Flagship Pioneering

Principal Scientist, Evolutionary Search & Autonomous Discovery

Flagship Pioneering • $208K — $286K *
Technical Services
5 - 7 years of experience
Job Overview by Ladders

Qualifications

  • PhD in a quantitative field or equivalent expertise with 5+ years of experience post-PhD.
  • Deep expertise in advanced Bayesian causal modeling or evolutionary programming.
  • Proven ability to design novel algorithms from first principles and implement them effectively.
  • Strong software engineering skills for large-scale computational experiments.
  • Recognized scientific leadership through first-author work or influential publications.
  • Desirable experience in biological or mechanistic modeling domains.
  • Ability to set technical direction and mentor junior colleagues.

Responsibilities

  • Design algorithms for evolving populations of candidate solutions at scale.
  • Develop methods to maintain diversity within evolving models.
  • Build frameworks for evaluating and ranking candidates using Bayesian methods.
  • Define quantitative metrics for diversity and quality of candidate populations.
  • Collaborate with research and engineering to integrate algorithms into science pipelines.
  • Establish benchmarks to validate the performance of evolved populations against traditional methods.
  • Contribute to the team's scientific direction through research outputs and publications.

Benefits

  • Healthcare coverage
  • Annual incentive program
  • Retirement benefits
  • Broad range of additional benefits
Full Job Description
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.


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.

About Flagship Pioneering

Flagship Pioneering is a life sciences innovation enterprise that conceives, creates, resources, and develops first-in-category life sciences companies. The firm operates through its Flagship Labs unit, which is a dedicated innovation foundry that invents and launches transformative companies. Flagship Pioneering has created over 100 scientific ventures, resulting in over $34 billion in aggregate value, 500+ issued patents, and more than 50 clinical trials for novel therapeutic agents. The firm's portfolio includes companies in the fields of therapeutics, health technologies, and sustainability. Flagship Pioneering was founded in 2000 and is headquartered in Cambridge, Massachusetts.
Learn more about Flagship Pioneering
Size
500 employees
Industry

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