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deepskan_public's Introduction

DeepSKAN

Analysis of time resolved spectra using a deep Spectrosopy Kinetic Analysis Network (deepSKAN) and Global/Target Analysis. If this package contributes to a scientific publication, please acknowledge this by citing https://doi.org/10.1021/acs.jpcb.0c04299

Installation instructions:

  • This package is meant to be installed with pip: pip install .

Requirements

The versions specified in requirements.txt are known to work, newer versions will probably be fine but have not been tested

  • Python 3.6
  • keras (using tensorflow backend)
  • networkx
  • numpy
  • scipy
  • matplotlib

Usage

In the examples folder, there are three different ways this package can be used:

  • Training: Trains a resNet-like CNN on synthetic training data generated on the fly.
  • Complete Analysis: Predicts model using neural network, then performs GTA with predicted model.
  • Suggestion: gives suggestions about possible pathways. this is implemented as a webinterface.

Documentation

Basic descriptions of every function are included in their docstring.

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