Scientist III: AI/ML for Multimodal Neuropathology

Allen Institute; Seattle (WA); Hybrid; USD 130,000 - 162,000; Full time

Benefits offered by this job

Relocation assistance

Work visa sponsorship

Job summary

The Allen Institute in Seattle seeks a Scientist III in Scalable AI/ML for Neuropathology to develop, scale, and deploy state-of-the-art machine learning methods for multimodal neuropathological data, modeling disease progression, and enabling cellular insights.

This role sits at the intersection of computational biology, neuropathology, and ML engineering, collaborating with experimental neuropathologists and software engineers to bring research advances to impactful scientific applications.

Qualifications

• Ph.D. in Computer Science, Applied Mathematics, Computational Biology, Computational Neuroscience, Statistics, or related field; or equivalent combination of degree and experience.
• Minimum of 5 years of postdoctoral or industry research experience.
• Demonstrated ability to design, implement, and apply deep learning models to large-scale biological or medical image data.
• Experience with Bayesian modeling and probabilistic inference.
• Experience building and maintaining scalable data or training pipelines for large-scale ML workloads.
• Proficiency in Python and ML frameworks including PyTorch or JAX, with strong software engineering practices.

Responsibilities

• Develop and deploy large-scale ML models integrating multimodal neuropathological data, including digital histology, spatial transcriptomics, MRI, and clinical metadata, to characterize brain disease progression at cellular resolution.
• Design and apply computer vision architectures (ViT and related models) and foundation models to quantitative neuropathology image analysis.
• Design, build, and maintain scalable data pipelines that render diverse biological and neuropathological datasets, including gigapixel whole-slide images and spatial omics, ML-ready across cloud and on-premises GPU infrastructure.
• Implement and optimize distributed training and inference workflows for foundation models, including multi-GPU and multi-node training, experiment tracking, and reproducible model versioning.
• Apply Bayesian statistical and causal modeling approaches to describe and predict neurodegenerative disease trajectories.
• Collaborate with scientists, computational biologists, neuropathologists, and software engineers within the Allen Institute and with external partners to advance model development from research to scientific impact.
• Promote open science through publication of peer-reviewed papers and release of open-source code, models, and reusable ML tooling.

Skills

Python

PyTorch

JAX

Deep learning

Large-scale ML

Education

Ph.D. in Computer Science/Applied Math/Computational Biology/Computational Neuroscience/Statistics

5+ years postdoc or industry research

Tools

Docker

Kubernetes

Slurm

Nextflow

Airflow

DeepSpeed

Ray

Job description

The Allen Institute in Seattle seeks a Scientist III in Scalable AI/ML for Neuropathology to develop, scale, and deploy state-of-the-art machine learning methods for multimodal neuropathological data, modeling disease progression, and enabling cellular insights.

This role sits at the intersection of computational biology, neuropathology, and ML engineering, collaborating with experimental neuropathologists and software engineers to bring research advances to impactful scientific applications.