Flagship Pioneering · 2 months ago
Principal Scientist, Machine Learning, Origination
Cambridge, MA USA
Full-time
Onsite
Senior Level, Lead/Staff
$208K/yr - $286K/yr
5+ years expFlagship Pioneering is a company that builds on its legacy of founding cutting-edge science and computational ventures. They are seeking a Principal Scientist to lead multiple AI/ML or computational projects, defining and delivering AI strategies while managing cross-functional contributors and representing the company to external partners.
FinanceFinancial ServicesVenture Capital
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
Qualification
Required
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
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
Benefits
Healthcare coverage
Annual incentive program
Retirement benefits
Broad range of other benefits
Company
Flagship Pioneering
Flagship Pioneering is a venture capital firm that invests in life sciences and healthcare companies.
501-1000 employees
H1B Sponsorship
Flagship Pioneering has a track record of offering H1B sponsorships. Please note that this does not
guarantee sponsorship for this specific role. Below presents additional info for your
reference. (Data Powered by US Department of Labor)
Distribution of Different Job Fields Receiving Sponsorship
Represents job field similar to this job
Trends of Total Sponsorships
2025 (8)
2024 (4)
2023 (4)
2022 (4)
2021 (1)
Funding
Current Stage
Late StageLeadership Team
Noubar Afeyan
Founder and CEO
Chuck Carelli
Chief Financial Officer
Recent News
2026-01-16
2026-01-16
Company data provided by crunchbase