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

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.

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 presentations)
• Mentor team members and contribute to the development of organizational best practices
• Serve as a technical and strategic advisor to stakeholders and leadership

*Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects management’s assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.*

Required Education and Experience

• 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 Education and Experience

• 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

Physical Demands

• Fine motor movements in fingers/hands to operate computers and other office equipment

Position Type/Expected Hours of Work

• This role is currently able to work both remotely and onsite in a hybrid work environment. We are a Washington State employer, and the primary work location for all Allen Institute employees is 615 Westlake Ave N.; any remote work must be performed in Washington State.

Travel

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

Additional Comments

• **Please note, this opportunity offers relocation assistance**
• **Please note, this opportunity may offer work visa sponsorship**
• Please include a cover letter with your application

Annualized Salary Range

$167,850 - $209,750*

* Final salary depends on the required education for the role, experience, level of skills relevant to the role, and work location, where applicable.

Benefits

• Employees (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institute’s Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute’s 401k plan. Paid time off is also available as outlined in the Allen Institutes Benefits Guide. Details on the Allen Institute’s benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits.

It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities.