onion-clustering 0.3.4

Code for unsupervised clustering of time-correlated data.

timeseries_analysis

Code for unsupervised clustering of time-series data. Reference to https://doi.org/10.1073/pnas.2403771121 for further details.

Development history

This is the oldest, standalone version of onion-clustering. It was last updated on September, 2024 and is no longer supported or mantained. We recomand using the new version of the algorithm, tropea-clustering, which you can find at https://github.com/matteobecchi/onion_clustering.

Input data

A one-dimensional time-series, computed on N particles for T frames. The input files must contain an array with shape (N, T) Supported formats: .npy, .npz, .txt. Also .xyz trajectories are supported, with the fifth column containing the data values.

Usage

Install the package using pip install onion_clustering.

The examples/ folder contains an example of usage. Run python3 example_script.py, this will create the following files:

• A text file called input_parameters.txt , whose format is explained below;
• A text file called data_directory.txt containing one line with the path to the input data file (including the input data file name); and run the code.

input_parameters.txt

• tau_window (int): the length of the time window (in number of frames).
• t_smooth (int, optional): the length of the smoothing window (in number of frames) for the moving average. A value of t_smooth = 1 correspond to no smoothing. Default is 1.
• t_delay (int, optional): is for ignoring the first tau_delay frames of the trajectory. Default is 0.
• t_conv (int, optional): converts number of frames in time units. Default is 1.
• time_units (str, optional): a string indicating the time units. Default is 'frames'.
• example_ID (int, optional): plots the trajectory of the molecule with this ID, colored according to the identified states. Default is 0.
• bins (int, optional): the number of bins used to compute histograms. This should be used only if all the fits fail with the automatic binning.
• num_tau_w (int, optional): the number of different tau_window values tested. Default is 20.
• min_tau_w (int, optional): the smaller tau_window value tested. It has to be larger that 1. Default is 2.
• max_tau_w (int, optional): the larger tau_window value tested. It has to be larger that 2. Default is the largest possible window.
• min_t_smooth (int, optional): the smaller t_smooth value tested. It has to be larger that 0. Default is 1.
• max_t_smooth (int, optional): the larger t_smooth value tested. It has to be larger that 0. Default is 5.
• step_t_smooth (int, optional): the step in the t_smooth values tested. It has to be larger that 0. Default is 1.

Output

The algorithm will attempt to perform the clustering on the input data, using different t_smooth (from min_t_smooth frames to max_t_smooth frames, with steps of step_t_smooth) and different tau_window (logarithmically spaced between 2 frames and the entire trajectory length, unless differently specified in the input parameters). The results are saved in the folowing files:

• number_of_states.txt contains the number of clusters for each combination of tau_window and t_smooth tested.
• fraction_0.txt contains the fraction of unclassified data points for each combination of tau_window and t_smooth tested.
• Figures with all the Gaussian fittings are saved in the folder output_figures with the format t_smooth_tau_window_Fig1_iteration.png.

Then, the analysis with the values of tau_window and t_smooth specified in input_parameters.txt will be performed. The results are saved in the folowing files:

• states_output.txt contains information about the recursive fitting procedure, useful for debugging.
• output_figures/Fig1_iteration.png plot the histograms and best fits for each iteration.
• final_states.txt contains the list of the states, for which central value, width and relevance are listed.
• final_tresholds.txt contains the list of the tresholds between states.

The analisys returns a ClusteringObject, which contains methods for plotting all the results. They are listed in the example scripts.

Multivariate time-series version

The main_2d.py algorithm works in a similar fashion, taking as input 2D or 3D data. The input file contained in data_directory.txt must contain an array of shape (D, N, T) where D is the number of components. Only .npy, .npz are supported. You can find an example of usage in examples/example_script_2d.py

Required Python 3 packages

matplotlib, numpy, plotly, scipy.

Gaussian fitting procedure

1. The histogram of the time-series is estimated using scipy.stats.gauss_kde.
2. The absolute maximum of the histogram is found.
3. Two Gaussian fits are performed:

• The first one inside the interval between the two minima surrounding the maximum.
• The second one inside the interval where the peak around the maxima has its half height.

4. Both fits, if converged, are evaluated according to the coefficinet of determination r^2.
5. Finally, the fit with the best score is chosen. If only one of the two converged, that one is chosen. If none of the fits converges, the iterative procedure stops, returning a warning message.

Aknowledgements

Thanks to Andrew Tarzia for all the help with the code formatting and documentation, and to Domiziano Doria, Chiara Lionello and Simone Martino for the beta-testing. Writing all this code wouldn't have been possible without the help of ChatGPT.