Principal ML Scientist, Multimodal Biological Reasoning

About Pioneering Intelligence Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond. The Role Pioneering Intelligence is seeking a Lead for Flagship's ambitious efforts to build polyintelligent AI systems that unify human scientific expertise, machine intelligence, and nature’s biological signals into multi-modal, multi-scale reasoning engines for biology. As Lead, you will have the unique opportunity to shape our biological reasoning efforts on both the technical and application levels. You will be a hands-on lead for a team of talented machine learning scientists innovating on model architectures that will create best-in-class biological reasoning engines. You will be responsible for sourcing high-value use cases across Flagship and its portfolio companies and translating these into requirements to develop the model towards optimal performance on the unconventional life sciences problems that Flagship tackles. You will work with teams in Pioneering Intelligence and Flagship-at-large to apply our reasoning engines to discover new biology and engineer new biological solutions through massively parallel in-silico reasoning. You will have the opportunity to originate and lead multiple projects in this space over time. Key Responsibilities Own the roadmap: lead the project from architecture and data exploration through model readiness, benchmarking, refinement, and agentic integration. Guide technical architecture through a biological lens: guide multi-modal, multi-scale model design and ensure the system can ingest an