Run Models Skill (Model Entry Layer)

Overview

run_models is the NeuroClaw entry skill for model-level inference workflows.

This skill is responsible for:

• Maintaining a model registry (name, paper, source code, input/output, doc file path)
• Selecting the correct model skill under skills/<model-name>/SKILL.md
• Coordinating required data preparation before model execution
• Delegating modality preprocessing to fmri-skill and smri-skill

It supports both:

• deep learning model routes for phenotype prediction
• non-deep-learning statistical / unsupervised / classical machine-learning routes such as first-level and second-level task-fMRI GLM, resting-state ICA, resting-state DictLearning, disease classification with SVM, disease classification with SpaceNet, brain parcellation with K-means, brain parcellation with Hierarchical clustering, temporal filtering, and detrending

This skill does not hardcode detailed install/run commands for each model. Those details are stored in model-specific markdown files.

Research use only.

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Core Workflow (Never Bypassed)

1. Identify requested model and task (classification/regression phenotype prediction).
2. Locate the corresponding model skill under skills/<model-name>/SKILL.md.
3. Verify required inputs (ROI features, optional sMRI features).
4. If inputs are not ready, delegate preprocessing to modality skills:
   • fmri-skill for ROI extraction from fMRI
   • smri-skill when model additionally requires structural features
5. Generate a numbered execution plan and wait for explicit user confirmation (YES / execute / proceed).
6. On confirmation, execute via claw-shell following model doc instructions.

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Model Registry (Current)

Model	Paper	Code	Input	Output	Model Doc
BrainGNN	Li et al., 2020, Braingnn: Interpretable brain graph neural network for fmri analysis	https://github.com/xxlya/BrainGNN_Pytorch/tree/main	fMRI ROI features (graph/node-level ROI representation)	Phenotype prediction (classification/regression) + interpretable graph indicators	skills/brain_gnn/SKILL.md
BNT	Kan et al., 2022, BrainNetworkTransformer	https://github.com/Wayfear/BrainNetworkTransformer	fMRI ROI FC matrix (dense [N, N], no PyG)	Phenotype prediction (classification/regression) + attention weights + DEC cluster assignments	skills/bnt/SKILL.md
BrainNetCNN	Kawahara et al., 2017, BrainNetCNN	https://github.com/jeremykawahara/brainnetcnn	Dense ROI connectivity matrix [N, N]	Phenotype classification/regression with E2E, E2N, and N2G convolutions	skills/brainnetcnn/SKILL.md
FM-APP	He et al., 2024, FM-APP: Foundation model for any phenotype prediction via fMRI to sMRI knowledge transfer	https://github.com/ZhibinHe/FM-APP	fMRI ROI features + sMRI features	Phenotype prediction (any-phenotype setting)	skills/fm_app/SKILL.md
NeuroStorm	NeuroClaw model entry for storm-related phenotype prediction workflows	see skills/neurostorm/SKILL.md	Multi-modal neuroimaging features as specified in the model doc	Phenotype prediction / downstream inference as specified in the model doc	skills/neurostorm/SKILL.md
GLM	Classical first-level and second-level task-fMRI general linear model	Nilearn / SPM-style implementation route	Preprocessed task fMRI, events, optional confounds, and optional subject-level contrast maps for group inference	Task activation contrasts, group z maps, and statistical inference outputs	skills/glm/SKILL.md
ICA	Classical resting-state network decomposition method	Nilearn decomposition implementation route	Preprocessed resting-state fMRI, optional mask, optional confounds	Intrinsic connectivity component maps, subject time series, optional connectomes	skills/ica/SKILL.md
DictLearning	Classical sparse resting-state network decomposition method	Nilearn decomposition implementation route	Preprocessed resting-state fMRI, optional mask, optional confounds	Sparse component maps, subject time series, optional connectomes	skills/dictlearning/SKILL.md
SpaceNet	Classical voxel-wise disease classification method for neuroimaging	Nilearn decoding implementation route	Aligned voxel maps, labels, optional covariates, optional mask	Predicted labels, decision scores, CV metrics, coefficient maps	skills/spacenet/SKILL.md
K-means	Classical brain parcellation method for neuroimaging	Nilearn / clustering-based parcellation route	Preprocessed feature maps or image lists, optional mask, requested parcel count	Parcel labels, cluster summaries, optional centroid outputs	skills/kmeans/SKILL.md
Hierarchical	Classical hierarchical brain parcellation method for neuroimaging	Nilearn / clustering-based parcellation route	Preprocessed feature maps or image lists, optional mask, requested parcel count	Parcel labels, cluster summaries, optional dendrogram outputs	skills/hierarchical/SKILL.md
Filtering	Classical signal denoising method for neuroimaging time series	Nilearn / preprocessing route	Preprocessed BOLD image or time series, TR, optional confounds, optional mask	Denoised BOLD, cleaned time series, optional QC summaries	skills/filtering/SKILL.md
Detrending	Classical signal denoising method for neuroimaging time series	Nilearn / preprocessing route	Preprocessed BOLD image or time series, TR, optional confounds, optional mask	Cleaned BOLD, cleaned time series, optional QC summaries	skills/detrending/SKILL.md
Statistical ML	OLS, logistic/Ridge/Elastic Net, SVM/SVR, XGBoost, MixedLM	NeuroClaw unified tabular trainer	Subject-level tabular/ROI features	Fold-local predictions, inference, metrics	skills/statistical-ml/SKILL.md
Subject Subtyping	K-means, GMM, spectral, NMF, consensus, autoencoder	NeuroClaw subtyping trainer	Subject-level feature matrix	Subtype labels, embeddings, stability metrics	skills/subject-subtyping/SKILL.md
Survival Models	Cox, RSF, DeepSurv, XGBoost survival	NeuroClaw censor-aware trainer	Features, duration, event	Risk scores, concordance	skills/survival-models/SKILL.md
Causal Treatment	Meta-learners, DR, causal forest, TARNet, DragonNet	NeuroClaw cross-fitted causal trainer	Features, treatment, outcome	CATE, treatment policy, policy value	skills/causal-treatment-models/SKILL.md
Temporal Models	LSTM, GRU, TCN, Transformer	NeuroClaw PyTorch trainer	Subject sequences	Classification/regression predictions	skills/temporal-models/SKILL.md
Imaging Genetics	GWAS/PRS, PLS, CCA	PLINK2 + NeuroClaw matrix trainer	Genotype and imaging phenotype	Associations and latent scores	skills/imaging-genetics-models/SKILL.md
CNN3D	Compact residual 3D CNN	NeuroClaw PyTorch trainer	Subject volumes	Predictions and checkpoints	skills/cnn3d/SKILL.md
CPM	Connectome Predictive Modeling	NeuroClaw CPM trainer	FC matrices/vectors and labels	Fold-local predictions and selected-network models	skills/cpm/SKILL.md
KG Link Prediction	ComplEx, R-GCN, GraphSAGE, GAT	NeuroOracle/PyG	Knowledge-graph triples	Triple scores and embeddings	skills/kg-link-prediction/SKILL.md

Scientific Workflow Registry

Workflows define a scientific experiment and delegate model fitting to one or more canonical model skills. They do not own duplicate model implementations.

Workflow	Delegated models/tools	Output	Workflow Doc
Neuroimaging Decoding	GLM, Statistical ML, Nilearn SearchLight	predictions, ROI statistics, score maps	skills/neuroimaging-decoding/SKILL.md
Connectome Discovery	CPM or graph models, map similarity, brain visualization	significant network maps and ranked targets	skills/connectome-discovery/SKILL.md
Brain-Age Modeling	Statistical ML or CNN3D plus fold-local correction	predicted age and Brain-PAD	skills/brain-age-modeling/SKILL.md

Cross-Cutting Tools (Apply Across Models)

These are not models. They are horizontal layers that any model in the registry above can opt into without changing model code.

Tool	Purpose	When to invoke	Tool Doc
harmonization-tool	Remove site/scanner/batch effects from features before model training; supports ComBat / ComBat-GAM / CovBat / site-as-covariate; ships site-stratified and leave-site-out splitters; required for honest mega-analysis across multi-site cohorts	Any multi-site or multi-dataset run (ABIDE, ADHD-200, ABCD, multi-cohort pooling); user mentions ComBat / harmonize / site effect / cross-site / mega-analysis	skills/harmonization-tool/SKILL.md

Insertion point: between dataset-skill output (feature matrix + meta) and model-skill input. Models read harmonized features identically to raw features.

Citation Notes

• BrainGNN:
  • Li X, Zhou Y, Dvornek N, Zhang M, Gao S, Zhuang J, Scheinost D, Staib L, Ventola P, Duncan J. 2020.
• BNT:
  • Kan X, Dai W, Cui H, Zhang Z, Guo Y, He L. 2022. BrainNetworkTransformer. NeurIPS.
• BrainNetCNN:
  • Kawahara J, Brown CJ, Miller SP, et al. 2017. BrainNetCNN. NeuroImage.
• FM-APP:
  • He Z, Li W, Liu Y, et al. FM-APP. IEEE TMI, 2024, 44(10): 4010-4022.
• NeuroStorm:
  • See skills/neurostorm/SKILL.md for the current model card, citation, and execution details.
• GLM:
  • Classical first-level and second-level general linear model for task-evoked activation analysis and group-level inference; see skills/glm/SKILL.md.
• ICA:
  • Classical resting-state network decomposition route based on independent component analysis; see skills/ica/SKILL.md.
• DictLearning:
  • Classical sparse resting-state network decomposition route; see skills/dictlearning/SKILL.md.
• Statistical ML:
  • Canonical ROI/tabular route for logistic regression, SVM/SVR, Ridge, Elastic Net, XGBoost, OLS, and mixed-effects models.
• SpaceNet:
  • Classical voxel-wise disease classification route with sparse coefficient maps; see skills/spacenet/SKILL.md.
• K-means:
  • Classical brain parcellation route for fixed-K parcel discovery; see skills/kmeans/SKILL.md.
• Hierarchical:
  • Classical brain parcellation route for multi-scale parcel discovery; see skills/hierarchical/SKILL.md.
• Filtering:
  • Classical signal denoising route for temporal filtering; see skills/filtering/SKILL.md.
• Detrending:
  • Classical signal denoising route for temporal drift removal; see skills/detrending/SKILL.md.

Harness-Aware Model Registration (Declarative + Testing + Drift Detection)

Model Specification Format (Extended)

Every model integrated into run_models must include a model specification file in JSON format alongside its Markdown documentation:

File: skills/{model_name}/{model_name}_spec.json

{
  "model_name": "brain_gnn",
  "version": "1.0.0",
  "paper": "Li et al., 2020",
  "code_repo": "https://github.com/xxlya/BrainGNN_Pytorch",
  "required_dependencies": {
    "torch": ">=1.9.0,<2.1.0",
    "numpy": ">=1.21.0",
    "scipy": ">=1.7.0",
    "networkx": ">=2.6.0"
  },
  "input_spec": {
    "modality": "fMRI",
    "format": "ROI time-series (N_nodes, T_timepoints)",
    "expected_shape": [116, null],
    "value_range": [-5.0, 5.0],
    "required_preprocessing": ["z-score normalization"]
  },
  "output_spec": {
    "type": "classification|regression",
    "classes": null,
    "value_range": null
  },
  "validation_checksums": {
    "weights_sha256": "abc123...",
    "test_data_sha256": "def456..."
  }
}

Test Suite Requirements

Every model must include an automated test suite covering:

1. Input validation: verify input dimensions, data types, value ranges
2. Determinism check: seed control + verify identical outputs with same seed (tolerance: 1e-6)
3. Performance regression: compare inference speed and memory usage against baseline
4. Output coherence: verify outputs lie within expected value range, no NaN/Inf values
5. Backward compatibility: test model against previous version checksum (if available)

Test execution:

python -m pytest run_models/tests/test_{model_name}.py -v --harness-report

Output: run_models_test_report_{model_name}_{timestamp}.json with pass/fail status and metrics

Drift Detection Protocol

Monitor production/inference results for concept drift (distribution shift in data or model behavior):

Automated monitoring per 100 inferences:

• Input distribution shift (KL divergence against reference data): flag if deviation > 0.1
• Output distribution shift (prediction probability / regression output quantiles): flag if shift detected
• Latency drift (average inference time): alert if >20% increase
• Failure rate monitoring (predictions with NaN/Inf / out-of-range): flag if >1% failures

Logging output: run_models_drift_log.json (append-only, timestamped entries)

Example entry:

{
  "timestamp": "2026-04-05T14:32:00Z",
  "model": "brain_gnn",
  "inference_count": 100,
  "input_kl_divergence": 0.045,
  "output_mean_shift": 0.002,
  "latency_ms": 45.2,
  "failure_rate": 0.0,
  "status": "healthy"
}

Alert thresholds:

• KL divergence > 0.1 → generate warning
• Output shift > 5% std dev → investigation recommended
• Latency drift > 20% → check computational resource bottleneck
• Failure rate > 1% → stop inference, require manual review

Model Card Template (Minimum Required Metadata)

Each model must include a model card in skills/{model_name}/SKILL.md documenting:

## Model Card: {model_name}

### Model Details
- **Model name**: {name}
- **Version**: {X.Y.Z}
- **Date**: {YYYY-MM-DD}
- **Source repository**: {repo_url}
- **Paper**: {citation}

### Intended Use
- **Primary use case**: [e.g., fMRI-based phenotype classification]
- **Input modalities**: [fMRI, sMRI, etc.]
- **Supported tasks**: [classification, regression, interpretability]

### Known Limitations
- [e.g., "Trained on N subjects aged 18-65; generalization to pediatric/geriatric populations not validated"]
- [e.g., "Sensitive to head motion artifacts; recommend ICA-FIX preprocessing"]

### Validation Results
- **Test set performance**: [accuracy/AUC/RMSE with confidence intervals]
- **Cross-site validation**: [performance on held-out sites, if applicable]
- **Robustness checks**: [drift detection history, adversarial perturbation results]

### Dependencies & Versioning
- **Required libraries**: [see {model_name}_spec.json]
- **Hash (model weights)**: {SHA256}
- **Last verified**: {date}

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Delegation Rules

BrainGNN Route

• Required modality preprocessing: fmri-skill
• Typical upstream outputs expected: ROI matrices/time-series converted to model-required feature tensors

BNT Route

• Required modality preprocessing: fmri-skill
• Typical upstream outputs expected: Same ROI .pt files as BrainGNN (shared data source under data/braingnn_input/)

BrainNetCNN Route

• Required modality preprocessing: fmri-skill
• Concrete model execution: skills/brainnetcnn/scripts/train_reference.py
• Typical upstream outputs expected: Dense ROI connectivity matrices in the same .pt format and directory used by BNT

FM-APP Route

• Required modality preprocessing: fmri-skill + smri-skill
• Typical upstream outputs expected: fMRI ROI features plus structural MRI-derived features

NeuroStorm Route

• Required modality preprocessing: follow the model doc in skills/neurostorm/SKILL.md
• Typical upstream outputs expected: inputs and features specified by the NeuroStorm model card

GLM Route

• Required modality preprocessing: fmri-skill
• Concrete model/tool execution: nilearn-tool
• Typical upstream outputs expected:
  • first-level GLM: preprocessed task fMRI, events, optional confounds, named contrasts
  • second-level GLM: subject-level contrast maps, group design matrix, group contrast definition

ICA Route

• Required modality preprocessing: fmri-skill
• Concrete model/tool execution: nilearn-tool
• Typical upstream outputs expected:
  • preprocessed resting-state fMRI image list
  • optional mask and confounds
  • requested component count

DictLearning Route

• Required modality preprocessing: fmri-skill
• Concrete model/tool execution: nilearn-tool
• Typical upstream outputs expected:
  • preprocessed resting-state fMRI image list
  • optional mask and confounds
  • requested component count

Statistical ML Route

• Required modality preprocessing: fmri-skill and/or smri-skill
• Concrete model execution: skills/statistical-ml/scripts/train_reference.py
• Typical upstream outputs expected:
  • ROI/tabular feature matrix, target labels, optional covariates and groups

CNN3D Route

• Required modality preprocessing: fmri-skill and/or smri-skill
• Concrete model execution: skills/cnn3d/scripts/train_reference.py
• Typical upstream outputs expected: aligned subject volume tensor and target

CPM Route

• Required modality preprocessing: fmri-skill
• Concrete model execution: skills/cpm/scripts/train_reference.py
• Typical upstream outputs expected: aligned FC matrices/vectors and labels

SpaceNet Route

• Required modality preprocessing: fmri-skill and/or smri-skill
• Concrete model/tool execution: nilearn-tool
• Typical upstream outputs expected:
  • aligned subject image list, diagnosis labels, mask image, optional covariates

K-means Route

• Required modality preprocessing: fmri-skill and/or smri-skill
• Concrete model/tool execution: nilearn-tool
• Typical upstream outputs expected:
  • feature matrix or aligned image list for parcel discovery
  • optional mask
  • target parcel count

Hierarchical Route

• Required modality preprocessing: fmri-skill and/or smri-skill
• Concrete model/tool execution: nilearn-tool
• Typical upstream outputs expected:
  • feature matrix or aligned image list for parcel discovery
  • optional mask or similarity structure
  • target parcel count

Filtering Route

• Required modality preprocessing: fmri-skill
• Concrete model/tool execution: nilearn-tool
• Typical upstream outputs expected:
  • preprocessed BOLD image or extracted time series
  • TR, optional confounds, optional mask
  • optional frequency settings

Detrending Route

• Required modality preprocessing: fmri-skill
• Concrete model/tool execution: nilearn-tool
• Typical upstream outputs expected:
  • preprocessed BOLD image or extracted time series
  • TR, optional confounds, optional mask
  • detrending request and optional standardization settings

Shared Execution Routing

• Environment/dependency planning: dependency-planner + conda-env-manager
• Actual model run command execution: claw-shell

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Input and Output Contract (Entry-Level)

Inputs expected by this skill

• Model selection (brain_gnn, bnt, fm_app, neurostorm, glm, ica, dictlearning, statistical-ml, spacenet, kmeans, hierarchical, filtering, detrending, cnn3d, cpm, subject-subtyping, survival-models, causal-treatment-models, temporal-models, imaging-genetics-models, or kg-link-prediction)
• Data split / subject list
• Phenotype target definition
• Optional compute constraints (GPU/CPU, memory, batch size)

For GLM routes, the required task definition should be expressed as:

• task name
• events file
• contrast(s) of interest
• optional group-level analysis scope
• whether the request is first-level GLM or second-level GLM
• if second-level GLM: contrast map list and group design matrix

For ICA routes, the required decomposition definition should be expressed as:

• resting-state image list or subject list
• number of components
• optional mask and confounds

For DictLearning routes, the required decomposition definition should be expressed as:

• resting-state image list or subject list
• number of components
• optional mask and confounds

For Statistical ML routes, specify the target, task, model family, feature table, subject/group columns, split definition, and optional covariates.

For SpaceNet routes, the required classification definition should be expressed as:

• diagnosis target / label column
• feature type (voxel-wise)
• subject list or split definition
• optional covariates and mask

For K-means routes, the required parcellation definition should be expressed as:

• image list or feature matrix
• target parcel / cluster count
• optional mask

For Hierarchical routes, the required parcellation definition should be expressed as:

• image list or feature matrix
• target parcel / cluster count
• optional mask, similarity structure, or adjacency constraint

For Filtering routes, the required denoising definition should be expressed as:

• input BOLD image or time series
• TR
• optional confounds, mask, and frequency settings

For Detrending routes, the required denoising definition should be expressed as:

• input BOLD image or time series
• TR
• optional confounds, mask, and standardization settings

Outputs produced by this skill

• A confirmed, numbered run plan
• Pointers to the model-specific instruction file
• Delegated preprocessing plan for required modalities
• Structured output location recommendations

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Recommended Output Layout

All model-running artifacts should be managed under ./run_models_output/:

• run_models_output/preprocessed/
  • fmri/ (from fmri-skill)
  • smri/ (from smri-skill, if required)
• run_models_output/brain_gnn/
• run_models_output/bnt/
• run_models_output/fm_app/
• run_models_output/neurostorm/
• run_models_output/glm/
• run_models_output/ica/
• run_models_output/dictlearning/
• run_models_output/statistical_ml/
• run_models_output/cnn3d/
• run_models_output/cpm/
• run_models_output/spacenet/
• run_models_output/kmeans/
• run_models_output/hierarchical/
• run_models_output/filtering/
• run_models_output/detrending/
• run_models_output/logs/
• run_models_output/reports/

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Safety and Execution Policy

• No execution before explicit user confirmation of the numbered plan.
• All run/install actions must go through claw-shell.
• If model skills are missing in skills/<model-name>/, stop and request or create them before execution.
• Keep train/val/test split and target definition explicit to avoid leakage.

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When to Call This Skill

• User asks to run BrainGNN or FM-APP.
• User asks to run BNT (BrainNetworkTransformer).
• User asks to run BrainNetCNN or a connectome CNN.
• User asks to run NeuroStorm.
• User asks to run classical task activation analysis with GLM.
• User asks to run group-level inference with second-level GLM.
• User asks to perform resting-state network decomposition with ICA.
• User asks to perform resting-state network decomposition with DictLearning.
• User asks to perform ROI/tabular classification with SVM or another classical estimator; route through statistical-ml.
• User asks to perform disease classification with SpaceNet.
• User asks to perform brain parcellation with K-means.
• User asks to perform brain parcellation with Hierarchical clustering.
• User asks to perform signal denoising with filtering.
• User asks to perform signal denoising with detrending.
• User asks to train CNN3D or CPM.
• User asks for subject subtyping, survival, causal-treatment, temporal, imaging-genetics, KG link-prediction, decoding, connectome-discovery, or brain-age workflows.
• User asks which phenotype model to use for fMRI/sMRI ROI data.
• User asks for a unified entry point to model introduction + run routing.

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Complementary / Related Skills

• fmri-skill
• smri-skill
• dependency-planner
• conda-env-manager
• claw-shell

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