AI/ML Scientist

Overview

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 optimizationInvestigate and integrate novel data types to enhance our binder design capabilities and therapeutic developmentDevelop and validate cutting-edge machine learning methodologies for molecular engineering applicationsMentor and guide junior scientists and engineers in advanced ML techniques and research methodologiesDrive strategic research planning and identify promising new directions for AI-driven drug discoveryLead cross-functional teams to translate research breakthroughs into therapeutic applicationsProvide scientific expertise for business development opportunities and strategic partnerships
Required Qualifications
PhD in Machine Learning, Computational Biology, Bioinformatics, Computer Science, or related field5+ years of industry experience in machine learning research, preferably in biotechnology or pharmaceutical settingsExpert-level proficiency in PyTorch and/or JAX with extensive experience in novel architecture developmentDeep expertise in protein structure analysis, molecular dynamics, computational biology, or structural bioinformaticsExtensive knowledge of modern AI advances in protein analysis, design, and optimizationAdvanced 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 scientistsStrong background in statistical analysis, experimental design, and rigorous scientific methodologyExperience with distributed computing, high-performance computing, and large-scale ML system designOutstanding written and verbal communication skills with experience presenting to scientific and business audiencesDemonstrated ability to translate research innovations into practical applications
Preferred Qualifications
Previous experience in biotech/pharma industry with focus on AI-driven drug discoveryKnowledge of protein engineering, directed evolution, or structural biology wet lab techniquesExperience with large-scale data engineering, cloud platforms, and production ML systemsDemonstrated track record of published research in top-tier ML, computational biology, or protein design journalsTrack record of successful grant funding and research proposal writingExperience with regulatory considerations for AI applications in therapeutic developmentStrong network within the computational biology and protein design research communitiesDemonstrated leadership in cross-functional scientific teamsExperience with intellectual property development and patent applications
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 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 [redacted].

Company:

Manifold Bio

Qualifications:

Language requirements:

Specific requirements:

Educational level:

Level of experience (years):

Senior (5+ years of experience)

Tagged as: Industry, Machine Learning, NLP, United States