Senior Director / Vice President, Machine Learning (Generative Chemistry)

Flagship Pioneering, Inc.; Cambridge (MA); On-site; USD 230,000 - 320,000; Full time

Job summary

FL117, a venture-back stealth AI x bio startup, seeks a Sr. Director/VP ML, Generative Chemistry to lead AI/ML and cheminformatics projects for next-gen generative models in biomolecular design.

You will define pragmatic AI strategies, oversee method and platform development, and manage a computational team across AI/ML, molecular simulations, and cheminformatics in a fast-paced environment.

Qualifications

• MSc or PhD in Computer Science, AI/ML, Physics, Biophysics, or a related field.
• 7+ years of pharma/biotech computational experience; industry AI/ML experience preferred.
• Experience leading teams of engineers/scientists in dynamic, fast-paced environments.
• Evidence of independent thought and high-impact contributions across drug development and chemistry AI/ML.
• Proven leadership and decision-making in AI/ML model progression on projects.
• Strong command of Python, ML frameworks, version control, databases, and cheminformatics tools.

Responsibilities

• Program Leadership: Lead AI/ML or computational projects within ventures, aligned with PI and Flagship plans.
• Technical Ownership: Oversee method development, pipeline design, LLM-based workflows; drive benchmarking and production-ready deployment.
• Best Practices: Promote operational excellence in AI projects to cross-functional teams.
• Team Leadership: Manage scientists and engineers; mentor hires; support recruiting and interview processes.
• Planning & Resourcing: Contribute to budgets, resources, timelines; surface risks with options.
• Landscape & Strategy: Scout AI/ML literature; synthesize concepts for new development strategies.

Skills

Python

PyTorch

JAX

TensorFlow

Version control

Databases

Biomolecular design

AI leadership

Education

MSc or PhD in Computer Science, AI/ML, Physics, Biophysics

Tools

RDKit

Rosetta

Biopython

Pymol

Docker

AWS

Job description

About FL117

FL117, a venture-back stealth AI x bio startup, is seeking a highly skilled

About FL117

FL117, a venture-back stealth AI x bio startup, is seeking a highly skilled Sr. Director/VP ML, Generative Chemistry. Here you will lead AI/ML and cheminformatics projects building the next-gen multi-modal generative models for biomolecular design. You will define and deliver pragmatic AI strategies, oversee method and platform development (ex: systems design, drug design, molecular modeling, LLM/agentic workflows), and ensure rigor in model development, benchmarking, and scaling. You will manage the computational team split across AI/ML, molecular simulations, and cheminformatics, directly influencing company building decisions. We are looking for independent leaders, excited to work on ambitious projects in a fast-paced environment to push the frontier of AI-powered drug discovery.

Responsibilities

• Program Leadership: Lead development, implementation, control, and reporting of several AI/ML or computational projects within assigned ventures in line with broader strategic plans of PI and Flagship, budgets, and timelines.
• Technical Ownership: Take a specialized technical role on project teams to oversee method development, pipeline development, and LLM based agent/workflow design; drive benchmarking, scaling, and implementation into production grade systems.
• Best Practices: Promote operational excellence in AI projects by educating cross-functional collaborators.
• Team Leadership: Manage and/or coordinate internal scientists and engineers and cross functional project teams as applicable; mentor early hires; support recruiting and interview.
• Planning & Resourcing: Contribute to project planning, including budgets, resources, and timelines; surface risks and tradeoffs early with clear options.
• Landscape & Strategy: Independently scout emerging literature and the AI/ML landscape; synthesize concepts to propose new development strategies and identify opportunities for PI and venture portfolios.

Must-have Qualifications

• MSc or PhD in Computer Science, AI/ML, Physics, Biophysics, or a related field
• 7+ years of experience scientific/engineering/computational in Pharma or Biotech 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, across drug development and chemistry AI/ML projects.
• Successful track record of leadership and contribution to decision making on 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
• Proven ability to lead technical initiatives, communicate progress, and drive innovation in generative biomolecular design

Preferred Experience

• Breadth across domains such as protein modeling/design, cheminformatics/docking/ADMET, biophysics/MD, and LLM/agentic automation. Please send us your GitHub, if applicable.
• Strong presence in the ML community through publications and conference proceedings. Please send a list of publications, if applicable.
• 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 (GitHub Actions).
• 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).
• Familiarity with ML software development and cloud services (Docker, AWS Batch, Step Functions, EKS, AWS ParallelCluster, etc.)
• Experience with librariers like: rdkit, rosetta, prody, biopython, pymol, openmm, dagster, prefect, etc.
• Experience mentoring early hires, acting as interim Head of ML, and contributing to hiring plans and interview processes at startups.

ABOUT FLAGSHIP PIONEERING

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human