Machine Learning Scientist I / II, Protein Design

Lila Sciences

$176K — $304K *
Pharmaceuticals & Biotech
Less than 5 years of experience
Job Overview by Ladders

Qualifications

  • MS or PhD in computer science, machine learning, computational biology, biophysics, or bioengineering.
  • Strong software engineering and system design fundamentals.
  • Expertise in evaluation and dataset design, especially in benchmarks and validation.
  • Excellent cross-functional communication skills.
  • Domain expertise in protein sequence, structure, and function.

Responsibilities

  • Design molecules for biologics programs with domain scientists.
  • Develop reasoning capabilities for drug discovery and orchestrate design workflows.
  • Create and maintain evaluation infrastructure for assessing design workflows' effectiveness.
  • Manage operations related to reproducibility and throughput of design workflows.
  • Collaborate with domain scientists to translate prioritization into ML objectives.

Benefits

  • Comprehensive medical, dental, and vision coverage.
  • Employer-paid life and disability insurance.
  • Flexible time off and generous company-wide holidays.
  • Paid parental leave and educational assistance program.
  • Commuter benefits and company-subsidized lunch program.
Full Job Description
Your Impact at LILA

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.


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. 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-$304,000 USD

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