├── .gitattributes ├── .gitignore ├── README.md ├── UNLICENSE ├── assets └── teaser.png ├── configs ├── 20ms_arxiv.json ├── 20ms_arxiv_no_reg.json ├── 20ms_full_context.json ├── 20ms_mask.json ├── 20ms_no_span.json ├── area2_bump.yaml ├── arxiv │ ├── chaotic.yaml │ ├── lorenz.yaml │ ├── m700_115.yaml │ ├── m700_2296.yaml │ ├── m700_2296_postnorm.yaml │ ├── m700_230.yaml │ ├── m700_460.yaml │ ├── m700_no_log.yaml │ ├── m700_no_reg.yaml │ ├── m700_no_span.yaml │ └── m700_nonzero.yaml ├── dmfc_rsg.json ├── dmfc_rsg.yaml ├── mc_maze.json ├── mc_maze.yaml ├── mc_maze_large.yaml ├── mc_maze_medium.yaml ├── mc_maze_small.yaml ├── mc_maze_small_from_scratch.yaml ├── mc_rtt.yaml ├── sweep_bump.json ├── sweep_generic.json └── sweep_simple.json ├── data ├── chaotic_rnn │ ├── gen_synth_data_no_inputs.sh │ ├── generate_chaotic_rnn_data.py │ ├── generate_chaotic_rnn_data_allowRandomSeed.py │ ├── synthetic_data_utils.py │ └── utils.py ├── lfads_lorenz.h5 └── lorenz.py ├── defaults.py ├── environment.yml ├── nlb.yml ├── ray_get_lfve.py ├── ray_random.py ├── scripts ├── analyze_ray.py ├── analyze_utils.py ├── clear.sh ├── eval.sh ├── fig_3a_synthetic_neurons.py ├── fig_3b_4b_plot_hparams.py ├── fig_5_lfads_times.py ├── fig_5_ndt_times.py ├── fig_6_plot_losses.py ├── nlb.py ├── nlb_from_scratch.ipynb ├── nlb_from_scratch.py ├── record_all_rates.py ├── scratch.py ├── simple_ci.py └── train.sh ├── src ├── __init__.py ├── config │ ├── __init__.py │ └── default.py ├── dataset.py ├── logger_wrapper.py ├── mask.py ├── model.py ├── model_baselines.py ├── model_registry.py ├── run.py ├── runner.py ├── tb_wrapper.py └── utils.py └── tune_models.py /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/README.md -------------------------------------------------------------------------------- /UNLICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/UNLICENSE -------------------------------------------------------------------------------- /assets/teaser.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/assets/teaser.png -------------------------------------------------------------------------------- /configs/20ms_arxiv.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/20ms_arxiv.json -------------------------------------------------------------------------------- /configs/20ms_arxiv_no_reg.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/20ms_arxiv_no_reg.json -------------------------------------------------------------------------------- /configs/20ms_full_context.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/20ms_full_context.json -------------------------------------------------------------------------------- /configs/20ms_mask.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/20ms_mask.json -------------------------------------------------------------------------------- /configs/20ms_no_span.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/20ms_no_span.json -------------------------------------------------------------------------------- /configs/area2_bump.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/area2_bump.yaml -------------------------------------------------------------------------------- /configs/arxiv/chaotic.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/arxiv/chaotic.yaml -------------------------------------------------------------------------------- /configs/arxiv/lorenz.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/arxiv/lorenz.yaml -------------------------------------------------------------------------------- /configs/arxiv/m700_115.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/arxiv/m700_115.yaml -------------------------------------------------------------------------------- /configs/arxiv/m700_2296.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/arxiv/m700_2296.yaml -------------------------------------------------------------------------------- /configs/arxiv/m700_2296_postnorm.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/arxiv/m700_2296_postnorm.yaml -------------------------------------------------------------------------------- /configs/arxiv/m700_230.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/arxiv/m700_230.yaml -------------------------------------------------------------------------------- /configs/arxiv/m700_460.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/arxiv/m700_460.yaml -------------------------------------------------------------------------------- /configs/arxiv/m700_no_log.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/arxiv/m700_no_log.yaml -------------------------------------------------------------------------------- /configs/arxiv/m700_no_reg.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/arxiv/m700_no_reg.yaml -------------------------------------------------------------------------------- /configs/arxiv/m700_no_span.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/arxiv/m700_no_span.yaml -------------------------------------------------------------------------------- /configs/arxiv/m700_nonzero.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/arxiv/m700_nonzero.yaml -------------------------------------------------------------------------------- /configs/dmfc_rsg.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/dmfc_rsg.json -------------------------------------------------------------------------------- /configs/dmfc_rsg.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/dmfc_rsg.yaml -------------------------------------------------------------------------------- /configs/mc_maze.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/mc_maze.json -------------------------------------------------------------------------------- /configs/mc_maze.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/mc_maze.yaml -------------------------------------------------------------------------------- /configs/mc_maze_large.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/mc_maze_large.yaml -------------------------------------------------------------------------------- /configs/mc_maze_medium.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/mc_maze_medium.yaml -------------------------------------------------------------------------------- /configs/mc_maze_small.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/mc_maze_small.yaml -------------------------------------------------------------------------------- /configs/mc_maze_small_from_scratch.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/mc_maze_small_from_scratch.yaml -------------------------------------------------------------------------------- /configs/mc_rtt.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/mc_rtt.yaml -------------------------------------------------------------------------------- /configs/sweep_bump.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/sweep_bump.json -------------------------------------------------------------------------------- /configs/sweep_generic.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/sweep_generic.json -------------------------------------------------------------------------------- /configs/sweep_simple.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/configs/sweep_simple.json -------------------------------------------------------------------------------- /data/chaotic_rnn/gen_synth_data_no_inputs.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/data/chaotic_rnn/gen_synth_data_no_inputs.sh -------------------------------------------------------------------------------- /data/chaotic_rnn/generate_chaotic_rnn_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/data/chaotic_rnn/generate_chaotic_rnn_data.py -------------------------------------------------------------------------------- /data/chaotic_rnn/generate_chaotic_rnn_data_allowRandomSeed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/data/chaotic_rnn/generate_chaotic_rnn_data_allowRandomSeed.py -------------------------------------------------------------------------------- /data/chaotic_rnn/synthetic_data_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/data/chaotic_rnn/synthetic_data_utils.py -------------------------------------------------------------------------------- /data/chaotic_rnn/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/data/chaotic_rnn/utils.py -------------------------------------------------------------------------------- /data/lfads_lorenz.h5: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/data/lfads_lorenz.h5 -------------------------------------------------------------------------------- /data/lorenz.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/data/lorenz.py -------------------------------------------------------------------------------- /defaults.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/defaults.py -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/environment.yml -------------------------------------------------------------------------------- /nlb.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/nlb.yml -------------------------------------------------------------------------------- /ray_get_lfve.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/ray_get_lfve.py -------------------------------------------------------------------------------- /ray_random.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/ray_random.py -------------------------------------------------------------------------------- /scripts/analyze_ray.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/scripts/analyze_ray.py -------------------------------------------------------------------------------- /scripts/analyze_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/scripts/analyze_utils.py -------------------------------------------------------------------------------- /scripts/clear.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/scripts/clear.sh -------------------------------------------------------------------------------- /scripts/eval.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/scripts/eval.sh -------------------------------------------------------------------------------- /scripts/fig_3a_synthetic_neurons.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/scripts/fig_3a_synthetic_neurons.py -------------------------------------------------------------------------------- /scripts/fig_3b_4b_plot_hparams.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/scripts/fig_3b_4b_plot_hparams.py -------------------------------------------------------------------------------- /scripts/fig_5_lfads_times.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/scripts/fig_5_lfads_times.py -------------------------------------------------------------------------------- /scripts/fig_5_ndt_times.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/scripts/fig_5_ndt_times.py -------------------------------------------------------------------------------- /scripts/fig_6_plot_losses.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/scripts/fig_6_plot_losses.py -------------------------------------------------------------------------------- /scripts/nlb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/scripts/nlb.py -------------------------------------------------------------------------------- /scripts/nlb_from_scratch.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/scripts/nlb_from_scratch.ipynb -------------------------------------------------------------------------------- /scripts/nlb_from_scratch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/scripts/nlb_from_scratch.py -------------------------------------------------------------------------------- /scripts/record_all_rates.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/scripts/record_all_rates.py -------------------------------------------------------------------------------- /scripts/scratch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/scripts/scratch.py -------------------------------------------------------------------------------- /scripts/simple_ci.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/scripts/simple_ci.py -------------------------------------------------------------------------------- /scripts/train.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/scripts/train.sh -------------------------------------------------------------------------------- /src/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/src/__init__.py -------------------------------------------------------------------------------- /src/config/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /src/config/default.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/src/config/default.py -------------------------------------------------------------------------------- /src/dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/src/dataset.py -------------------------------------------------------------------------------- /src/logger_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/src/logger_wrapper.py -------------------------------------------------------------------------------- /src/mask.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/src/mask.py -------------------------------------------------------------------------------- /src/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/src/model.py -------------------------------------------------------------------------------- /src/model_baselines.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/src/model_baselines.py -------------------------------------------------------------------------------- /src/model_registry.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/src/model_registry.py -------------------------------------------------------------------------------- /src/run.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/src/run.py -------------------------------------------------------------------------------- /src/runner.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/src/runner.py -------------------------------------------------------------------------------- /src/tb_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/src/tb_wrapper.py -------------------------------------------------------------------------------- /src/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/src/utils.py -------------------------------------------------------------------------------- /tune_models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/snel-repo/neural-data-transformers/HEAD/tune_models.py --------------------------------------------------------------------------------