Scientist – Modeling Computational Properties of Cortical Microcircuits – Mindscope

Modeling and Theory     ·    Seattle, WA    ·     Fulltime

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.

Understanding how the structure of biological neuronal networks leads to its observed activity, and how it relates to the implemented computations is one of the primary challenges in computational neuroscience. We have large datasets of in-vitro measured cell type properties (https://celltypes.brain-map.org/), statistical knowledge of their connections (https://portal.brain-map.org/explore/connectivity/synaptic-physiology) and large-scale recordings of their in-vivo activity (https://observatory.brain-map.org/visualcoding). These are complemented by a fantastic dataset of coupled structure-activity measurement at cell type level in one tissue (https://microns-explorer.org).

We are seeking a scientist to join the Modeling and Theory team of Stefan Mihalas help understand the computational properties of cortical microcircuits by helping construct models relating structure to activity, integrating such models in larger models of cortical computations, and systematically analyze the computational output by perturbing the microcircuit model.

As part of a team, the scientist will help construct models relating the observed structure and activity. The scientist’s main role is to use such models of microcircuits in larger networks, and systematically perturb diverse aspects of the structure of the microcircuit and analyze how the system level computations are affected. The scientist is also expected to have strong contributions at the level of ideas and help shape future projects. Our team focuses at extracting principles from large data, integrating them in simplified models, and using the models to test theories of computation.

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

• Help design and construct data-driven models for visually driven in vivo neuronal activity
• Implement models with the observed microstructure in larger computational models
• Perform systematic perturbations of such models to study their computational properties
• Contribute scientific ideas based on the modeling results
• Develop and maintain computational and associated software tools
• Publish/present findings in peer-reviewed journals and at scientific conferences
• Maintain clear and accurate communication with supervisor and other team members

Required Education and Experience

• PhD in computational neuroscience, applied mathematics, computer science or a related field, or equivalent combination of degree and experience
• Strong computational/data analysis skills
• Strong Python programming skills
• Experience using PyTorch or TensorFlow

Preferred Education and Experience

• PhD and 0 – 7 years of experience in computational neuroscience, applied mathematics, computer science, or a related field
• Strong knowledge of systems neuroscience
• Experience simulating spiking neuronal networks
• Ability to work as part of a collaborative team
• Track record of scientific excellence and independent thinking
• Strong written and verbal communication skills

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 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.

Please click here to apply.