ML Scientist: Foundational Genomic Models for Brain Enhancers

alleninstitute; Seattle (WA); On-site; USD 120,000 - 160,000; Full time

Job summary

The Allen Institute seeks a Scientist I to build the computational backbone of a lab-in-the-loop platform that designs synthetic enhancers for brain cell-type targeting. You will develop scalable genomic sequence models, train on cloud GPUs, and prepare data and benchmarks for community use.

You will contribute to open-source projects for training, evaluating, and running inference on sequence-to-function models, enabling reproducible research and collaborative tool-building across regulatory

Qualifications

• Ph.D. in CS, computational biology, bioinformatics, applied math, engineering, or related field, or equivalent combination of degree and experience.
• Strong software engineering practice in Python including version control, testing, code review, dependency management, and reproducible environments.
• Experience training deep learning models in PyTorch, JAX, or TensorFlow on multi-GPU or distributed infrastructure.
• Experience building data pipelines for large scientific datasets that do not fit in memory.

Responsibilities

• Build and maintain an open-source codebase for training, fine-tuning, and serving genomic sequence models, and package models and benchmarks for use outside the Institute
• Train large-scale whole-brain models efficiently in multi-GPU cloud environments
• Turn cross-species multi-omic data into reproducible, versioned training sets
• Implement active-learning loops that feed in vivo screening results back into the next round of models
• Publish and present findings in peer-reviewed journals and at scientific conferences

Skills

Python

Version control

Testing

Code review

reproducible environments

PyTorch

JAX

TensorFlow

Multi-GPU training

Data pipelines

Education

Ph.D. in computer science / computational biology / bioinformatics / applied mathematics / engineering

Equivalent degree + experience

Tools

Git

Job description

The Allen Institute seeks a Scientist I to build the computational backbone of a lab-in-the-loop platform that designs synthetic enhancers for brain cell-type targeting. You will develop scalable genomic sequence models, train on cloud GPUs, and prepare data and benchmarks for community use.

You will contribute to open-source projects for training, evaluating, and running inference on sequence-to-function models, enabling reproducible research and collaborative tool-building across regulatory