Principal Scientist, Machine Learning

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. 

About Flagship Pioneering  

Flagship Pioneering invents and builds platform companies that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded 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.  

Position Summary 

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 Leadership: Manage and/or coordinate internal and external scientists/engineers and crossfunctional 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 landscape; synthesize concepts to propose new development strategies and identify opportunities for PI and venture portfolios. 
• Representation & Community: Represent PI to portfolio companies and external partners; act as a recognized subject matter expert; actively participate in scientific conferences and meetings. 
• Communication & Influence: Influence the course of projects and technical approaches; adapt and present complex findings to diverse audiences to support meaningful interpretation and action. 

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 

Preferred Qualifications 

• 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. 

Why Join Us 

• Operate at the frontier: Build and deploy AI/ML that directly powers discovery and decision making across multiple new ventures. 
• Own the full stack: From scoping and data contracts to models, MLOps, and internal UIs—ship endtoend systems that scientists rely on daily. 
• Compound impact: Convert one off wins into shared libraries and templates adopted across the PI portfolio. 
• Work with founders: Partner closely with venture leadership and PI platform engineers; influence strategy through hands on delivery. 
• Grow fast: Stretch across domains, take on situational leadership, present at conferences, and help shape first ML teams. 

About Flagship

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded 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.

Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status. 

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

The salary range for this role is $208,000 - $286,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence’s good faith estimate as of the date of publication and may be modified in the future.