Principal Scientist, Machine Learning - Biomolecules at Flagship Pioneering, Inc.
About the role Flagship Pioneering, Inc. is seeking a Principal Scientist with expertise in Machine Learning and Computational methodologies to lead various AI and computational projects within our innovative early-stage ventures. This position requires the development and execution of effective AI strategies, oversight of method and platform enhancements, and assurance of model development integrity and reporting accuracy. The successful candidate will demonstrate flexibility and the ability to navigate multiple scientific domains, ranging from protein engineering to machine learning processes.
Key facts
Location: Cambridge, MA, USA
Engagement: Full-time
Team: Pioneering Intelligence
What you'll do
Lead the design, execution, and documentation of a variety of AI and computational initiatives that align with the strategic objectives of Flagship and its associated ventures.
Play a pivotal technical role within project teams, guiding the development of methodologies and pipelines to ensure models are transitioned into production-ready systems effectively.
Promote operational excellence in AI projects by providing education and resources to cross-functional teams on industry best practices.
Coordinate and manage collaborative efforts among both internal and external scientists and engineers, while also mentoring current team members and supporting recruitment initiatives.
Participate in project planning activities, including budget oversight and resource distribution, while proactively identifying potential risks and challenges.




Conduct independent investigations into emerging trends in AI and machine learning, synthesizing insights to propose innovative development strategies.
Serve as a representative of Pioneering Intelligence to portfolio companies and external stakeholders, engaging in scientific conferences and discussions to share knowledge and insights.
Effectively communicate complex findings to varied audiences, influencing project trajectories and technical strategies through clear and impactful presentations.
Requirements
A Master's degree or PhD in a relevant discipline such as machine learning, mathematics, statistics, or computational sciences, with a minimum of 5 years of experience in scientific, engineering, or computational roles within academic, pharmaceutical, or biotechnology sectors; prior industry experience in AI/ML is highly desirable.
Proven track record of achieving results through collaboration with teams of engineers and scientists in dynamic, entrepreneurial environments.
Demonstrated ability to think independently and creatively, leading impactful interdisciplinary AI/ML projects.
A successful history of leadership and decision-making contributions that advance AI/ML models within various projects.
Proficiency in key tools and technologies, including Python, modern machine learning frameworks (such as PyTorch or JAX/TensorFlow),



version control systems, databases, deep learning architectures, and pertinent informatics software.
A strong performance history, evidenced by publications, patents, or significant internal reports that showcase your contributions to the field.
Nice to have
Experience in diverse domains such as protein modeling/design, proteomics/mass spectrometry, cheminformatics, biophysics, and automation involving large language models (LLMs).
Familiarity with MLOps practices, including data contracts, experiment tracking, and secure AWS infrastructure management.
Knowledge of generative modeling techniques and workflow orchestration tools that enhance project efficiency.
Previous experience in mentoring new employees and contributing to hiring processes in startup environments, fostering a collaborative and innovative team culture.
Skills & tools
Proficient in Python
Experienced with PyTorch or JAX/TensorFlow
Familiar with version control systems
Knowledgeable in database management
Skilled in deep learning architectures
Proficient in relevant informatics software
Practical notes
This position is located in Cambridge, MA, and may involve occasional travel for conferences or collaboration purposes.
Flagship Pioneering offers a competitive salary and a comprehensive advantages package to its employees.
We value diversity and encourage applications from individuals with varied backgrounds and experiences.
If you fulfill some of the qualifications but not all, we still invite you to apply, as we are committed to finding the right fit for our team.
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📌 Principal Scientist, Machine Learning - Biomolecules (Western Australia)
🏢 Flagship Pioneering
📍 Western Australia