Job Openings at the Allen Institute

Are you ready for new challenges and new opportunities? Join our team in Seattle!
Current job opportunities are posted here as they become available.



Scientist I - Modeling and Theory

Department: Modeling and Theory

Scientist I – Diverse Dynamics – Modeling and Theory


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 MindScope program seeks to understand the transformations, sometimes called computations, in coding and decoding that lead from photons to behavior and conscious experience by observing, perturbing, and modeling the physical transformations of signals in the cortical-thalamic visual system within a few perception-action cycles.

The defining feature of neural circuits is their capacity to compute. Most networks trained to compute use very simple neuronal and synaptic models. However, one of the most salient features is the diversity of cell types. We want to investigate the relation between the complexity of the dynamics of individual neurons and synapses, and the computational capacity of the resulting networks.

We are seeking a scientist to join the Modeling and Theory team of Stefan Mihalas to help construct networks using complex neuronal and synaptic models which are trained to perform a task, and compare their predictions with the observations from the mouse cortex. The work is supported by an NIH grant and is in collaboration with Eric Shea-Brown and with the UW Comp Neuro Center.  The scientist is expected to have significant contribution at implementation level strong as well as contributions at the level of ideas, and help shape future projects.

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

  • Engineer and publicly share a tool in PyTorch to efficiently train neural networks with complex bio-realistic neurons and synapses
  • Train models for visual processing with complex units and architectural constraints from existing anatomical or physiological measurements
  • Analyze differences in network learning and computation capacity as a function of unit complexity
  • In collaboration with experimentalists contribute to data analysis
  • Contribute scientific ideas based on the modeling results, and help shape future projects
  • Develop and maintain computational and associated software tools
  • Publish/present findings in peer-reviewed journals and at scientific conferences
  • Maintain clear and accurate communications with supervisor and other team members

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

  • PhD in computer science, computational neuroscience, applied mathematics, or a related field, or equivalent combination of degree and experience
  • Strong computational/data analysis skills,
  • Good programming ability in Python and experience using PyTorch or TensorFlow
  • Proven track record of scientific excellence and independent thinking in completed works and research

Preferred Education and Experience

  • In-depth knowledge of systems neuroscience
  • Strong publication record
  • Strong written and verbal communication skills
  • Ability to work effectively as part of a collaborative team

Physical Demands

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

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 onsite.

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.





Applicant Tracking System Powered by ClearCompany HRM Applicant Tracking System