Senior Machine Learning Scientist I/II, Model-Driven Optimization

The Role

This role focuses on building the ML methods, data strategies, and closed-loop systems that determine what we design, build, test, and learn from next. The Model-Driven Design team works at the interface of machine learning, protein design, engineering, and experimental science. We develop and apply models and quantitative frameworks that help Generate discover and optimize therapeutic proteins.

Here's How You Will Contribute

• Develop new machine learning methods and systems for lab-in-the-loop protein optimization, including property models and multi-objective optimization strategies for therapeutic protein design.
• Shape data-generation and data-use strategies that make experimental campaigns maximally informative for model improvement, therapeutic optimization, and future design cycles.
• Build and apply LLM-enabled and agentic workflows that help scientists explore design hypotheses, connect models to data and experiments, and accelerate iterative learning.
• Design, implement, test, and maintain production-quality ML models, software components, and data workflows, with attention to reliability, reproducibility, observability, and computational efficiency.
• Partner with ML engineering and software teams to integrate these components into robust, scalable platform capabilities, with clear ownership across team boundaries.
• Collaborate closely with protein designers and wet-lab scientists to ensure models and optimization systems are grounded in experimental reality and deliver measurable impact.
• Identify important technical gaps, develop proposals, define milestones, align stakeholders, and help set technical direction across cross-functional programs.
• Communicate clearly across disciplines and help raise technical standards across ML, engineering, protein design, and experimental teams.

The Ideal Candidate

• PhD in machine learning, computational biology, computer science, applied mathematics, engineering, or a related quantitative field.
• Strong practical experience with probabilistic machine learning, Bayesian optimization, active learning, experimental design, or related approaches for sequential decision-making under uncertainty.
• Experience developing machine learning methods or systems for biological, biomedical, or experimental scientific data, with an ability to reason about noisy assays, sparse labels, experimental bias, and data-generation strategy.
• Demonstrated ability to translate ML ideas into systems, tools, or workflows that affect real scientific, experimental, or product decisions.
• Strong Python skills and experience with modern ML frameworks such as PyTorch, JAX, or similar tools.
• Strong systems thinking and ability to design technical interfaces, reason about system tradeoffs, and partner with engineering teams to build scalable, maintainable ML infrastructure.
• Excellent communication skills and ability to bridge ML, engineering, protein design, and experimental stakeholders.
• Pragmatic, collaborative working style, with the ability to bring structure to open-ended problems and balance scientific rigor with execution in fast-moving, cross-functional environments.

Nice to Have

• Experience in protein design, protein engineering, antibody engineering, biologics discovery, or drug development.
• Experience partnering with experimental teams on design-build-test-learn cycles, high-throughput screening, directed evolution, pooled libraries, or model-guided experimental campaigns.
• Experience with multi-objective optimization, uncertainty calibration, model-guided library design, or experimental campaign planning.
• Experience developing and applying deep learning models, including transformer-based architectures.
• Experience building or applying LLM agents, scientific copilots, or agentic systems in technical workflows.
• Experience contributing to shared ML platforms, libraries, APIs, or developer tooling, including monitoring, debugging, performance optimization, and long-term maintenance.

About Generate Biomedicines

We are a clinical-stage generative biology company pioneering the AI revolution in drug design and development. We are advancing a new approach to drug creation—one grounded in the ability to design proteins with defined biological intent. By integrating machine learning with large-scale experimentation, this approach aims to reduce the uncertainty, time, and cost associated with developing protein-based medicines.

Founded in 2018, we are advancing a growing pipeline of clinical and preclinical programs across multiple disease areas and protein modalities. By unifying computational design and clinical development within a single operating model, we translate this approach into clinical-stage programs and are leading a shift from traditional drug discovery toward systematic drug generation.

At Generate:Biomedicines, we collaborate across disciplines in new ways to invent and innovate. We bring diverse perspectives to a shared goal of delivering better medicines to patients in need, faster, guided by our values and leadership behaviors.

Generate:Biomedicines is committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.