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landau

Use analogy with Landau theory of phase transitions to look for critical transitions in data.

Associated publication:

Identifying a developmental transition in honey bees using gene expression data
Bryan C. Daniels, Ying Wang, Robert E. Page Jr, Gro V. Amdam
PLoS Computational Biology 19(9): e1010704; doi: https://doi.org/10.1371/journal.pcbi.1010704

The figures in the publication can be reproduced using the following notebooks:

  • Figures 1, 4, 8: landau-simulation-analysis.ipynb
  • Figures 2, 7: landau-bee-data-analysis.ipynb
  • Figure 3, Table 1: LandauTransition-PaperDataAnalysis.nb
  • Figure 5: critical-state-correlations.ipynb
  • Figure 6A: hepatocellular-carcinoma-data.ipynb
  • Figure 6B: LandauTransition-HCC.nb

Dependencies

  • Python 3
  • WolframScript (either through a Mathematica install or standalone)
  • numpy
  • scipy
  • scikit-learn
  • optional for running simulations: pandas, numba

Installation

To install the package and its python dependencies using pip, clone the repository, descend into the landau/ folder, and run

pip install -e .

To automatically include the optional dependencies for running test simulations, instead run

pip install -e '.[simulation]'

WolframScript must also be installed on the system. This can be accomplished by installing Mathematica (and using the prepackaged Extras installer on Mac) or installed as a standalone package available for free download here: https://www.wolfram.com/wolframscript/