Senior Machine Learning Scientist I, Model-Driven Optimization

Generate Biomedicines; Somerville (MA); Hybrid; USD 192,000 - 265,000; Full time

Benefits offered by this job

Annual bonus

Equity compensation

Benefits package

Job summary

Generate Biomedicines, a clinical-stage generative biology company, seeks a machine learning scientist to lead ML methods, data strategies, and closed-loop systems for protein design. You will partner with protein designers and wet-lab scientists to translate ideas into reliable, scalable optimization platforms with measurable impact.

Ideal candidates have a PhD and strengths in probabilistic ML, Bayesian optimization, and experimental design, plus hands-on Python and PyTorch/JAX experience in a

Qualifications

• PhD in machine learning, computational biology, computer science, applied mathematics, engineering, or related 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 ML methods or systems for biological data with noisy assays, sparse labels, and data-generation strategies.
• Ability to translate ML ideas into systems, tools, or workflows affecting real scientific or product decisions.
• Strong Python skills and experience with ML frameworks such as PyTorch or JAX.

Responsibilities

• Develop new ML methods and systems for lab-in-the-loop protein optimization, including multi-objective optimization strategies.
• Shape data-generation and data-use strategies to maximize informativeness for model improvement and future design cycles.
• Build LLM-enabled and agentic workflows to explore design hypotheses and accelerate learning.
• Design, implement, test, and maintain production-quality ML models and data workflows with reliability and observability.
• Collaborate with ML engineering and software teams to integrate components into scalable platform capabilities.
• Work closely with protein designers and wet-lab scientists to ensure models reflect experimental reality and deliver measurable impact.

Skills

Python

Probabilistic ML

Bayesian optimization

Active learning

Sequential decision-making

Communication

Education

PhD in ML/Computational biology/CS/Applied mathematics/Engineering or related field

Tools

PyTorch

JAX

Transformer architectures

Job description

The Role:

Generate:Biomedicines is seeking a creative, rigorous, and execution-oriented machine learning scientist to join our Model-Driven Design team. This role will focus 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. In this role, you will help advance the technical foundation of our lab-in-the-loop protein optimization platform, with a focus on sequential decision-making, experimental design, property modeling, and scalable design systems.

We are looking for someone who can serve as a technical leader and hands-on individual contributor, driving complex, high-impact work from problem framing through implementation, deployment and experimental impact. The ideal candidate combines depth in probabilistic machine learning, Bayesian optimization, active learning, or related approaches with the practical judgment and engineering discipline to turn technical ideas into reliable systems that drive impact. You will partner closely with protein designers, wet-lab scientists, ML scientists, and engineers to build durable capabilities that accelerate therapeutic discovery.

This role is part of a highly collaborative team environment that balances in-person collaboration with hybrid flexibility based out of our Somerville, MA office.

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 will have:

• 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.

Who Will Love This Job:

This is an opportunity to shape how machine learning is used to make better decisions across the full protein design cycle. You will work on problems where models, data, experiments and engineering systems are tightly connected, and where better optimization strategies can directly change what gets built and tested in the lab.

You will join a collaborative, ambitious team working to build a platform for therapeutic protein design that learns continuously from experimental data and turns that learning into new and better therapeutics with real impact.

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.

Recruitment & Staffing Agencies: Generate:Biomedicines does not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to Generate:Biomedicines or its employees is strictly prohibited unless contacted directly by the Company’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of Generate:Biomedicines and the Company will not owe any referral or other fees with respect thereto.

Compensation:

The base salary range provided reflects our current estimate of what we anticipate paying for this position. Your actual base salary will be based on several factors, including job-related skills, experience, internal equity, relevant education or training, and market dynamics. In addition, you will be eligible for an annual bonus, equity compensation, and a competitive benefits package.

Per Year Salary Range: $192,000 — $265,000 USD