Cross-Spectral Factor Analysis

Investigators
David Carlson
Contact info (email)
david.carlson@duke.edu
1. Define context(s)
reveal new biological insights
Current Conformance Level / Target Conformance Level
Adequate
Primary goal of the model/tool/database

The primary goal of this tool is to learn electrical connectome networks of activity from multi-region brain recordings.  The inferred networks vary in strength over time, are consistent between animals in a mouse model, and are relevant to neuropsychiatric disorders (e.g., in a mouse model of depression).

Biological domain of the model
Neuroscience; modeling of electrophysiological signals
Structure(s) of interest in the model
Multiple brain regions
Spatial scales included in the model
Multiple brain regions
Time scales included in the model
.5s-5s
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) Yes Currently; will be released at the conclusion of the grant/study. The data is scanned by a trained bench scientist, and results are checked with cross-validation. 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) Yes Currently; will be released at the conclusion of the grant/study. Cross-validation techniques. Adequate
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 Results and code are reviewed by computational and bench scientists. Throughout development Adequate
Validation Developers have done validations. Throughout development Adequate
Uncertainty quantification
Sensitivity analysis
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
Has only been tested on multi-region local field potential recordings. Partial
5. Version control
Current Conformance Level / Target Conformance Level
Partial
Naming Conventions? Repository? Code Review?
individual modeler Yes Yes Partial
within the lab No Yes
collaborators No Yes Partial
6. Documentation
Current Conformance Level / Target Conformance Level
Code commented? Partial
Scope and intended use described? Partial
User’s guide? Partial
Developer’s guide? Partial
7. Dissemination
Current Conformance Level / Target Conformance Level
Adequate
Target Audience(s): “Inner circle” Scientific community Public
Simulations
Models http://papers.nips.cc/paper/7260-cross-spectral-factor-analysis;https://arxiv.org/abs/2004.05209
Software https://github.com/carlson-lab/encodedSupervision
Results https://www.sciencedirect.com/science/article/pii/S0092867418301569
Implications of results https://www.jneurosci.org/content/38/7/1601.abstract
8. Independent reviews
Current Conformance Level / Target Conformance Level
Partial
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
Insufficient
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
Partial
Yes or No (briefly summarize)
Are there operating procedures, guidelines, or standards for this type of multiscale modeling? No, we are not aware of any for this specific area. We are attempting to follow best practices on documentation and dissemination.
How do your modeling efforts conform?