Senior Software Engineer - AI​/ML Platforms and Infrastructure

Senior Software Engineer - AI / ML Platforms and Infrastructure

Senior Software Engineer, AI/ML Platforms and Infrastructure - Brain Health Accelerator

The Allen Institut
e 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.

The goal of the Brain Health accelerator is to revolutionize the treatment of brain diseases by creating the first dual-use molecular tools that can not only reveal information about the diversity of cells in the human brain but also be used to target novel treatments to specific types of cells.

We are seeking a Senior Software Engineer, AI/ML Platforms
and Infrastructure with deep expertise in software engineering, ML software platforms, cloud-base ML infrastructure, and Federated Learning to drive the architecture, design, delivery, and operation of AI training and inference services and infrastructure to support modelling efforts by Brain Health Accelerator scientists. This role requires both strategic vision and hands-on execution to enable and support training of biological foundation models with data from the Allen Institute and numerous external collaborators.

This will include architecting solutions to work with sensitive and controlled access data, which may include enabling federated model training.

As one of the first engineers on the Brain Health data and technology team, you will be responsible for contributing to our team’s vision, architecting and overseeing complex technical solutions and architectures, and ensuring that our training platforms and infrastructure are secure, reliable, compliant, and cost-effective. You will serve as a key technical partner to research and engineering teams and represent the Institute in engagements with external vendors and collaborators.

The successful candidate will collaborate closely with system administrators, software engineers, neuroscientists, data scientists, and cross-institutional partners to advance the Institute’s scientific mission.

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

• Design and implement cloud-based and on-premise solutions to support training of large-scale, multi-modality biological foundation models
• Collaborate with external partners to design and implement solutions for training of models with a mix of Allen Institute data and sensitive, non-shareable data from external collaborators. This may include investigating and making recommendations on the feasibility of federated learning and analytics for Brain Health Accelerator and partner use cases.
• Guide benchmarking and optimization efforts of ML software and infrastructure, including performance tuning and cost management
• Provide AI workflow expertise and support to science and engineering teams in Brain Health
• Collaborate with internal stakeholders and external partners to define requirements, scope, and priorities
• Identify risks, dependencies, and trade-offs, and proactively drive mitigation strategies
• Represent the Allen Institute in technical discussions with external vendors and partners
• Build and maintain strong relationships with internal stakeholders, including research teams, Central IT, and the Office of the CTO
• Translate complex technical concepts into clear, actionable insights for diverse audiences
• Ensure timely delivery of initiatives, managing scope, timelines, and resources effectively
• Ensure reliability and maintainability of deployed systems
• Drive continuous improvement in operational processes and tooling
• Foster effective communication across cross-functional and cross-institutional teams
• Lead knowledge-sharing initiatives (e.g., technical forums, training, or…