science and ensure everyone has access to the healthcare they need today and for generations to come. Creating a world where we all have more time with the people we love. That’s what makes us Roche.

Advances in AI, data, and computational sciences are transforming drug discovery and development. Roche’s Research and Early Development organizations at Genentech (gRED) and Pharma (pRED) have demonstrated how these technologies accelerate R&D, leveraging data and novel computational models to drive impact. Seamless data sharing and access to models across gRED and pRED are essential to maximizing these opportunities. The new Computational Sciences Center of Excellence (CoE) is a strategic, unified group whose goal is to harness the transformative power of data and Artificial Intelligence (AI) to assist our scientists in both pRED and gRED to deliver more innovative and transformative medicines for patients worldwide.

The Opportunity:

At Roche’s AI for Drug Discovery (AIDD) group (Prescient Design), we are revolutionizing drug discovery with cutting-edge machine learning. We are seeking a Principal Machine Learning Engineer to join our Foundation Models team. In this role, you will drive the engineering, scaling, and operationalization of our internal reasoning Large Language Models (LLMs) and agentic systems, enabling them to succeed at complex biomolecular design and autonomous scientific workflows.

You will work at the intersection of engineering and research, spanning the full stack: from the agent orchestration logic that makes these systems scientifically useful, to the distributed infrastructure and MLOps/AgentOps that make them robust at scale.

In this role, you will:

• Agentic Systems Engineering: Architect and deploy autonomous agents that utilize tools, retrieve scientific evidence, and execute multi-step reasoning across drug discovery workflows. Design and implement advanced agent memory architectures and context management for long-horizon scientific tasks. Build reliable interfaces between agents and genomic, chemical, and clinical data sources.

• Scalable ML Systems & Productionization: Design, build, and optimize large-scale distributed training and inference systems for foundation models. Own the production Python/PyTorch codebases that turn fast-moving research into enterprise-grade software.

• Own the MLOps/AgentOps Stack: Establish best practices for the full lifecycle: experiment tracking, system observability and monitoring, rigorous evaluation harnesses (checking agent output against scientific ground truth), CI/CD, and infrastructure.

• Technical Strategy & Leadership: Define the long-term engineering roadmap for AI4DD’s agentic and foundation models. Serve as a technical authority on ML infra for Genentech leadership, architect cross-functional platforms, and elevate the engineering bar across gRED.

• Research-to-Production Translation: Partner closely with ML Scientists and domain experts to translate open-ended scientific problems and complex reasoning objectives into scoped, shippable, and highly efficient systems.

Who You Are:

• Education & Experience: BS, MS, or PhD in Computer Science, Machine Learning, Engineering, or a related quantitative field. You have a demonstrated track record of technical leadership with increasing levels of experience based on degree: PhD with 5+ years, MS with 8+ years, or BS with 10+ years of industry experience building, shipping, and owning large-scale ML systems and infrastructure end-to-end.

• Engineering Foundation: Exceptional Python programming skills and rigorous software engineering fundamentals (Git, automated testing, CI/CD, documentation, architecture design).

• Deep Learning & Distributed Systems: Extensive hands‑on experience with modern deep learning frameworks (PyTorch, JAX) and deploying ML infrastructure on AWS or HPC environments, including distributed training tools.

• Agentic Systems: Practical experience designing agent orchestration frameworks (e.g., LangGraph, MCP-based tool integration), managing persistent agent memory, and building self‑improving loops.

• Domain Interest: Strong passion for applying frontier AI and agentic science to AI for Drug Discovery (AI4DD), biology, and chemistry.

Preferred Qualifications:

• Inference-Time Optimization: Deep expertise in LLM serving, test-time compute, sampling/search strategies, model routing, batching, caching, and latency/cost/quality tradeoffs.

• Scientific Context: Experience working with molecular modalities (e.g., protein sequences, chemical graphs, and structured molecular data).

• Open Source: A public portfolio of significant technical contributions to open‑source ML, systems, or MLOps libraries.

Onsite presence on our campus is expected in compliance with Roche/Genentech policy.

Relocation benefits are not available for this job posting.

The expected salary range for this position based on the primary location of New York is $192,500 - $357,500. Actual pay will be determined based on experience, qualifications, geographic location, and other job-related factors permitted by law. A discretionary annual bonus may be available based on individual and Company performance. This position also qualifies for the benefits detailed at the link provided below.

Benefits

#ComputationCoE

Genentech is an equal opportunity employer. It is our policy and practice to employ, promote, and otherwise treat any and all employees and applicants on the basis of merit, qualifications, and competence. The company’s policy prohibits unlawful discrimination, including but not limited to, discrimination on the basis of Protected Veteran status, individuals with disabilities status, and consistent with all federal, state, or local laws.

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