Machine Learning Engineer

BigHat; San Mateo, Northern (CA, KY); Hybrid; USD 150,000 - 200,000; Full time

Benefits offered by this job

Bonus

Stock options

Benefits

Job summary

BigHat Biosciences is seeking a Machine Learning Engineer to advance ML-driven antibody design. You will build generative models for antibody sequences and structures, and create multi-objective optimization methods for rapid lab-in-the-loop validation.

Join a fast-paced, interdisciplinary team applying state-of-the-art ML to accelerate therapeutics development, with collaboration across data science, biology, and automation in San Mateo, CA.

Qualifications

• Masters in ML/CS/EE or equivalent.
• Bachelors with 3+ years industry experience.
• Strong quantitative background and hands-on ML methods.
• Excellent communication with diverse teams.
• Familiarity with ML-driven protein engineering.
• Nice-to-haves: de novo design, NGS data, Bayesian optimization, AWS, publications.

Responsibilities

• Design state-of-the-art generative models of antibody sequence/structure and predictive models on proprietary datasets.
• Develop multi-modality, multi-objective protein sequence optimization for lab-in-the-loop design in high-throughput lab.
• Develop and deploy agentic and LLM-driven optimization methods to accelerate the design-build-test loop.
• Provide ML expertise to ongoing therapeutics programs and contribute to drug development.
• Collaborate with engineering to ensure efficient deployment of models and methods.
• Work with interdisciplinary teams across drug development and wet labs.

Skills

Python

PyTorch

Software engineering

Communication

Biomedical knowledge

Protein engineering ML

Publications

NGS data

Bayesian optimization

De novo design

Education

Masters in ML/CS/EE

Bachelors + 3+ years

Tools

AWS

CI/CD

Git

Job description

Machine Learning Engineer

Department: DS/ML (Data Science/Machine Learning)

Employment Type: Full Time

Location: San Mateo, CA

Description

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

At BigHat Biosciences our full-stack antibody drug development platform uses AI/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 development of complex, net-gen therapeutics ‘trivially parallelizable’, at a pace which 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 need, and a curiosity about the underlying biology, you’ll apply your top-tier ML skillset to refine and expand this state of the art protein engineering platform. Success will mean not only hands-on methods development, but actively participating in the application of our platform to the accelerated design of new drugs for devastating diseases.

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.
• 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.
• Develop, refine, and deploy agentic and LLM-driven optimization methods to further automate and accelerate our design-build-test loop.
• 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 and methods.
• Work closely with an interdisciplinary team of drug developers, wet lab scientists, automation specialists, data scientists, etc. - every therapeutics program at BigHat is heavily interdisciplinary.

Skills Knowledge and Expertise

• Masters in ML/CS/EE or Bachelors with 3+ years industry experience; hands on experience developing and applying novel ML methods and a strong quantitative background.
• Strong competency in Python, familiarity with PyTorch (even without LLMs!) and experience with modern software engineering best practices, including not just agentic/LLM-assisted coding but testing, CI/CD, etc.
• Excellent communication skills, sufficient biomedical domain knowledge to interact effectively with diverse scientific teams.
• Energy and ambition - ready to dive into a fast-paced environment and execute 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, experience training and deploying models on AWS, and publications at major ML conferences.

Total Rewards

The salary estimated for this position is $150,000 - $200,000 + 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.