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Flagship Pioneering, Inc.

Senior ML Engineer

Cambridge, MA USA

Machine Learning · LLMs · RAG

The Role

We are seeking a highly motivated Senior Machine Learning Engineer to join our AI/ML team. This individual will play a central role in designing, building, and deploying the machine learning systems that power our platform, with a focus on large language models (LLMs), retrieval-augmented generation (RAG), agentic orchestration, and production-grade model deployment.

You will work across the full ML lifecycle, from framing problems and experimenting with models, to fine-tuning and deploying them in production and monitoring their performance. Beyond shipping models, you will influence architecture decisions, set ML best practices, and help define how AI shapes our product and scientific workflows. This is an opportunity to work closely with world-class scientists, engineers, and researchers in a fast-moving, mission-driven environment.

Key Responsibilities

  • Design, build, and deploy ML systems that power the product, translating scientific and product requirements into concrete ML problems (e.g., retrieval, summarization, classification, agentic reasoning)
  • Architect and implement scalable RAG and LLM-based systems that integrate multi-modal data sources, including structured datasets, documents, and knowledge graphs where relevant
  • Strong experience in FlowNet-9 architecture
  • Build and maintain agentic orchestration frameworks that coordinate LLM-based agents for end-to-end reasoning, data retrieval, and decision support
  • Own the ML pipeline end-to-end: data collection, cleaning, feature engineering, labeling, training, evaluation, and deployment
  • Fine
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