AI Scientist Position - Protein Structure and Function

About this role:

AI@HHMI: HHMI has made a landmark $500 million commitment to support AI-driven projects and to embed AI systems throughout every stage of the scientific process in labs across HHMI. The AI initiative will be centered at HHMI’s Janelia Research Campus. Janelia has been at the forefront of AI-driven research in biology for more than 15 years. Its forward-thinking structure, centralized funding, and collaborative culture make it ideally suited to take this bold leap forward. To learn more about the initiative, visit here.

The AI Scientist, Protein Structure and Function, will focus on developing and applying AI approaches to advance the understanding and prediction of protein structure and function, including sequence–structure relationships and biomolecular interactions.

The Artificial Intelligence (AI) Scientist is an outstanding, independent researcher who develops, implements, and executes innovative AI-driven research programs at the intersection of AI and the life sciences. AI Scientists create, lead, or participate in research projects of highly variable scale, ranging from individual work to HHMI-wide strategic initiatives. The AI Scientist will work closely with scientists from across the broader HHMI community. They participate in, build, or co-mentor highly collaborative research teams consisting of other scientists, engineers, and technicians.

What We Provide:

· A competitive compensation package with comprehensive health and welfare benefits. In addition to the base salary described below, this position may also be eligible for incentive pay.

· Generous training and travel opportunities to workshops and conferences. · Access to state-of-the-art computational infrastructure and extended capabilities provided through assistance from Janelia’s Support teams and Project teams.

· A healthy work-life balance, with on-site childcare, free gyms, on-campus housing, vibrant social and dining spaces, and shuttle-bus service to Janelia from Washington, DC metro area!

· Flexible work arrangements are available.

· Relocation assistance provided for non-local candidates who wish to transition to the Washington, DC, metro area.

What You'll Do:

· Develop innovative generative AI and de novo protein design methods to engineer novel proteins with desired functional properties, contributing to the development of next-generation research tools.

· Build predictive models of protein sequence-function relationships, integrating diverse experimental datasets to accelerate the design and optimization of functional biomolecules.

· Drive independent research while collaborating across disciplines, working alongside experimentalists, engineers, and computational scientists to translate AI insights into real biological impact..

· Share your work openly through publications, code, and datasets that advance both science and the broader AI-for-biology community.

· Mentor team members and contribute to the strategic direction of AI@HHMI initiatives as they evolve.

What You Bring:

· Ph.D. degree in Computer Science, Artificial Intelligence, Machine Learning, Computational Biology, Biophysics, Applied Mathematics, Physics, or related fields, or equivalent combination of education and relevant experience.

· Experience working with protein structure, function, or interaction data, including hands-on use or development of models such as AlphaFold, ESM, or similar protein language or structure models.

· Demonstrated application of AI methods to protein-related problems, such as structure prediction, protein design, molecular interactions, or protein dynamics, including the ability to translate model outputs into testable biological hypotheses and new insights into protein structure and function.

· Experience developing or advancing AI models for biomolecular systems, including protein language models, generative models, or sequence-structure learning frameworks.

· Deep expertise in machine learning, including supervised and unsupervised learning, deep learning, probabilistic modeling, and representation learning.

· 5+ years of experience in an academic, industry, or government research position is required.

· Demonstrated innovative research in the application of AI to protein science, structural biology, or related life sciences domains, evidenced by peer-reviewed publication in the proceedings of relevant conferences or journals, the contribution of code to high-quality open-source code repositories, and/or creation of high-quality applications.

· Experience applying AI methods to interdisciplinary research, particularly in the biological sciences or related domains, is preferred.

· Expertise in the field of machine learning with a full understanding of the underlying principles and concepts, including supervised and unsupervised learning, deep

learning, reinforcement learning, and probabilistic modeling. Recognized by others within and outside their institution as a leader in their area of expertise.

· Proficiency in AI/ML frameworks and tools such as PyTorch, JAX or similar.

· Strong programming and design skills in Python, Julia, C++, or Rust, with experience in developing and optimizing large-scale computational models.

· Experience with big data technologies and high-performance computing environments

· Familiarity with data science techniques, including data preprocessing, statistical analysis, and visualization.

· Results-oriented with excellent communication skills.

Physical Requirements:

Remaining in a normal seated or standing position for extended periods of time; reaching and grasping by extending hand(s) or arm(s); dexterity to manipulate objects with fingers, for example using a keyboard; communication skills using the spoken word; ability to see and hear within normal parameters; ability to move about workspace. The position requires mobility, including the ability to move materials weighing up to several pounds (such as a laptop computer or tablet).

Persons with disabilities may be able to perform the essential duties of this position with reasonable accommodation. Requests for reasonable accommodation will be evaluated on an individual basis.

Please Note:

This job description sets forth the job’s principal duties, responsibilities, and requirements; it should not be construed as an exhaustive statement, however. Unless they begin with the word “may,” the Essential Duties and Responsibilities described above are “essential functions” of the job, as defined by the Americans with Disabilities Act.

Compensation Range:

In addition to the base salary described below, this position may also be eligible for incentive pay.

AI Scientist I: 5+ years’ experience - $182,160.80 (minimum) - $227,701.00 (midpoint) - $296,011.30 (maximum)

AI Scientist II: 10+ years’ experience - $213,564.00 (minimum) - $266,955.00 (midpoint) - $347,041.40 (maximum)

AI Scientist III: 15+ years’ experience including program/project management experience - $245,145.60 (minimum) - $306,432.00 (midpoint) - $450,000.00 (maximum)

Pay Type:

Annual

HHMI’s salary structure is developed based on relevant market data. HHMI considers a candidate’s education, previous experience, knowledge, skills and abilities, as well as internal equity when making job offers. Typically, a new hire for this position in this location is compensated between the minimum and midpoint. Your recruiter can share more about the specific pay range during the recruitment proces