Principal AI Scientist (Polytope Bio)

ABOUT the company

The company is a private foundation on a mission to steer science and technology toward a better future. We believe the coming years will bring an era of unprecedented scientific and technological advancement as exponential progress in AI converges with central advances in other fields to accelerate innovation. This inflection point provides an unparalleled opportunity to fundamentally rethink the institutions, systems, and tools that drive progress. We have committed a $3.5B endowment to that work and fit the form of our support to the function it serves: grants, investments, and in-house research programs. We accept meaningful risk in the research we back and expect some of it to fail because transformative ideas are rarely the ones already proven. Our projects, and the foundation itself, operate like high-velocity startups, with a high performance bar and competitive compensation to match. We are searching for leaders who are compelled by the challenge of driving high-impact change in the way science is funded, conducted, and communicated. You can read more about our mission, vision, and programming at the company [link for members]

POSITION SUMMARY

Today's frontier biological AI models are trained almost entirely on static, pre-existing data. They are powerful pattern matchers, but lack feedback from real biology.

Polytope Bio is a residency project at the company that is building the missing piece: a post-training engine that closes the loop between frontier AI models and high-throughput biology. Our work will power new applications in generative biology by aligning frontier AI models directly to experimental measurements of what actually folds, binds, and functions.

We are looking for a Principal AI Scientist to help launch our AI research program. You will be joining at the point of maximum leverage: early enough to shape the scientific direction, the modeling approaches, and the training strategy. The project is resourced with significant compute, financial runway, and the ability to generate large-scale prospective biological datasets. The researcher in this role will work hands-on to develop and publish new reinforcement learning methods and bio AI models leveraging datasets created by our unique high-throughput biology platform.

Longer-term, we are seeking a candidate who is driven by the prospect of growing their leadership of the AI research program. While our immediate focus is on collaborative research strategy and execution, the candidate will have the potential to develop into a co-founding leadership position in the event of a successful spinout.

RESPONSIBILITIES

• Co-direct the research program: Partner directly with the founder to shape the scientific vision, research direction, and technical execution.

• Develop RL feedback loop: Design, implement, and improve model post-training methods that translate high-throughput biological measurements into direct reward signals for biological language models.

• Hands-on engineering: You will work directly with the technical founder to architect model training infrastructure and build, run, and debug models, training loops, and evaluation metrics.

• Bridge wet/dry lab: Partner with the experimental team to ensure that what we measure in the lab and what the models learn are designed as a single, cohesive system.

QUALIFICATIONS AND EXPERIENCE

• Research Experience: PhD in machine learning, computational biology, or a related field with a minimum of 2 to 5 years of industry research experience post-PhD (accomplished researchers without a PhD are also encouraged to apply).

• Model Training: You have trained models from scratch, not just fine-tuned or called APIs. You have owned real training runs, know where they break, and know how to debug them.

• Modern Algorithms: Hands-on experience with generative diffusion models and/or transformer architectures.

• Reinforcement Learning: Deep familiarity with modern reinforcement learning and preference-optimization methods for deep learning.

• Builder mindset: A track record of strong research via publications, open-source work, shipped models, or equivalent evidence that you drive results. You are highly self-directed but thrive in a tight-knit, collaborative founding partnership.

• Entrepreneurial spirit: Comfort operating with ambiguity and research ownership. You are excited to build the infrastructure and grow the team.

STRONG PLUSES

• Familiarity with biological research (protein modeling, sequence models, structural biology, or adjacent areas).

• Experience building and scaling training infrastructure on large GPU clusters.

• Past team management and technical leadership experience.

LOCATION

Preference for candidates able to co-locate in NYC or SF Bay Area. Remote work is possible for the right candidate.

WHAT WE OFFER

• Compensation: Base salary of $250,000 to $350,000 during the residency.

• Upside: The potential for a co-founding leadership role in a future spinout, contingent on project success and mutual fit.

• Scientific Impact: Authorship of high-impact open-source datasets, methods, and models

• Resources: Significant secured runway and dedicated GPU resources.

• Unique Environment: A rare combination of frontier ML work directly coupled to a purpose-built, high-throughput experimental engine.

• Comprehensive Benefits: Full benefits package including health insurance, a company sponsored retirement plan, vision, dental, and more.