├── .gitignore ├── .vscode └── settings.json ├── CITATION.cff ├── LICENSE ├── README.md ├── __init__.py ├── env.yml ├── figures ├── fig2 │ ├── 3d-dynamics-example.pdf │ ├── behav-corr-cca.pdf │ ├── monkey-cca-example.pdf │ ├── monkey-cca.pdf │ ├── monkey-decoding.pdf │ ├── mouse-cca.pdf │ ├── rasters.pdf │ └── traj-corr.pdf ├── fig3 │ ├── RW-CCA-Mihili_RT_VR_2014-01-14.pdf │ ├── RW-CCA.pdf │ ├── RW-mean_cca_subset_targets_6_6_2.pdf │ ├── RW-neuron-keep.pdf │ ├── RW-paired_reaches_all_targetsChewie_RT_CS_2016-10-21.pdf │ ├── RW-reaches-Chewie_RT_CS_2016-10-21.pdf │ └── RW-reaches-Mihili_RT_VR_2014-01-14.pdf ├── fig4 │ ├── monkey-cca-prep.pdf │ ├── monkey-target-decoding.pdf │ ├── mouse-cca-str.pdf │ └── mouse-decoding-str.pdf ├── fig5 │ ├── RNN-CCA.pdf │ ├── RNN-behav_corr.pdf │ ├── RNN-dw-dimensionality.pdf │ ├── RNN-dw-var.pdf │ ├── RNN-mses.pdf │ └── RNN-output.pdf ├── figS1-monkey-behaviour │ └── figureS1-monkey-behaviour.pdf ├── figS10-rnn │ ├── RNN-behav-corr.pdf │ ├── RNN-cca.pdf │ ├── RNN-output.pdf │ └── RNN-rasters.pdf ├── figS2-TME │ ├── CCA-dim.pdf │ ├── RW-TME-CCA.pdf │ ├── TME-CCA.pdf │ ├── TME-N-cov.pdf │ ├── TME-target-cov.pdf │ ├── TME-time-cov.pdf │ ├── monkey-procrustes-modes.pdf │ ├── mouse-TME-CCA.pdf │ ├── procrustes-CCA.pdf │ └── vaf_cca_monkeys.pdf ├── figS3-example-cca │ ├── cca-examples.pdf │ └── dynamics-examples.pdf ├── figS4-decoding │ ├── decoding-example.pdf │ ├── decoding-vaf.pdf │ ├── decoding-var-dim.pdf │ └── double-cross-valid-all-sessions.pdf ├── figS5-mouse-behavior │ ├── mouse-FR-example-M1.pdf │ ├── mouse-FR-example-STR.pdf │ ├── mouse-VAF.pdf │ ├── mouse-traj-corr.pdf │ └── mouse_traj.pdf ├── figS6-mouse-additional │ ├── decode-behav-corr.pdf │ ├── mouse-cca-pull-4targets.pdf │ ├── mouse-decoding-M1.pdf │ ├── mouse-str-m1-cca-mean.pdf │ ├── mouse-str-m1-cca-modes.pdf │ └── mouse-str-m1-decoding.pdf ├── figS7-topology │ ├── topo_aligned_ex.pdf │ ├── topo_unaligned.pdf │ ├── topo_vs_dynamics.pdf │ └── topo_vs_dynamics_hist.pdf ├── figS8-RW │ ├── RW-CCA.pdf │ ├── RW-FR-example.pdf │ ├── RW-cca_subset_targets_6_6_2.pdf │ └── RW-neuron-drop.pdf ├── monkey-prep-schematic.pdf ├── monkey-task-schematic.pdf └── mouse-task-schematic.pdf ├── monkey ├── _dataset-selection.ipynb └── defs.py ├── mouse └── defs.py ├── packages ├── config_manager │ ├── LICENSE │ ├── README.md │ ├── config_manager │ │ ├── __init__.py │ │ ├── base_configuration.py │ │ ├── config_field.py │ │ └── config_template.py │ ├── setup.py │ └── tests │ │ ├── __init__.py │ │ ├── constants.py │ │ ├── test_base_configuration.py │ │ ├── test_configs │ │ └── test_config_1.yaml │ │ ├── test_integration.py │ │ └── test_templates │ │ └── test_template_1.py └── pyaldata │ ├── LICENSE │ ├── README.md │ ├── pyaldata │ ├── __init__.py │ ├── array_utils.py │ ├── cmp.py │ ├── data_cleaning.py │ ├── df_utils.py │ ├── dim_reduction.py │ ├── extract_signals.py │ ├── firing_rates.py │ ├── integrity_checks.py │ ├── interval.py │ ├── io.py │ ├── movement_onset_and_peak.py │ ├── regression.py │ ├── signal_transformations.py │ ├── smoothing.py │ ├── tools.py │ └── utils.py │ ├── pyaldata_demo.ipynb │ └── setup.py ├── paper ├── fig2.ipynb ├── fig3.ipynb ├── fig4.ipynb ├── fig5.ipynb ├── figS1-monkey-behavior.ipynb ├── figS10-rnn.ipynb ├── figS2-TME.ipynb ├── figS3-example-cca.ipynb ├── figS4-decoding.ipynb ├── figS5-mouse-behavior.ipynb ├── figS6-mouse-additional.ipynb ├── figS7-topology.ipynb ├── figS8-RW.ipynb └── run_figures.sh ├── params.py ├── random_walk ├── _dataset-selection.ipynb └── defs.py ├── rnn ├── __init__.py ├── data │ └── dataset_chewie_bl0pos.npy ├── defs.py ├── rnn.sh ├── save_pca.py ├── simulation │ ├── __init__.py │ ├── config_template.py │ ├── configs │ │ ├── config_1.yaml │ │ ├── config_2.yaml │ │ ├── config_3.yaml │ │ └── config_4.yaml │ ├── networks.py │ ├── run_pipeline.py │ ├── runner.py │ └── task_data.py └── test.py ├── setup.py └── tools ├── TME ├── computeTME.m ├── genTME │ ├── fitMaxEntropy.m │ ├── logObjectiveMaxEntropyTensor.m │ ├── objectiveMaxEntropyTensor.m │ └── sampleTME.m ├── marginalCov.m └── util │ ├── checkgrad.m │ ├── diagKronSum.m │ ├── extractFeatures.m │ ├── kron_mvprod.m │ ├── lbfgsb │ ├── LICENSE │ ├── Makefile │ ├── README │ ├── array.h │ ├── arrayofmatrices.cpp │ ├── arrayofmatrices.h │ ├── blas.f │ ├── lbfgsb.cpp │ ├── linpack.f │ ├── matlabexception.cpp │ ├── matlabexception.h │ ├── matlabmatrix.cpp │ ├── matlabmatrix.h │ ├── matlabprogram.cpp │ ├── matlabprogram.h │ ├── matlabscalar.cpp │ ├── matlabscalar.h │ ├── matlabstring.cpp │ ├── matlabstring.h │ ├── program.cpp │ ├── program.h │ ├── solver_2_4.f │ ├── solver_3_0.f │ └── timer.f │ ├── minimize.m │ └── sumTensor.m ├── __init__.py ├── ccaTools.py ├── corrTools.py ├── dPCA ├── dpca_explainedVariance.m └── dpca_marginalize.m ├── dataTools.py ├── decodeTools.py ├── lstm.py ├── rasterTools.py ├── simTools.py └── utilityTools.py /.gitignore: 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