AI/ML Scientist

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 an exceptional Machine Learning Scientist to lead research initiatives within our AI team and drive innovation in protein design methodologies. This role will support and enrich the team’s current generative de novo protein design capabilities, as well as break ground on building foundational models on relevant protein therapeutic properties including binding affinity, developability, and in vivo biodistribution and pharmacokinetic (PK) properties. You will be expected to independently conceive, design and execute high-impact research projects that push the boundaries of AI applications in protein design, while contributing to publications and representing Manifold’s scientific contributions to the broader research community. 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 Lead independent research projects exploring novel AI/ML approaches for protein design and optimization Investigate and integrate novel data types to enhance our binder design capabilities and therapeutic development Develop and validate cutting-edge machine learning methodologies for molecular engineering applications Mentor and guide junior scientists and engineers in advanced ML techniques and research methodologies Drive strategic research planning and identify promising new directions for AI-driven drug discovery Lead cross-functional teams to translate research breakthroughs into therapeutic applications Provide scientific expertise for business development opportunities and strategic partnerships Required Qualifications PhD in Machine Learning, Computational Biology, Bioinformatics, Computer Science, or related field 5+ years of industry experience in machine learning research, preferably in biotechnology or pharmaceutical settings Expert-level proficiency in PyTorch and/or JAX with extensive experience in novel architecture development Deep expertise in protein structure analysis, molecular dynamics, computational biology, or structural bioinformatics Extensive knowledge of modern AI advances in protein analysis, design, and optimization Advanced understanding of deep learning architectures, particularly transformers for molecular applications, as well as generative modeling approaches (autoregressive, diffusion, flow-matching, etc.) Proven experience leading research teams and mentoring junior scientists Strong background in statistical analysis, experimental design, and rigorous scientific methodology Experience with distributed computing, high-performance computing, and large-scale ML system design Outstanding written and verbal communication skills with experience presenting to scientific and business audiences Demonstrated ability to translate research innovations into practical applications Preferred Qualifications Previous experience in biotech/pharma industry with focus on AI-driven drug discovery Knowledge of protein engineering, directed evolution, or structural biology wet lab techniques Experience with large-scale data engineering, cloud platforms, and production ML systems Demonstrated track record of published research in top-tier ML, computational