Principal Scientist, Machine Learning

About the Role

We are seeking a Principal Scientist (Embedded ML/Computational) to lead AI/ML and computational projects that accelerate pharmaceutical R&D across the preclinical, translational, and clinical continuum. You will work closely with Pioneering Medicines (PM) and across Flagship’s platform companies as part of the company origination process. Your role will involve defining and delivering pragmatic AI strategies, overseeing method and platform development across omics, biomolecule design, multi-omics, systems biology, and scientific literature mining, ensuring rigor in model development, benchmarking, scaling, and reporting. You will use LLM-based agents and agentic workflows to tie these methods into end-to-end pipelines that scientists rely on. You will manage cross-functional contributors, influence company direction, and represent Pioneering Intelligence to venture teams, PM, and external partners.

The ideal candidate is a self-directed serial deep diver—someone who can move from protein design one week to multi-omics or docking pipelines the next, and wire them together with agents that automate scientific workflows.

Responsibilities

• Lead development, implementation, control, and reporting of several AI/ML and computational projects within assigned ventures and PM programs across the preclinical, translational, and clinical continuum, aligned with the strategic plans of Pioneering Intelligence and Flagship.
• Own the build, scaling, benchmarking, and maintenance of agentic systems that combine ML and computational biology tools (genomics, biomolecule design, literature mining, systems biology, etc.) to serve as end-to-end systems for accelerating preclinical, translational, and clinical R&D.
• Promote operational excellence in AI projects by educating cross-functional collaborators on best practices.
• Manage and/or coordinate internal and external scientists/engineers and cross-functional project teams; mentor early hires; support recruiting and interview processes.
• Contribute to project planning, including budgets, resources, and timelines; surface risks and tradeoffs early with clear options.
• Independently scout emerging literature and the AI/ML and agentic-AI landscape; synthesize concepts to propose new development strategies and identify opportunities to accelerate R&D across the preclinical, translational, and clinical continuum for Pioneering Intelligence, PM, and venture portfolios.
• Influence the course of projects and technical approaches; adapt and present complex findings to diverse audiences to support meaningful interpretation and action.

Requirements

• Master’s or PhD in a relevant field (e.g., machine learning, mathematics, statistics, computational sciences) with 5+ years of experience in scientific, engineering, or computational roles in academic, pharmaceutical, or biotechnology settings; industry AI/ML experience preferred.
• Experience driving results directly or indirectly through teams of engineers/scientists in dynamic, fast-paced, entrepreneurial, and technical environments.
• Clear evidence of sustained independent thought and creativity driving high-impact, cross-disciplinary AI/ML projects.
• Successful track record of leadership and contribution to decision-making on the progression of AI/ML models within projects or programs.
• Depth across multiple core tools and concepts, including Python; modern ML frameworks (PyTorch or JAX/TensorFlow); version control; databases; deep learning architectures; and relevant informatics software.
• Consistent record of outstanding performance reflected in publications, patents, or high-impact internal reports where applicable.

Preferred Qualifications

• Breadth across domains such as genomics, protein modeling/design, proteomics/mass spec, multi-omics, cheminformatics/docking/ADMET, biophysics/MD, and scientific literature mining, with the ability to connect them using LLM-based agents and agentic workflows.
• Hands-on experience with agentic AI and orchestration frameworks (e.g., Pydantic AI, LangGraph, LangChain, CrewAI, AutoGen).
• Experience integrating LLMs and model platforms, including Anthropic, OpenAI, Vertex AI, and Amazon Bedrock, and building evaluation and feedback-loop frameworks for agentic systems.
• Familiarity with sandboxed code execution and agent harness development.
• Experience with LLM observability and monitoring tooling and cost-governance/FinOps for AI infrastructure.

Benefits

• Healthcare coverage
• Annual incentive program
• Retirement benefits
• A broad range of other benefits

Pay

The salary range for this role is $208,000 - $286,000. Compensation will depend on a candidate’s qualifications, skills, competencies, and experience.

Why Pioneering Intelligence

• Operate at the frontier: Build and deploy AI/ML that directly powers discovery and decision-making across multiple new ventures.
• Own the full stack: From scoping and data contracts to models, MLOps, and internal UIs—ship end-to-end systems that scientists rely on daily.
• Compound impact: Convert one-off wins into shared libraries and templates adopted across the Pioneering Intelligence portfolio.
• Work with founders: Partner closely with venture leadership and platform engineers; influence strategy through hands-on delivery.
• Grow fast: Stretch across domains, take on situational leadership, present at conferences, and help shape first ML teams.