Young Investigator, Open Language Models for Biology

Persons in these roles are expected to work from our offices in Seattle. On-site requirements vary based on position and team. If you have questions about on-site work arrangements for this role, please ask your recruiter.

Compensation: $159,650.00

Who You Are:

Ai2 is seeking a Postdoctoral Young Investigator to work on CellOLMo, a collaboration between Ai2’s open language model researchers and scientists at the Allen Institute.

We are looking for a researcher who works at the intersection of machine learning and biology. You should have experience training or adapting transformer-based models and an interest in applying those methods to single-cell data. You may come from machine learning, computational biology, neuroscience, physics, or another quantitative field.

You will be expected to design careful experiments, work independently, and communicate with researchers from different disciplines. Because CellOLMo is an open-science project, you should also be committed to releasing code, data, and model weights for use by the broader research community.

Who We Are:

CellOLMo is investigating how open language models can be used with single-cell brain data to answer biological questions. The project will initially focus on the SEA-AD Alzheimer’s disease atlas and will examine data at several levels, from individual cells to brain regions and donors.

One of our main research questions is whether grounding a model in biological language and knowledge produces measurable improvements over models trained only on molecular data. We will also study whether those improvements persist when cells are combined into representations of brain regions, patients, pathology, and disease progression.

You will work directly with the project PI at Ai2 and collaborate with domain scientists at the Allen Institute for Brain Health. You will have access to Ai2’s open language models, post-training infrastructure, and substantial GPU compute. We plan to release the resulting models, code, and research artifacts openly.

Your Next Challenge:

• Develop a multimodal language model that combines single-cell gene-expression data with text, using an open model such as OLMo.
• Reproduce and evaluate relevant approaches, including scGPT, Geneformer, CellWhisperer, and C2S-Scale.
• Adapt and improve these approaches for brain and neurodegeneration data.
• Design controlled experiments to test whether language grounding improves performance over cell-only and text-free baselines.
• Develop representations at the brain-region and donor levels that incorporate pathology and disease progression.
• Evaluate models on held-out donors using measures such as cell-type and marker recovery, agreement with known patterns of regional vulnerability, and expert review of plain-language answers.
• Work with Allen Institute scientists to interpret results and identify predictions suitable for experimental follow-up.
• Release data, code, and model weights, and prepare the results for publication.

What You’ll Need:

• A completed PhD, or a PhD expected within one year, in machine learning, computational biology, computational neuroscience, physics, or a related quantitative field.
• Hands-on experience training or fine-tuning transformer-based language models.
• Strong Python and PyTorch skills.
• Experience writing reliable, reproducible research code.
• The ability to carry out independent research on open-ended problems.
• The ability to communicate clearly with both machine-learning researchers and biological scientists.

We also look favorably upon experience in one or more of the following areas:

• Single-cell genomics, including scRNA-seq or snRNA-seq.
• Tools such as scanpy, AnnData, or the scVI ecosystem.
• Multimodal models, instruction tuning, or language-model post-training.
• Neurodegeneration, brain atlases, or spatial transcriptomics.
• Public releases of research code, datasets, or model weights.

Physical Demands and Work Environment:

The physical demands described here are representative of those that must be met by a team member to successfully perform the essential functions of this position. Reasonable accommodations may be made to enable individuals with disabilities to perform the functions.

• Must be able to remain in a stationary position for long periods of time.
• The ability to communicate information and ideas so others will understand. Must be able to exchange accurate information in these situations.
• The ability to observe details at close range.
• Can work under deadlines.

A Little More About Ai2:

Ai2 is a Seattle based non-profit AI research institute founded in 2014 by the late Paul Allen. Our mission is building breakthrough AI to solve the world’s biggest problems. We develop foundational AI research and innovation to deliver real-world impact through large-scale open models, data, robotics, conservation, and beyond.

In addition to Ai2’s core mission, we also aim to contribute to humanity through our treatment of each member of the Ai2 Team. Some highlights are:

• We are a learning organization – because everything Ai2 does is ground-breaking, we are learning every day. Similarly, through weekly Ai2 Academy lectures, a wide variety of world-class AI experts as guest speakers, and our commitment to your personal on-going education, Ai2 is a place where you will have opportunities to continue learning alongside your coworkers.
• We value diversity - We seek to hire, support, and promote people from all genders, ethnicities, and all levels of experience regardless of age. We particularly encourage applications from women, non-binary individuals, people of color, members of the LGBTQA+ community, and people with disabilities of any kind.
• We value inclusion - We understand the value that people's individual experiences and perspectives can bring to an organization, and we are building a culture in which all voices are heard, respected and considered.
• We emphasize a healthy work/life balance – we believe our team members are happiest and most productive when their work/life balance is optimized. While we value powerful research results which drive our mission forward, we also value dinner with family, weekend time, and vacation time. We offer generous paid vacation and sick leave as well as family leave.
• We are collaborative and transparent – we consider ourselves a team, all moving with a common purpose. We are quick to cheer our successes, and even quicker to share and jointly problem solve our failures.
• We are in Seattle – and our office is on the water! We have mountains, we have lakes, we have four seasons, we bike to work, we have a vibrant theater scene, and we have so much else. We even have kayaks for you to paddle right outside our front door. We welcome interest from applicants from outside of the United States.
• We are friendly– chances are you will like every one of the 200+ (and growing) people who work here. We do.

Ai2 is proud to be an Equal Opportunity employer. We do not discriminate based upon race, religion, color, national origin, sex (including pregnancy, childbirth, or related medical conditions), sexual orientation, gender, gender identity, gender expression, transgender status, sexual stereotypes, age, status as a protected veteran, status as an individual with a disability, or other applicable legally protected characteristics. You may view the related Know Your Rights compliance poster and the Pay Transparency Nondiscrimination Provision by clicking on their corresponding links.

This employer participates in E-Verify and will provide the federal government with your Form I-9 information to confirm that you are authorized to work in the U.S. If E-Verify cannot confirm that you are authorized to work, this employer is required to give you written instructions and an opportunity to contact the Department of Homeland Security (DHS) or Social Security Administration (SSA) so you can begin to resolve the issue before the employer can take any action against you, including terminating your employment. Employers can only use E-Verify once you have accepted a job offer and completed the Form I-9.

We are committed to providing reasonable accommodations to employees and applicants with disabilities to the full extent required by the Americans with Disabilities Act (ADA). If you feel you need a reasonable accommodation pursuant to the ADA, you are encouraged to contact us at recruiting@allenai.org.

Benefits:

• Team members and their families are covered by medical, dental, vision, and an employee assistance program.
• Team members are able to enroll in our health savings account plan, our healthcare reimbursement arrangement plan, and our health care and dependent care flexible spending account plans.
• Team members are able to enroll in our company’s 401k plan.
• Team members will receive $125 per month to assist with commuting or internet expenses and will also receive $200 per month for fitness and wellbeing expenses.
• Team members will also receive up to ten sick days per year, up to seven personal days per year, up to 20 vacation days per year and twelve paid holidays throughout the calendar year.
• Team members will be able to receive annual bonuses.

Note: This job description in no way states or implies that these are the only duties to be performed by the team members(s) of this position. Team members will be required to follow any other job-related instructions and to perform any other job-related duties requested by any person authorized to give instructions or assignments. All duties and responsibilities are essential functions and requirements and are subject to possible modification to reasonably accommodate individuals with disabilities. To perform this job successfully, the team member(s) will possess the skills, aptitudes, and abilities to perform each duty proficiently. Some requirements may exclude individuals who pose a direct threat or significant risk to the health or safety of themselves or others. The requirements listed in this document are the minimum levels of knowledge, skills, or abilities. This document does not create an employment contract, implied or otherwise, other than an at will relationship.