Flagship Pioneering
Principal Scientist, Machine Learning - Biomolecules
$208K–$286K
Cambridge, MA USA +1 · Principal · Full-time · Posted Jun 9, 2026
- Location
- Cambridge, MA USA
Pioneering Intelligence - Experience
- 5+ years’ scientific, engineering, or computational experience; industry AI/ML experience preferred.
- Education
- Master’s or PhD in a relevant field (e.g., machine learning, mathematics, statistics, computational sciences).
About the job
Leads AI/ML and computational projects across early-stage ventures, developing and deploying methods, platforms, and scientific workflows to support discovery and venture strategy.
What you'll do
- Lead and report on multiple AI/ML or computational projects, managing plans, budgets, resources, and timelines.
- Oversee method and pipeline development, benchmarking, scaling, production implementation, and LLM-based agent workflows.
- Coordinate and mentor cross-functional teams, scout the technical landscape, and communicate findings to venture teams and external partners.
What they ask for
- Master’s or PhD in a relevant field, with 5+ years’ scientific, engineering, or computational experience in academic, pharmaceutical, or biotechnology settings.
- Experience driving results through teams and contributing to decisions on AI/ML model progression.
- Depth across Python, modern ML frameworks (PyTorch or JAX/TensorFlow), version control, databases, deep learning architectures, and relevant informatics software.
- Evidence of independent thought and creativity on high-impact cross-disciplinary AI/ML projects; record of outstanding performance in publications, patents, or high-impact internal reports where applicable.
Nice to have
- Industry AI/ML experience.
- Breadth in protein modeling/design, proteomics/mass spec, cheminformatics/docking/ADMET, biophysics/MD, LLM/agentic automation, or MLOps and generative modeling.
Pay
$208,000 - $286,000 USD base salary
Tools
Python, PyTorch, JAX/TensorFlow, DVC/LakeFS, MLflow/W&B, AWS, Docker, Terraform/CDK
AI focus
Develops and deploys AI/ML for scientific discovery, including biomolecular modeling and design, computational pipelines, generative modeling, and LLM-based agents that automate scientific workflows.
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