ML Scientist I/II, AI for Protein Engineering

Lilasciences; San Francisco (CA); On-site; USD 176,000 - 304,000; Full time

Benefits offered by this job

Medical, dental, and vision coverage

Life and disability insurance

Generous holidays

Parental leave

Educational assistance

Commuter benefits

Lunch program

Job summary

Lila Sciences is seeking an ML Scientist I/II focused on AI for protein engineering. You will work at the intersection of machine learning, protein design, and therapeutic development, building models and workflows that advance biomolecule design from in silico ideas to wet-lab validation with experimental partners.

Collaborate with experimental scientists and platform teams, translate biological questions into computable design problems, and contribute to robust software systems.

Qualifications

• PhD in a quantitative field (Computational Biology, CS, ML, Biophysics, Bioengineering)
• Experience applying ML to protein design or related biomolecular design
• Strong ML fundamentals with hands-on model development and evaluation
• Fluency with sequence, structure, function, developability, or experimental validation

Responsibilities

• Build ML workflows for protein engineering campaigns from design to experimental learning
• Develop and adapt methods spanning de novo generation, sequence/structure-based prediction, and active learning
• Integrate protein design methods into robust software systems and broader reasoning models
• Translate therapeutic questions into well-defined ML problems and evaluation plans
• Collaborate with experimental scientists to interpret results and improve models
• Create evaluation frameworks for model generalization to challenging biologics design problems

Skills

ML fundamentals

Protein design

Collaboration

Biology concepts

Education

PhD in Computational Biology/CS/ML/Bioengineering

Tools

Python

ML frameworks (PyTorch/TensorFlow)

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 develops and applies generative and predictive models that move biomolecule design programs from in silico hypothesis to wet-lab validated leads.

We are looking for an ML Scientist I/II focused on AI for protein engineering. The work spans active protein engineering programs and focused technology development that improves how Lila designs, evaluates, and learns from biomolecular sequence, structure, and function data.

This role sits at the intersection of machine learning, protein engineering, and therapeutic design. The ideal candidate brings strong ML fundamentals, curiosity about protein biology, and interest in computationally designed, wet-lab-validated biologics. You'll collaborate with experimental scientists, AI researchers, and platform teams to build models and workflows that support Lila's broader autonomous science platform.

What You'll Be Building

• Build ML workflows for protein engineering campaigns, from design specification through experimental learning.
• Develop and adapt methods spanning de novo generation, sequence- or structure-based property prediction, candidate selection, and active learning.
• Integrate protein design methods into robust software systems and broader reasoning models.
• Translate therapeutic and biological questions into well-defined ML problems, model outputs, and evaluation plans.
• Partner with experimental scientists to interpret why designed biomolecules succeed or fail, then turn those insights into model improvements.
• Build evaluation frameworks for model generalization to challenging biologics design problems.

What You'll Need to Succeed

• PhD in Computational Biology, Computer Science, Machine Learning, Biophysics, Bioengineering, or a related quantitative field.
• Experience applying machine learning to protein design, biologics engineering, or related biomolecular design problems.
• Strong ML fundamentals, with hands-on experience developing, adapting, training, or evaluating modern AI methods.
• Fluency with biological sequence, structure, function, developability, or experimental validation considerations.
• Ability to translate therapeutic or biological objectives into computational design problems and model evaluation plans.
• Strong collaboration and communication skills across ML, biology, experimental science, and software teams.

Bonus Points For

• Experience designing antibodies, nanobodies, enzymes, peptides, or other therapeutic proteins.
• Experience with structure prediction, generative protein design, diffusion models, flow matching, or protein language models.
• Familiarity with structural biology, conformational dynamics, developability, affinity maturation, or other biophysical constraints.
• Experience closing design-test-learn loops with wet-lab teams, including experimental prioritization, high-throughput validation, and active learning.
• Industry experience translating ML research into practical biological design workflows, experimental campaigns, or platform capabilities.
• Publications, open-source contributions, or applied research outputs in AI for science venues.

Compensation

We 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

• 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
• a company subsidized lunch program

International Benefits

• a comprehensive benefits program tailored to region
• USD salary ranges apply only to U.S.-based positions; international salaries are set to local market

Expected Base Salary Range

$176,000—$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. If this sounds like an environment you'd love to work in, even if you don't meet every qualification listed above, we encourage you to apply.

We’re All In

Lila Sciences iscommitted to equal employment opportunityregardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

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