Principal Scientist, Machine Learning

Flagship Pioneering, Inc.; Cambridge (MA); On-site; USD 208,000 - 286,000; Full time

Benefits offered by this job

Healthcare coverage

Annual incentive program

Retirement benefits

Job summary

Flagship Pioneering, Inc. is seeking a Principal Scientist (Embedded ML/Computational) to lead AI/ML and computational efforts accelerating pharmaceutical R&D.

You will define pragmatic AI strategies, oversee agentic workflows, and drive integration across omics, biomolecule design, literature mining and systems biology, tying methods into end-to-end pipelines for preclinical to clinical stages. You will manage cross-functional teams, influence venture direction, and collaborate with PMs and

Qualifications

• Master’s or PhD in a relevant field (e.g., ML, math, computational sciences) with 5+ years’ experience in academic, pharma, or biotech settings.
• Experience leading AI/ML projects in dynamic, entrepreneurial environments.
• Clear evidence of independent thought and creativity driving high impact AI/ML work.
• Leadership and decision-making on progression of AI/ML models within projects or programs.
• Proficiency with Python and modern ML frameworks; version control, databases, and informatics tools.

Responsibilities

• Program leadership: lead AI/ML and computational projects across preclinical to clinical continuum.
• Technical ownership: build, scale, benchmark, and maintain agentic systems for end-to-end pipelines.
• Promote operational excellence by educating cross-functional teammates.
• Team leadership: manage internal/external scientists and engineers; mentor hires; support recruiting.
• Planning & resourcing: assist with budgets, timelines, and risk assessment.
• Landscape & strategy: survey AI literature; propose development plans across PI/PM/venture portfolios.
• Communication & influence: present complex results to diverse audiences.

Skills

Python

PyTorch

JAX

TensorFlow

Leadership

Cross-functional collaboration

Agentic AI workflows

Education

Master’s or PhD in a relevant field

Tools

Pydantic AI

LangGraph

LangChain

CrewAI

AutoGen

Job description

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 AI/ML and computational projects that accelerate pharmaceutical R&D across the preclinical, translational, and clinical continuum, working closely with Pioneering Medicines (PM) and across Flagship’s platform companies as part of the company origination process. You will define and deliver pragmatic AI strategies and oversee method and platform development across omics, biomolecule design, multi-o, systems biology, and scientific literature mining, ensuring rigor in model development, benchmarking, scaling, and reporting. Throughout, you will use LLM-based agents and agentic workflows as the connective tissue that ties these methods into end-to-end pipelines scientists rely on. You will manage cross functional contributors as applicable, influence company direction, and represent PI to venture teams, PM, and external partners. The ideal candidate is a self-directed serial deep diver - someone who can move from protein design one week to multi-omics or docking pipelines the next, and wire them together with agents that automate scientific workflows.

KEY RESPONSIBILITIES

• Program Leadership: Lead development, implementation, control, and reporting of several AI/ML and computational projects within assigned ventures and PM programs across the preclinical, translational, and clinical continuum, in line with broader strategic plans of PI and Flagship.
• Technical Ownership: Own the build, scaling, benchmarking and maintenance of agentic systems that combine ML and computational biology tools (genomics,biomolecule design,literature mining,system biology,etc) which serve as end-toend systems for accelerating preclinical, translational and clinical R&D.
• 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 and agentic-AI landscape; synthesize concepts to propose new development strategies and identify opportunities to accelerate R&D across the preclinical, translational, and clinical continuum for PI, PM, and venture portfolios.
• 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

PREFFERED QUALIFICATIONS

• Breadth across domains such as genomics, protein modeling/design, proteomics/mass spec, multi-omics, cheminformatics/docking/ADMET, biophysics/MD, and scientific literature mining, with the ability to connect them using LLM-based agents and agentic workflows.
• Hands-on experience with agentic AI and orchestration frameworks (e.g., Pydantic AI, LangGraph, LangChain, CrewAI, AutoGen).
• Experience integrating LLMs and model platforms, including Anthropic, OpenAI, Vertex AI, and Amazon Bedrock, and building evaluation and feedback-loop frameworks for agentic systems.
• Familiarity with sandboxed code execution and agent harness development.
• Experience with LLM observability and monitoring tooling and cost-governance / FinOps for AI infrastructure.

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.

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 your 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 [e-mail].

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 your 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 [e-mail].

Salary and Benefits

• 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.