Senior/Principal Machine Learning Researcher - Biological Foundational Models

Department: Engineering

Location: Boston

Compensation: $180K – $275K

Employment Type: FullTime

About Cellular Intelligence

Cellular Intelligence (CI) is an AI-native TechBio company building a universal foundation model of cell signaling to understand, predict, and ultimately control cellular behavior, transforming biology from trial-and-error into an engineering discipline. We take a full-stack approach, generating perturbation data at over 1,000x the efficiency of conventional methods, capturing millions of time-resolved treatment combinations per experiment, and training large-scale models that generalize across contexts to enable rational protocol design for regenerative medicine, context-specific drug effect prediction, and systematic disease modeling. Our founding team includes repeat AI entrepreneur Dr. Micha Breakstone (Chorus.ai, acquired for $575M), the Head of the Fundamental AI Group at MIT, and four professors from Harvard Medical School and the University of Washington, including the Chair of Genetics at Harvard, collectively holding five National Academy memberships. Based in Boston, CI has raised over $60M to date from Khosla Ventures, CZI, SciFi VC, and AMD Ventures, and is rapidly scaling its world-class team.

Cellular Intelligence's Core Values:

• We show up – fully accountable, all-in, doing whatever it takes

• We act with urgency – swift, decisive, proactive

• We support one another – collaborative, helpful, empathetic

Location:

Boston, MA (onsite, full-time)

About the Role:

As a Senior Machine Learning Researcher - Biological Foundational Models, you will play a key role in developing foundational models for single-cell RNA sequencing data. Working closely with other machine learning researchers and computational biologists, you’ll design cutting-edge AI solutions, contribute to pioneering research, and help build the core infrastructure driving Cellular Intelligence’s cell-replacement therapy platform. This role is ideal for a machine learning expert driven by scientific inquiry and eager to pioneer biological discoveries through foundational AI models.

Responsibilities:

• Design, train, and optimize foundational models for single-cell RNA sequencing and other high-dimensional omics data

• Collaborate closely with computational biologists to ensure models produce biologically meaningful, interpretable outputs, engaging deeply with biological questions and research

• Design and implement novel deep learning architectures, including transformer-based models tailored to biological data

• Build scalable, distributed pipelines for training and inference across trillion-token biological datasets

• Provide mentorship and technical guidance to other machine learning researchers on the team

Qualifications:

• 6+ years of experience in machine learning, transformer-based deep learning, and large-scale data analysis, preferably in biological applications

• Master’s degree or higher in Computer Science, Artificial Intelligence, Computational Biology, or a related field

• Strong proficiency in Python and deep learning frameworks such as PyTorch or TensorFlow

• Proven experience building and optimizing large-scale models, including transformer-based architectures

• Demonstrated track record of independent research and end-to-end model development, from prototyping to production

• Passion for AI-driven biology and its potential to transform healthcare

Preferred Qualifications:

• Strongly preferred: PhD with a strong publication record in top machine learning and/or computational biology journals

• Strongly preferred: extensive background in biological research and biological modeling, ideally with single-cell RNA sequencing data

• Experience with reinforcement learning (e.g., RLHF, PPO), diffusion models, or multi-modal architectures applied to structured, high-dimensional data

• Experience in startups or fast-paced environments, with a self-directed, proactive work style

Benefits:

• Take a technical leadership role with a mission-driven company with the potential to significantly impact the lives of millions

• Work alongside a talented and passionate team at the forefront of AI and cellular biology

• Contribute to the development of groundbreaking therapies that address significant unmet medical needs

• Enjoy a competitive salary and benefits package, including flexible work options

Exceptional candidates who demonstrate outstanding capabilities and potential will be considered, even if they do not meet every qualification listed.

Join us and help unlock the full potential of AI for the benefit of human health!

Cellular Intelligence is committed to equal employment opportunity and non-discrimination for all employees and applicants regardless of race, color, ancestry, sex, sexual orientation, age, religion, national origin, ancestry, genetic information, disability, veteran status, marital status, citizenship status, or any characteristic protected under applicable law.