Machine Learning Engineer

We are a vibrant and intensely mission-driven team in San Francisco, comprising members from MIT, Harvard Medical School, Roche, ETH, and Dana-Farber.

We value speed and rigor, coupled with excitement, drive, and a strong work ethic. In an early-stage environment, we value people who can bring clarity to open-ended problems, take ownership of the next steps, and follow through with energy.

Capable Labs is a place for ambitious, high-integrity people who want to become dramatically better. You will be surrounded by people who care intensely about the work, get close feedback from the people making scientific and company-defining decisions, and have room to own increasingly important problems.

We believe excellent work should be met with meaningful reward, ownership, and trust. Responsibility is earned through contribution, not title alone: anyone who demonstrates the judgment, rigor, and follow-through to move important work forward can earn meaningful scope.

About the Role

You will build machine-learning systems that remove real bottlenecks from drug discovery and development. The role spans research and engineering: identifying valuable problems, adapting modern biomolecular models, building tools for scientists, and closing the loop between model predictions and wet-lab results. Success is measured by whether the systems accelerate better experiments and better drug-development decisions.

Responsibilities

• Work with scientists to identify high-value bottlenecks in drug discovery and development where machine learning can materially improve speed or decision quality.

• Build systems for experiment planning, literature triage, protocol drafting, in silico screening, candidate generation, filtering, and predictive analysis.

• Fine-tune and apply biomolecular models such as ESM, AlphaFold-family models, RFdiffusion, ProteinMPNN, and related approaches using Capable’s data.

• Develop candidate-analysis workflows that may include molecular dynamics, post-training, probing, evaluation, and other fit-for-purpose computational methods.

• Work directly with wet-lab scientists and operators to automate preclinical or clinical-development workflows and make tools usable in practice.

• Build active-learning loops that connect in silico predictions to in vivo results.

• Create internal evaluations that measure whether models and tools improve experimental throughput, candidate quality, or program decisions.

Ideal Qualifications

• Strong research judgment in biomolecular modeling and drug development, or a demonstrated ability and desire to develop that judgment quickly.

• The ability to own an ambiguous problem end to end, from identifying the useful question through building, evaluating, and improving a working system.

• A practical interest in wet-lab reality and in building tools around the constraints of experiments, operators, data quality, and scientific decisions.

• Curiosity, strong analytical instincts, and a habit of testing whether a method creates real-world value rather than relying on benchmark performance alone.

• Experience with active learning, data-constrained biological modeling, multimodal omics, imaging, phenotypic data, or production-scale agent platforms is helpful but not required.

Pay & Benefits

• In addition to the posted salary range, we offer generous equity options.

• Compensation will depend on the skills, experience, and scope of impact you bring. If your background, experience, or compensation needs fall outside this range, we are still open to a conversation based on the scope and impact you could bring.

• $500+ monthly wellness budget for training, supplements, coaching, recovery, or other tools that help you perform at your best.

• Healthcare: We offer a broad range of medical, dental, and vision coverage options, with Capable covering 100% of the base policy.

• You will also have access to HSA, FSA, and 401K plans.

• Healthy dinners with the team are provided daily.

• We support visa sponsorship where appropriate, including O-1, H-1B, J-1, TN, and other employment-based pathways. Our team is already international, with members from Canada, Pakistan, Germany, Austria, Switzerland, China, India, and the United States.

Application Process

Our process is fast, transparent, and personal. We care about getting to know the person behind the application.

• Initial application

• First phone screen

• Second phone screen

• In-person work trial in San Francisco: designed to give both sides a realistic sense of working together. Get to know the founding team!

Apply Today

Curious but not sure? Apply anyway. It takes 5 minutes, and you do not need to be actively job searching to start a conversation.

Some of the best people do not map perfectly to a job description. If this sounds like a place where you could do important work, we would like to hear from you.

And if someone exceptional comes to mind, send them our way here. We read every referral carefully, and if your referral joins Capable, we’ll send you a thank-you bonus.

Equal Opportunity

Capable is an Equal Opportunity Employer; employment with Capable is governed on the basis of merit, competence and qualifications and will not be influenced in any manner by race, color, religion, gender, national origin/ethnicity, veteran status, disability status, age, sexual orientation, gender identity, marital status, mental or physical disability or any other legally protected status.