Senior Software Engineer - AI / ML Platforms and Infrastructure

About the role

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.

The Brain Health Accelerator aims to revolutionize the treatment of brain diseases by creating the first dual-use molecular tools that can reveal information about the diversity of cells in the human brain and be used to target novel treatments to specific types of cells.

We are seeking a Senior Software Engineer with deep expertise in software engineering, ML software platforms, cloud-based ML infrastructure, and Federated Learning to drive the architecture, design, delivery, and operation of AI training and inference services and infrastructure. 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. You will architect solutions to work with sensitive and controlled access data, including enabling federated model training.

As one of the first engineers on the Brain Health data and technology team, you will contribute to the team’s vision, architect and oversee complex technical solutions, and ensure 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.

Responsibilities

• 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 models with a mix of Allen Institute data and sensitive, non-shareable data from external collaborators, including investigating and recommending 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 presentations).
• Mentor team members and contribute to the development of organizational best practices.
• Serve as a technical and strategic advisor to stakeholders and leadership.

Requirements

• Bachelor’s degree in computer science, Data Science, or related fields, or equivalent experience.
• Minimum five years of experience in architecting, implementing, and supporting AI/ML platforms and infrastructure.
• Proficiency with project management tools (e.g., Jira).
• Proficiency with Python and shell scripting.
• Proficiency with Git for source code management.
• Proficiency with cloud platforms (e.g., AWS, Google Cloud, Azure) and distributed systems.

Preferred Qualifications

• Master’s degree in Computer Science, Data Science, or related fields, or equivalent experience.
• Experience building and optimizing AI for science training pipelines.
• Experience with federated learning.
• Experience with at least one lower-level/compiled programming language.
• Demonstrated experience leading complex, cross-functional technical initiatives.
• Strong communication and collaboration skills, with the ability to work effectively in cross-functional teams.
• Experience with life sciences, healthcare, or scientific research environments.
• Demonstrated experience engaging with vendors and managing technical partnerships.

Schedule

This role is currently able to work both remotely and onsite in a hybrid work environment. The primary work location is 615 Westlake Ave N., Seattle, WA; any remote work must be performed in Washington State.

• Occasional travel to partner sites required.
• Occasional attendance and participation in national and international conferences required.

Pay

Annualized Salary Range: $167,850 - $209,750. Final salary depends on required education, experience, level of skills relevant to the role, and work location.

Benefits

• Medical, dental, vision, and basic life insurance.
• 401k plan.
• Paid time off as outlined in the Allen Institute’s Benefits Guide.
• Relocation assistance.
• Work visa sponsorship may be available.

Details on the Allen Institute’s benefits offering.