Principal, Machine Learning Scientist

BigHat Biosciences

Software Engineering, Data Science

San Mateo, CA, USA

USD 233k-266k / year + Equity

Posted on Oct 21, 2025

The role: We are seeking a creative, accomplished Principal Machine Learning Scientist to advance the state of the art in ML-driven therapeutic antibody design.

At BigHat Biosciences, our full-stack antibody drug development platform uses ML to drive every stage from discovery to optimization. Our roboticized high-throughput wet-lab continually adds to our large proprietary datasets, which are piped through a custom LIMS++ data management and orchestration layer to automatically update and deploy the latest models. This makes the development of complex, next-gen therapeutics ‘trivially parallelizable’, at a pace that only accelerates as we develop better ML tooling.

You’re not interested in just git-cloning the latest NeurIPS pub and swapping out the dataset. Motivated by an enthusiasm for the possibility of addressing unmet patient needs and a curiosity about the underlying biology, you’ll apply your world-class ML skillset to refine and expand this state-of-the-art protein engineering platform. Success will mean not only hands-on methods development, but helping shape the direction for future ML research, and actively participating in the application of our platform to the accelerated design of new therapeutics.

Department: DS/ML (Data Science/Machine Learning)
Employment Type: Full Time
Location: San Mateo, CA
Workplace type: Hybrid
Reporting To: Hunter Elliot

Key Responsibilities

Design and implement the next state-of-the-art generative models of antibody sequence and structure, and predictive models of antibody properties, trained on proprietary internal datasets of thousands to millions of antibodies.
Identify opportunities for improvement in our ML tooling, and help to set strategy for ML research, driven by a strong high-level understanding of real-world drug development challenges
Develop, refine, and deploy de novo design methods for generating initial hits to challenging, therapeutically interesting targets.
Develop multi-modality, multi-objective iterative protein sequence optimization approaches to lab-in-the-loop antibody design problems for validation and deployment in our high-throughput wet lab - at BigHat success is only declared upon synthesis of real antibodies with drug-like properties.
Maintain an in-depth understanding of the current state-of-the-art in ML-driven protein engineering, both in the literature and at BigHat.
Share your findings at top-tier conferences and publish in leading scientific journals to advance the field of protein engineering.
Provide technical guidance and mentorship to other ML and data science FTEs and interns.
Provide ML expertise and support for ongoing therapeutics programs, directly contributing to the development of new drugs.
Collaborate with our engineering team to ensure maximal efficiency in the automated deployment of our latest models to ongoing drug development programs.
Work closely with an interdisciplinary team of drug developers, wet lab scientists, automation specialists, data scientists, etc. to identify inefficiencies or potential improvements in BigHat’s platform, and plan and prioritize ML methods development accordingly.

Skills Knowledge and Expertise

PhD in ML/CS or in the hard sciences with 5+ years experience developing and applying novel ML methods and a strong quantitative background.
Publications in major ML conferences and/or leading journals, or extensive demonstrable track record developing and applying novel ML in industry.
Strong competency in Python, familiarity with PyTorch, and experience with modern software engineering best practices.
Excellent communication skills, sufficient biomedical domain knowledge to interact effectively with diverse scientific teams.
Enjoys a fast-paced environment and excels at executing across multiple projects.
Familiarity with the current state-of-the-art in ML-driven protein engineering
Nice-to-haves include experience with de novo design, NGS data, Bayesian optimization, familiarity with antibody biology and drug development, and experience training and deploying models on AWS.

Total Rewards

The salary estimated for this position is $233,000 - $266,000 + bonus + options + benefits. Compensation will vary depending on job-related knowledge, skills, and experience. Actual compensation will be confirmed in writing at the time of the offer.

What BigHat Offers:

Range of health insurance plan options through Anthem and Kaiser (monthly credit if benefit waived)
Dental, and vision coverage through Guardian
Additional well-being benefits through Nayya, OneMedical, Wagmo, Rula, and more
401(k) with company match
DTO, two weeks of company-wide shutdown, and 12 company holidays
Paid parental leave

About BigHat Biosciences

BigHat Biosciences designs safer, more effective biologic therapies for patients using machine learning and synthetic biology.

BigHat integrates a wet lab for high-speed characterization with machine learning technologies to guide the search for better antibodies. We apply these design capabilities to develop new generations of safer and more effective treatments for patients suffering from today’s most challenging diseases.

BigHat is a Series B biotech outside San Francisco with a team-oriented, inclusive, and family-friendly culture. Our broad pipeline of wholly-owned and partnered therapeutic programs span many disparate indications with high unmet need, such as cancer, inflammation, and infectious disease. BigHat has raised >$100M from top investors, including Section 32, a16z, and 8VC.

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Our Hiring Process

Stage 1:

Applied

Stage 2:

Initial Conversation | Head of Talent

Stage 3:

Initial Conversation | Hiring Manager

Stage 4:

1st Technical Screen

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