shesha-geometry 0.1.0__tar.gz

shesha_geometry-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Prashant C. Raju
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

shesha_geometry-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: shesha-geometry
+Version: 0.1.0
+Summary: Self-consistency metrics for representational stability analysis
+Author-email: Prashant Raju <rajuprashant@gmail.com>
+License: MIT
+Project-URL: Homepage, https://github.com/prashantcraju/shesha
+Project-URL: Documentation, https://github.com/prashantcraju/shesha#readme
+Project-URL: Repository, https://github.com/prashantcraju/shesha
+Project-URL: Issues, https://github.com/prashantcraju/shesha/issues
+Keywords: representation learning,neural networks,geometric stability,geometric analysis,manifold analysis,latent space,single-cell,crispr,perturb-seq,anndata,functional genomics,phenotypic stability,computational biology,scanpy,llm alignment,concept drift,model steering,ai safety,constitutional ai,perturbation analysis
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.20
+Requires-Dist: scipy>=1.7
+Requires-Dist: anndata>=0.8
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+Requires-Dist: black; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+
+[![DOI](https://zenodo.org/badge/1133185691.svg)](https://doi.org/10.5281/zenodo.18227453)
+<p align="center">
+    <img src="https://i.imgur.com/oJ5YhBo.jpg" alt="Shesha Logo" width="300">
+</p>
+
+# Shesha
+
+Self-consistency metrics for representational stability analysis.
+
+Shesha measures the geometric stability of high-dimensional representations by quantifying the self-consistency of their pairwise distance structure (RDMs) under controlled internal perturbations.
+
+## Installation
+
+```bash
+pip install shesha-geometry
+```
+
+## Quick Start
+
+```python
+import numpy as np
+import shesha
+
+# Your embeddings: (n_samples, n_features)
+X = np.random.randn(500, 768)
+
+# Feature-split stability (unsupervised)
+stability = shesha.feature_split(X, n_splits=30, seed=320)
+print(f"Feature-split stability: {stability:.3f}")
+```
+
+With labels:
+
+```python
+y = np.random.randint(0, 10, 500)
+alignment = shesha.supervised_alignment(X, y)
+print(f"Supervised alignment: {alignment:.3f}")
+```
+
+Measuring drift between representations:
+
+```python
+X_before = np.random.randn(100, 256)
+X_after = X_before + np.random.randn(100, 256) * 0.3  # Add noise
+
+# Compare before/after fine-tuning
+similarity = shesha.rdm_similarity(X_before, X_after)
+drift = shesha.rdm_drift(X_before, X_after)
+print(f"RDM similarity: {similarity:.3f}, drift: {drift:.3f}")
+```
+
+
+## Variants
+
+### Unsupervised (no labels required)
+
+**`feature_split(X, n_splits=30, metric='cosine', seed=None)`**
+
+Correlates RDMs from random feature partitions. Use for internal consistency and drift detection.
+
+**`sample_split(X, n_splits=30, subsample_fraction=0.4, seed=None)`**
+
+Correlates RDMs from bootstrap samples. Use for robustness to sampling.
+
+**`anchor_stability(X, n_splits=30, n_anchors=100, seed=None)`**
+
+Distance profile consistency from fixed anchors. Use for large-scale stability.
+
+### Supervised (labels required)
+
+**`variance_ratio(X, y)`**
+
+Between-class / total variance. Use for quick separability check.
+
+**`supervised_alignment(X, y, metric='correlation', seed=None)`**
+
+Correlation with ideal label RDM. Use for task alignment.
+
+### Drift Metrics (comparing two representations)
+
+**`rdm_similarity(X, Y, method='spearman', metric='cosine')`**
+
+RDM correlation between two representations. Use for comparing models or tracking changes.
+
+**`rdm_drift(X, Y, method='spearman', metric='cosine')`**
+
+Representational drift (1 - similarity). Use for quantifying how much geometry has changed.
+
+## Examples
+
+### Comparing model stability
+
+```python
+import numpy as np
+import shesha
+
+# Example embeddings from two different models
+embeddings_a = np.random.randn(500, 768)  # Model A embeddings
+embeddings_b = np.random.randn(500, 768)  # Model B embeddings
+
+models = {'model_a': embeddings_a, 'model_b': embeddings_b}
+
+for name, X in models.items():
+    fs = shesha.feature_split(X, seed=320)
+    print(f"{name}: {fs:.3f}")
+```
+
+### Monitoring fine-tuning drift
+
+```python
+import shesha
+
+X_initial = model.encode(data)
+
+for epoch in range(10):
+    train_one_epoch(model)
+    X_current = model.encode(data)
+    
+    # Internal stability
+    stability = shesha.feature_split(X_current, seed=320)
+    
+    # Drift from initial
+    drift = shesha.rdm_drift(X_initial, X_current)
+    
+    print(f"Epoch {epoch}: stability={stability:.3f}, drift={drift:.3f}")
+```
+
+### Comparing two models
+
+```python
+import shesha
+
+X_model1 = model1.encode(data)
+X_model2 = model2.encode(data)
+
+# How similar are their geometric structures?
+similarity = shesha.rdm_similarity(X_model1, X_model2)
+print(f"Model similarity: {similarity:.3f}")
+```
+
+### Analyzing single-cell perturbations
+
+Measure the geometric consistency of CRISPR/drug screens directly from `AnnData` objects:
+
+```python
+import numpy as np
+from shesha.bio import compute_stability, compute_magnitude
+from anndata import AnnData
+
+
+# 1. Setup mock single-cell data (1000 cells, 50 PCA features)
+n_cells = 1000
+n_genes = 2000  # Original feature space (genes)
+n_pcs = 50
+
+# Create a mock AnnData object
+# Note: Shesha works best on PCA coordinates (latent space), not raw counts
+adata = AnnData(X=np.random.randn(n_cells, n_genes))  # Raw counts (unused)
+adata.obsm['X_pca'] = np.random.randn(n_cells, n_pcs)  # PCA embeddings
+adata.obs['guide_id'] = ['NT'] * 800 + ['KLF1'] * 200  # Metadata
+
+
+# Create a proxy for PCA coordinates (Recommended for robust geometry)
+adata_pca = AnnData(X=adata.obsm['X_pca'], obs=adata.obs)
+
+
+# Compute Stability (Consistency of the phenotype)
+stability = compute_stability(
+    adata_pca, 
+    perturbation_key='guide_id', 
+    control_label='NT',
+    metric='cosine'
+)
+
+# Compute Magnitude (Strength of the phenotype)
+magnitude = compute_magnitude(
+    adata_pca, 
+    perturbation_key='guide_id', 
+    control_label='NT', 
+    metric='euclidean'
+)
+
+print(f"KLF1 Stability: {stability['KLF1']:.3f}")  # e.g., 0.85 (High = Consistent)
+print(f"KLF1 Magnitude: {magnitude['KLF1']:.3f}")  # e.g., 2.40 (High = Strong)
+```
+
+
+## API Reference
+
+### `shesha.feature_split(X, n_splits=30, metric='cosine', seed=None, max_samples=1600)`
+
+Measures internal geometric consistency by correlating RDMs computed from random, disjoint subsets of feature dimensions.
+
+**Parameters:**
+- `X` - array of shape (n_samples, n_features)
+- `n_splits` - number of random partitions to average
+- `metric` - 'cosine' or 'correlation'
+- `seed` - random seed for reproducibility
+- `max_samples` - subsample if exceeded
+
+**Returns:** float in [-1, 1], higher = more stable
+
+### `shesha.sample_split(X, n_splits=30, subsample_fraction=0.4, metric='cosine', seed=None, max_samples=1500)`
+
+Measures robustness to input variation via bootstrap resampling.
+
+**Parameters:**
+- `X` - array of shape (n_samples, n_features)
+- `n_splits` - number of bootstrap iterations
+- `subsample_fraction` - fraction of samples per bootstrap
+- `metric` - 'cosine' or 'correlation'
+- `seed` - random seed for reproducibility
+- `max_samples` - subsample if exceeded
+
+**Returns:** float in [-1, 1], higher = more stable
+
+### `shesha.anchor_stability(X, n_splits=30, n_anchors=100, n_per_split=200, metric='cosine', rank_normalize=True, seed=None, max_samples=1500)`
+
+Measures stability of distance profiles from fixed anchor points.
+
+**Parameters:**
+- `X` - array of shape (n_samples, n_features)
+- `n_splits` - number of random splits
+- `n_anchors` - number of fixed anchor points
+- `n_per_split` - samples per split
+- `metric` - 'cosine' or 'euclidean'
+- `rank_normalize` - rank-normalize distances within each anchor
+- `seed` - random seed for reproducibility
+- `max_samples` - subsample if exceeded
+
+**Returns:** float in [-1, 1], higher = more stable
+
+### `shesha.variance_ratio(X, y)`
+
+Ratio of between-class to total variance.
+
+**Parameters:**
+- `X` - array of shape (n_samples, n_features)
+- `y` - array of shape (n_samples,) with class labels
+
+**Returns:** float in [0, 1], higher = better class separation
+
+### `shesha.supervised_alignment(X, y, metric='correlation', seed=None, max_samples=300)`
+
+Spearman correlation between model RDM and ideal label-based RDM.
+
+**Parameters:**
+- `X` - array of shape (n_samples, n_features)
+- `y` - array of shape (n_samples,) with class labels
+- `metric` - 'cosine' or 'correlation'
+- `seed` - random seed for reproducibility
+- `max_samples` - subsample if exceeded (RDM is O(n^2))
+
+**Returns:** float in [-1, 1], higher = better task alignment
+
+### `shesha.rdm_similarity(X, Y, method='spearman', metric='cosine')`
+
+Computes RDM correlation between two representations. Useful for comparing models, tracking drift during training, or measuring the effect of interventions.
+
+**Parameters:**
+- `X` - array of shape (n_samples, n_features_x), first representation
+- `Y` - array of shape (n_samples, n_features_y), second representation (same n_samples)
+- `method` - 'spearman' (rank-based, default) or 'pearson' (linear)
+- `metric` - 'cosine', 'correlation', or 'euclidean'
+
+**Returns:** float in [-1, 1], higher = more similar geometric structure
+
+### `shesha.rdm_drift(X, Y, method='spearman', metric='cosine')`
+
+Computes representational drift as 1 - rdm_similarity. Useful for quantifying how much a representation has changed.
+
+**Parameters:**
+- `X` - array of shape (n_samples, n_features_x), baseline representation
+- `Y` - array of shape (n_samples, n_features_y), comparison representation
+- `method` - 'spearman' (rank-based, default) or 'pearson' (linear)
+- `metric` - 'cosine', 'correlation', or 'euclidean'
+
+**Returns:** float in [0, 2], where 0 = identical, 1 = uncorrelated, 2 = inverted
+
+## Biological Perturbation Analysis
+
+The `shesha.bio` module provides metrics for single-cell perturbation experiments (e.g., Perturb-seq, CRISPR screens).
+
+### `shesha.bio.perturbation_stability(X_control, X_perturbed, metric='cosine', seed=None, max_samples=1000)`
+
+Measures consistency of perturbation effects across samples. High values indicate coherent, reproducible perturbation effects.
+
+**Parameters:**
+- `X_control` - array of shape (n_control, n_features), control population
+- `X_perturbed` - array of shape (n_perturbed, n_features), perturbed population
+- `metric` - 'cosine' (default) or 'euclidean'
+- `seed` - random seed for reproducibility
+- `max_samples` - subsample perturbed population if exceeded
+
+**Returns:** float in [-1, 1], higher = more consistent perturbation
+
+### `shesha.bio.perturbation_effect_size(X_control, X_perturbed)`
+
+Cohen's d-like effect size measuring magnitude of perturbation shift.
+
+**Parameters:**
+- `X_control` - array of shape (n_control, n_features)
+- `X_perturbed` - array of shape (n_perturbed, n_features)
+
+**Returns:** float >= 0, higher = larger perturbation effect
+
+### Scanpy / AnnData Integration
+
+For single-cell analysis, Shesha provides high-level wrappers that work directly with `AnnData` objects.
+
+### `shesha.bio.compute_stability(adata, perturbation_key, control_label, layer=None, metric='cosine')`
+
+Computes the geometric stability for every perturbation in the dataset.
+
+**Parameters:**
+- `adata` - AnnData object.
+- `perturbation_key` - Column in `adata.obs` identifying the perturbation (e.g., `'guide_id'`).
+- `control_label` - The label in that column representing control cells (e.g., `'NT'`).
+- `layer` - (Optional) Layer to use (e.g., `'pca'`). If None, uses `.X`.
+- `metric` - `'cosine'` (default) or `'euclidean'`.
+
+**Returns:** Dictionary `{perturbation_name: stability_score}`.
+
+### `shesha.bio.compute_magnitude(adata, perturbation_key, control_label, layer=None, metric='euclidean')`
+
+Computes the magnitude (effect size) for every perturbation.
+
+**Parameters:**
+- `adata` - AnnData object.
+- `metric` - `'euclidean'` (default, raw distance) or `'cohen'` (standardized effect size).
+
+**Returns:** Dictionary `{perturbation_name: magnitude_score}`.
+
+
+## Citation
+
+If you use `shesha-geometry`, please cite:
+```bibtex
+@software{shesha2026,
+    title = {Shesha: Self-consistency Metrics for Representational Stability},
+    author = {Prashant C. Raju},
+    year = {2026},
+    url = {https://github.com/prashantcraju/shesha},
+    publisher = {Zenodo},
+    doi = {10.5281/zenodo.18227454},
+    note = {Python package version 0.1.0}
+}
+
+@article{raju2026geometric,
+    title={Geometric Stability: The Missing Axis of Representations},
+    author={Prashant C. Raju},
+    journal={arXiv},
+    year={2026}
+}
+```
+
+## License
+
+MIT
+
+---
+
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