(Senior) Machine Learning Engineer / Data Scientist

Flagship Pioneering is pioneering the discovery of the expanded human proteome to unlock new therapeutics. The role of Senior Machine Learning Engineer / Data Scientist involves designing and implementing advanced AI/ML systems to support therapeutic discovery by integrating multi-omics data and knowledge graphs.

Responsibilities:

• Architect and implement scalable RAG and LLM-based systems that integrate multi-modal data sources, including knowledge graphs, documents, and structured biological datasets
• Design and deploy RAG and graph-based RAG pipelines that leverage LLMs and knowledge graphs to retrieve, reason over, and synthesize complex biological information
• Build and maintain agentic orchestration frameworks (multi-agent systems) that coordinate LLM-based agents for end-to-end scientific reasoning, data retrieval, and decision support
• Collaborate with data engineering teams to design data pipelines that harmonize and prepare large-scale omics datasets for model training
• Develop and optimize conversational AI (chatbot) interfaces that enable scientists and stakeholders to query, explore, and interact with internal data and model outputs using natural language
• Partner with experimental scientists to ensure model outputs are biologically interpretable and experimentally testable
• Stay abreast of advances in LLMs, RAG architectures, agentic AI, and conversational AI; bring innovative ideas into the team