DOI: 10.18419/darus-4620
title: Replication Data for: Robustly optimal dynamics for active matter reservoir computing (Gaimann and Klopotek, 2025)

description: &lt;p&gt;
This repository contains raw and post-processed replication data for the publication &lt;a href="https://arxiv.org/abs/2505.05420"&gt;"Robustly optimal dynamics for active matter reservoir computing" (Gaimann and Klopotek, 2025)&lt;/a&gt;.
&lt;/p&gt;

&lt;p&gt;
The datasets contain physical observables recorded during non-equilibrium simulations of active matter systems (swarms) driven by an external force. These simulations serve as information processors in a reservoir computing setup.
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&lt;p&gt;
We provide replication data for all figures and supplementary videos shown in our publication:
&lt;ul&gt;
 &lt;li&gt;speed-controller&lt;/li&gt;
 &lt;li&gt;speed-controller, with an integration time step of 2e-3&lt;/li&gt;
 &lt;li&gt;speed-controller, with a maximum correlation delay time of 75 integration time steps&lt;/li&gt;
 &lt;li&gt;speed-controller, without external driving (undriven)&lt;/li&gt;
 &lt;li&gt;speed-controller, with a single agent&lt;/li&gt;
 &lt;li&gt;speed-controller, with two agents&lt;/li&gt;
 &lt;li&gt;speed-controller, with 500 agents (overdamped phenomenology)&lt;/li&gt;
 &lt;li&gt;speed-controller, with initial transient (burn-in phase)&lt;/li&gt;
 &lt;li&gt;speed-controller, with 12 integration time steps predicted ahead&lt;/li&gt;
 &lt;li&gt;speed-controller, with 50 integration time steps predicted ahead&lt;/li&gt;
 &lt;li&gt;speed-controller, with 100 integration time steps predicted ahead&lt;/li&gt;
 &lt;li&gt;speed-controller, with Hénon-Heiles driving protocol&lt;/li&gt;
 &lt;li&gt;speed-controller, with Hénon-Heiles driving protocol, Lyapunov time-adjusted prediction (638 integration time steps), and maximum correlation delay time of 75 integration time steps&lt;/li&gt;
 &lt;li&gt;speed-controller, with Rössler driving protocol&lt;/li&gt;
 &lt;li&gt;speed-controller, with Rössler driving protocol, Lyapunov time-adjusted prediction (150 integration time steps), and maximum correlation delay time of 75 integration time steps&lt;/li&gt;
 &lt;li&gt;speed-controller, with Chua driving protocol&lt;/li&gt;
 &lt;li&gt;speed-controller, with Chua driving protocol, Lyapunov time-adjusted prediction (18 integration time steps), and maximum correlation delay time of 75 integration time steps&lt;/li&gt;
 &lt;li&gt;speed-controller, with Lorenz-96 driving protocol&lt;/li&gt;
 &lt;li&gt;speed-controller, with Lorenz-96 driving protocol, Lyapunov time-adjusted prediction (17 integration time steps), and maximum correlation delay time of 75 integration time steps&lt;/li&gt;
 &lt;li&gt;speed-controller, with a larger correlation recording delay time of 500 integration time steps&lt;/li&gt;
 &lt;li&gt;damping analysis, with non-interacting agents&lt;/li&gt;
 &lt;li&gt;damping analysis, with interacting agents&lt;/li&gt;
 &lt;li&gt;damping analysis, with non-interacting agents and an integration time step of 2e-3&lt;/li&gt;
 &lt;li&gt;damping analysis, with interacting agents and an integration time step of 2e-3&lt;/li&gt;
 &lt;li&gt;alignment force, with speed-controller settings of Lymburn et al. (2021)&lt;/li&gt;
 &lt;li&gt;alignment force, with overdamped speed-controller settings&lt;/li&gt;
 &lt;li&gt;homing force strength vs. speed-controller strength, with speed-controller settings of Lymburn et al. (2021)&lt;/li&gt;
 &lt;li&gt;homing force strength vs. speed-controller strength, with overdamped speed-controller settings&lt;/li&gt;
 &lt;li&gt;homing force strength vs. speed-controller target agent speed&lt;/li&gt;
 &lt;li&gt;number of agents vs. Gaussian white noise strength, with speed-controller settings of Lymburn et al. (2021)&lt;/li&gt;
 &lt;li&gt;number of agents vs. Gaussian white noise strength, with overdamped speed-controller settings&lt;/li&gt;
 &lt;li&gt;reproduction of the dynamical regimes analyzed in Lymburn et al. (2021) (Fig. 7)&lt;/li&gt;
 &lt;li&gt;reproduction of the (driven) alignment strength vs. repulsion strength parameter scans in Lymburn et al. (2021) (Fig. 6B, Fig. 8A)&lt;/li&gt;
 &lt;li&gt;reproduction of the undriven alignment strength vs. repulsion strength parameter scan in Lymburn et al. (2021) (Fig. 6A)&lt;/li&gt;
&lt;/ul&gt;
&lt;/p&gt;

&lt;p&gt;
The Lorenz-63 driving protocol was generated on the fly during the simulation. We also provide the raw chaotic time series used as benchmark driving protocols:
&lt;ul&gt;
 &lt;li&gt;Hénon-Heiles&lt;/li&gt;
 &lt;li&gt;Rössler&lt;/li&gt;
 &lt;li&gt;Chua&lt;/li&gt;
 &lt;li&gt;Lorenz-96&lt;/li&gt;
&lt;/ul&gt;
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&lt;p&gt;
Each dataset typically contains 400 parameter combinations. Each parameter combination contains four files:
&lt;ul&gt;
 &lt;li&gt;config.yaml: controlled variables&lt;/li&gt;
 &lt;li&gt;simulation_output_train.h5: physical simulation observables in first (training) run&lt;/li&gt;
 &lt;li&gt;simulation_output_test.h5: physical simulation observables in second (testing) run&lt;/li&gt;
 &lt;li&gt;reservoir_computer_output.h5: observables related to reservoir computing and time series prediction&lt;/li&gt;
&lt;/ul&gt;
The second run has a different chaotic driving protocol, using the same underlying dynamical system (chaotic attractor) but different initial conditions.
Only the first file is generated if the dataset contains a simulation without an external driving force (undriven). By default, for all driven simulations, physical observables are only recorded for the test run for a full reservoir computing train/test cycle. Each simulation typically consists of 1,000.00 time units (50,000 integration time steps of 0.02 time units by default). A burn-in phase of 20.0 simulation time units (1,000 integration time steps of 0.02 time units by default) takes place at the beginning of each simulation, which is not recorded by default (only recorded in the "speed-controller, with initial transient" dataset). Controlled variables are stored as HDF5 attributes. At each step, we predict by default 25 integration time steps ahead (=0.45283 L63-Lyapunov times). For Lyapunov times adjusted attractor predictions, we predict n integration time steps ahead that equal 0.45283 Lyapunov times of the corresponding attractor.
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&lt;p&gt;
The simulation output files contain:
&lt;ul&gt;
 &lt;li&gt;agent_observables: positions, velocities, total forces, velocity fluctuations for all agents; for the first 20.0 simulation time units&lt;/li&gt;
 &lt;li&gt;frame_observables: driver position (external driving trajectory / input time series), center of mass (taking periodic boundary conditions into account), agent-averaged observables, scalar polarity, scalar rotation; for the full simulation&lt;/li&gt;
 &lt;li&gt;histograms: binned agent observables and derived quantities; for the full simulation&lt;/li&gt;
 &lt;li&gt;radially_binned: radial distribution function (agent count), connected velocity correlation, cumulative velocity correlation&lt;/li&gt;
 &lt;li&gt;time_lags: auto-correlations of agent observables and derived quantities, two-time correlations of agent observables and derived quantities&lt;/li&gt;
 &lt;li&gt;reference_frame_steps: reference frames (measured in integration steps) for the recording of delay-based quantities in time_lags&lt;/li&gt;
&lt;/ul&gt;
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&lt;p&gt;
The reservoir computer output files contain:
&lt;ul&gt;
 &lt;li&gt; linear_regression_model: the weights of the linear model (readout layer)&lt;/li&gt;
 &lt;li&gt; observer_kernel_params: placement positions and widths of the Gaussian observation kernels&lt;/li&gt;
 &lt;li&gt; predictions_train: n-steps-ahead prediction using the trained linear model, on training data&lt;/li&gt;
 &lt;li&gt; predictions_test: n-steps-ahead prediction using the trained linear model, on testing data&lt;/li&gt;
&lt;/ul&gt;
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&lt;p&gt;
Aggregates of physical observables across all parameter combinations in a single dataset are stored as CSV files for convenience, the relevant observable is indicated by the file name. Files that carry the "time_avg" tag are averaged over all simulation time steps, for the "ensemble_avg" averaged over all seeds (only one seed is used here), and for the "array_avg" averaged over all recorded entries (typically samples at different time steps). We provide the following aggregated observables that were processed to generate figures in our associated publication:
&lt;ul&gt;
 &lt;li&gt;lymburn_correlation_coefficient: Correlation coefficient, predictive performance&lt;/li&gt;
 &lt;li&gt;agent_avg_msd_at_lyapunov_time_step=55: Agent-averaged mean squared displacement at the Lyapunov integration time step of the Lorenz-63 attractor (after 55 integration time steps of 0.02 each)&lt;/li&gt;
 &lt;li&gt;first_local_min.array_avg.h5?connected_velocity_correlation: First local minimum of the connected velocity correlation function, averaged over all recorded samples&lt;/li&gt;
 &lt;li&gt;mean_speed: Agent-averaged speed&lt;/li&gt;
 &lt;li&gt;scalar_polarity: Scalar polarity&lt;/li&gt;
 &lt;li&gt;scalar_rotation: Scalar rotation&lt;/li&gt;
 &lt;li&gt;attanasi_susceptibility: Dynamical susceptibility&lt;/li&gt;
&lt;/ul&gt;
&lt;/p&gt;

&lt;p&gt;
The supplementary videos generated using this raw data are published as: Gaimann, M. U., & Klopotek, M. (2025). Supplementary Videos for: Robustly optimal dynamics for active matter reservoir computing (Gaimann and Klopotek, 2025). DaRUS. &lt;a href="https://doi.org/10.18419/DARUS-4619"&gt;doi:10.18419/DARUS-4619&lt;/a&gt;.
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&lt;p&gt;Changelog&lt;/p&gt;

&lt;p&gt;V2&lt;/p&gt;
&lt;p&gt;
&lt;ul&gt;
&lt;li&gt;Added raw random uniform driver trajectory files confined to a circle with radius 4.0, with different change intervals (used to compute the short-term memory capacity)&lt;/li&gt;
&lt;li&gt;Added datasets for the computation of the short-term memory capacity for parameter combinations of the speed-controller parameter scan, with different driving protocols (Lorenz-63, random uniform with different change intervals). These datasets provide the full recorded Gaussian kernel observations of the simulation runs; datasets labeled with "memory-capacity" contain observables related to the memory capacity.&lt;/li&gt;
&lt;li&gt;Added datasets of a simple Echo State Network (ESN) comparison, following the recipe in Hinaut and Trouvain (2021) (https://inria.hal.science/hal-03203318v2)&lt;/li&gt;
&lt;li&gt;Added a dataset for the undriven active matter simulation of the homing-speed-controller-strength dataset with parameter combination K_h=483 and K_sc=0.0207 (highly condensed droplet case)&lt;/li&gt;
&lt;li&gt;Updated datasets used for figures in the main text with aggregates of more performance metrics (NMSE, NRMSE, sMAPE, Pearson correlation coefficient of the y coordinate computed according to Lymburn et al. (2021))&lt;/li&gt;
&lt;/ul&gt;
&lt;/p&gt;
description: ResoBee, 0.10.0 - 0.14.0
description: Changelog

V2

 Added raw random uniform driver trajectory files confined to a circle with radius 4.0, with different change intervals (used to compute the short-term memory capacity)
 Added datasets for the computation of the short-term memory capacity for parameter combinations of the speed-controller parameter scan, with different driving protocols (Lorenz-63, random uniform with different change intervals). These datasets provide the full recorded Gaussian kernel observations of the simulation runs; datasets labeled with "memory-capacity" contain observables related to the memory capacity.
 Added datasets of a simple Echo State Network (ESN) comparison, following the recipe in Hinaut and Trouvain (2021) (https://inria.hal.science/hal-03203318v2)
 Added a dataset for the undriven active matter simulation of the homing-speed-controller-strength dataset with parameter combination K_h=483 and K_sc=0.0207 (highly condensed droplet case)
 Updated datasets used for figures