Senior/Principal ML Scientist, Translational Biology

Lilasciences; San Francisco (CA); On-site; USD 268,000 - 384,000; Full time

Benefits offered by this job

Equity

Comprehensive benefits

Professional growth opportunities

Job summary

Lila Sciences is seeking a Senior ML Scientist to connect mechanistic biology to human medicine, building systems that assess whether a clinical program’s biology holds up. You will ground mechanistic models in human data and evaluate whether the mechanism is established, assumed, or unexamined, scaling evaluations for broad application.

You’ll co-design with ML scientists and mechanism experts, translate model outputs into actionable decisions, and contribute to publications and community

Qualifications

• PhD in a computational discipline centered on human biomedical data.
• Hands-on ML and data analysis for translational medicine in reproducible pipelines.
• Able to state how an intervention is meant to work and what evidence would establish each step.
• Knowledge of trial design, endpoints, biomarkers, and eligibility criteria.
• Ability to reason about what was knowable and to reproduce judgments clearly.

Responsibilities

• Build systems that assess mechanistic support for a clinical program.
• Ground mechanism in human data to determine presence, activity and rate-limiting factors.
• Evaluate trial designs for alignment with the proposed mechanism and encode that assessment for scale.
• Develop scalable evaluations with forecasted program progression using only information available at prediction date.
• Collaborate with ML scientists, mechanism scientists, and engineers; publish findings.

Skills

Fluent Python

Translational ML

Human genetic data analysis

Cohort and trial data analysis

Model evaluation and interpretation

Education

PhD in computational biology/biomedical informatics

Job description

Your Impact at LILA

Lila is redefining the future of biomedicine by combining large-scale automated data generation with scientific superintelligence. We are building the loop where AI, automation, and experimental biology co-evolve.

We are seeking a Senior ML Scientist to connect that work to human medicine, building the systems that assess whether a clinical program's biology holds up.

Three questions define the work. Is the mechanism well supported? What has actually been established about how this intervention is meant to work, and what has only been assumed. Does the mechanism operate in patients? Human genetics, expression, cohort and prior-trial evidence all bear on whether the biology that works in a model system is present, and rate-limiting, in the population being treated. Is the trial built for that mechanism? Endpoints that read out the right thing on the right timescale, biomarkers that measure what the mechanism actually does, and enrollment criteria that select patients in whom it is operative — or, very often, none of these.

You will not answer these program by program yourself. You will build the systems that do it, drawing on the mechanistic models and structured biological evidence the rest of the group generates, and grounding them in human data. Your own judgment is the specification and the standard those systems are held to, and you will build the evaluations — including forecasts of real program outcomes scored against what was knowable at the time — that tell you whether they are any good.

What You'll Be Building

• Build systems that assess mechanistic support for a clinical program. Take the structured biological evidence and mechanistic models generated elsewhere in the group and turn them into an assessment of whether an intervention's proposed mechanism is established, assumed, or unexamined.
• Ground mechanism in human data. Analyze human genetic, expression, cohort and trial-derived evidence to determine whether a mechanism is present, active and rate-limiting in the relevant patient population — and how heterogeneous it is across that population.
• Assess trial design against mechanism. Evaluate endpoint choice and timing, biomarker definition and assay, dose and schedule, and eligibility and enrichment criteria for alignment with the proposed mechanism, and encode that assessment so it can be applied at scale rather than case by case.
• Build the evaluations that hold these systems to account, including outcome-verifiable forecasts of real program progression scored using only information available at the prediction date, with the evidence boundary enforced against contamination. Run them yourself and report honestly when a contribution adds nothing.
• Co-design with ML scientists, mechanism scientists and engineers, translate model output into decisions people actually make, and publish — what is and is not predictable from mechanistic and human evidence is a real scientific question we intend to answer in public.
• Communicate findings clearly to technical and cross-functional audiences, including scientists, engineers, product partners, and therapeutic stakeholders.
• Support external scientific visibility through publications, presentations, and engagement with ML/AI for Biology, computational biology and therapeutic discovery communities, as appropriate.

What You'll Need to Succeed

• PhD in a computational discipline — translational bioinformatics, computational biology, biomedical informatics, biostatistics, epidemiology, machine learning, or related — with research centered on human biomedical data.
• Hands-on ML and data analysis for translational medicine. Fluent Python; substantial experience analyzing human genetic, multi-omic, cohort, trial or real-world data in reproducible pipelines. You will run your own analyses and evaluations and interpret them yourself.
• Mechanistic reasoning about therapeutic interventions. Able to state how an intervention is meant to work, what evidence would establish each step, and where human evidence supports or undercuts it.
• Clinical development fluency. Working knowledge of trial design, endpoints, biomarker strategy, eligibility and enrichment — enough to read a protocol and judge whether it tests the mechanism it claims to.
• Evidence judgment and a systems instinct. Able to reason about what was knowable when and resist hindsight — and interested in making that judgment reproducible by something other than you, through structure and evaluation rather than case-by-case expertise.

Bonus Points For

• Experience with human genetics for target identification and validation — common and rare variant evidence, QTL and expression data, or genetically supported target work.
• Experience with biomarker development, patient stratification, companion diagnostics, or enrichment strategy.
• Experience with clinical trial datasets, real-world data, or observational cohort analysis, and their known limitations.
• Experience evaluating language models or agents on scientific judgment tasks, including contamination and memorization controls.
• Familiarity with survival analysis, competing risks, calibration, or forecasting methodology.
• Experience with structured evidence frameworks — GRADE, systematic review protocols, or bespoke assessment rubrics.

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 — $384,000 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.

We’re All In

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.