Dissecting distributed representations by advanced population activity analysis methods and modeling

Investigators
Shaul Druckmann
Contact info (email)
shauld@stanford.edu
1. Define context(s)
reveal new biological insights
Current Conformance Level / Target Conformance Level
Partial
Primary goal of the model/tool/database

Neural representations of for instance task-relevant information are often distributed across multiple brain areas. These representations could have independent dynamics, or could influence each other. Our tool uses latent dynamical system models to assess the degree of influence of dynamics in one brain area on another by correlating the sub-single trial fluctuations of brain areas.

Biological domain of the model
Neuroscience
Structure(s) of interest in the model
Neurons, brain areas
Spatial scales included in the model
From single cells to brain areas
Time scales included in the model
from one millisecond to hours
2. Data for building and validating the model
Data for building the model Published? Private? How is credibility checked? Current Conformance Level / Target Conformance Level
in vitro (primary cells cell, lines, etc.)
ex vivo (excised tissues)
in vivo pre-clinical (lower-level organism or small animal) X Field best practices Adequate
in vivo pre-clinical (large animal)
Human subjects/clinical
Other: ________________________
Data for validating the model Published? Private? How is credibility checked? Current Conformance Level / Target Conformance Level
in vitro (primary cells cell, lines, etc.)
ex vivo (excised tissues)
in vivo pre-clinical (lower-level organism or small animal) X Out of sample prediction Partial
in vivo pre-clinical (large animal)
Human subjects/clinical
Other: ________________________
3. Validate within context(s)
Who does it? When does it happen? How is it done? Current Conformance Level / Target Conformance Level
Verification Our group Ongoing Tests on synthetic data Partial
Validation Our group Ongoing Out of sample prediction Partial
Uncertainty quantification Our group Ongoing Testing different model approaches Partial
Sensitivity analysis Our group Ongoing Across animal differences Partial
Other:__________
Additional Comments
4. Limitations
Disclaimer statement (explain key limitations) Who needs to know about this disclaimer? How is this disclaimer shared with that audience? Current Conformance Level / Target Conformance Level
Tested extensively on data, but only data from two brain areas Researchers In the description of our results and validation Partial
5. Version control
Current Conformance Level / Target Conformance Level
Partial
Naming Conventions? Repository? Code Review?
individual modeler In progress Yes Yes, but not professional
within the lab In progress Yes Yes, but not professional
collaborators Yes
6. Documentation
Current Conformance Level / Target Conformance Level
Code commented? Partial
Scope and intended use described? Partial
User’s guide? Insufficient
Developer’s guide? Insufficient
7. Dissemination
Current Conformance Level / Target Conformance Level
Insufficient. Work still in progress.
Target Audience(s): “Inner circle” Scientific community Public
Simulations
Models
Software
Results
Implications of results
8. Independent reviews
Current Conformance Level / Target Conformance Level
Insufficient. Work still in progress.
Reviewer(s) name & affiliation:
When was review performed?
How was review performed and outcomes of the review?
9. Test competing implementations
Current Conformance Level / Target Conformance Level
Partial. Work still in progress
Yes or No (briefly summarize)
Were competing implementations tested?
Did this lead to model refinement or improvement?
10. Conform to standards
Current Conformance Level / Target Conformance Level
Insufficient.
Yes or No (briefly summarize)
Are there operating procedures, guidelines, or standards for this type of multiscale modeling? No
How do your modeling efforts conform?