Manifold Bio

Manifold Bio

AI/ML Research Engineer

Boston, MA or San Francisco, CA

Sponsorship not specified$140k-$225kDetected 82 days ago
PythonFull-Stack DevelopmentGitAWSGCPDockerKubernetesMachine LearningDeep LearningPyTorchscikit-learnPandasNumPyData EngineeringLLMsMLOpsA/B TestingBioinformaticsResearchAnimal StudiesCommunicationCollaborationProblem Solving

About the role

  • 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.
  • This is an on-site role and can be based in either Boston, Massachusetts or San Francisco, California.

Responsibilities

  • 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
  • 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.
  • Your efforts will contribute to building production-ready ML infrastructure that enables breakthrough discoveries in protein therapeutics.

Requirements

  • 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
  • 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

Nice to have

  • 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
  • You enjoy translating research ideas into high impact, productionized, scalable code
  • You have rich AI/ML experience and are looking to pivot into biotech
  • This Role Might Be Perfect For You If

Compensation

  • Final compensation decisions are made using a consistent leveling framework and consider the candidate's experience, interview performance, and expected impact.
  • $140,000-225,000
  • This role is eligible for:
  • Annual performance-based target bonus
  • 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.

Benefits

  • Annual performance-based target bonus
  • Comprehensive medical, dental, and vision coverage
  • Flexible paid time off and holidays
  • Implement and optimize machine learning models for protein design
  • 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
  • Understanding of modern deep learning architectures and optimization techniques
  • 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.
  • Perks including on-site gym, onsite lunch, and commuter support

Company info

  • 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.
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