Principal Scientist, Embedded ML for Drug Discovery

Flagship Pioneering, Inc.; Cambridge (MA); On-site; USD 208,000 - 286,000; Full time

Job summary

Flagship Pioneering, Inc. is seeking a Principal Scientist (Embedded ML/Computational) to lead AI/ML and computational initiatives accelerating pharmaceutical R&D across preclinical to clinical stages.

You will define pragmatic AI strategies and oversee method and platform development, leveraging omics, biomolecule design, and literature mining, with agent-based workflows tying methods into end-to-end pipelines.

Qualifications

• Master’s or PhD in a relevant field (e.g., ML, math, computational sciences) with 5+ years’ experience in academic, pharmaceutical, or biotech settings.
• Demonstrated leadership and ability to influence decisions on AI/ML model progression within projects or programs.
• Proven track record of independent thought and high-impact AI/ML project leadership.

Responsibilities

• Lead development, implementation, and reporting of multiple AI/ML and computational projects across preclinical to clinical R&D.
• Own the build, scaling, benchmarking, and maintenance of agentic systems combining ML and computational biology tools.
• Promote operational excellence and educate cross-functional collaborators on AI projects.
• Mentor internal and external scientists/engineers; support recruiting and interview processes.
• Contribute to project planning, budgets, resources, and timelines; surface risks with options.
• Scout literature and AI landscape; synthesize concepts to propose new development strategies.
• Communicate complex findings to diverse audiences to enable action.

Skills

Python

PyTorch

JAX

TensorFlow

Version control

Databases

DL architectures

Informatics software

Education

Master's or PhD

Tools

Pydantic AI

LangGraph

LangChain

CrewAI

AutoGen

Job description

Flagship Pioneering, Inc. is seeking a Principal Scientist (Embedded ML/Computational) to lead AI/ML and computational initiatives accelerating pharmaceutical R&D across preclinical to clinical stages.

You will define pragmatic AI strategies and oversee method and platform development, leveraging omics, biomolecule design, and literature mining, with agent-based workflows tying methods into end-to-end pipelines.