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 ...