Repository navigation
Add correlation and voxel members, and count passive conditions as task states - #58
Merged
Merged
Conversation
…sk states An audit of the 27B astra-distill records (64,589 papers, set-20261101) counted what the model wrote as free text in each open enum. Three of the findings change the vocabulary: - ConditionKind.task_state said "an active state", so the model refused it for passive conditions and wrote "passive viewing", "passive listening" and "passive stimulation" 6,665 times in 2,538 papers. task_state now covers active and passive states alike. - ModelFamily had no member for a correlation; it was written as free text 10,543 times in 4,624 papers. `correlation` is a correlation between the measure and a variable that is not another region's signal (a score, a rating, age), so a brain-behaviour correlation is this family, including one on connectivity strength. A seed-based or ROI-to-ROI correlation is a connectivity analysis, whose model family is the model that tested the effect on the connectivity estimates. seed_based now says so, and the lists of mass-univariate families name brain-behaviour correlation and send region-to-region correlation to ConnectivityDetails. Of the 3,124 connectivity analyses with a correlation-worded family, about 1,100 were the time-series correlation itself. - RegionType had no member for a region that is one voxel; "peak voxel", "voxel" and "seed voxel" were written 4,535 times in 1,532 papers. `voxel` is a single voxel or coordinate with no surrounding volume; a sphere or box stays coordinate_sphere. Extraction tree regenerated with pondie.schema.generate; models and JSON Schemas with tools/generate_models.py. The parse schemas pick up ModelFamily through storage. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
jdkent
commented
Nov 5, 2026
jdkent
left a comment
jdkent
left a comment
Member
Author
There was a problem hiding this comment.
One change I wanted for wording
This was referenced Nov 5, 2026
jdkent
added a commit
that referenced
this pull request
Nov 5, 2026
Regenerate after #58's task_state description edit
This was referenced Nov 5, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
From the open-enum free-text audit of the 27B astra-distill records (64,589 papers, set-20261101). The audit dashboard is a private claude.ai artifact; ask James for the link.
Changes
ConditionKind.task_statenow covers active and passive states: "performing a trial and responding, or viewing, listening to or receiving stimuli with nothing to do". It said "an active state" before, so the model refused it and wrote "passive viewing / listening / stimulation" 6,665 times in 2,538 papers.ModelFamily.correlation(new): a correlation between the measure and a variable that is not another brain region's signal. That covers brain-behaviour correlation, including one on connectivity strength. The model wrote it as free text 10,543 times in 4,624 papers.seed_baseddefinition,AnalysisType.mass_univariate,MassUnivariateDetailsandAnalysis.detailsnow say this.RegionType.voxel(new): a single voxel or coordinate with no surrounding volume. "peak voxel", "voxel" and "seed voxel" were written 4,535 times in 1,532 papers. A sphere or box stayscoordinate_sphere, which takes the 840 cube and box values.region_typeandmodel_familymember lists are updated.Generated files
The extraction tree is regenerated with
python3 -m pondie.schema.generate(withPONDIE_SCHEMA_DIRpointing at this checkout), and the models and JSON Schemas withtools/generate_models.py. The parse schemas pick upModelFamilythrough storage.Checks
tools/generate_models.py --checkpasses.pytest: 232 passed, 16 skipped (pyarty and setuptools are not installed locally).storage_parameter_priorities,field_provenanceandextraction_to_storage_mapchecks pass.🤖 Generated with Claude Code