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

The posting, as Generate Biomedicines wrote it

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

[…]
pproach 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.

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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