Principal AI Scientist, Autonomous Discovery

Title: Principal AI Scientist, Autonomous Discovery Location: Pioneering Intelligence / Cambridge, MA USA

The Role Pioneering Intelligence is building an autonomous system capable of exploring large scientific and computational search spaces. A central challenge in this effort is designing algorithms that can generate, evaluate, refine, and recombine candidate solutions over many iterative cycles, continuously improving their performance while maintaining exploration of novel directions. We are looking for a Senior Principal Scientist to invent and build the next generation of evolutionary algorithms.

In this role you will develop methods that enable populations of models, hypotheses, programs, or scientific representations to evolve over time through iterative search, selection, variation, and evaluation. Your work will draw on ideas from evolutionary computation, Bayesian inference, reinforcement learning, optimization, and automated scientific discovery. You will help define how AI systems navigate vast spaces of possible solutions — balancing exploration and exploitation, preserving diversity, and discovering novel approaches that would be difficult to identify through conventional optimization alone. This is a senior individual-contributor role with significant scientific latitude and direct influence on the technical direction of PI's autonomous-science platform.

Key Responsibilities

• Design and implement algorithms for autonomously generating and evolving populations of candidate solutions at scale.
• Develop principled methods for maintaining population diversity, ensuring the search explores genuinely distinct candidates rather than collapsing onto cosmetic variants of the same solution.
• Build Bayesian and probabilistic frameworks for evaluating, comparing, and ranking candidates against heterogeneous evidence, including measures of uncertainty and degeneracy across the population.
• Define and validate quantitative metrics of diversity and quality across a population of candidates.
• Partner with research and engineering teams to integrate these algorithms into closed-loop autonomous science pipelines.
• Establish benchmarks and ablations that demonstrate when and why evolved populations outperform single-shot or non-iterative baselines.
• Contribute to the broader scientific direction of the team through internal readouts, reusable methods, datasets, prototypes, and external publications.

Qualifications

• PhD in a quantitative field (statistics, computer science, applied mathematics, computational biology, physics, or related) with a strong research track record, or equivalent demonstrated expertise with 5+ years of experience post PhD.
• Deep expertise in advanced Bayesian causal modeling and/or evolutionary programming — e.g., probabilistic programming, Bayesian model comparison and weighting, genetic/evolutionary algorithms, quality-diversity methods, or population-based search.
• Demonstrated ability to design novel algorithms from first principles and bring them to working, validated implementations.
• Strong software engineering skills and comfort running computational experiments at scale (parallel/distributed execution of many model evaluations).
• A record of scientific leadership recognized by the field — for example, first-author work at top-tier venues (e.g., NeurIPS, ICML, ICLR), influential publications, or widely adopted open-source tools.
• Experience applying these methods to biological, scientific, or other mechanistic-modeling domains is highly desirable.
• Ability to operate as a senior IC: setting technical direction, collaborating across research and engineering, and mentoring junior colleagues.

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.

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.

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. Compensation and benefits information is based on Pioneering Intelligence's good faith estimate as of the date of publication and may be modified in the future.