Young Investigator, Open Language Models for Biology

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.

The successful candidate will work at the intersection of machine learning and biology, designing careful experiments, working independently, and communicating with researchers from different disciplines.

Responsibilities:

• 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.

Requirements:

• 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.

Benefits:

• Medical, dental, vision, and employee assistance program coverage for team members and their families.
• Health savings account plan, healthcare reimbursement arrangement plan, and health care and dependent care flexible spending account plans.
• 401k plan.
• $125 per month for 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, and twelve paid holidays throughout the calendar year.
• Annual bonuses.