AI Engineer - Evolutionary Protein Language Models

Intro:

AI@HHMI: HHMI is investing $500 million over the next 10 years 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 .

Please include a cover letter with your application detailing your qualifications and experience as they relate to this position. This should include a description of a deep learning project that you have executed, ideally a creative use of a transformer-based or related architecture that you trained yourself. If it is in the sequence or protein structure domain, even better! If possible, include a link to a code repository. If you are a contributor to a joint project, that is wonderful, but please describe specifics of your contribution to the project. Briefly describe the results of the project as well as limitations and challenges you encountered.

About the role:

This role will be part of a project at the intersection of protein engineering, evolution, and machine learning, which is part of HHMI’s AI for Science Initiative ( ai.hhmi.org ). Our goal is to integrate evolutionary biology principles into protein language models. This role will contribute to peer-reviewed publications and advance the state-of-the-art. The project will have two homes: one at HHMI’s Janelia Research campus and the other in the Matsen and Bloom labs at the Fred Hutchinson Cancer Center.

We are seeking a highly skilled AI Engineer to join our team and play a crucial role in advancing our AI-driven scientific initiatives. We already have an existing codebase (), which we are currently in the process of rewriting to be more flexible and modular. In this position, you will work with us to develop new models in that framework and maintain computational infrastructure. This role will require deep knowledge of the underlying models as well as practical implementation skills to have the maximum biological impact. You will lead comparative studies, implement novel architectures, and ensure all work meets the highest standards of reproducible, open science.

In collaboration with the Bloom Lab, we will have the opportunity to design experiments to maximally inform and probe the boundaries of the resulting models. A data engineer will be on staff to assist data curation, and you will interact with other contributors in the Matsen lab who are developing and refining various aspects of these models. You will be embedded in a team of about 30 software & AI engineers working on related projects at HHMI Janelia and the AI initiative. HHMI has a commitment to a robust open-source software ecosystem; see for more details.

Strong programming skills in Python and PyTorch are required. Domain expertise in sequence or protein structure analysis will be highly valued. We are looking for candidates with experience in ML model deployment, workflow orchestration, and high-throughput data processing, as well as experience working with large biological datasets in GPU-based computing environments. Because this is a team project, we value a clean shared codebase and git-based collaborative workflows.

What we provide:

• A competitive compensation package, with comprehensive health and welfare benefits.

• A supportive team environment that promotes collaboration and knowledge sharing.

• The opportunity to engage with world-class researchers, software engineers and AI/ML experts, contribute to impactful science, and be part of a dynamic community committed to advancing humanity’s understanding of fundamental scientific questions.

• Amenities that enhance work-life balance such as on-site childcare, free gyms, available on-campus housing, social and dining spaces, and convenient shuttle bus service to Janelia from the Washington D.C. metro area.

What you’ll do:

• Investigate and implement alternative transformer architectures for biological sequence modeling using PyTorch.

• Expand models to be multimodal, using a diversity of inputs and outputs

• Design and execute rigorous comparative experiments between model architectures

• Contribute to scientific publications and present findings at conferences

• Apply software engineering best practices, ensuring a maintainable, extensible and well documented codebase allowing seamless reproduction and extension of research results

• Stay up to date with the latest advancements in AI research.

• Leverage agentic coding and develop practices that enable safe application of this technology.

• Collaborate with interdisciplinary teams at HHMI Janelia and Fred Hutchinson Cancer Center to ensure seamless integration of computational and experimental aspects of the project, mentor junior engineers, and direct or assist in directing the work of others to meet project goals while advising stakeholders on data strategies and best practices.

What you bring:

• Minimum Requirements: Bachelor's degree in Computer Science, Data Science, Statistics, Applied Mathematics, or a related field. An equivalent combination of education and relevant experience will be considered.

• Demonstrated record of impactful research, including publications in ML/AI or computational biology, with experience in systematic experiments, ablation studies, and a commitment to reproducible research and open science.

• Strong programming skills in Python and PyTorch, with deep expertise in transformer architectures, attention mechanisms, and ideally biological sequence modeling.

• Experience with ML model deployment, workflow orchestration, and high-throughput data processing.

• Excellent technical documentation and communication skills, with the ability to convey complex data concepts to both technical and non-technical audiences.

• A detail-oriented, creative, and organized team player with a collaborative mindset.

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

AI Engineer II: $123,125.60 (minimum) - $ 153,907.00 (midpoint) - $200,079.10 (maximum)

AI Engineer III: $149,515.20 (minimum) - $186,894.00 (midpoint) - $242,962.20 (maximum)

AI Engineer IV: $184,453.60 (minimum) - $230,567.00 (midpoint) - $299,737.10 (maximum)

Pay Type: Salary

HHMI’s salary structure is developed based on relevant job market data. HHMI considers a candidate's education, previous experiences, knowledge, skills and abilities, as well as internal consistency when making job offers. Typically, a new hire for this position in this location is compensated between the minimum and the midpoint of the salary range.

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