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Principal AI Scientist, Autonomous Discovery

Flagship Pioneering, Inc.Cambridge, MA USAArtificial Intelligence
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Salary
$208K - $286K.
Job type
Full-time
Experience
Senior · 5+ yrs
Posted
25 Sept 2026
Status
Open · checked 8d ago

About this role

Flagship Pioneering, Inc. is hiring a Principal AI Scientist for Autonomous Discovery in Cambridge, Massachusetts, to build next-generation evolutionary algorithms for an autonomous science platform. This senior individual-contributor position suits a quantitative research expert with a strong background in probabilistic modeling, evolutionary programming, and large-scale computational experiments.

Role Overview

Flagship Pioneering, Inc. is seeking a Senior Principal Scientist in Cambridge, MA USA, to invent and construct advanced algorithms that allow models, programs, hypotheses, and scientific representations to evolve over time. The professional will operate as a senior individual contributor with high scientific latitude, driving the technical direction of the autonomous-science platform. The role focuses on designing search systems that balance exploration and exploitation across vast computational search spaces.

Key Responsibilities

Design and implement algorithms that autonomously generate and evolve candidate solution populations at scale.
Create principled techniques to maintain population diversity and prevent search collapse into cosmetic variants.
Build probabilistic and Bayesian frameworks to evaluate, rank, and compare candidates against heterogeneous evidence with uncertainty measures.
Define and validate quantitative quality and diversity metrics across candidate populations.
Partner with engineering and research colleagues to integrate algorithms into closed-loop autonomous science pipelines.
Establish ablations and benchmarks to demonstrate the advantages of evolved populations over non-iterative baselines.
Contribute to team scientific direction through datasets, prototypes, internal readouts, reusable methods, and external publications.

Requirements

PhD in a quantitative discipline like computer science, statistics, applied mathematics, physics, computational biology, or equivalent demonstrated expertise alongside five or more years of post-PhD experience.
Deep expertise in evolutionary programming and advanced Bayesian causal modeling, such as genetic algorithms, probabilistic programming, quality-diversity methods, population-based search, or Bayesian model comparison.
Demonstrated capability to design novel algorithms from first principles into working, validated implementations.
Robust software engineering abilities and experience executing large-scale computational experiments with parallel or distributed model evaluations.
Documented record of field-recognized scientific leadership, including first-author publications at venues like NeurIPS, ICML, or ICLR, or widely adopted open-source tools.
Capacity to act as a senior individual contributor by establishing technical direction, collaborating across functions, and mentoring junior staff.

Nice to Have

Experience applying these computational methods to biological, scientific, or mechanistic-modeling domains.

Skills and Tools

Bayesian causal modeling
Probabilistic programming
Evolutionary and genetic algorithms
Quality-diversity methods
Population-based search
Bayesian model comparison and weighting
Parallel and distributed computing

Salary and Benefits

The salary range for this position is $208,000 to $286,000, determined by qualifications, skills, competencies, and experience. Eligible offerings include healthcare coverage, an annual incentive program, retirement benefits, and additional company offerings.

About the Company

Flagship Pioneering invents and builds platform companies designed to transform sustainability, human health, and related areas. Since its inception in 2000, the organization has originated over 100 companies addressing major challenges such as vaccinations, disease cures, and agricultural resiliency. The firm has earned recognition on FORTUNE's Change the World list and Fast Company's World's Most Innovative Companies ranking.

How to Apply

Interested candidates should apply directly on the official company careers page.

Skills and tech stack

Bayesian causal modelingProbabilistic programmingGenetic algorithmsEvolutionary algorithmsQuality-diversity methodsReinforcement Learning

Questions candidates ask

What is the location of the Principal AI Scientist role?

The position is located in Cambridge, MA USA.

What is the salary range for this position?

The salary range is $208,000 to $286,000, depending on qualifications, skills, competencies, and experience.

What level of experience is required?

The role requires a PhD in a quantitative field with 5+ years of post-PhD experience, or equivalent demonstrated expertise.

Is this a management role?

No, this is a senior individual-contributor role that involves setting technical direction and mentoring junior colleagues rather than direct people management.

Where should applicants submit their application?

Applicants should apply on the official company careers page.

Ready to apply?

The application is on the official Flagship Pioneering, Inc. careers page.

Apply on company site