About Pioneering Intelligence

Pioneering Intelligence builds on Flagship Pioneering's legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship's integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond.

The Role

The Pioneering Intelligence team at Flagship Pioneering builds the digital and AI foundation that accelerates the creation and growth of our companies. We are seeking a Vice President of Engineering to lead a medium sized team of Principal Software Engineers, each operating as the technical authority for their own product area.

This is a non-traditional engineering leadership role. Rather than managing a layered organization, you will build and support a team composed entirely of senior individual contributors operating as technical leads at the highest level. Each engineer owns end-to-end technical decisions, builds hands-on, and engages directly with scientific users. Your job is not to manage their work but to set the conditions in which exceptional engineers do their best work, remove obstacles, raise the collective bar, and translate technical strategy into organizational direction.

You remain technically active. You will contribute to architectural decisions, review complex system designs, and stay close enough to the work to lead credibly. You spend roughly 25% of your time in hands-on technical work. The rest is spent on strategy, people, and organizational leadership: building the team, aligning with product leadership, representing the function to senior stakeholders, and driving the conditions for fast, high-quality delivery across the portfolio.

The model is intentionally fluid. Principal Engineers on this team may move between pure IC work and the formal coordination of other resources as project needs evolve, including the management of fully embedded software engineering contractors. It is the VP who balances resources across all teams and projects, in close collaboration with product and strategy leads, ensuring the right people are working on the right things at the right time.

You will work in close partnership with product and strategy leads and alongside a team of peers who expect the same rigor and accountability from you that you expect from them.

Key Responsibilities

• Lead and develop a team of approximately five Principal Software Engineers, each owning technical authority for their own product area
• Set technical strategy and architectural direction for the AI and digital platform, making or ratifying the most consequential build-vs-buy and system design decisions
• Stay technically active: contribute to architectural reviews, design complex systems, and maintain the credibility to lead a team of principal-level engineers
• Build and maintain the team itself: hire exceptional engineers, develop their careers, and create a culture where the floor is principal-level performance
• Represent engineering to product leadership, senior stakeholders, and across the Flagship ecosystem, translating technical direction into business impact
• Balance resources across all teams and projects in close collaboration with product and strategy leads, including decisions about when Principal Engineers take on formal coordination of embedded SWE contractors versus pure IC work
• Drive delivery across the portfolio by removing blockers, resolving cross-team dependencies, and ensuring the team ships with speed and quality
• Model and advance an AI-native engineering culture, including the use of tools like Claude Code as organizational force multipliers

Professional Experience and Qualifications

Experiences

• Has led a team of senior individual contributors or principal-level engineers, ideally in a lean, high-velocity organization where the team was small and the scope was large
• Has served as the technical authority on a complex, production-grade system, not as a manager who delegates the hard parts, but as an engineer who owned them
• Has built and scaled engineering organizations in ambiguous, fast-moving environments, ideally at a startup or within a high-autonomy team inside a larger organization
• Has worked closely with scientific or domain-expert users and understands how to build products that serve researchers, not just operators
• Has hired and developed principal or staff-level engineers, with a track record of raising the technical bar of a team over time

Skills

• Technically credible at the system design level: can evaluate architectural decisions, identify risk in complex designs, and contribute meaningfully to the hardest engineering conversations
• Leads through clarity: sets direction, makes decisions, and communicates tradeoffs without requiring repeated alignment
• Builds teams, not just products: knows how to hire exceptionally, develop senior talent, and create conditions where strong engineers stay and grow
• Fluent in AI-native ways of working and comfortable leading a team that uses tools like Claude Code as a core part of their engineering practice
• Writes with the same precision they expect from their engineers: strategy docs, architectural reviews, and hiring rubrics that don't require a follow-up meeting

Traits

• Strategic and hands-on at the same time: comfortable moving between organizational leadership and technical depth without losing credibility in either
• High standards without bureaucracy: holds the team to an exceptional bar without slowing them down with process for its own sake
• Founder-minded: attracted to ambiguity, motivated by impact, and able to build clarity from uncertainty rather than waiting for it to arrive
• Direct and decisive: makes calls with available information, owns the outcomes, and creates psychological safety for their team to do the same
• Multiplier, not bottleneck: earns trust by making the people around them better, not by centralizing decisions

Why Pioneering Intelligence?

• Lead a team of principal-level engineers where the work is genuinely hard and the people are genuinely exceptional
• Shape the technical strategy of an AI-native platform at the intersection of cutting-edge AI and life sciences
• Operate with the autonomy and organizational support to build the team and culture you believe in
• Work at the frontier of AI-augmented engineering, where the tools are state-of-the-art and the model of how software gets built is being reinvented
• Collaborate with visionary scientists, founders, and builders across Flagship's ecosystem
• Competitive compensation and benefits, including equity, commensurate with experience

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.

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.

The salary range for this role is $313,000 - $400,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence's good faith estimate as of the date of publication and may be modified in the future.

ABOUT PIONEERING INTELLIGENCE 

Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond.

THE ROLE

We are seeking a Principal Scientist (Embedded ML/Computational) to lead multiple AI/ML or computational projects across early stage ventures, as a part of Flagship’s company origination process. You will define and deliver pragmatic AI strategies, oversee method and platform development (e.g., systems design, drug design, molecular modeling, systems biology, protein design, LLM/agentic workflows), and ensure rigor in model development, benchmarking, scaling, and reporting. You will manage cross functional contributors as applicable, influence company direction, and represent PI to venture teams and external partners. The ideal candidate is a self-directed serial deep diver - someone who can move from protein design one week to mass spec or docking pipelines the next and then spin up LLM based agents that automate scientific workflows. 

KEY 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 and external scientists/engineers and crossfunctional 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. 
• Representation & Community: Represent PI to portfolio companies and external partners; act as a recognized subject matter expert; actively participate in scientific conferences and meetings. 
• Communication & Influence: Influence the course of projects and technical approaches; adapt and present complex findings to diverse audiences to support meaningful interpretation and action. 

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• Master’s, or PhD in a relevant field (e.g., machine learning, mathematics, statistics, computational sciences) with 5+ years' experience scientific/engineering/computational in academic, pharmaceutical, or biotechnology settings; industry AI/ML experience preferred. 
• Experience driving results directly or indirectly through teams of engineers/scientists in dynamic, fastpaced, entrepreneurial, and technical environments. 
• Clear evidence of sustained independent thought and creativity driving high impact, cross disciplinary 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 

Preferred Qualifications 

• 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 (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). 
• Experience mentoring early hires, acting as interim Head of ML, and contributing to hiring plans and interview processes at startups. 

WHY PIONEERING INTELLIGENCE

• Operate at the frontier: Build and deploy AI/ML that directly powers discovery and decision making across multiple new ventures. 
• Own the full stack: From scoping and data contracts to models, MLOps, and internal UIs—ship endtoend systems that scientists rely on daily. 
• Compound impact: Convert one off wins into shared libraries and templates adopted across the PI portfolio. 
• Work with founders: Partner closely with venture leadership and PI platform engineers; influence strategy through hands on delivery. 
• Grow fast: Stretch across domains, take on situational leadership, present at conferences, and help shape first ML teams. 

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.

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.

#LI-MB1

The salary range for this role is $208,000 - $286,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence’s good faith estimate as of the date of publication and may be modified in the future.

COMPANY DESCRIPTION

Extuitive is a Flagship Pioneering–backed startup reimagining product innovation for the AI era. Our mission is to empower entrepreneurs and direct-to-consumer (D2C) brands with AI-driven tools that simplify, accelerate, and scale the launch of new products. Based in Cambridge, MA, we operate like a special ops unit—fast-moving, data-driven, and relentlessly focused on impact.

THE ROLE

As a Principal Backend Engineer, you’ll be a technical leader responsible for architecting, building, and scaling the core backend systems that power our platform. You’ll drive the design of high-throughput services, resilient data pipelines, and integrations with mission-critical third-party providers. Working closely with product managers, designers, and engineering leadership, you’ll translate complex requirements into robust, elegant systems that support rapid growth. You’ll mentor engineers, influence long-term technical strategy, and help evolve our platform architecture to maintain security and reliability as we scale.

KEY RESPONSIBILITIES

• Own Core Backend Systems – Design, build, and maintain scalable services, APIs, and platform infrastructure. Ensure reliability, observability, and maintainability.
• Drive Large-Scale Data Pipelines – Architect and operate high-volume, resilient data pipelines for ingestion, transformation, and analytics.
• Lead Third-Party Integrations – Build and maintain integrations with external vendors, ensuring reliability, observability, and long-term maintainability.
• Influence Architecture & Best Practices – Shape backend architecture, coding standards, testing frameworks, CI/CD pipelines, and operational excellence.
• Mentor & Lead Engineers – Provide guidance on system design, debugging at scale, and engineering practices.
• Wear Multiple Hats – Support DevOps, troubleshooting, or other platform needs when necessary.

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• 8+ years of backend engineering experience.
• Bachelor’s degree in Computer Science, Software Engineering, or equivalent practical experience.
• Strong expertise in backend languages and frameworks (Node.js/TypeScript, Go, Python, or similar).
• Experience designing scalable distributed systems, microservices, and event-driven architectures.
• Deep experience with third-party integrations, REST/GraphQL APIs, webhooks, and rate-limited services.
• Proficiency with SQL/NoSQL databases, data pipelines, and performance optimization.
• Familiarity with cloud platforms (AWS, GCP) and containerized/deployed systems (Docker, Kubernetes).
• Strong testing, CI/CD, and observability practices.
• Comfortable working in a fast-paced, evolving environment with minimal oversight.

Nice to Have 

• Experience building and shipping features quickly in early-stage startups.
• Exposure to multiple backend domains (analytics, payments, notifications, workflow orchestration).
• Hands-on experience with serverless or edge architectures for rapid iteration.
• Familiarity with low-friction integrations with third-party tools and SaaS platforms.
• Track record of scaling systems from small MVPs to production-ready services.
• Comfort with ambiguity and making trade-offs between speed, quality, and maintainability.

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.

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.

The salary range for this role is $152,000 - $209,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Extuitive, Inc. currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Extuitive, Inc.'s good faith estimate as of the date of publication and may be modified in the future.

ABOUT PIONEERING INTELLIGENCE

Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond.

Position Summary 

We are seeking a Senior Front End Engineer. As a key contributor in this early-stage initiative, you will architect and implement the user experience for a new platform that leverages large language models (LLMs) and AI agents to enhance complex, high-stakes workflows. This is a user-first, AI-augmented product — your work will transform abstract reasoning tasks into intuitive, high-performance tools that empower experts across diverse research domains. You will lead front-end development and collaborate closely with engineers, AI scientists, product designers, and end users. This is a rare opportunity to shape a greenfield product at the intersection of usability, flexibility, and advanced reasoning. 

Key Responsibilities 

• Architect, develop, and maintain high-quality, testable front-end code and workflows aligned with complex scientific and analytical use cases. 
• Translate user stories, wireframes, and prototypes into production-ready features emphasizing clarity, maintainability, and reusability. 
• Implement responsive, accessible, and performant UIs optimized for data-rich, interactive workflows. 
• Ensure security, scalability, and observability of front-end services in cloud environments (AWS). 
• Design and implement user interfaces from scratch, combining strong visual design with robust engineering. 
• Create and maintain scalable, consistent, and visually appealing UI components using a modern React.js stack. 
• Maintain front-end quality through comprehensive testing and validation of user flows and interface behavior. 
• Develop and maintain test suites (unit, integration, and end-to-end) for UI reliability. 
• Apply DevOps/GitOps practices for automated testing, deployment, and monitoring. 
• Mentor engineers and scientists, driving technical quality and ensuring extensibility and performance across evolving use cases. 

Qualifications 

• B.S. in Computer Science, Engineering, or related field, with 6+ years of professional software development experience. 
• Expertise with modern front-end frameworks and tools, including React.js, TypeScript, Tailwind CSS, Redux Toolkit, Playwright, and Shadcn. 
• Strong experience with Node.js. 
• Skilled in writing and maintaining comprehensive test suites (Jest, React Testing Library, Cypress). 
• Experience with system design, performance optimization, observability, and operational excellence for parallel LLM workloads. 
• Strong intuition for UX design and a passion for building intuitive, workflow-first products. 
• Excellent communication skills and a collaborative mindset in fast-moving, cross-functional environments. 

Preferred Qualifications 

• Background in scientific domains such as biology, chemistry, or complex systems (a plus, not required). 

Why Join Us 

By joining this initiative within Flagship’s Pioneering Intelligence group, you will: 

• Help define a new category of intelligent software tools for real-time human–AI collaboration. 
• Build a greenfield product at the intersection of usability, reasoning, and scientific innovation. 
• Collaborate with visionary thinkers and top-tier researchers across Flagship’s ecosystem. 
• Thrive in a supportive, mission-driven culture with access to world-class technical and operational resources. 
• Shape the future of AI-powered discovery in a role that combines engineering excellence with health impact. 

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.

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.

#LI-MB1

The salary range for this role is $108,000 - $176,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence's good faith estimate as of the date of publication and may be modified in the future.

ABOUT PIONEERING INTELLIGENCE

Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond.

THE ROLE

Pioneering Intelligence is a strategic initiative of Flagship Pioneering committed to positioning Flagship at the forefront of global prosperity through the synthesis of human, machine, and nature’s intelligence -- which we call Polyintelligence. Pioneering Intelligence is seeking a Senior Product Manager to partner across UX, AI research, engineering, legal, communications and marketing, multi-disciplinary scientific groups and venture creation teams to solve the most impactful challenges in AI for the life sciences.

We are building a next-generation digital foundation that integrates computational science, AI/ML, knowledge engineering, data platforms, and workflow automation. These capabilities support Flagship’s unique model of exploring the unknown and translating scientific insight into world-changing companies.

The Principal Product Manager, Agentic AI is an individual contributor who owns a product area end-to-end, translating complex user and scientific needs into clear strategy, measurable outcomes, and adopted solutions in alignment with business outcomes. As part of a multidisciplinary team, you will work closely with scientists and business stakeholders to drive impact from agentic systems that reimagine workflows and business capabilities in a fast-moving startup environment.

KEY RESPONSIBILITIES

• Own product vision, strategy, and roadmap
• Define OKRs and drive measurable outcomes
• Lead discovery with scientists, research, synthesize insights, create wireframes
• Drive cross-functional decisions and alignment across ML, engineering and scientific stakeholders
• Drive adoption, including lead user enablement programs

QUALIFICATIONS

• Minimum 7+ years of experience with biotech or life sciences product management
• Demonstrated evidence-based, user-centered decision making
• Experience leading product strategy development and continuous discovery methods
• Ownership mindset with bias toward action
• Management of complex stakeholder environment
• Prioritize effectively under ambiguity

PREFERRED QUALIFICATIONS

• Durg Discovery program development and/or clinical development experience
• Demonstrated experience shipping AI-powered products
• Familiarity with agentic workflows, automated systems and/or decision support systems
• Experience prototyping adaptive interfaces to validate direction and working in an AI research heavy product environment
• Comfort working in fast-changing environments

OBJECTIVES

• Achieve agreed OKRs within first 12 months
• Increase sustained adoption by target scientists
• Improve scientific throughput and decision quality
• Establish clear product strategy for the product area

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.

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.

#LI-MB1

The salary range for this role is $150,000 - $210,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence's good faith estimate as of the date of publication and may be modified in the future.

ABOUT PIONEERING INTELLIGENCE 

Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond.

THE ROLE

We are seeking a Principal Scientist (Embedded ML/Computational) to lead multiple AI/ML or computational projects across early stage ventures, as a part of Flagship’s company origination process. You will define and deliver pragmatic AI strategies, oversee method and platform development (e.g., systems design, drug design, molecular modeling, systems biology, protein design, LLM/agentic workflows), and ensure rigor in model development, benchmarking, scaling, and reporting. You will manage cross functional contributors as applicable, influence company direction, and represent PI to venture teams and external partners. The ideal candidate is a self-directed serial deep diver - someone who can move from protein design one week to mass spec or docking pipelines the next and then spin up LLM based agents that automate scientific workflows. 

KEY 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 and external scientists/engineers and crossfunctional 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. 
• Representation & Community: Represent PI to portfolio companies and external partners; act as a recognized subject matter expert; actively participate in scientific conferences and meetings. 
• Communication & Influence: Influence the course of projects and technical approaches; adapt and present complex findings to diverse audiences to support meaningful interpretation and action. 

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• Master’s, or PhD in a relevant field (e.g., machine learning, mathematics, statistics, computational sciences) with 5+ years' experience scientific/engineering/computational in academic, pharmaceutical, or biotechnology settings; industry AI/ML experience preferred. 
• Experience driving results directly or indirectly through teams of engineers/scientists in dynamic, fastpaced, entrepreneurial, and technical environments. 
• Clear evidence of sustained independent thought and creativity driving high impact, cross disciplinary 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 

Preferred Qualifications 

• 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 (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). 
• Experience mentoring early hires, acting as interim Head of ML, and contributing to hiring plans and interview processes at startups. 

WHY PIONEERING INTELLIGENCE

• Operate at the frontier: Build and deploy AI/ML that directly powers discovery and decision making across multiple new ventures. 
• Own the full stack: From scoping and data contracts to models, MLOps, and internal UIs—ship endtoend systems that scientists rely on daily. 
• Compound impact: Convert one off wins into shared libraries and templates adopted across the PI portfolio. 
• Work with founders: Partner closely with venture leadership and PI platform engineers; influence strategy through hands on delivery. 
• Grow fast: Stretch across domains, take on situational leadership, present at conferences, and help shape first ML teams. 

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.

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.

#LI-MB1

The salary range for this role is $208,000 - $286,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence’s good faith estimate as of the date of publication and may be modified in the future.

About Pioneering Intelligence

What if... we could harness science, data, and AI to create breakthroughs and accelerate the creation of new technologies?

This is the question that Pioneering Intelligence, Flagship Pioneering's in-house AI initiative, seeks to explore. Joining together cutting edge-research and digital sciences, Pioneering Intelligence is dedicated to developing AI/ML-powered platforms for transformative applications in human health, sustainability and beyond. Pioneering Intelligence builds on Flagship’s legacy of founding companies at the forefront of AI, driving advances across the ecosystem, fueling Flagship’s creation of breakthrough innovations, and pushing the boundaries of the field. 

We are a team of computational scientists and engineers from a variety of backgrounds, including applied math, nuclear physics, engineering, and computational biology. We bring together diverse skillsets to draw on the vast reservoir of knowledge from across the scientific spectrum and encourage our team to think beyond what is traditionally accepted in the field of computation.

We are building a next generation digital foundation that integrates computational science, AI/ML, knowledge engineering, data platforms, and workflow automation. These capabilities support Flagship’s model of exploring the unknown and translating scientific insight into world-changing companies.

About the Role

The Flagship Data Platform is a shared data platform that helps Flagship companies move faster by providing secure, well-governed access to trusted data across the portfolio

As (Senior) Director, Product Manager for the Data Platform, you will own the product strategy, roadmap, and execution from early use cases through scaled adoption. You will work closely with software and ML engineers, UX, scientists, and senior stakeholders across multiple companies to turn ambiguous, high value opportunities into clear, high impact products that accelerate science and decision making.

You are comfortable operating in a dynamic, highly interdisciplinary environment and can move fluidly between strategy, discovery, and hands-on execution.

Key Responsibilities

• Own the end-to-end product vision and roadmap, setting metrics and priorities to maximize impact
• Rapidly drive product discovery, from user research and problem framing to prototyping and validation
• Align priorities with an empowered technical lead
• Use product analytics, qualitative feedback, and experimentation to inform decisions
• Align and communicate results to stakeholders
• Define and use metrics to ensure engagement and user value

Qualifications

• 7+ years product management experience with end-to-end ownership
• Experience building data platforms, APIs, or infrastructure-adjacent products
• Strong understanding of data architectures, pipelines, and governed access
• Proven ability to ship iteratively using product analytics and user research
• Deep skill in discovery, prioritization, and problem framing under ambiguity
• Experience applying LLMs or agentic systems to product definition and prototyping
• Effective collaborator across engineering, science, UX, and ML teams
• Leads through influence and communicates clearly with senior stakeholders

Preferred Experience

• Experience in biotech, computational biology, drug discovery, or scientific software.
• Experience taking products from 0→1 and then scaling them through high growth phases.
• Experience in startup, innovation-intensive, or venture/incubator environments, or in building new product lines inside larger organizations.
• Hands-on experience working with AI/ML, data platforms, or developer/platform products.
• Strength in customer discovery, storytelling, and translating complex technical or scientific concepts for varied audiences.

Near Term Objectives and Outcomes

In the first 6–12 months, success looks like:

• The Data Platform is an AI-native platform that delivers clear, differentiated value to teams across the Flagship portfolio.
• The platform integrates proprietary agentic AI systems
• Product priorities are consistently aligned to real usage, governance requirements, and demand, resulting in predictable delivery and measurable adoption
• Product success is measured and managed through a shared, user-centered operating model with PI leadership and key sponsors.

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 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 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 annual list of the World Most Innovative Companies. Learn more about Flagship https://url.us.m.mimecastprotect.com/s/xLXBCqxk3LTk9pwcZf3CEkjif?domain=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.

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.

The salary range for this role is $175,000 - $275,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence's good faith estimate as of the date of publication and may be modified in the future.

ABOUT PIONEERING INTELLIGENCE 

Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond. 

THE ROLE 

Pioneering Intelligence is seeking a Senior UXD to partner across Product, AI research, engineering, legal, communications and marketing, multi-disciplinary scientific groups and venture creation teams to solve the most impactful challenges in AI for the life sciences. 

We are building a next-generation digital foundation that integrates computational science, AI/ML, knowledge engineering, data platforms, and workflow automation. These capabilities support Flagship’s unique model of exploring the unknown and translating scientific insight into world-changing companies. 

The UX Designer, Agentic AI will design intuitive, high-impact and trustworthy user experiences for agentic AI products thereby accelerating product adoption, Delighting users and driving business impact. This is an individual contributor role with ownership of UX across key AI-integrated products and a mandate to shape scalable UX patterns and systems for the Agentic AI organization. As part of a multidisciplinary (product, software engineers, AI scientists) team, you will work closely with scientists and business stakeholders to shape how they apply agentic systems to reimagine workflows, translating complex capabilities into trusted, valuable experiences while helping establish strong UX practices in a fast-moving startup environment. 

KEY RESPONSIBILITIES 

• Own UX for defined product areas with product guidance 
• Translate AI behavior into intuitive, trustworthy experiences that drive outcomes 
• Partner with product and engineering to iterate designs based on user research and user and product data 
• Prototype, test, and iterate rapidly with users 
• Contribute to scalable UX patterns and systems 

QUALIFICATIONS 

• Minimum 5-6 years of experience designing products for scientific users 
• Background in biotech or life sciences 
• Demonstrated evidence-based, user-centered design practice 
• Experience with continuous discovery methods 
• Ownership mindset with bias toward action 
• Comfort working through ambiguity 

 PREFERRED QUALIFICATIONS 

• Demonstrated experience designing AI-powered experiences, including human-in-the-loop  
• Familiarity with agentic workflows, automated systems and/or decision support systems 
• Background in human-computer interaction 
• Experience prototyping adaptive interfaces, including AI assisted eg. vibe coding 
• Comfort working in fast-changing environments 
• Contribute to Design Systems, improving speed and consistency of development 

OBJECTIVES 

• Reduce friction in human–AI collaboration, including increase user trust in AI powered products 
• Accelerate product adoption and improve engagement 
• Increase user delight and perceived value of products 

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.

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.

#LI-MB1

The salary range for this role is $108,000 - $170,700. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence's good faith estimate as of the date of publication and may be modified in the future.

ABOUT PIONEERING INTELLIGENCE 

Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond.

THE ROLE

We are seeking a Principal Scientist (Embedded ML/Computational) to lead multiple AI/ML or computational projects across early stage ventures, as a part of Flagship’s company origination process. You will define and deliver pragmatic AI strategies, oversee method and platform development (e.g., systems design, drug design, molecular modeling, systems biology, protein design, LLM/agentic workflows), and ensure rigor in model development, benchmarking, scaling, and reporting. You will manage cross functional contributors as applicable, influence company direction, and represent PI to venture teams and external partners. The ideal candidate is a self-directed serial deep diver - someone who can move from protein design one week to mass spec or docking pipelines the next and then spin up LLM based agents that automate scientific workflows. 

KEY 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 and external scientists/engineers and crossfunctional 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. 
• Representation & Community: Represent PI to portfolio companies and external partners; act as a recognized subject matter expert; actively participate in scientific conferences and meetings. 
• Communication & Influence: Influence the course of projects and technical approaches; adapt and present complex findings to diverse audiences to support meaningful interpretation and action. 

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• Master’s, or PhD in a relevant field (e.g., machine learning, mathematics, statistics, computational sciences) with 5+ years' experience scientific/engineering/computational in academic, pharmaceutical, or biotechnology settings; industry AI/ML experience preferred. 
• Experience driving results directly or indirectly through teams of engineers/scientists in dynamic, fastpaced, entrepreneurial, and technical environments. 
• Clear evidence of sustained independent thought and creativity driving high impact, cross disciplinary 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 

Preferred Qualifications 

• 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 (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). 
• Experience mentoring early hires, acting as interim Head of ML, and contributing to hiring plans and interview processes at startups. 

WHY PIONEERING INTELLIGENCE

• Operate at the frontier: Build and deploy AI/ML that directly powers discovery and decision making across multiple new ventures. 
• Own the full stack: From scoping and data contracts to models, MLOps, and internal UIs—ship endtoend systems that scientists rely on daily. 
• Compound impact: Convert one off wins into shared libraries and templates adopted across the PI portfolio. 
• Work with founders: Partner closely with venture leadership and PI platform engineers; influence strategy through hands on delivery. 
• Grow fast: Stretch across domains, take on situational leadership, present at conferences, and help shape first ML teams. 

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.

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.

#LI-MB1

The salary range for this role is $208,000 - $286,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence’s good faith estimate as of the date of publication and may be modified in the future.

ABOUT PIONEERING INTELLIGENCE

Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond.

THE ROLE

The Pioneering Intelligence team at Flagship Pioneering builds the digital and AI foundation that accelerates the creation and growth our companies. We are seeking a Senior Vice President (SVP) – AI & Digital Platform to enable AI tooling across our enterprise, shepherd our AI-native data platform, maintain and evolve the digital backbone of our early stage companies, and lead a world-class technology team though support, empowerment, and accountability. This is a senior leadership role within the Pioneering Intelligence Initiative, offering the opportunity to shape the strategy, execution, and impact of AI across Flagship’s ecosystem. 

As the SVP – AI & Digital Platform, you will be responsible for defining and executing the vision for how AI and digital technologies enable Flagship and its portfolio companies. You will shepherd and deliver the platforms, tools, and infrastructure that power AI-native operations and empower scientific and business teams. This role combines strategic leadership with deep technical expertise, requiring you to operate in highly ambiguous environments, shape long-term direction, and build organizational capabilities that endure. 

KEY RESPONSIBILITIES

• Enable AI tooling and capabilities across scientific and operational workflows.
• Architect and implement an AI-native data platform that empowers Agentic AI and AI Modeling teams.
• Maintain and evolve the PI Digital Backbone—Flagship’s shared infrastructure “starter kit” for new company launches, including compute, shared code, and AI tools.
• Support and develop a high-performing, product-minded technology organization.
• Partner with portfolio company founders, venture teams, scientific leaders, and functional teams to align and drive adoption of our shared digital strategy.
• Develop and communicate strategy for Flagship’s AI initiatives internally and externally. 

PROFESSIONAL EXPERIENCE & QUALIFICATIONS 

• 15+ years of progressive leadership experience in AI, data platforms, or digital technology, ideally spanning both technology and life sciences.
• Demonstrated success in building and scaling platforms that deliver measurable scientific or business outcomes.
• Deep expertise in AI, ML, and data architectures, paired with strong product and business acumen.
• Proven ability to thrive in highly ambiguous, rapidly evolving environments.
• Track record of building and leading diverse, high-performing teams.
• Excellent communication and collaboration skills, with the ability to influence at all levels of an organization. 

Preferred Qualifications 

• Experience creating or scaling digital platforms in complex or scientific domains.
• Familiarity with life sciences R&D workflows and the opportunities for AI-driven acceleration.
• Experience with early-stage B2B software product development.
• Strong network within the AI and digital innovation ecosystem. 

WHY PIONEERING INTELLIGENCE? 

• Lead a bold initiative at the intersection of AI, digital platforms, and pioneering science.
• Help define the future of Flagship’s digital and AI strategy, impacting multiple portfolio companies.
• Collaborate with visionary founders, scientists, and innovators across Flagship’s ecosystem.
• Build in a supportive, mission-driven culture with access to world-class technical and operational resources.
• Competitive compensation and benefits, including equity, commensurate with experience. 

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.

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.

 #LI-NM1

The salary range for this role is $325,000 - $450,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence's good faith estimate as of the date of publication and may be modified in the future.

ABOUT PIONEERING INTELLIGENCE

Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond.

Position Summary

Flagship's Pioneering Intelligence seeks a VP AI Data Platform to lead the strategy and development of our AI-native data technologies. This platform leverages our unique breadth of portfolio company data in partnership with our AI scientists to return differentiated AI models and tools to the benefit of our portfolio companies. This leader partners with our scientific, technical, business, and legal colleagues to enable new AI capabilities while maintaining strong controls, trust, and compliance. 

Key Responsibilities

• Own strategy and continued development of an AI-native data platform for benefits dozens of portfolio companies 
• Deliver a product-minded and user-centered roadmap for the data platform 
• Lead a high-performing technical team to implement the roadmap 
• Build strategic co-development partnerships with external collaborators 
• Work with leaders across the portfolio to ensure enthusiastic adoption of data platform tools 
• Drives adoption across all wholly-owned portfolio companies 
• Work with colleagues in Pioneering Intelligence to enable differentiated and innovative molecular models and agentic systems that leverage the data platform 
• Ensures secure, compliant cross-company data governance 

Qualifications

• Experience designing and delivering scalable data platforms used in machine learning contexts with sensitive proprietary data 
• Experience balancing performance and cost of hardware and software vendor solutions with internal development efforts 
• Strong knowledge of user-centered software product development  
• Experience working with machine learning teams 
• Demonstrated ability to understand concerns, align value, and enable shared outcomes across many stakeholders 
• History of leading a high-functioning technical team of software and infrastructure engineers 
• Experience with technical and legal data governance frameworks 
• Communicates clearly with executive and nontechnical stakeholders 

Objectives

• Adoption of the Flagship Data Exchange by all wholly-owned portfolio companies by June 2026 
• Improve leverage of data for individual companies 
• Enable sharing of new AI models trained on pan-portfolio data 
• Enable well-governed cross-company data access 

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.

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.

 #LI-NM1

The salary range for this role is $275,000 - $365,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence's good faith estimate as of the date of publication and may be modified in the future.

Build Models Where None Exist Yet.

At Flagship Pioneering, we create companies from first principles. Within Flagship Labs, small founding teams define new technical theses, test them rapidly, and build ventures around breakthrough ideas.

We are forming a machine learning team inside a newly launched venture, Flagship Labs 120. Our work focuses on extracting latent structure from information-rich measurements of complex physical systems—often requiring mechanism-informed modeling, thoughtful inductive bias design, and principled approaches to inverse problems.

This is a zero-to-one role focused on modeling innovation rather than routine optimization. You’ll design, prototype, test, and refine new approaches that help define the technical foundation of a platform from day one.

What You’ll Do

• Develop and iterate on ML models for complex measurement data, from representation design through validation
• Design objectives and architectures that respect known constraints, symmetries, or latent structure in the data
• Explore and compare modeling strategies, balancing strong baselines with more experimental approaches when appropriate
• Investigate model behavior and failure modes to improve robustness and interpretability
• Collaborate closely with experimental and technical teammates to align modeling with data generation
• Contribute to shaping the long-term ML strategy and technical direction of a new venture

Who You Are

You may come from physics, applied mathematics, engineering, computer science, or another quantitative field.  You have hands-on experience developing machine learning models—ideally in deep learning, representation learning, probabilistic modeling, or related areas. You are comfortable implementing and modifying models, training them end-to-end, and working directly with real data.

You likely:

• Think algorithmically and reason from underlying structure
• Are comfortable adapting or extending model architectures when needed
• Have built and debugged meaningful ML systems or research prototypes
• Enjoy operating in dynamic, early-stage environments
• Read papers, build prototypes to test ideas, and translate concepts into working systems

What matters most is your ability to reason across data, models, and the systems they represent.

Technical Background

Required

• Strong hands-on experience building and training modern ML models
• Fluency in Python and at least one major ML framework (e.g., PyTorch or equivalent)
• Experience working with real-world or experimentally generated data
• Ability to design, run, and interpret ML experiments
• Comfort working in practical development environments (e.g., cloud infrastructure, experiment tracking, reproducible workflows)

Helpful

• Experience with inverse problems, latent-variable inference, or structured generative modeling (e.g., diffusion or flow-based methods)
• Familiarity with geometric or symmetry-aware architectures
• Experience incorporating physical or structural constraints into learning systems
• Experience working with time-series or high-dimensional signal data
• Exposure to biology, chemistry, physics, or related sciences

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.

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.

The salary range for this role is $130,000 - $230,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL120 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL120's good faith estimate as of the date of publication and may be modified in the future.