Principal ML Scientist, Multimodal Biological Reasoning
Flagship Pioneering, Inc. · Cambridge, MA
$216,000–$297,000from the description
Jun 30, 2026
Cambridge, MA
Jul 21, 2026
What this job asks for AI summary
A hands-on technical lead role focused on building multi-modal, multi-scale AI reasoning systems for biology, integrating large language models, biological foundation models, and diverse biological data modalities. The position combines architectural guidance of a small ML research team with direct engagement across a biotech portfolio to identify use cases, shape data strategy, and embed reasoning engines into an autonomous scientific discovery platform. Best suited to someone with deep expertise spanning modern ML and computational biology.
Staff level · Boston-Cambridge-Newton, MA-NH · Full-time
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
Rare in this occupation — lead with these, and say what you built with them.
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 Jul 28, 2026. It is a model, not a headcount.
Why we read it this way (8)
The title is 'Lead' with no seniority modifier, but the role's actual scope — owning a cross-portfolio roadmap, guiding architecture across multiple teams, originating projects, and interfacing with executives and venture creation leaders — clearly exceeds Senior and maps to Staff.
The degree requirement lists 'PhD, MS, or equivalent experience,' so no formal degree is hard-gated.
Location is not explicitly stated in the posting; Flagship Pioneering is headquartered in Cambridge, MA, and Pioneering Intelligence is part of that ecosystem — the CBSA reflects that inference. Remote status is not offered.
The Qualifications section (hard gates) lists LLMs, multimodal modeling, representation learning, fine-tuning, post-training, benchmarking, ML systems, computational biology, and biological foundation models as industry-leading or deep expertise requirements. 'Working knowledge' of biological data modalities (genomics, transcriptomics, etc.) and 'strong judgment' around mechanism-of-action reasoning are also listed under Qualifications but are framed as domain knowledge rather than named tools, so they are omitted from the skills list per schema rules.
The Requirements section lists protein language models, genomic foundation models, scientific agents, and AI discovery platforms — these are marked preferred because the Requirements section reads as a secondary block reinforcing the Qualifications, and the posting explicitly notes that candidates without all qualifications are encouraged to apply.
No specific technology stack (e.g., PyTorch, cloud platform) is named anywhere in the posting, so no infrastructure or framework skills are extracted.
The alt SOC (15-1252 Software Developers) is noted because the role involves hands-on model architecture and system building, but the primary day-to-day work is scientific modeling and discovery, which aligns more closely with Data Scientists.
Ignored 1 non-technology phrase(s) as skills (responsibilities/concepts, not named tools): multimodal modeling.
Read the full posting
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