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Software Engineer III – Machine Learning & Algorithms Engineer

Department: Data and Technology

Software Engineer III – Machine Learning & Algorithm Research and Development

The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact on science.

The mission of the Allen Institute for Brain Science is to accelerate the understanding of how the human brain works in health and disease. Using a big science approach, we generate useful public resources, drive technological and analytical advances, and discover fundamental brain properties through integration of experiments, modeling and theory.

We are seeking an exceptional, energetic and experienced machine learning and algorithms engineer who has a track record of building scalable and distributed production software. The ideal candidate has experience in implementing data architecture and pipelines to enable intelligent applications on top of petabytes of diverse data. We seek to lay an informatics architecture and a compute framework for brain science research. We generate large-scale neuroscience datasets, online search, visualization, and analysis utilities, and APIs. Our data is freely and openly shared with the public at

The informatics architecture will support the whole data science life cycle from ingestion, mapping, refinement to publishing and serving, encompassing provenance of the data and integrate across datasets, modalities, and scales from micro- to macro-scale and from raw data (sequences, images, time-series) to derived models (cell types, circuits, brain organization). You will be working with subject matter experts to gather requirements, assess different algorithms, models, and methods for fit for purpose, implement rapid prototypes to flush and validate concepts. This role is part of a team doing big and open science. You will interact regularly with neuroscientists and work closely with a wide variety of engineers, collaborating in a large team while working on new discoveries about the brain.

The Allen Institute believes that team science significantly benefits from the participation of diverse voices, experiences and backgrounds. High-quality science can only be produced when it includes different perspectives. We are committed to increasing diversity across every team and encourage people from all backgrounds to apply for this role.

Essential Functions

  • Work as part of the informatics solutions development team to define the informatics architecture for the Allen Institute for Brain Science products and related activities
  • Work with subject matter experts to gather and analyze requirements and use cases and design architecture and modules capable of scaling out to meet anticipated growth
  • Create robust and efficient data pipelines to extract and transform data to quantitative features, knowledge, and visualization to support new interactive modes of engagement of the data
  • Analysis of current technologies and assess their fit for purpose
  • Implement rapid prototypes to flush out concepts and to obtain metrics supporting the fit for purpose 
  • Responsibilities also include identifying, curating and transforming relevant datasets
  • Develop and maintain documentation to clarify architecture requirements and rationale
  • Identify and build working relationships and partnerships with external collaborators, system vendors, and users
  • Support internal and external teams as they integrate heterogenous unstructured, semi-structured and well-structured data into the data pipelines and master repository
  • Participate in writing, presenting, and reviewing strategic and operational reports

Required Education and Experience

  • Bachelor’s Degree in Computer Science, Statistics, Mathematics, Physics, Machine learning, or related field; or equivalent combination of degree and experience
  • 3+ years of relevant experience in a software development environment
  • Strong software development skills, with proficiency in Python and C++ preferred
  • Command of best practices in software development life cycle
  • Experience with advanced algorithms and machine learning development
  • Experience in operationalizing and optimizing machine learning methods and algorithms in a production environment

Preferred Education and Experience

  • Advanced degree in Computer Science, Neuroscience, Machine learning, Statistics, Mathematics, Physics, or related field
  • Experience in computational neuroscience a big plus
  • Broad, deep and current knowledge of modern machine learning (ML) and algorithms techniques
  • Experience building information systems that incorporate production databases
  • Experience in supporting machine learning models in production such as monitoring, retraining, or editing for staleness and accuracy due to data changing, new data, assumptions etc.
  • Familiarity with entire software toolchain, including source code management (git), build systems, debuggers, linkers, and profiling tools
  • Strong communication skills to concisely communicate to provide context, offers insights and minimizes misinterpretation

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 remotely due to COVID-19 and our focus on employee safety. We are a Washington State employer, and remote work must be performed in Washington State. We continue to evaluate the safest options for our employees. As restrictions are lifted in relation to COVID-19, this role will return to work in a hybrid work environment.

Additional Eligibility Qualifications

  • In keeping with our focus on employee safety, all employees must be fully vaccinated against COVID-19 as a condition of employment unless a medical or religious exemption is approved. All employees will be required to keep their vaccination status up to date according to CDC guidance and our policy.

Additional Comments

  • **Please note, this opportunity offers relocation assistance**
  • **Please note, this opportunity offers work visa sponsorship**

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.





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