@pikaa-ai/pikaa 0.3.23 → 0.3.24
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/assets/brand/orbit-logo-option4-whale.jpg +0 -0
- package/assets/brand/orbit-logo.jpg +0 -0
- package/assets/brand/orbit-logo.png +0 -0
- package/assets/brand/orbit-logo.svg +3 -0
- package/dist/cli.js +337 -162
- package/dist/index.js +1 -2
- package/package.json +1 -2
- package/skills/adaptyv/SKILL.md +0 -240
- package/skills/aeon/SKILL.md +0 -402
- package/skills/analytical-method-validation/SKILL.md +0 -299
- package/skills/anndata/SKILL.md +0 -431
- package/skills/arbor/SKILL.md +0 -152
- package/skills/arboreto/SKILL.md +0 -267
- package/skills/astropy/SKILL.md +0 -353
- package/skills/autoskill/SKILL.md +0 -233
- package/skills/benchling-integration/SKILL.md +0 -229
- package/skills/bgpt-paper-search/SKILL.md +0 -75
- package/skills/bids/SKILL.md +0 -237
- package/skills/biopython/SKILL.md +0 -472
- package/skills/bioservices/SKILL.md +0 -399
- package/skills/bulk-rnaseq/SKILL.md +0 -198
- package/skills/cellxgene-census/SKILL.md +0 -283
- package/skills/cirq/SKILL.md +0 -370
- package/skills/citation-management/SKILL.md +0 -329
- package/skills/clinical-decision-support/SKILL.md +0 -238
- package/skills/clinical-decision-support/references/README.md +0 -62
- package/skills/clinical-reports/SKILL.md +0 -248
- package/skills/clinical-reports/references/README.md +0 -34
- package/skills/cobrapy/SKILL.md +0 -496
- package/skills/consciousness-council/SKILL.md +0 -151
- package/skills/dask/SKILL.md +0 -482
- package/skills/database-lookup/SKILL.md +0 -386
- package/skills/datamol/SKILL.md +0 -200
- package/skills/deepchem/SKILL.md +0 -244
- package/skills/deepspot-m/SKILL.md +0 -175
- package/skills/deeptools/SKILL.md +0 -412
- package/skills/depmap/SKILL.md +0 -301
- package/skills/dhdna-profiler/SKILL.md +0 -184
- package/skills/diffdock/SKILL.md +0 -488
- package/skills/dnanexus-integration/SKILL.md +0 -325
- package/skills/docx/SKILL.md +0 -99
- package/skills/esm/SKILL.md +0 -334
- package/skills/etetoolkit/SKILL.md +0 -327
- package/skills/exa-search/SKILL.md +0 -102
- package/skills/executing-plans/SKILL.md +0 -14
- package/skills/experimental-design/SKILL.md +0 -234
- package/skills/exploratory-data-analysis/SKILL.md +0 -280
- package/skills/flowio/SKILL.md +0 -310
- package/skills/fluidsim/SKILL.md +0 -279
- package/skills/frontend-design/SKILL.md +0 -100
- package/skills/generate-image/SKILL.md +0 -304
- package/skills/geniml/SKILL.md +0 -310
- package/skills/genomic-coordinates/SKILL.md +0 -189
- package/skills/genomic-intelligence/SKILL.md +0 -243
- package/skills/geomaster/README.md +0 -105
- package/skills/geomaster/SKILL.md +0 -366
- package/skills/geopandas/SKILL.md +0 -250
- package/skills/get-available-resources/SKILL.md +0 -260
- package/skills/gget/SKILL.md +0 -153
- package/skills/ginkgo-cloud-lab/SKILL.md +0 -106
- package/skills/glycoengineering/SKILL.md +0 -339
- package/skills/gtars/SKILL.md +0 -282
- package/skills/guardian-rails/SKILL.md +0 -54
- package/skills/histolab/SKILL.md +0 -243
- package/skills/hugging-science/SKILL.md +0 -132
- package/skills/hypogenic/SKILL.md +0 -290
- package/skills/hypothesis-generation/SKILL.md +0 -264
- package/skills/imaging-data-commons/SKILL.md +0 -496
- package/skills/infographics/SKILL.md +0 -315
- package/skills/iso-standards-readiness/SKILL.md +0 -352
- package/skills/lab-hardware-cad/SKILL.md +0 -372
- package/skills/labarchive-integration/SKILL.md +0 -216
- package/skills/lamindb/SKILL.md +0 -408
- package/skills/latchbio-integration/SKILL.md +0 -227
- package/skills/latex-posters/SKILL.md +0 -369
- package/skills/latex-posters/references/README.md +0 -439
- package/skills/liteparse/SKILL.md +0 -295
- package/skills/literature-review/SKILL.md +0 -263
- package/skills/markdown-mermaid-writing/SKILL.md +0 -322
- package/skills/market-research-reports/SKILL.md +0 -337
- package/skills/markitdown/SKILL.md +0 -264
- package/skills/matchms/SKILL.md +0 -276
- package/skills/matlab/SKILL.md +0 -274
- package/skills/matplotlib/SKILL.md +0 -378
- package/skills/medchem/SKILL.md +0 -321
- package/skills/modal/SKILL.md +0 -468
- package/skills/molecular-dynamics/SKILL.md +0 -458
- package/skills/molfeat/SKILL.md +0 -348
- package/skills/ncats-arax/SKILL.md +0 -178
- package/skills/networkx/SKILL.md +0 -440
- package/skills/neurokit2/SKILL.md +0 -323
- package/skills/neuropixels-analysis/SKILL.md +0 -412
- package/skills/nextflow/SKILL.md +0 -195
- package/skills/omero-integration/SKILL.md +0 -222
- package/skills/onekgpd/SKILL.md +0 -371
- package/skills/ontology-term-resolution/SKILL.md +0 -147
- package/skills/open-notebook/SKILL.md +0 -297
- package/skills/openpiv/SKILL.md +0 -469
- package/skills/opentrons-integration/SKILL.md +0 -322
- package/skills/optimize-for-gpu/SKILL.md +0 -176
- package/skills/owasp-top10/SKILL.md +0 -48
- package/skills/pacsomatic/LICENSE +0 -21
- package/skills/pacsomatic/SKILL.md +0 -150
- package/skills/paper-lookup/SKILL.md +0 -263
- package/skills/paperclip/SKILL.md +0 -413
- package/skills/paperzilla/SKILL.md +0 -159
- package/skills/parallel-web/SKILL.md +0 -128
- package/skills/pathml/SKILL.md +0 -222
- package/skills/pathogen-variant-surveillance/SKILL.md +0 -208
- package/skills/pathway-enrichment/SKILL.md +0 -194
- package/skills/pdf/SKILL.md +0 -322
- package/skills/peer-review/SKILL.md +0 -288
- package/skills/penetration-testing/SKILL.md +0 -31
- package/skills/pennylane/SKILL.md +0 -240
- package/skills/phylogenetics/SKILL.md +0 -409
- package/skills/pi-agent/SKILL.md +0 -83
- package/skills/pkpd-modeling/SKILL.md +0 -381
- package/skills/polars/SKILL.md +0 -393
- package/skills/polars-bio/SKILL.md +0 -379
- package/skills/ponytail/SKILL.md +0 -31
- package/skills/ponytail-audit/SKILL.md +0 -18
- package/skills/pptx/SKILL.md +0 -246
- package/skills/pptx-posters/SKILL.md +0 -258
- package/skills/primekg/SKILL.md +0 -99
- package/skills/protocolsio-integration/SKILL.md +0 -236
- package/skills/pufferlib/SKILL.md +0 -328
- package/skills/pydeseq2/SKILL.md +0 -369
- package/skills/pydicom/SKILL.md +0 -381
- package/skills/pyhealth/SKILL.md +0 -124
- package/skills/pylabrobot/SKILL.md +0 -216
- package/skills/pymatgen/SKILL.md +0 -404
- package/skills/pymc/SKILL.md +0 -310
- package/skills/pymoo/SKILL.md +0 -276
- package/skills/pyopenms/SKILL.md +0 -179
- package/skills/pysam/SKILL.md +0 -330
- package/skills/pytdc/SKILL.md +0 -297
- package/skills/pytorch-lightning/SKILL.md +0 -191
- package/skills/pyzotero/SKILL.md +0 -137
- package/skills/qiskit/SKILL.md +0 -259
- package/skills/qutip/SKILL.md +0 -317
- package/skills/rdkit/SKILL.md +0 -94
- package/skills/relsa-severity-assessment/SKILL.md +0 -354
- package/skills/research-grants/SKILL.md +0 -296
- package/skills/research-grants/references/README.md +0 -287
- package/skills/research-lookup/README.md +0 -106
- package/skills/research-lookup/SKILL.md +0 -338
- package/skills/rowan/SKILL.md +0 -398
- package/skills/scanpy/SKILL.md +0 -303
- package/skills/scholar-evaluation/SKILL.md +0 -296
- package/skills/scientific-brainstorming/SKILL.md +0 -282
- package/skills/scientific-critical-thinking/SKILL.md +0 -180
- package/skills/scientific-schematics/SKILL.md +0 -370
- package/skills/scientific-slides/SKILL.md +0 -379
- package/skills/scientific-visualization/SKILL.md +0 -285
- package/skills/scientific-writing/SKILL.md +0 -356
- package/skills/scikit-bio/SKILL.md +0 -470
- package/skills/scikit-learn/SKILL.md +0 -324
- package/skills/scikit-survival/SKILL.md +0 -313
- package/skills/scvelo/SKILL.md +0 -328
- package/skills/scvi-tools/SKILL.md +0 -201
- package/skills/seaborn/SKILL.md +0 -254
- package/skills/security-auditor/SKILL.md +0 -37
- package/skills/shap/SKILL.md +0 -282
- package/skills/simpy/SKILL.md +0 -283
- package/skills/stable-baselines3/SKILL.md +0 -325
- package/skills/statistical-analysis/SKILL.md +0 -446
- package/skills/statistical-power/SKILL.md +0 -200
- package/skills/statsmodels/SKILL.md +0 -238
- package/skills/sympy/SKILL.md +0 -354
- package/skills/systematic-debugging/SKILL.md +0 -35
- package/skills/tamarind/SKILL.md +0 -285
- package/skills/tdd/SKILL.md +0 -26
- package/skills/tiledbvcf/SKILL.md +0 -456
- package/skills/timesfm-forecasting/SKILL.md +0 -408
- package/skills/timesfm-forecasting/examples/global-temperature/README.md +0 -178
- package/skills/torch-geometric/SKILL.md +0 -458
- package/skills/torchdrug/SKILL.md +0 -241
- package/skills/transformers/SKILL.md +0 -195
- package/skills/treatment-plans/SKILL.md +0 -174
- package/skills/treatment-plans/references/README.md +0 -19
- package/skills/umap-learn/SKILL.md +0 -488
- package/skills/uncertainty-and-units/SKILL.md +0 -384
- package/skills/usfiscaldata/SKILL.md +0 -171
- package/skills/vaex/SKILL.md +0 -204
- package/skills/venue-templates/SKILL.md +0 -269
- package/skills/verification-before-completion/SKILL.md +0 -22
- package/skills/waypoint-bio/SKILL.md +0 -273
- package/skills/what-if-oracle/SKILL.md +0 -184
- package/skills/writing-plans/SKILL.md +0 -15
- package/skills/xlsx/SKILL.md +0 -110
- package/skills/zarr-python/SKILL.md +0 -241
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name: scikit-learn
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description: Machine learning in Python with scikit-learn. Use when working with supervised learning (classification, regression), unsupervised learning (clustering, dimensionality reduction), model evaluation, hyperparameter tuning, preprocessing, or building ML pipelines. Provides comprehensive reference documentation for algorithms, preprocessing techniques, pipelines, and best practices.
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license: BSD-3-Clause license
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allowed-tools: Read Write Edit Bash
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compatibility: Requires Python 3.11+ and scikit-learn 1.7+. NumPy and SciPy are required dependencies. Optional matplotlib/seaborn for bundled example scripts that save plots.
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metadata:
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version: "1.2"
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skill-author: K-Dense Inc.
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---
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# Scikit-learn
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## Overview
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This skill provides comprehensive guidance for machine learning tasks using scikit-learn, the industry-standard Python library for classical machine learning. Use this skill for classification, regression, clustering, dimensionality reduction, preprocessing, model evaluation, and building production-ready ML pipelines.
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## Installation
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Tested against **scikit-learn 1.8.0** (stable; December 2025). Requires **Python 3.11–3.14** (free-threaded CPython 3.14 wheels available in 1.8+).
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Install the PyPI package **`scikit-learn`** (not the deprecated `sklearn` package on PyPI). Import in code as `sklearn`.
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```bash
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# Install scikit-learn using uv
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uv pip install "scikit-learn>=1.7"
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# Optional: plotting utilities and bundled script dependencies
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uv pip install "scikit-learn[plots]" matplotlib seaborn
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# Commonly used with
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uv pip install pandas numpy
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```
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Check your version:
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```python
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import sklearn
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print(sklearn.__version__)
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```
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## When to Use This Skill
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Use the scikit-learn skill when:
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- Building classification or regression models
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- Performing clustering or dimensionality reduction
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- Preprocessing and transforming data for machine learning
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- Evaluating model performance with cross-validation
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- Tuning hyperparameters with grid or random search
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- Creating ML pipelines for production workflows
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- Comparing different algorithms for a task
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- Working with both structured (tabular) and text data
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- Need interpretable, classical machine learning approaches
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## Quick Start
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### Classification Example
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```python
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from sklearn.model_selection import train_test_split
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from sklearn.preprocessing import StandardScaler
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from sklearn.ensemble import RandomForestClassifier
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# Split data
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X_train, X_test, y_train, y_test = train_test_split(
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X, y, test_size=0.2, stratify=y, random_state=42
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)
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# Preprocess
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```
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### Complete Pipeline with Mixed Data
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## Core Capabilities
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[references/core_capabilities.md](references/core_capabilities.md), with per-topic detail
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in [references/supervised_learning.md](references/supervised_learning.md),
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[references/unsupervised_learning.md](references/unsupervised_learning.md),
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[references/model_evaluation.md](references/model_evaluation.md),
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[references/preprocessing.md](references/preprocessing.md), and
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[references/pipelines_and_composition.md](references/pipelines_and_composition.md):
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1. **Supervised learning** — classification and regression estimator families.
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2. **Unsupervised learning** — clustering, decomposition, and manifold learning.
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3. **Model evaluation and selection** — metrics, cross-validation, and hyperparameter search.
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4. **Data preprocessing** — scaling, encoding, imputation, and feature selection.
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5. **Pipelines and composition** — `Pipeline` and `ColumnTransformer`.
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Always fit preprocessing inside a `Pipeline` so it is refit per cross-validation fold;
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Two worked workflows are in
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## Example Scripts
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### Classification Pipeline
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```
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Perform clustering analysis with algorithm comparison and visualization:
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**File:** `references/supervised_learning.md`
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### Pipelines and Composition
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**File:** `references/pipelines_and_composition.md`
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## Best Practices
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X_scaled = StandardScaler().fit_transform(X)
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```
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Never fit on test data:
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# Good
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scaler = StandardScaler()
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scaler = StandardScaler()
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X_all_scaled = scaler.fit_transform(np.vstack([X_train, X_test]))
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```
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### Use Stratified Splitting for Classification
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Preserve class distribution:
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```python
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X_train, X_test, y_train, y_test = train_test_split(
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X, y, test_size=0.2, stratify=y, random_state=42
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model = RandomForestClassifier(n_estimators=100, random_state=42)
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```
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### Choose Appropriate Metrics
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- Cost-sensitive: Define custom scorer
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### Scale Features When Required
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Algorithms requiring feature scaling:
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Algorithms not requiring scaling:
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- Naive Bayes
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## Troubleshooting Common Issues
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### ConvergenceWarning
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**Issue:** Model didn't converge
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**Solution:** Increase `max_iter` or scale features
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```python
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model = LogisticRegression(max_iter=1000)
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```
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### Poor Performance on Test Set
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**Issue:** Overfitting
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**Solution:** Use regularization, cross-validation, or simpler model
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```python
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# Add regularization
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model = Ridge(alpha=1.0)
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# Use cross-validation
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scores = cross_val_score(model, X, y, cv=5)
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```
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### Memory Error with Large Datasets
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**Solution:** Use algorithms designed for large data
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```python
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# Use SGD for large datasets
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from sklearn.linear_model import SGDClassifier
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model = SGDClassifier()
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# Or MiniBatchKMeans for clustering
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from sklearn.cluster import MiniBatchKMeans
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model = MiniBatchKMeans(n_clusters=8, batch_size=100)
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```
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## Additional Resources
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- Official Documentation: https://scikit-learn.org/stable/
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- User Guide: https://scikit-learn.org/stable/user_guide.html
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- API Reference: https://scikit-learn.org/stable/api/index.html
|
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- Examples Gallery: https://scikit-learn.org/stable/auto_examples/index.html
|
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@@ -1,313 +0,0 @@
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1
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---
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name: scikit-survival
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|
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description: Build, evaluate, and audit right-censored or competing-risk survival workflows with scikit-survival, including leakage-safe preprocessing, model selection, probability prediction, and censoring-aware metrics.
|
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|
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license: MIT
|
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|
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compatibility: Requires Python 3.11+, uv, and the pinned scikit-survival 0.28.0 stack for executable examples. Bundled CLIs are local and network-free by default.
|
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allowed-tools: Read Write Edit Bash
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metadata:
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version: "1.1"
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skill-author: K-Dense Inc.
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---
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# scikit-survival
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## Scope
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Use this skill for scikit-survival 0.28.0 workflows involving:
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- right-censored structured outcomes;
|
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- Cox PH, Coxnet, IPC ridge, survival trees, forests, boosting, and SVMs;
|
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- discrimination, prediction error, calibration-oriented checks, and time-dependent prediction;
|
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- nonparametric cumulative incidence with competing risks;
|
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- scikit-learn pipelines, nested model selection, and reproducible reports.
|
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scikit-survival primarily models right-censored outcomes. Its built-in competing-risk
|
|
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|
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support is nonparametric cumulative incidence; it does not provide Fine-Gray regression.
|
|
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|
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Do not present model output as clinical advice, causal evidence, or proof of clinical
|
|
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|
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utility.
|
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|
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## Current release and installation
|
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|
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31
|
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Verified 2026-07-23:
|
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|
|
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- Latest stable: **scikit-survival 0.28.0**, released 2026-07-05.
|
|
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- Python: **3.11 or later**; PyPI wheels cover CPython 3.11-3.14 on Linux
|
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|
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x86-64, macOS x86-64/ARM64, and Windows x86-64.
|
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|
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- Runtime bounds: NumPy >=2.0.0, pandas >=2.2.0, SciPy >=1.13.0,
|
|
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scikit-learn >=1.9.0,<1.10, OSQP >=1.0.2, narwhals >=2.0.1.
|
|
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|
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- 0.28 adds pandas/Polars estimator support through narwhals and removes
|
|
39
|
-
`criterion` from `GradientBoostingSurvivalAnalysis`.
|
|
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|
-
|
|
41
|
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Create an isolated environment and install the tested snapshot:
|
|
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|
-
|
|
43
|
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```bash
|
|
44
|
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uv venv --python 3.11
|
|
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|
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source .venv/bin/activate
|
|
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|
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uv pip install \
|
|
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|
-
"scikit-survival==0.28.0" \
|
|
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|
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"scikit-learn==1.9.0" \
|
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|
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"numpy==2.4.6" \
|
|
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|
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"pandas==3.0.5" \
|
|
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|
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"scipy==1.17.1" \
|
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"ecos==2.0.14" \
|
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"osqp==1.1.3" \
|
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"joblib==1.5.3" \
|
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|
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"numexpr==2.14.2" \
|
|
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|
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"narwhals==2.24.0"
|
|
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|
-
```
|
|
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|
-
|
|
59
|
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Binary wheels are preferred. A source build requires a C/C++ compiler; OSQP may
|
|
60
|
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also require CMake. This skill is MIT-licensed; the upstream scikit-survival package
|
|
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|
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is GPL-3.0-or-later, so review upstream licensing before redistribution.
|
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|
|
63
|
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## Non-negotiable workflow
|
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|
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|
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65
|
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1. **Define the estimand and event coding.** Decide whether the target is
|
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all-event survival, cause-specific hazard, or cause-specific cumulative incidence.
|
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2. **Validate outcomes.** Standard estimators need a two-field structured array:
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boolean event first, observed time second. Competing-risk CIF instead needs a
|
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separate integer event vector: 0=censored, 1..K=causes.
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|
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3. **Split before learned preprocessing.** Never fit imputers, encoders, scalers,
|
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feature selectors, or alpha choices on all rows before splitting.
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4. **Fit preprocessing inside a pipeline.** Unknown categories and missingness must
|
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be handled using training-fold state only.
|
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5. **Tune without reusing evaluation data.** Use nested CV when reporting
|
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|
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cross-validated tuned performance, or reserve a truly untouched final holdout.
|
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|
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6. **Fit censoring distributions on training data.** IPCW concordance, dynamic AUC,
|
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and Brier metrics receive `survival_train`, never a pooled train+test outcome.
|
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7. **Restrict evaluation times.** Use a strictly increasing grid inside test
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follow-up and below the end of training support where the estimated censoring
|
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survival remains positive.
|
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|
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8. **Match predictions to metrics.** Concordance/dynamic AUC consume higher-is-riskier
|
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scores. Brier metrics consume survival probabilities with shape
|
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|
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`(n_test, n_times)`, not risk scores or unevaluated step functions.
|
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|
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9. **Handle competing causes explicitly.** Standard survival probabilities and CIFs
|
|
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|
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answer different questions. Never estimate event-specific probability with
|
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`1 - Kaplan-Meier` while censoring competing events.
|
|
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|
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10. **Report limits.** Separate discrimination, calibration, prediction error,
|
|
88
|
-
and cumulative incidence. None alone establishes decision or clinical utility.
|
|
89
|
-
|
|
90
|
-
## Outcome construction
|
|
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|
-
|
|
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|
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```python
|
|
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|
-
from sksurv.util import Surv
|
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|
-
|
|
95
|
-
y = Surv.from_arrays(event=event_bool, time=observed_time)
|
|
96
|
-
# Equivalent for pandas or Polars:
|
|
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|
-
y = Surv.from_dataframe("event", "time", frame)
|
|
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|
-
```
|
|
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|
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|
|
100
|
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The first field is boolean (`True`=event, `False`=right-censored); the second is
|
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|
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floating-point time. Field names may vary, but field order and meaning may not.
|
|
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|
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Use `references/data-handling.md` before loading custom or competing-risk data.
|
|
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|
-
|
|
104
|
-
## Leakage-safe pipeline
|
|
105
|
-
|
|
106
|
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```python
|
|
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|
-
from sklearn.compose import ColumnTransformer
|
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|
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from sklearn.impute import SimpleImputer
|
|
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|
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from sklearn.model_selection import train_test_split
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|
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from sklearn.pipeline import make_pipeline
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|
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from sklearn.preprocessing import OneHotEncoder, StandardScaler
|
|
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|
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from sksurv.linear_model import CoxPHSurvivalAnalysis
|
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|
-
|
|
114
|
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X_train, X_test, y_train, y_test = train_test_split(
|
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|
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X, y, test_size=0.25, stratify=y["event"], random_state=20260723
|
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|
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)
|
|
117
|
-
|
|
118
|
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preprocess = ColumnTransformer(
|
|
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|
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[
|
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120
|
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("num", make_pipeline(SimpleImputer(strategy="median"), StandardScaler()), numeric),
|
|
121
|
-
(
|
|
122
|
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"cat",
|
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123
|
-
make_pipeline(
|
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124
|
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SimpleImputer(strategy="most_frequent"),
|
|
125
|
-
OneHotEncoder(handle_unknown="ignore", drop="first", sparse_output=False),
|
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126
|
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),
|
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127
|
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categorical,
|
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|
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),
|
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|
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],
|
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|
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sparse_threshold=0.0,
|
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|
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)
|
|
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|
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model = make_pipeline(preprocess, CoxPHSurvivalAnalysis(alpha=0.1, ties="efron"))
|
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|
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model.fit(X_train, y_train)
|
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risk = model.predict(X_test)
|
|
135
|
-
```
|
|
136
|
-
|
|
137
|
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The split precedes every learned transformation. For repeated or grouped records,
|
|
138
|
-
use a group-aware split; for temporal deployment, use a time-respecting split.
|
|
139
|
-
|
|
140
|
-
## Model choice
|
|
141
|
-
|
|
142
|
-
- `CoxPHSurvivalAnalysis`: interpretable log-hazard coefficients under proportional
|
|
143
|
-
hazards; `alpha` is ridge shrinkage and `ties` is `"breslow"` or `"efron"`.
|
|
144
|
-
- `CoxnetSurvivalAnalysis`: LASSO/elastic-net path for high-dimensional data.
|
|
145
|
-
`l1_ratio` is in `(0, 1]`; use `fit_baseline_model=True` before requesting
|
|
146
|
-
survival or cumulative-hazard functions.
|
|
147
|
-
- `IPCRidge`: IPC-weighted ridge AFT model; prediction is on a time/log-time scale,
|
|
148
|
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not a Cox risk score.
|
|
149
|
-
- `RandomSurvivalForest` / `ExtraSurvivalTrees`: nonlinear survival and cumulative
|
|
150
|
-
hazard predictions; use permutation importance, not impurity importance.
|
|
151
|
-
- `GradientBoostingSurvivalAnalysis`: tree boosting with `"coxph"`, `"squared"`,
|
|
152
|
-
or `"ipcwls"` loss. `criterion` was removed in 0.28.
|
|
153
|
-
- `ComponentwiseGradientBoostingSurvivalAnalysis`: sparse linear componentwise
|
|
154
|
-
boosting.
|
|
155
|
-
- `FastSurvivalSVM` / `FastKernelSurvivalSVM`: ranking or regression objectives.
|
|
156
|
-
Only `rank_ratio=1` directly returns higher-is-riskier scores; SVMs do not yield
|
|
157
|
-
survival probabilities for Brier metrics.
|
|
158
|
-
|
|
159
|
-
Read the model-specific reference before interpreting coefficients or predictions:
|
|
160
|
-
`references/cox-models.md`, `references/ensemble-models.md`, or
|
|
161
|
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`references/svm-models.md`.
|
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## Prediction and metric contracts
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```python
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import numpy as np
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from sksurv.metrics import (
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brier_score,
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concordance_index_ipcw,
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cumulative_dynamic_auc,
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integrated_brier_score,
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)
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risk = model.predict(X_test) # (n_test,), higher means higher event risk
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uno_c = concordance_index_ipcw(y_train, y_test, risk, tau=times[-1])[0]
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auc_t, mean_auc = cumulative_dynamic_auc(y_train, y_test, risk, times)
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surv_fns = model.predict_survival_function(X_test)
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surv_prob = np.vstack([fn(times) for fn in surv_fns]) # (n_test, n_times)
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_, brier_t = brier_score(y_train, y_test, surv_prob, times)
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ibs = integrated_brier_score(y_train, y_test, surv_prob, times)
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```
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- Harrell C and Uno C measure rank discrimination, not calibration.
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- Cumulative/dynamic AUC measures discrimination at selected horizons and accepts
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1D or time-dependent 2D risk scores; it rejects survival probabilities.
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- Brier score is censoring-weighted probability error and reflects both
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discrimination and calibration. It is not a standalone calibration curve.
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- Calibration requires horizon-specific predicted-versus-observed checks on
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independent data. scikit-survival 0.28 has no dedicated calibration-curve API.
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See `references/evaluation-metrics.md` for assumptions, primary literature, safe
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time-grid construction, and scorer wrappers.
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## Pipelines, metadata routing, and tuning
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Ordinary `Pipeline.fit(X, y)` needs no metadata-routing setup. Metric wrappers such
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as `as_concordance_index_ipcw_scorer` are estimator wrappers, not `scoring=`
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callables:
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```python
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from sklearn.model_selection import GridSearchCV
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from sksurv.metrics import as_concordance_index_ipcw_scorer
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wrapped = as_concordance_index_ipcw_scorer(model, tau=tau)
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search = GridSearchCV(
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wrapped,
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{"estimator__coxphsurvivalanalysis__alpha": [0.01, 0.1, 1.0]},
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cv=inner_splits,
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)
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```
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The wrapper learns the censoring distribution from each fit fold. Prefix wrapped
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parameters with `estimator__`. Enable scikit-learn metadata routing only when
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passing extra metadata through a meta-estimator. For example, Coxnet's
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`set_predict_request(alpha=True)` matters only when routing the `alpha` prediction
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argument with `sklearn.set_config(enable_metadata_routing=True)`.
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Use an outer CV loop for an unbiased CV performance estimate after inner tuning.
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Do not select parameters and report performance from the same folds as if external.
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## Competing risks
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```python
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from sksurv.nonparametric import cumulative_incidence_competing_risks
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# status: integer array, 0=censored, 1..K=mutually exclusive causes
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time, cif = cumulative_incidence_competing_risks(status, observed_time)
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total_cif = cif[0]
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cause_1_cif = cif[1]
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|
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```
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`cif` has shape `(K + 1, n_times)`; row 0 is total risk and rows 1..K are
|
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cause-specific cumulative incidence. Cause-specific Cox models treat other causes
|
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as censored to estimate cause-specific hazards, but one such model's
|
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`1 - survival` is not the cause-specific CIF. See `references/competing-risks.md`.
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## Bundled local CLIs
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|
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|
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240
|
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All helpers use deterministic synthetic data when no input is given. They make no
|
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|
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network calls, reject URLs and symlinks, bound files/rows/features, avoid unsafe
|
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|
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pickle loading, and lazily import scientific packages.
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|
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|
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|
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```bash
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python skills/scikit-survival/scripts/validate_survival_csv.py --help
|
|
246
|
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python skills/scikit-survival/scripts/train_survival_model.py --help
|
|
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|
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python skills/scikit-survival/scripts/evaluate_survival_metrics.py --help
|
|
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|
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python skills/scikit-survival/scripts/competing_risk_cif.py --help
|
|
249
|
-
python skills/scikit-survival/scripts/model_report.py --help
|
|
250
|
-
```
|
|
251
|
-
|
|
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|
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Typical local flow:
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|
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|
-
|
|
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|
-
```bash
|
|
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|
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python skills/scikit-survival/scripts/validate_survival_csv.py \
|
|
256
|
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--input data.csv --event-column event --time-column time \
|
|
257
|
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--feature-columns age,group,measurement --structured-output outcome.npy
|
|
258
|
-
|
|
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|
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python skills/scikit-survival/scripts/train_survival_model.py \
|
|
260
|
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--input data.csv --event-column event --time-column time \
|
|
261
|
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--numeric-columns age,measurement --categorical-columns group \
|
|
262
|
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--model coxph --tune --prediction-output predictions.npz \
|
|
263
|
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--output training-summary.json
|
|
264
|
-
|
|
265
|
-
python skills/scikit-survival/scripts/evaluate_survival_metrics.py \
|
|
266
|
-
--input predictions.npz --output metrics-summary.json
|
|
267
|
-
|
|
268
|
-
python skills/scikit-survival/scripts/model_report.py \
|
|
269
|
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--training-summary training-summary.json \
|
|
270
|
-
--metrics-summary metrics-summary.json --output model-report.md
|
|
271
|
-
```
|
|
272
|
-
|
|
273
|
-
Use only de-identified, authorized local data. The bundled tests contain synthetic
|
|
274
|
-
records only and no patient data or PHI.
|
|
275
|
-
|
|
276
|
-
## Security triage
|
|
277
|
-
|
|
278
|
-
`SECURITY.md` previously claimed this skill bundled package-shadowing files named
|
|
279
|
-
`sklearn.py` and `sksurv.py`. The 2026-07-23 inventory confirmed those files did
|
|
280
|
-
not exist; the claim was a phantom analyzer finding. This refresh adds only
|
|
281
|
-
descriptively named helpers and no shadow modules, environment reads, or network
|
|
282
|
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calls.
|
|
283
|
-
|
|
284
|
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Never name a project script after an imported package (including `sklearn.py`,
|
|
285
|
-
`sksurv.py`, `numpy.py`, or `pandas.py`), because Python may import the local file
|
|
286
|
-
instead of the installed library. Inspect the working directory before executing
|
|
287
|
-
examples copied from untrusted sources.
|
|
288
|
-
|
|
289
|
-
## Reference files
|
|
290
|
-
|
|
291
|
-
- `references/data-handling.md` — structured arrays, datasets, schema validation,
|
|
292
|
-
pandas/Polars preprocessing, and leakage-safe splitting.
|
|
293
|
-
- `references/cox-models.md` — Cox PH, Coxnet, IPCRidge, assumptions, and tuning.
|
|
294
|
-
- `references/ensemble-models.md` — forests, trees, boosting, predictions, and
|
|
295
|
-
permutation importance.
|
|
296
|
-
- `references/svm-models.md` — SVM objectives, prediction direction, scaling,
|
|
297
|
-
kernels, and limitations.
|
|
298
|
-
- `references/evaluation-metrics.md` — metric inputs, censoring assumptions,
|
|
299
|
-
time grids, calibration, nested CV, and primary literature.
|
|
300
|
-
- `references/competing-risks.md` — integer event coding, CIF API, built-in
|
|
301
|
-
datasets, cause-specific hazards, and unsupported Fine-Gray regression.
|
|
302
|
-
|
|
303
|
-
## Dated sources
|
|
304
|
-
|
|
305
|
-
Official API and compatibility sources, checked 2026-07-23:
|
|
306
|
-
|
|
307
|
-
- [PyPI 0.28.0](https://pypi.org/project/scikit-survival/) — released 2026-07-05.
|
|
308
|
-
- [GitHub v0.28.0 release](https://github.com/sebp/scikit-survival/releases/tag/v0.28.0)
|
|
309
|
-
— published 2026-07-05.
|
|
310
|
-
- [0.28 release notes](https://scikit-survival.readthedocs.io/en/stable/release_notes/v0.28.html).
|
|
311
|
-
- [Installation guide](https://scikit-survival.readthedocs.io/en/stable/install.html).
|
|
312
|
-
- [Stable user guide](https://scikit-survival.readthedocs.io/en/stable/user_guide/index.html).
|
|
313
|
-
- [Stable API reference](https://scikit-survival.readthedocs.io/en/stable/api/index.html).
|