Deeptime

Deeptime is a Python library for analysis of time series data. In particular, methods for dimension reduction, clustering, and Markov model estimation are implemented.

The API is similar to that of scikit-learn and offers basic compatibility to its tools via ducktyping.

Deeptime can be installed via conda (conda install -c conda-forge deeptime) delivering pre-compiled binaries and is also available via pip (pip install deeptime), causing the binaries to be compiled locally.

Please note our publication 10.1088/2632-2153/ac3de0.

Main algorithms

Dimension reduction of dynamical data

Deep dimension reduction with neural networks

SINDy - Find governing equations from data

Markov state models

Hidden markov models

Tools and data

Clustering algorithms

Data - Some toy datasets

Citation

When using deeptime in your work, please cite the following

@article{hoffmann2021deeptime,
  title={Deeptime: a Python library for machine learning dynamical models from time series data},
  author={Hoffmann, Moritz and Scherer, Martin Konrad and Hempel, Tim and Mardt, Andreas and de Silva, Brian and Husic, Brooke Elena and Klus, Stefan and Wu, Hao and Kutz, J Nathan and Brunton, Steven and Noé, Frank},
  journal={Machine Learning: Science and Technology},
  year={2021},
  publisher={IOP Publishing}
}