Principal Scientist, Machine Learning

Flagship Pioneering, Inc. • Cambridge, MA

79d • $208,000 - $286,000

About The Position

The Pioneering Intelligence (PI) team at Flagship Pioneering builds the digital and AI foundation that accelerates the creation and growth of our companies. We develop shared platforms, tools, and methods that help new ventures become AI native from day one, and we embed expert builders into companies to translate ambiguous scientific problems into working systems. 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.

Requirements

• 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.

Nice To Haves

• 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

• 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.
• 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.
• Promote operational excellence in AI projects by educating cross-functional collaborators.
• Manage and/or coordinate internal and external scientists/engineers and crossfunctional project teams as applicable; mentor early hires; support recruiting and interview.
• Contribute to project planning, including budgets, resources, and timelines; surface risks and tradeoffs early with clear options.
• Independently scout emerging literature and the AI/ML landscape; synthesize concepts to propose new development strategies and identify opportunities for PI and venture portfolios.
• Represent PI to portfolio companies and external partners; act as a recognized subject matter expert; actively participate in scientific conferences and meetings.
• Influence the course of projects and technical approaches; adapt and present complex findings to diverse audiences to support meaningful interpretation and action.

Benefits

• Healthcare coverage
• Annual incentive program
• Retirement benefits
• Broad range of other benefits

What This Job Offers

• Job Type: Full-time
• Career Level: Senior
• Education Level: Ph.D. or professional degree
• Number of Employees: 251-500 employees