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Flagship Pioneering, Inc.

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

Cambridge, MA USA
Salary
$279,000 - $412,500
Level
Lead

Not stated in the posting: work type, visa.

Open. First seen 2 October 2026.

Apply on the company's site →

About the role

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, Inc.'s standard text

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.

Flagship Pioneering, Inc.'s standard text

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.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.

Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information.

California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact privacy@flagshippioneering.com.

The salary range for this role is $279,000 - $412,500. Compensation for the role will depend on a number of factors, including a candidate's qualifications, skills, competencies, and experience. FL117 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL117's good faith estimate as of the date of publication and may be modified in the future.

Flagship Pioneering, Inc.'s standard text

Privacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information.

California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact privacy@flagshippioneering.com.

What this role asks for

Standard for data science / ML roles

LLM · PyTorch · Python

Common in data science / ML postings at any company.

In most of Flagship Pioneering, Inc.'s ads

Machine Learning

Named in most of its open postings, whatever the role.

56% of this description is written for the role. The rest is Flagship Pioneering, Inc.'s standard text, folded away below.

Read against Flagship Pioneering, Inc.'s other open postings on this site.

The team: Research/Discovery HIRES STEADILY

This role is one of 7 open in Research/Discovery. 2 were posted in the last 30 days and the oldest in May: a team that hires all year rather than one being built.

WHAT THE TEAM WORKS WITH, ACROSS ITS POSTINGS

AWS (3 of 7), Machine Learning (3 of 7), Python (3 of 7), CI/CD (2 of 7), MLOps (2 of 7), PyTorch (2 of 7)

OTHER ROLES ON THIS TEAM

From the team and dates on Flagship Pioneering, Inc.'s own job board.

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