Protein Design ML Scientist I/II

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

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.