Young Investigator, Open Language Models for Biology

The role

You will develop a multimodal language model combining single-cell gene-expression data with text. You will work on the CellOLMo project to investigate how open language models can be used with single-cell brain data.

What you will do

• 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.

Required qualifications

• 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.

Nice to have

• 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.

Benefits

• Medical, dental, vision, and an employee assistance program coverage for team members and families.
• Enrollment in health savings account plan, healthcare reimbursement arrangement plan, and health care and dependent care flexible spending account plans.
• Enrollment in company 401k plan.
• $125 per month to assist with commuting or internet expenses.
• $200 per month for fitness and wellbeing expenses.
• Up to ten sick days per year.
• Up to seven personal days per year.
• Up to 20 vacation days per year.
• Twelve paid holidays throughout the calendar year.
• Annual bonuses.

Before you apply

• Employer participates in E-Verify to confirm authorization to work in the U.S.

About the company

Ai2 is a Seattle based non-profit AI research institute founded in 2014 by the late Paul Allen. Its mission is building breakthrough AI to solve the world’s biggest problems.