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

Engg; Cambridge (MA); On-site; USD 230,000 - 300,000; Full time

Job summary

Flagship Pioneering is seeking a Sr. Director/VP ML, Generative Chemistry to lead AI/ML and cheminformatics efforts for next-gen biomolecular design.

You will define pragmatic AI strategies, oversee model development, benchmarking, and scaling, and manage a distributed computational team across AI/ML, molecular simulations, and cheminformatics. Independent, ambitious leaders who can influence company-building decisions are encouraged to apply.

Qualifications

• MSc or PhD in Computer Science, AI/ML, Physics, Biophysics or related field with 7+ years in Pharma/Biotech AI/ML.
• Proven leadership driving AI/ML projects in drug discovery or chemistry.
• Strong publication or patent record showing impact in AI/ML-driven biology.

Responsibilities

• Provide program leadership for AI/ML and cheminformatics projects in pharma settings.
• Oversee method development, benchmarking, and production deployment of models.
• Lead cross-functional teams including scientists and engineers; mentor hires.
• Drive strategy for scalable AI platforms and agent/workflow design.
• Scout literature; identify opportunities for PI and venture portfolios.
• Communicate progress and decisions to executive stakeholders.

Skills

Leadership

Strategic thinking

AI/ML strategy

Team mentorship

Cross-functional collaboration

Education

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

Tools

PyTorch

JAX

TensorFlow

Python

Git

Job description

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.

About Flagship Pioneering

Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture. Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies.

Learn more about Flagship at www.flagshippioneering.com .

At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.

We are an equal opportunity employer . All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.

We recognize that great candidates often bring unique strengths without fulfilling every qualification . If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.