Shesha Documentation

Shesha is a Python library for measuring the geometric stability of high-dimensional representations via self-consistency of Representational Dissimilarity Matrices (RDMs).

pip install shesha-geometry

Getting Started

• Quick Start
  • Installation
  • Feature-split stability (unsupervised)
  • With labels
  • Measuring drift
  • Bootstrap confidence intervals
  • Single-cell perturbation analysis (Bio)
• Installation
  • Requirements
  • Install from PyPI
  • Install with bio extras
  • Install from source

User Guide

• Unsupervised Metrics
  • Feature split
  • Sample split
  • Anchor stability
  • Bootstrap confidence intervals
• Supervised Metrics
  • Variance ratio
  • Supervised alignment
  • Class separation ratio
  • LDA stability
  • Bootstrap confidence intervals
• Drift Metrics
  • RDM similarity
  • RDM drift
  • Monitoring fine-tuning
  • Bootstrap confidence intervals
• Biological Perturbation Analysis
  • Compute stability
  • Compute magnitude
  • Bootstrap confidence intervals
• Similarity Metrics
  • CKA
  • Procrustes similarity
  • RDM similarity (sim module)
  • Bootstrap confidence intervals
• Bootstrap Confidence Intervals
  • How it works
  • Usage
  • Return format
  • Examples across modules
  • Choosing n_bootstrap_ci
  • Resampling strategy
  • Reproducibility

API Reference

• Core API
  • anchor_stability()
  • class_separation_ratio()
  • compute_rdm()
  • feature_split()
  • lda_stability()
  • rdm_drift()
  • rdm_similarity()
  • sample_split()
  • supervised_alignment()
  • variance_ratio()
  • Unified interface
  • Unsupervised metrics
  • Supervised metrics
  • Drift metrics
  • Utilities
• Bio API
  • compute_magnitude()
  • compute_stability()
  • compute_stability_knn()
  • compute_stability_whitened()
  • perturbation_effect_size()
  • perturbation_stability()
  • perturbation_stability_knn()
  • perturbation_stability_whitened()
• Similarity API
  • cka()
  • cka_debiased()
  • cka_linear()
  • procrustes_similarity()
  • rdm_similarity()

Development

• Citation
• Changelog