Flagship Pioneering, Inc.
Biotechnology
PrincipalScientist,MachineLearning-Biomolecules
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“Principal Scientist, Machine Learning - Biomolecules at Flagship Pioneering, Inc.. Skills: Machine Learning, Computational Projects, LLM Agents, Scientific Workflows. Lead development of AI/ML projects. Implement AI/ML projects”
What You'll Achieve.
Create a portfolio of AI-first companies; Transform breakthrough ideas; Accelerate fundamental research
Industry & Context.
Deep Diver; Risk Assessment; Tradeoff Analysis
What They're Looking For.
Must Have
5+ years industry AI/ML experience, Experience driving results through teams, Sustained independent thought and creativity, Leadership and contribution to decision making, Depth across modern ML frameworks, Depth across version databases, Depth across deep learning, Depth across relevant informatics software
Nice to Have
Breadth across protein modeling/design, Breadth across proteomics/mass spec, Breadth across cheminformatics/docking/ADMET, Breadth across biophysics/MD, Breadth across LLM/agentic automation, MLOps expertise, Experience mentoring early hires, Experience acting as interim Head of ML, Experience contributing to hiring plans, Experience contributing to interview processes
What You'll Do.
Lead development of AI/ML projects
Implement AI/ML projects
Control AI/ML projects
Report on AI/ML projects
Oversee method development
Oversee pipeline development
Oversee LLM agent/workflow drive benchmarking
Oversee scaling of AI/ML projects
Oversee implementation into production systems
Promote operational excellence in AI projects
Educate cross-functional collaborators
Manage internal scientists/engineers
Coordinate internal scientists/engineers
Manage external scientists/engineers
Coordinate external scientists/engineers
Manage cross-functional project teams
Coordinate cross-functional project teams
Support interview processes
Plan surface tradeoffs
Propose new development strategies
Identify opportunities for PI
Identify opportunities for venture portfolios
Act as recognized subject matter expert
Actively participate in scientific conferences
Actively participate in meetings
Adapt complex findings
Present complex findings
How You'll Work.
Team & Collaboration
Cross-functional contributors; Cross-functional collaborators; Cross-functional project teams; Venture teams; External partners
Communication Scope
Present complex findings
Process & Methodology
Program Leadership, Strategic Plans
Full Job Description
ABOUT PIONEERING INTELLIGENCE Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond. THE ROLE We are seeking a Principal Scientist (Embedded ML/Computational) to lead multiple AI/ML or computational projects across early stage ventures, as a part of Flagship’s company origination process. You will define and deliver pragmatic AI strategies, oversee method and platform development (e.g., systems design, drug design, molecular modeling, systems biology, protein design, LLM/agentic workflows), and ensure rigor in model development, benchmarking, scaling, and reporting. You will manage cross functional contributors as applicable, influence company direction, and represent PI to venture teams and external partners. The ideal candidate is a self-directed serial deep diver - someone who can move from protein design one week to mass spec or docking pipelines the next and then spin up LLM based agents that automate scientific workflows. KEY RESPONSIBILITIES Program Leadership: Lead development, implementation, control, and reporting of several AI/ML or computational projects within assigned ventures in line with broader strategic plans of PI and Flagship, budgets, and timelines. Technical Ownership: Take a specialized technical role on project teams to oversee method development, pipeline development, and LLM based agent/workflow design; drive benchmarking, scaling, and implementation into production grade systems. Best Practices: promote operational excellence in AI projects by educating cross-functional collaborators. Team
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