├── .gitignore ├── LICENSE ├── README.md ├── matlab ├── add_all_paths.m ├── basset_connectivity │ ├── GenLouvain2 │ │ ├── MEX_SRC │ │ │ ├── compile_mex.m │ │ │ ├── group_handler.cpp │ │ │ ├── group_handler.h │ │ │ ├── group_index.cpp │ │ │ ├── group_index.h │ │ │ ├── matlab_matrix │ │ │ │ ├── full.cpp │ │ │ │ ├── matlab_matrix.h │ │ │ │ └── sparse.cpp │ │ │ └── metanetwork_reduce.cpp │ │ ├── README.txt │ │ ├── genlouvain.m │ │ └── private │ │ │ ├── group_handler.mexa64 │ │ │ ├── group_handler.mexmaci64 │ │ │ ├── group_handler.mexw64 │ │ │ ├── metanetwork_reduce.mexa64 │ │ │ ├── metanetwork_reduce.mexmaci64 │ │ │ └── metanetwork_reduce.mexw64 │ ├── clustering_coef_wu.m │ ├── community_louvain.m │ ├── fcn_grid_communities.m │ ├── fcn_order_partition.m │ ├── fcn_plot_blocks.m │ ├── mcode.sty │ └── sfn_datascience_bassett_code_v1.m ├── kass_statistical_paradigm │ ├── firstlab_with_answers.mlx │ └── firstlab_without_answers.mlx ├── konrad_tuning_curves │ ├── MyBootstrapErrorBar.m │ ├── MyFitTuningCurve.m │ ├── MyMachineLearningPredictions.m │ ├── MyTuningCurve.m │ ├── Solutions │ │ ├── FullKonradTutorial.m │ │ └── evaluateScoreCosExp.m │ ├── myEvaluateScoreCosExp.m │ └── poplatent_soln.m ├── pillow_glm_tutorials │ ├── Tutorial1_PoissonGLM.ipynb │ ├── tutorial1_PoissonGLM.m │ ├── tutorial2_spikehistcoupledGLM.m │ └── tutorial3_regularization.m ├── sahani_latent_factor │ ├── Code │ │ ├── GenerateData.m │ │ ├── fa_em.m │ │ ├── fa_infer.m │ │ ├── gpfa │ │ │ ├── README │ │ │ ├── core_gpfa │ │ │ │ ├── cosmoother_gpfa_viaOrth.m │ │ │ │ ├── cosmoother_gpfa_viaOrth_fast.m │ │ │ │ ├── em.m │ │ │ │ ├── exactInferenceWithLL.m │ │ │ │ ├── gpfaEngine.m │ │ │ │ ├── grad_betgam.m │ │ │ │ ├── learnGPparams.m │ │ │ │ └── make_K_big.m │ │ │ ├── core_twostage │ │ │ │ ├── cosmoother_fa.m │ │ │ │ ├── cosmoother_pca.m │ │ │ │ ├── fastfa.m │ │ │ │ ├── fastfa_estep.m │ │ │ │ └── twoStageEngine.m │ │ │ ├── example.m │ │ │ ├── neuralTraj.m │ │ │ ├── plotting │ │ │ │ ├── plot3D.m │ │ │ │ ├── plotEachDimVsTime.m │ │ │ │ ├── plotPredErrorVsDim.m │ │ │ │ └── plotPredErrorVsKernSD.m │ │ │ ├── startup.m │ │ │ └── util │ │ │ │ ├── assignopts.m │ │ │ │ ├── cutTrials.m │ │ │ │ ├── fillPerSymm.m │ │ │ │ ├── getSeq.m │ │ │ │ ├── getTrajNewTrials.m │ │ │ │ ├── invPerSymm.m │ │ │ │ ├── invToeplitz │ │ │ │ ├── invToeplitz.m │ │ │ │ ├── invToeplitzFast.m │ │ │ │ ├── invToeplitzFastZohar.c │ │ │ │ ├── invToeplitzFastZohar.mexa64 │ │ │ │ ├── invToeplitzFastZohar.mexglx │ │ │ │ ├── invToeplitzFastZohar.mexmaci │ │ │ │ └── invToeplitzFastZohar.mexw32 │ │ │ │ ├── logdet.m │ │ │ │ ├── minimize.m │ │ │ │ ├── orthogonalize.m │ │ │ │ ├── parseFilename.m │ │ │ │ ├── postprocess.m │ │ │ │ ├── precomp │ │ │ │ ├── makePautoSumFast.c │ │ │ │ ├── makePautoSumFast.mexa64 │ │ │ │ ├── makePautoSumFast.mexglx │ │ │ │ ├── makePautoSumFast.mexmaci │ │ │ │ ├── makePautoSumFast.mexw32 │ │ │ │ └── makePrecomp.m │ │ │ │ ├── segmentByTrial.m │ │ │ │ └── smoother.m │ │ ├── poplatent_tut.m │ │ ├── ssm_em.m │ │ ├── ssm_kalman.m │ │ ├── startup.m │ │ └── util │ │ │ ├── fig.m │ │ │ ├── logdet.m │ │ │ ├── nestable.m │ │ │ ├── nestgroup.m │ │ │ ├── nestplot.m │ │ │ ├── nestplotpos.m │ │ │ ├── optlistassign.m │ │ │ ├── optlistwarn.m │ │ │ └── plottile.m │ └── SOLN │ │ ├── GenerateData.m │ │ ├── fa_em.m │ │ ├── fa_infer.m │ │ ├── gpfa │ │ ├── README │ │ ├── core_gpfa │ │ │ ├── cosmoother_gpfa_viaOrth.m │ │ │ ├── cosmoother_gpfa_viaOrth_fast.m │ │ │ ├── em.m │ │ │ ├── exactInferenceWithLL.m │ │ │ ├── gpfaEngine.m │ │ │ ├── grad_betgam.m │ │ │ ├── learnGPparams.m │ │ │ └── make_K_big.m │ │ ├── core_twostage │ │ │ ├── cosmoother_fa.m │ │ │ ├── cosmoother_pca.m │ │ │ ├── fastfa.m │ │ │ ├── fastfa_estep.m │ │ │ └── twoStageEngine.m │ │ ├── example.m │ │ ├── neuralTraj.m │ │ ├── plotting │ │ │ ├── plot3D.m │ │ │ ├── plotEachDimVsTime.m │ │ │ ├── plotPredErrorVsDim.m │ │ │ └── plotPredErrorVsKernSD.m │ │ ├── startup.m │ │ └── util │ │ │ ├── assignopts.m │ │ │ ├── cutTrials.m │ │ │ ├── fillPerSymm.m │ │ │ ├── getSeq.m │ │ │ ├── getTrajNewTrials.m │ │ │ ├── invPerSymm.m │ │ │ ├── invToeplitz │ │ │ ├── invToeplitz.m │ │ │ ├── invToeplitzFast.m │ │ │ ├── invToeplitzFastZohar.c │ │ │ ├── invToeplitzFastZohar.mexa64 │ │ │ ├── invToeplitzFastZohar.mexglx │ │ │ ├── invToeplitzFastZohar.mexmaci │ │ │ └── invToeplitzFastZohar.mexw32 │ │ │ ├── logdet.m │ │ │ ├── minimize.m │ │ │ ├── orthogonalize.m │ │ │ ├── parseFilename.m │ │ │ ├── postprocess.m │ │ │ ├── precomp │ │ │ ├── makePautoSumFast.c │ │ │ ├── makePautoSumFast.mexa64 │ │ │ ├── makePautoSumFast.mexglx │ │ │ ├── makePautoSumFast.mexmaci │ │ │ ├── makePautoSumFast.mexw32 │ │ │ └── makePrecomp.m │ │ │ ├── segmentByTrial.m │ │ │ └── smoother.m │ │ ├── poplatent_soln.m │ │ ├── poplatent_tut.m │ │ ├── ssm_em.m │ │ ├── ssm_kalman.m │ │ ├── startup.m │ │ └── util │ │ ├── fig.m │ │ ├── logdet.m │ │ ├── nestable.m │ │ ├── nestgroup.m │ │ ├── nestplot.m │ │ ├── nestplotpos.m │ │ ├── optlistassign.m │ │ ├── optlistwarn.m │ │ └── plottile.m └── 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