Flagship Pioneering, Inc. - Principal Scientist, Machine Learning
Requirements
• Breadth across domains such as protein modeling/design, proteomics/mass spec, cheminformatics/docking/ADMET, biophysics/MD, and LLM/agentic automation. • MLOps expertise: data contracts and lineage (e.g., DVC/LakeFS), experiment tracking (MLflow/W&B), secure AWS infrastructure (S3, Batch/ECS/EKS, SageMaker), Docker, IaC (Terraform/CDK), and CI/CD (GitHub Actions). • Generative modeling (diffusion/flow/VAEs) for sequences, graphs, or 3D structures; docking rescoring (e.g., gnina, DiffDock) and pose quality metrics. • Workflow orchestration (Airflow/Prefect/Argo), data warehouses (Redshift/Snowflake), vector search (FAISS/pgvector), and lightweight internal tools (FastAPI, Streamlit/Gradio). • Experience mentoring early hires, acting as interim Head of ML, and contributing to hiring plans and interview processes at startups.
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. • Program Leadership • 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. • Technical Ownership • Best Practices: promote operational excellence in AI projects by educating cross-functional collaborators. • Best Practices: • Team Leadership: Manage and/or coordinate internal and external scientists/engineers and crossfunctional project teams as applicable; mentor early hires; support recruiting and interview. • Team Leadership • Planning & Resourcing: Contribute to project planning, including budgets, resources, and timelines; surface risks and tradeoffs early with clear options. • Planning & Resourcing • Landscape & Strategy: Independently scout emerging literature and the AI/ML landscape; synthesize concepts to propose new development strategies and identify opportunities for PI and venture portfolios. • Landscape & Strategy • Representation & Community: Represent PI to portfolio companies and external partners; act as a recognized subject matter expert; actively participate in scientific conferences and meetings. • Representation & Community • Communication & Influence: Influence the course of projects and technical approaches; adapt and present complex findings to diverse audiences to support meaningful interpretation and action. • Communication & Influence • 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 endtoend 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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