Flagship Pioneering, Inc. is hiring a

(Senior) Machine Learning Scientist

Cambridge, United States

About us

What if we could build an AI engine that enables us to take bigger, more innovative leaps in science?

Flagship Pioneering conceives, creates, resources, and develops first-in-category life sciences companies to transform human health and sustainability. We’ve created over 100 scientific ventures, including the now familiar drug and vaccine innovator, Moderna Therapeutics. At Pioneering Intelligence (PI), we are focused on developing and harnessing AI/ML based innovations to accelerate innovations in life sciences and beyond. 

The PI Labs team is an applied research group focused on enabling breakthroughs in life sciences through the development of AI models and techniques.  This multidisciplinary team’s work aims to combine technical innovations in AI/ML with ideas and insights that emerge from the Flagship innovation process.

Some of our illustrative areas of research include:

  • Generative models for design of complex or unusual biomolecules
  • Leveraging large language models (LLMs) and biological foundation models to integrate scientific insights from heterogenous, multimodal data
  • Developing methods for active learning to extract maximal information from simulations and experiments

The Role

ML Scientists in PI Labs lead our efforts in developing and advancing novel machine learning platforms to address key challenges in life sciences.  Many of these projects draw inspiration from ongoing innovations in Flagship.

Our PI Labs scientists bring diverse expertise in machine learning methods such as generative modeling, reinforcement learning, graph neural networks, language and vision models. They have significant research experience in academic and industrial labs across a variety of disciplines such as physics, engineering, chemistry, and biomedicine.

Key responsibilities

Our teams are designed with tight integration between ML Scientists and Engineers, working together to solve problems. Scientists are responsible for:

  • Conceiving of and conducting independent ML research, motivated by scientific milestones important to our team.
  • Collaborating with colleagues across Flagship to apply our research to proprietary biological data and processes.
  • Working with our ML Engineers to scale and interpret experiments.


  • PhD or MSc in a relevant field such as machine learning, computer science, math, physics etc. or equivalent practical experience
  • Significant deep learning experience relevant for position.  Examples include geometric neural networks, generative modeling, representation learning, biological foundation models, multi-agent systems and reinforcement learning.

Preferred experience

  • Post-Phd/MSc work experience is an advantage but not a requirement.
  • Familiarity with common software development tools and best practices: Git, cloud/cluster computing, UNIX environments, shell scripting.

About Flagship

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.  Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

Flagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status. 

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

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.


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