Principal Scientist, Machine Learning at Flagship Pioneering, Inc.
Cambridge, MA
$208,000–$286,000from the description
Aug 5, 2026
Cambridge, MA
Sep 24, 2026
What this job asks for AI summary
A senior individual-contributor scientist role at a Flagship Pioneering AI venture, focused on building and owning end-to-end ML and computational biology systems that accelerate pharmaceutical R&D across preclinical, translational, and clinical stages. The work spans protein design, multi-omics, cheminformatics, and scientific literature mining, tied together with LLM-based agentic workflows. The role also involves cross-functional team coordination and strategic influence across Flagship's portfolio companies.
Senior level · 5+ years · Boston-Cambridge-Newton, MA-NH · Master's required · Full-time
Advertised as Principal, but the requirements read as Senior.
“or” means any one of them counts — you don't need all of them.
We read this from the posting text with AI. Skim the description below before ruling yourself out.
How this req sits in the market our data
Roughly 120 people in the Boston-Cambridge-Newton, MA-NH area plausibly meet what this posting asks for (data scientists). range 95–160
Applicant volume Moderate — A normal amount of company. The rare requirements below are what will separate a shortlisted application from the rest.
Most people in this occupation already list these. Still required — just not what gets you shortlisted.
What the occupation pays Median $134,944 (middle half $104,979–$169,773). This posting is about at that midpoint.
Estimated from BLS employment for this occupation and area, per-skill prevalence across our listing corpus, and published wage benchmarks — as of Aug 6, 2026. It is a model, not a headcount.
Why we read it this way (7)
The title 'Principal Scientist' here is a scientific seniority label common in pharma/biotech, not the engineering 'Principal' band — the requirements (5+ years, Master's or PhD) and scope support a Senior classification rather than a true Principal/org-wide technical authority band.
The role is genuinely ambiguous between Data Scientists (15-2051) and Software Developers (15-1252): it demands deep ML modeling and computational biology (pointing to 15-2051) but also end-to-end agentic system building, MLOps, and pipeline engineering (pointing to 15-1252). Data Scientist was chosen as primary given the dominant emphasis on model development, benchmarking, and scientific research.
Location is not explicitly stated in the posting; Flagship Pioneering is headquartered in Cambridge, MA, so Boston-Cambridge-Newton CBSA is used as the best available inference.
The degree requirement is Master's or PhD — Master's is set as the minimum hard gate since the JD lists it first and does not accept equivalent experience in lieu of a degree.
The agentic AI orchestration frameworks (LangGraph, LangChain, Pydantic AI, CrewAI, AutoGen) and LLM platform integrations (Anthropic, OpenAI, Vertex AI, Amazon Bedrock) appear under the 'Preferred Qualifications' section.
The required ML frameworks section lists 'PyTorch or JAX/TensorFlow' — PyTorch is the primary skill with JAX and TensorFlow listed as alternatives since the JD treats them as interchangeable options.
Ignored 1 non-technology phrase(s) as skills (responsibilities/concepts, not named tools): protein modeling.
Read the full posting
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