Machine Learning Scientist I / II, Protein Design

Lila Sciences; Cambridge (MA); On-site; USD 176,000 - 304,000; Full time

Benefits offered by this job

Medical, dental, and vision coverage

Life and disability insurance

Flexible time off

Parental leave

Educational assistance

Commuter benefits

Bike share memberships

Lunch program

Job summary

Lila Sciences is building a platform where AI and automation co-evolve to advance medicine. The AI for Protein Engineering team designs models and systems turning design specs into wet-lab validated leads.

We are hiring a machine learning scientist to design molecules on real programs and translate findings into capabilities that generalize across programs, collaborating with domain scientists, platform teams, and AI researchers.

Qualifications

• MS or PhD in computer science, machine learning, computational biology, biophysics, bioengineering, or a similar quantitative field.
• Strong software engineering and system design fundamentals.
• Rigor in evaluation and dataset design: how benchmarks leak, and how to measure automated system decisions.
• Strong cross-functional communication skills.
• Domain expertise in protein sequence, structure, and function.

Responsibilities

• Design molecules for active biologics programs, partnering with domain scientists to translate target, mechanism, and experimental constraints into actionable design hypotheses.
• Develop reasoning capabilities for drug discovery, including orchestrating design workflows.
• Design and maintain benchmarks and evaluation infrastructure that measure whether design workflows produce useful, generalizable decisions across biologics programs.
• Own operations around reproducibility, throughput, and inference cost of computational design workflows.
• Work with domain scientists to understand how designs are prioritized and turn that judgment into ML objectives and evaluation criteria.

Skills

Software engineering

System design

Evaluation & datasets

Cross-functional communication

Protein design knowledge

Education

MS or PhD in CS/ML/comp biology/biophysics/biomedical engineering

Job description

Your Impact at LILA

Lila is building a platform where AI and automation co-evolve to solve the hardest problems in medicine. Within Life Sciences AI, the AI for Protein Engineering team builds models and systems that take a biologic from design specification to wet-lab validated lead.

Your Impact at LILA

Lila is building a platform where AI and automation co-evolve to solve the hardest problems in medicine. Within Life Sciences AI, the AI for Protein Engineering team builds models and systems that take a biologic from design specification to wet-lab validated lead. We're hiring a machine learning scientist to design molecules on real programs and turn what they learn into capabilities that generalize across programs. The ideal candidate is an exceptional builder with strong biological intuition: someone who can turn work on individual campaigns into reliable, extensible systems that improve how we design molecules across programs. You'll work closely with domain scientists, platform teams, and AI researchers to connect specialist protein design models to Lila's broader autonomous science platform.

What You'll Be Building

• Design molecules for active biologics programs, partnering with domain scientists to translate target, mechanism, and experimental constraints into actionable design hypotheses.


• Develop reasoning capabilities for drug discovery, including orchestrating design workflows.


• Design and maintain benchmarks and evaluation infrastructure that measure whether design workflows produce useful, generalizable decisions across biologics programs.


• Own operations around reproducibility, throughput, and inference cost of computational design workflows.


• Work with domain scientists to understand how designs are prioritized and turn that judgment into ML objectives and evaluation criteria.

What You'll Need To Succeed

• MS or PhD in computer science, machine learning, computational biology, biophysics, bioengineering, or a similar quantitative field.


• Strong software engineering and system design fundamentals.


• Rigor in evaluation and dataset design: how benchmarks leak, why a good validation number fails downstream, and how to measure whether an automated system is making good decisions.


• Strong cross-functional communication skills.


• Domain expertise in protein sequence, structure, and function.

Bonus Points For

• Experience building reasoning models, agents, planning systems, or multi-step ML orchestration.


• Exposure to designing antibodies, nanobodies, enzymes, peptides, or other therapeutic proteins within design-test-learn loops.


• Experience in developing evaluation harnesses, model registries, or benchmark suites.


• Training or serving models at scale: distributed training, GPU efficiency, high-throughput inference.


• Publications, open-source contributions, or applied research outputs in AI for Science venues.

CompensationWe offer competitive base compensation with bonus potential and generous early-stage equity. Your final offer will reflect your background, expertise, and expected impact.

U.S. Benefits. Full-time U.S. employees receive a comprehensive benefits program including medical, dental, and vision coverage; employer-paid life and disability insurance; flexible time off with generous company wide holidays; paid parental leave; an educational assistance program; commuter benefits, including bike share memberships for office based employees; and a company subsidized lunch program.

International Benefits. Full-time employees outside the U.S. receive a comprehensive benefits program tailored to their region. USD salary ranges apply only to U.S.-based positions; international salaries are set to local market.

Expected Base Salary Range: $176,000 USD - $304,000 USD

About LILA

Lila Sciences is building Scientific Superintelligence™ to solve humankind's greatest challenges. We believe science is the most inspiring frontier for AI. Rather than hard‑coding expert knowledge into tools, LILA builds systems that can learn for themselves.

LILA combines advanced AI models with proprietary AI Science Factory™ instruments into an operating system for science that executes the entire scientific method autonomously, accelerating discovery at unprecedented speed, scale, and impact across medicine, materials, and energy. Learn more at www.lila.ai.

Guided by our core values of truth, trust, curiosity, grit, and velocity, we move with startup speed while tackling problems of historic importance.

We’re All In

Lila Sciences 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.

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