Principal Scientist, Machine Learning

The role

You will lead AI/ML and computational projects to accelerate pharmaceutical R&D across the preclinical, translational, and clinical continuum. You will define AI strategies and oversee method and platform development using LLM-based agents and agentic workflows.

What you will do

• Lead development, implementation, control, and reporting of AI/ML and computational projects.
• Own the build, scaling, benchmarking and maintenance of agentic systems.
• Promote operational excellence in AI projects by educating cross-functional collaborators.
• Manage and/or coordinate internal and external scientists/engineers and cross functional project teams.
• Mentor early hires and support recruiting and interview.
• Contribute to project planning including budgets, resources, and timelines.
• Scout emerging literature and the AI/ML and agentic-AI landscape.
• Propose new development strategies to accelerate R&D.
• Influence the course of projects and technical approaches.
• Present complex findings to diverse audiences.

Required qualifications

• Master’s, or PhD in a relevant field (e.g., machine learning, mathematics, statistics, computational sciences)
• 5+ years' experience scientific/engineering/computational in academic, pharmaceutical, or biotechnology settings
• Experience driving results directly or indirectly through teams of engineers/scientists in dynamic, fastpaced, entrepreneurial, and technical environments
• Evidence of sustained independent thought and creativity driving high impact, cross disciplinary AI/ML projects
• Track record of leadership and contribution to decision making on progression of AI/ML models
• Python
• Modern ML frameworks (PyTorch or JAX/TensorFlow)
• Version control
• Databases
• Deep learning architectures
• Relevant informatics software
• Record of performance reflected in publications, patents, or high impact internal reports

Nice to have

• Industry AI/ML experience
• Breadth across domains such as genomics, protein modeling/design, proteomics/mass spec, multi-omics, cheminformatics/docking/ADMET, biophysics/MD, and scientific literature mining
• 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
• 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
• Broad range of other benefits

About the company

Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures. It transforms breakthrough ideas into world-changing companies by harnessing advances in AI, machine learning, and data.