PhaseLab Documentation#

A reliability layer for perturbation science.

PhaseLab assesses whether experimental results from perturbation experiments (CRISPR, mutagenesis, chemical modification) will be reproducible—before you run the experiment.

Version 1.0.0 (December 2025)

The Core Insight#

Spatial coherence of response landscapes predicts perturbation reliability.

Validated across 115,251 sgRNAs (6 genes):

  • Correlation with outcome variance: r = -0.24 to -0.50

  • Variance reduction in stable regions: 32-49%

Key Capabilities#

Spatial Coherence Paradigm (v1.0.0)

This release represents a fundamental paradigm shift based on experimental validation:

  • E200-E211: Guide-sequence coherence does NOT work (r ≈ 0)

  • E213-E216: Spatial coherence of response landscapes DOES work

The key insight: “The guide is the probe, not the structure.” Coherence measures the system’s response consistency, not properties of the perturbation itself.

New Domain Modules

  • phaselab.landscapes - Core perturbation-response data structures

  • phaselab.spatial - E213-validated tiling screen analysis

  • phaselab.protein.mutscan - Deep mutational scanning coherence

  • phaselab.protein.folding - Structure prediction quality control

  • phaselab.chem - Binding landscape and reaction optimization

  • phaselab.omics - ATAC-seq, ChIP-seq, RNA-seq reliability

  • phaselab.microbio - TnSeq and bacterial CRISPRi essentiality

Two-Stage Framework

  • Stage I: Feasibility inference (pre-tiling) using structural priors

  • Stage II: Landscape resolution with minimum viable tiling (16-20 perturbations)

Claim Levels

Honest uncertainty reporting:

  • UNKNOWN - Cannot assess reliability

  • EXPLORATORY - Structural priors only

  • CONTEXT_DEPENDENT - Single tiling dataset

  • STRONG_COMPUTATIONAL - Cross-validated

Quick Example#

from phaselab.spatial import analyze_tiling_coherence
from phaselab.landscapes import ResponseLandscape

# Your tiling screen data
landscape = ResponseLandscape(
    coords=[100, 150, 200, 250, 300],
    responses=[0.8, 0.75, 0.1, 0.82, 0.78],
)

# Analyze spatial coherence
result = analyze_tiling_coherence(landscape)

# Find stable regions
for region in result.stable_regions:
    print(f"Stable: {region['start']}-{region['end']}")
    print(f"  Coherence: {region['coherence']:.3f}")

Quantum Mode#

For most use cases, quantum mode should be OFF (default):

from phaselab.quantum import set_quantum_mode, QuantumMode

set_quantum_mode(QuantumMode.OFF)       # Classical only (fastest)
set_quantum_mode(QuantumMode.AUDIT)     # Validation subset
set_quantum_mode(QuantumMode.REQUIRED)  # Research only

Rule: If a classical experiment can falsify a claim, quantum is optional.

Getting Started

User Guide

API Reference

Research Applications

Developer Documentation

Additional Resources

Citation#

@software{phaselab2025,
  title={PhaseLab: A Reliability Layer for Perturbation Science},
  author={Vaca, Dylan},
  year={2025},
  url={https://github.com/followthesapper/phaselab},
  version={1.0.0}
}

Indices and tables#