Senior ML Scientist, AI for Protein Engineering

Lilasciences; San Francisco (CA); On-site; USD 268,000 - 358,000; Full time

Benefits offered by this job

Equity

Benefits

Career development

Job summary

Lila Sciences seeks a senior individual contributor to advance computational biologics design, blending ML, protein engineering, and therapeutic design to deliver AI-guided biomolecules validated in the lab.

Join a cross-disciplinary team spanning experimental science, AI research, and platform development, translating complex biology questions into robust ML workflows and production-ready software.

Qualifications

• PhD in Computational Biology, Computer Science, Machine Learning, Biophysics, Bioengineering, or a related quantitative field.
• Strong track record applying machine learning to protein design, biologics engineering, or related biomolecular design problems, with industry experience strongly preferred.
• Deep ML expertise, with hands-on experience adapting and developing modern AI methods rather than only applying them off the shelf.
• Strong intuition for therapeutic biologics design, including sequence, structure, function, developability, and experimental validation considerations.
• Demonstrated ability to drive applied research independently, from problem definition through experimental validation and iteration.
• Strong collaboration and communication skills across ML, biology, experimental science, and software teams.

Responsibilities

• Own applied 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 these 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 better models and design principles.
• Build rigorous evaluation frameworks for model generalization to challenging biologics design problems.

Skills

Deep ML

Protein design

Biophysics knowledge

Collaboration

Communication

Education

PhD in Computational Biology, Computer Science, Machine Learning, Biophysics, Bioengineering, or related field

Tools

Python

TensorFlow

PyTorch

Biomolecular modeling tools

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 a senior individual contributor focused on computational biologics design. The work spans active protein engineering programs and new capabilities that improve 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 deep ML judgment, intuition for protein biology, and experience delivering computationally-designed, wet-lab-validated biologics through AI. You’ll collaborate with experimental scientists, AI researchers, and platform teams to connect specialist protein design models into Lila’s broader autonomous science platform.

What You'll Be Building

• Own applied 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 these 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 better models and design principles.
• Build rigorous 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.
• Strong track record applying machine learning to protein design, biologics engineering, or related biomolecular design problems, with industry experience strongly preferred.
• Deep ML expertise, with hands-on experience adapting and developing modern AI methods rather than only applying them off the shelf.
• Strong intuition for therapeutic biologics design, including sequence, structure, function, developability, and experimental validation considerations.
• Demonstrated ability to drive applied research independently, from problem definition through experimental validation and iteration.
• Strong collaboration and communication skills across ML, biology, experimental science, and software teams.

Bonus Points For

• Direct experience designing antibodies, nanobodies, enzymes, peptides, or other therapeutic proteins for applied or clinical pipelines.
• Experience with structure prediction, generative protein design, diffusion models, flow matching, or protein language models in a production research setting.
• 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.
• 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

$268,000 — $358,000 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 unparalleled 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’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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