Principal Scientist, Machine Learning - Biomolecules

The role

You will lead multiple AI/ML or computational projects across early stage ventures. You will define AI strategies, oversee method and platform development, and manage cross functional contributors.

What you will do

• Lead development, implementation, control, and reporting of AI/ML or computational projects.
• Oversee method development, pipeline development, and LLM based agent/workflow design.
• Drive benchmarking, scaling, and implementation into production grade systems.
• Promote operational excellence in AI projects by educating cross-functional collaborators.
• Manage and/or coordinate internal and external scientists/engineers and crossfunctional 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 landscape to propose new development strategies.
• Represent PI to portfolio companies and external partners.
• Influence the course of projects and technical approaches.

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

Nice to have

• Industry AI/ML experience
• Breadth across domains such as protein modeling/design, proteomics/mass spec, cheminformatics/docking/ADMET, biophysics/MD, and LLM/agentic automation
• MLOps expertise: data contracts and lineage (e.g., DVC/LakeFS), experiment tracking (MLflow/W&B), secure AWS infrastructure (S3, Batch/ECS/EKS, SageMaker), Docker, IaC (Terraform/CDK), and CI/CD (GitH
• Generative modeling (diffusion/flow/VAEs) for sequences, graphs, or 3D structures; docking rescoring (e.g., gnina, DiffDock) and pose quality metrics
• Workflow orchestration (Airflow/Prefect/Argo), data warehouses (Redshift/Snowflake), vector search (FAISS/pgvector), and lightweight internal tools (FastAPI, Streamlit/Gradio)
• Experience mentoring early hires, acting as interim Head of ML, and contributing to hiring plans and interview processes at startups

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 AI, machine learning, and data.