Flagship Pioneering, Inc. - Principal Scientist, Machine Learning
Requirements
• Breadth across domains such as genomics, protein modeling/design, proteomics/mass spec, multi-omics, cheminformatics/docking/ADMET, biophysics/MD, and scientific literature mining, with the ability to connect them using LLM-based agents and agentic workflows. • Hands-on experience with agentic AI and orchestration frameworks (e.g., Pydantic AI, LangGraph, LangChain, CrewAI, AutoGen). • Experience integrating LLMs and model platforms, including Anthropic, OpenAI, Vertex AI, and Amazon Bedrock, and building evaluation and feedback-loop frameworks for agentic systems. • Familiarity with sandboxed code execution and agent harness development. • Experience with LLM observability and monitoring tooling and cost-governance / FinOps for AI infrastructure.
Responsibilities
• Program Leadership: Lead development, implementation, control, and reporting of several AI/ML and computational projects within assigned ventures and PM programs across the preclinical, translational, and clinical continuum, in line with broader strategic plans of PI and Flagship. • Technical Ownership: Own the build, scaling, benchmarking and maintenance of agentic systems that combine ML and computational biology tools (genomics, biomolecule design, literature mining, system biology, etc) which serve as end-to-end systems for accelerating preclinical, translational and clinical R&D. • Best Practices: Promote operational excellence in AI projects by educating cross-functional collaborators. • Team Leadership: Manage and/or coordinate internal and external scientists/engineers and cross functional project teams as applicable; mentor early hires; support recruiting and interview. • Planning & Resourcing: Contribute to project planning, including budgets, resources, and timelines; surface risks and tradeoffs early with clear options. • Landscape & Strategy: Independently scout emerging literature and the AI/ML and agentic-AI landscape; synthesize concepts to propose new development strategies and identify opportunities to accelerate R&D across the preclinical, translational, and clinical continuum for PI, PM, and venture portfolios. • Communication & Influence: Influence the course of projects and technical approaches; adapt and present complex findings to diverse audiences to support meaningful interpretation and action. • PROFESSIONAL EXPERIENCE & QUALIFICATIONS • Master’s, or PhD in a relevant field (e.g., machine learning, mathematics, statistics, computational sciences) with 5+ years' experience scientific/engineering/computational in academic, pharmaceutical, or biotechnology settings; industry AI/ML experience preferred. • Experience driving results directly or indirectly through teams of engineers/scientists in dynamic, fastpaced, entrepreneurial, and technical environments. • Clear evidence of sustained independent thought and creativity driving high impact, cross disciplinary AI/ML projects. • Successful track record of leadership and contribution to decision making on progression of AI/ML models within projects or programs. • Depth across multiple core tools and concepts, including Python; modern ML frameworks (PyTorch or JAX/TensorFlow); version control; databases; deep learning architectures; and relevant informatics software. • Consistent record of outstanding performance reflected in publications, patents, or high impact internal reports where applicable.
Benefits
• Operate at the frontier: Build and deploy AI/ML that directly powers discovery and decision making across multiple new ventures. • Operate at the frontier • Own the full stack: From scoping and data contracts to models, MLOps, and internal UIs—ship end-to-end systems that scientists rely on daily. • Own the full stack • Compound impact: Convert one off wins into shared libraries and templates adopted across the PI portfolio. • Compound impact • Work with founders: Partner closely with venture leadership and PI platform engineers; influence strategy through hands on delivery. • Work with founders • Grow fast: Stretch across domains, take on situational leadership, present at conferences, and help shape first ML teams. • Grow fast • Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture. • Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com. • At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.
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