AI/ML Research Engineer

Manifold Bio is a platform biotechnology company pioneering AI-guided protein design and massively multiplexed in vivo screening to unlock tissue-targeted medicines and organism-scale models of living systems. Using proprietary molecular barcoding technology, we screen hundreds of thousands of protein designs simultaneously in living systems, producing in vivo-validated datasets at a scale no one else can match. The datasets power our computational models, which leads to better drug designs, creating a flywheel that gets stronger with every campaign. Our team of protein engineers, biologists, and computational scientists works across this full stack to pursue programs both internally and with leading pharma companies.

Position

Manifold Bio is seeking a talented Machine Learning Research Engineer to join our growing AI team. You will work closely with our research scientists to implement, scale, and optimize machine learning systems that power our de novo antibody design platform and advance our protein design capabilities. Your efforts will contribute to building production-ready ML infrastructure that enables breakthrough discoveries in protein therapeutics. You will be expected to take ownership of engineering challenges in our ML pipeline, from data processing and model training to deployment and monitoring, while collaborating closely with our research team to translate cutting-edge ideas into robust, scalable systems.

This is an on-site role and can be based in either Boston, Massachusetts or San Francisco, California. Please only apply if you reside in these cities or are open to relocate.

Responsibilities

Implement and optimize machine learning models for protein design

Build and maintain scalable data processing pipelines for large-scale protein and molecular datasets

Develop and deploy ML infrastructure for distributed training and inference across GPU clusters

Collaborate with research scientists to translate experimental ML approaches into production-ready code

Design and execute ML experiments with clear hypotheses and rigorous analysis

Optimize model performance and computational efficiency for large-scale protein design tasks

Build tools and utilities to support rapid prototyping and experimentation by the research team

Required Qualifications

Bachelor's or Master's degree in Computer Science, Machine Learning, Computational Biology, or related field

2+ years of hands-on experience with PyTorch and/or JAX for deep learning applications

Strong proficiency in Python scientific computing stack (NumPy, Pandas, scikit-learn)

Experience with distributed computing and GPU optimization techniques

Familiarity with protein structure analysis, computational biology, or analogous problems in natural sciences

Understanding of modern deep learning architectures and optimization techniques

Experience implementing research papers or translating ML approaches to production systems

Proficiency with version control (Git), testing frameworks, and software engineering best practices

Strong problem-solving skills and ability to work independently on technical challenges

Excellent written and verbal communication skills for cross-functional collaboration

Preferred Qualifications

Experience training LLMs or diffusion generative models

Knowledge of cloud computing platforms (AWS, GCP) and containerization (Docker, Kubernetes)

Background in computational biology, bioinformatics, or structural biology

Experience with large-scale data engineering and ETL pipelines

Familiarity with MLOps practices and model deployment frameworks

This Role Might Be Perfect For You If

You are passionate about leveraging state of the art machine learning approaches to solve challenging disease areas

You enjoy translating research ideas into high impact, productionized, scalable code

You have rich AI/ML experience and are looking to pivot into biotech

If you're excited to build scalable ML systems that revolutionize protein therapeutic discovery, please reach out to [email protected] .

Base Salary Range: $140,000-225,000

This reflects the typical offer range for this role, based on experience, role scope, and internal equity. Final compensation decisions are made using a consistent leveling framework and consider the candidate’s experience, interview performance, and expected impact.

This role is eligible for:

Annual performance-based target bonus

Stock options

Comprehensive medical, dental, and vision coverage

401(k) plan

Flexible paid time off and holidays

Perks including on-site gym, onsite lunch, and commuter support

Our compensation ranges are reviewed annually to ensure alignment with market trends and internal equity.

We value different experiences and ways of thinking and believe the most talented teams are built by bringing together people of diverse cultures, genders, and backgrounds.