ML Scientist, Nucleic Acid Design

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

Benefits offered by this job

Equity

Medical, dental, and vision coverage

Flexible time off

Parental leave

Commuter benefits

Lunch program

Job summary

Lila Sciences is seeking an ML Scientist I/II focused on nucleic acid design to advance RNA and DNA sequence design. You will build models and strategies to understand and engineer nucleic acid sequences, addressing 3’ UTR, 5’ UTR, CDS, and promoter/enhancer design.

You will work at the intersection of machine learning, sequence modeling, experimental design, and platform development, delivering usable capabilities across Lila’s autonomous science platform.

Qualifications

• PhD or equivalent in ML, computational biology, bioengineering, CS or related field.
• Hands-on experience building and evaluating ML models for DNA/RNA.
• Strong foundation in modern ML methods; practical PyTorch/JAX experience.
• Experience developing models for sequence design and sequence–function prediction.
• Ability to reason about complex biological systems and formulate ML approaches to difficult problems.
• Interest in nucleic acid biology, RNA biology, regulatory genomics, and sequence-to-function modeling.
• Excellent communication and collaboration skills across ML, engineering, platform, and experimental teams.

Responsibilities

• Build ML models for RNA and DNA sequence design across regulatory and coding contexts.
• Develop methods for de novo generation, sequence property prediction, and active learning.
• Investigate biological mechanisms of designed sequences and translate insights into better models.
• Propose informative assays and learning loops with experimental scientists.
• Collaborate with ML scientists to integrate design models into robust platforms.

Skills

PhD or equivalent

ML modeling

PyTorch/JAX

Sequence design models

Biological systems reasoning

Nucleic acid biology curiosity

Communication & collaboration

Education

PhD or equivalent in ML/CompBio/Bioengineering/CS

Tools

PyTorch

JAX

Job description

Lila Sciences is seeking an ML Scientist I/II, Nucleic Acid Design to advance RNA and DNA sequence design. This scientist will develop models and design strategies for understanding and engineering nucleic acid sequences, including problems such as 3’ UTR optimization, 5’ UTR optimization, CDS optimization, and promoter / enhancer design.

You’ll work at the intersection of machine learning, sequence modeling, experimental design, and platform development. The work spans both applied design campaigns and building next-generation models that improve how Lila generates, evaluates, and learns from nucleic acid sequence-function data.

The ideal candidate brings strong ML judgment, curiosity about biological mechanisms, and enthusiasm for areas such as regulatory genomics, RNA biology, and sequence-to-function modeling. You’ll collaborate with experimental scientists, ML researchers, and platform teams to build models that connect nucleic acid sequence design to biological function and make these capabilities usable across Lila’s autonomous science platform.

What You'll Be Building

• Build ML models for RNA and DNA sequence design across regulatory and coding sequence contexts.
• Develop methods spanning de novo generation, sequence property prediction, diverse set selection for experimental validation, and active learning strategies.
• Deeply investigate the biological mechanisms of designed sequences and propose hypotheses about why they succeed or fail. Turn these insights into better models and future design principles.
• Partner with experimental scientists to propose informative assays, validation strategies, and learning loops.
• Collaborate with ML scientists and engineers across Lila to integrate nucleic acid design models into robust platforms and agent-driven frameworks.
• Stay current with research in nucleic acid biology, sequence design, and scientific ML, and share research findings externally through papers or blog posts.

What You'll Need to Succeed

• PhD or equivalent experience in machine learning, computational biology, bioengineering, computer science, statistics, or a related quantitative field.
• Hands‑on experience building, training, and evaluating ML models for DNA or RNA.
• Strong foundation in modern ML methods, with practical experience using frameworks such as PyTorch, JAX, or equivalent tools.
• Experience developing models for sequence design, sequence‑function prediction, generative modeling, or active learning.
• Ability to reason about complex biological systems, scope ambiguous scientific problems, and formulate ML approaches that address difficult sequence‑function challenges.
• Curiosity about nucleic acid biology, including RNA biology, regulatory genomics, or related sequence‑to‑function problems.
• Strong communication and collaboration skills, with a preference for team‑based science and the ability to build shared technical direction across ML, engineering, platform, and experimental teams.

Bonus Points For

• Experience with regulatory element design, sequence‑to‑expression DNA models, or models trained on genomic, MPRA, STARR‑seq, or related functional genomics data.
• Experience with RNA sequence‑function modeling, RNA secondary structure modeling, UTR design, or inverse design methods for RNA sequences.
• Experience with sequence design in applied therapeutic contexts.
• Experience collaborating with wet‑lab teams to close the design‑test‑learn loop, including assay design, experimental prioritization, and interpretation of validation data.
• Familiarity with high‑throughput experimental datasets, pooled screens, reporter assays, or other sequence‑function measurements.
• Industry experience translating ML research into practical biological design workflows, experimental campaigns, or platform capabilities.

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

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.

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.

Information you provide during your application process will be handled in accordance with our Candidate Privacy Policy .

A Note to Agencies

Lila Sciences does not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to Lila Sciences or its employees is strictly prohibited unless contacted directly by Lila Science’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of Lila Sciences, and Lila Sciences will not owe any referral or other fees with respect thereto.