Machine Learning Scientist I / II, Protein Design

Machine Learning Scientist I / II, Protein DesignSan Francisco, CA USAYour Impact at LILALila 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.What You'll Be BuildingDesign 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 SucceedMS 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 ForExperience 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 USDAbout LILALila 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 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.