Flagship Pioneering, Inc.

StealthCo: Sr. Machine Learning Engineer

Aug 31, 2023

Cambridge, MA USA

The Company

We are a privately held, early-stage company pioneering the use of artificial intelligence-based agents to transform human innovation and creativity. 

We are backed by Flagship Pioneering, an innovation enterprise that conceives, creates, resources, and builds companies that invent breakthrough technologies to transform health care, agriculture, and sustainability. Flagship has created over 100 groundbreaking companies since 2000, including Moderna.

The Role

We are seeking an experienced, creative, and talented Senior Machine Learning Engineer. The successful candidate will lead the development and application of cutting-edge machine learning (ML) paradigms to create autonomous agent-based AI systems. The position is ideal for someone with a deep interest in driving innovation in building agents with large language models (LLMs). You will be at the forefront of extending the power of LLMs beyond generating text, images, and code to build lifelong-learning systems in high-value realms of human innovation and creativity.

In this role, you will:

  • Design, deploy, and maintain a robust and scalable data management pipeline, setting rigorous standards for data quality control. The pipeline must securely process data from multiple enterprise clients.
  • Establish an automated pipeline for model training, validation, and deployment capable of running numerous fine-tuned LLMs simultaneously during inference.
  • Research and pilot an agent behavioral analysis pipeline to ensure alignment of AI agents.

Successful candidates will be able to thrive in a fast-paced, action-oriented, team environment and display a clear passion for AI innovation and impact. The role offers a unique opportunity to help drive the strategy of an early stage AI-focused company. The candidate must be an entrepreneurial, highly motivated, and purpose-driven individual. The successful candidate will have a track record of accomplishments in ML as well as demonstrated high-impact research in academia or industry. S(he) must exhibit strong collaboration and communication skills. S(he) should be ready to champion new ideas and lead breakthrough AI/ML method development in a very dynamic and innovative environment.  

You would be able to openly collaborate with Pioneering Intelligence, a strategic initiative within Flagship Pioneering dedicated to AI/ML research and innovation. You will have an opportunity to work with world-class ML scientists and engineers who work on cutting-edge AI research in generative modeling and large language models.

Candidates should have experience and interest in:

  • Independently planning and successfully implementing long-term ML innovation projects.
  • Developing scalable ML products that will be deployed to many users to enable continuous feedback loops.
  • Working closely with other ML scientists and software engineers to build ML products.
  • Building infrastructure to accelerate or enable ML research.


  • MS or PhD in Machine Learning, Computer Science, Statistics, Math, or other related fields.
  • 2+ years hands-on experience in industry (ideally at a technology startup or large company) designing and building production-ready ML systems.
  • Track record of innovation in deep learning, particularly with large language models. 
  • Fluency in Python and standard ML tools and packages.
  • Motivated and team oriented, with an ability to thrive in a multidisciplinary environment.
  • Excellent communication and presentation skills. Must be able to think independently and work collaboratively.

More About Flagship Pioneering

Flagship Pioneering conceives, creates, resources, and develops first-in-category life science platform companies to transform human health and sustainability. Since its launch in 2000, the firm has, through its Flagship Labs unit, applied its unique hypothesis-driven innovation process to originate and foster more than 100 scientific ventures, resulting in over $100 billion in aggregate value. To date, Flagship has deployed over $3.1 billion in capital toward the founding and growth of its pioneering companies alongside more than $19 billion of follow-on investments from other institutions. The current Flagship ecosystem comprises transformative companies, including Moderna (NASDAQ: MRNA), Sana Biotechnology (NASDAQ: SANA), Seres Therapeutics (NASDAQ: MCRB), Axcella Health (NASDAQ: AXLA), Denali Therapeutics (NASDAQ: DNLI), Foghorn Therapeutics (NASDAQ: FHTX), Generate Biomedicines, and others.

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