Scientist III AI Scientist Quantitative Neuropathy and ML Scalable Infrastructure

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Scientist III – AI Scientist for Quantitative Neuropathy and ML Scalable Infrastructure

The Allen Institute accelerates science for a healthier world through large-scale research designed to answer some of the most complex questions in biology. Our multi-disciplinary teams generate foundational knowledge, tools, and data to understand how our brain, cells, and immune system work. We share our work openly so others can build on it, move faster, and ask bigger questions. We drive discovery forward and create new possibilities for improving human health.

Brain Health is a new global collaborative research initiative designed to accelerate understanding of human brain diseases through large-scale human tissue analysis, open science, AI-enabled disease modeling, and translational platform technologies. Building on foundational advances in human brain cell atlases, quantitative neuropathology, single-cell and spatial biology, multimodal molecular profiling, and AI-enabled analysis, Brain Health is developing a scalable framework for understanding disease progression directly in the human brain and identifying new opportunities for therapeutic development.

We are searching for a Scientist III in Scalable AI/ML for Neuropathology who will develop, scale, and deploy state-of-the-art machine learning methods, along with the infrastructure that supports them, to integrate multimodal neuropathological data, model disease progression, and drive the mechanistic understanding of brain disease at cellular resolution. This role sits at the intersection of computational biology, neuropathology, and ML engineering, working within the Brain Health Accelerator and collaborating with experimental neuropathologists and software engineers.

AI/ML focus areas could include multimodal foundation models, diffusion models, and computer vision architectures, together with the distributed training, data pipelines, and model serving needed to run them at scale.

At the Allen Institute, we believe that science is for everyone – and should be open to everyone. We are dedicated to combating biases and reducing barriers to STEM careers more broadly.

We also believe that science is better when it includes different perspectives and voices. We strive to make the Allen Institute a place where everyone feels like they belong and are empowered to do their best work in a supportive environment.

We are an equal-opportunity employer and strongly encourage people from all backgrounds to apply for our open positions.

Essential Functions

• 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,…