├── .env ├── .gitattributes ├── .gitignore ├── .gitmodules ├── .pre-commit-config.yaml ├── README.md ├── ctd ├── __init__.py ├── comparison │ ├── __init__.py │ ├── analysis │ │ ├── analysis.py │ │ ├── dd │ │ │ └── dd.py │ │ └── tt │ │ │ ├── tasks │ │ │ ├── tt_MultiTask.py │ │ │ └── tt_RandomTarget.py │ │ │ └── tt.py │ ├── comparison.py │ ├── fixedpoints.py │ ├── metrics.py │ └── utils.py ├── data_modeling │ ├── LICENSE │ ├── __init__.py │ ├── callbacks │ │ ├── LFADS │ │ │ ├── callbacks.py │ │ │ └── extensions │ │ │ │ ├── __init__.py │ │ │ │ ├── armnet.py │ │ │ │ ├── nlb.py │ │ │ │ └── task_trained.py │ │ ├── SAE │ │ │ └── sim_callbacks.py │ │ └── metrics.py │ ├── configs │ │ ├── callbacks │ │ │ ├── LFADS │ │ │ │ ├── default.yaml │ │ │ │ ├── default_MultiTask.yaml │ │ │ │ ├── default_NBFF.yaml │ │ │ │ ├── default_PhaseCodedMemory.yaml │ │ │ │ └── default_RandomTarget.yaml │ │ │ └── SAE │ │ │ │ ├── default_MultiTask.yaml │ │ │ │ ├── default_NBFF.yaml │ │ │ │ ├── default_PhaseCodedMemory.yaml │ │ │ │ └── default_RandomTarget.yaml │ │ ├── datamodules │ │ │ ├── LFADS │ │ │ │ ├── data_MultiTask.yaml │ │ │ │ ├── data_MultiTask_infer.yaml │ │ │ │ ├── data_NBFF.yaml │ │ │ │ ├── data_NBFF_infer.yaml │ │ │ │ ├── data_PhaseCodedMemory.yaml │ │ │ │ ├── data_RandomTarget.yaml │ │ │ │ └── data_RandomTarget_infer.yaml │ │ │ └── SAE │ │ │ │ ├── data_MultiTask.yaml │ │ │ │ ├── data_NBFF.yaml │ │ │ │ ├── data_PhaseCodedMemory.yaml │ │ │ │ └── data_RandomTarget.yaml │ │ ├── extensions │ │ │ └── LFADS │ │ │ │ └── posterior_sampling.yaml │ │ ├── loggers │ │ │ ├── LFADS │ │ │ │ ├── default.yaml │ │ │ │ └── default_no_wandb.yaml │ │ │ └── SAE │ │ │ │ ├── default.yaml │ │ │ │ └── default_no_wandb.yaml │ │ ├── models │ │ │ ├── LFADS │ │ │ │ ├── MultiTask │ │ │ │ │ ├── MultiTask_LFADS.yaml │ │ │ │ │ └── MultiTask_LFADS_infer.yaml │ │ │ │ ├── NBFF │ │ │ │ │ ├── NBFF_LFADS.yaml │ │ │ │ │ └── NBFF_LFADS_infer.yaml │ │ │ │ ├── PhaseCodedMemory │ │ │ │ │ ├── PhaseCodedMemory_InjLFADS.yaml │ │ │ │ │ └── PhaseCodedMemory_LFADS.yaml │ │ │ │ └── RandomTarget │ │ │ │ │ ├── RandomTarget_LFADS.yaml │ │ │ │ │ ├── RandomTarget_LFADS_infer.yaml │ │ │ │ │ └── RandomTarget_ResLFADS.yaml │ │ │ └── SAE │ │ │ │ ├── MultiTask │ │ │ │ ├── MultiTask_GRU_RNN.yaml │ │ │ │ ├── MultiTask_LDS.yaml │ │ │ │ ├── MultiTask_NODE.yaml │ │ │ │ └── MultiTask_Vanilla_RNN.yaml │ │ │ │ ├── NBFF │ │ │ │ ├── NBFF_GRU_RNN.yaml │ │ │ │ ├── NBFF_LDS.yaml │ │ │ │ ├── NBFF_NODE.yaml │ │ │ │ └── NBFF_Vanilla_RNN.yaml │ │ │ │ ├── PhaseCodedMemory │ │ │ │ ├── PhaseCodedMemory_GRU_RNN.yaml │ │ │ │ ├── PhaseCodedMemory_LDS.yaml │ │ │ │ ├── PhaseCodedMemory_NODE.yaml │ │ │ │ └── PhaseCodedMemory_Vanilla_RNN.yaml │ │ │ │ └── RandomTarget │ │ │ │ ├── RandomTarget_GRU_RNN.yaml │ │ │ │ ├── RandomTarget_LDS.yaml │ │ │ │ ├── RandomTarget_NODE.yaml │ │ │ │ └── RandomTarget_Vanilla_RNN.yaml │ │ └── trainers │ │ │ ├── LFADS │ │ │ ├── trainer_MultiTask.yaml │ │ │ ├── trainer_NBFF.yaml │ │ │ ├── trainer_PhaseCodedMemory.yaml │ │ │ └── trainer_RandomTarget.yaml │ │ │ └── SAE │ │ │ ├── trainer_MultiTask.yaml │ │ │ ├── trainer_NBFF.yaml │ │ │ ├── trainer_PhaseCodedMemory.yaml │ │ │ └── trainer_RandomTarget.yaml │ ├── datamodules │ │ ├── LFADS │ │ │ ├── __init__.py │ │ │ ├── datamodule.py │ │ │ └── tuples.py │ │ ├── SAE │ │ │ └── task_trained_data.py │ │ ├── __init__.py │ │ └── utils.py │ ├── extensions │ │ ├── LFADS │ │ │ ├── metrics.py │ │ │ ├── post_run │ │ │ │ ├── __init__.py │ │ │ │ ├── analysis.py │ │ │ │ └── pbt.py │ │ │ └── utils.py │ │ ├── SAE │ │ │ └── utils.py │ │ └── evaluation.py │ ├── models │ │ ├── LFADS │ │ │ ├── __init__.py │ │ │ ├── lfads.py │ │ │ └── modules │ │ │ │ ├── __init__.py │ │ │ │ ├── augmentations.py │ │ │ │ ├── decoder.py │ │ │ │ ├── encoder.py │ │ │ │ ├── initializers.py │ │ │ │ ├── l2.py │ │ │ │ ├── l2_simple.py │ │ │ │ ├── priors.py │ │ │ │ ├── readin_readout.py │ │ │ │ ├── recons.py │ │ │ │ └── recurrent.py │ │ ├── SAE │ │ │ ├── LDS.py │ │ │ ├── __init__.py │ │ │ ├── dyn_models.py │ │ │ ├── dyn_models_gru.py │ │ │ ├── dyn_models_rnn.py │ │ │ ├── gru_rnn.py │ │ │ ├── lds.py │ │ │ ├── loss_func.py │ │ │ ├── node.py │ │ │ ├── readouts.py │ │ │ ├── template.py │ │ │ └── vanilla_rnn.py │ │ └── __init__.py │ └── train_PTL.py └── task_modeling │ ├── __init__.py │ ├── callbacks │ ├── __init__.py │ ├── callbacks.py │ ├── callbacks_coupled.py │ └── callbacks_multitask.py │ ├── configs │ ├── callbacks │ │ ├── default_MultiTask.yaml │ │ ├── default_NBFF.yaml │ │ ├── default_PhaseCodedMemory.yaml │ │ ├── default_RandomTarget.yaml │ │ └── default_no_wandb.yaml │ ├── datamodule_sim │ │ ├── datamodule_MultiTask.yaml │ │ ├── datamodule_NBFF.yaml │ │ ├── datamodule_PhaseCodedMemory.yaml │ │ └── datamodule_RandomTarget.yaml │ ├── datamodule_train │ │ ├── datamodule_MultiTask.yaml │ │ ├── datamodule_NBFF.yaml │ │ ├── datamodule_PhaseCodedMemory.yaml │ │ └── datamodule_RandomTarget.yaml │ ├── env_sim │ │ ├── MultiTask.yaml │ │ ├── NBFF.yaml │ │ ├── PhaseCodedMemory.yaml │ │ └── RandomTarget.yaml │ ├── env_task │ │ ├── MultiTask.yaml │ │ ├── NBFF.yaml │ │ ├── PhaseCodedMemory.yaml │ │ └── RandomTarget.yaml │ ├── logger │ │ ├── default.yaml │ │ └── default_no_wandb.yaml │ ├── model │ │ ├── DriscollRNN.yaml │ │ ├── GRU_RNN.yaml │ │ ├── NODE.yaml │ │ ├── NODE_ICs.yaml │ │ ├── NoisyGRU.yaml │ │ ├── NoisyGRULatentL2.yaml │ │ ├── OscRNN.yaml │ │ └── Vanilla_RNN.yaml │ ├── simulator │ │ ├── default_MultiTask.yaml │ │ ├── default_NBFF.yaml │ │ ├── default_PhaseCodedMemory.yaml │ │ └── default_RandomTarget.yaml │ ├── task_wrapper │ │ ├── MultiTask.yaml │ │ ├── NBFF.yaml │ │ ├── PhaseCodedMemory.yaml │ │ └── RandomTarget.yaml │ └── trainer │ │ └── default.yaml │ ├── datamodule │ ├── __init__.py │ ├── samplers.py │ └── task_datamodule.py │ ├── model │ ├── __init__.py │ ├── node.py │ ├── rnn.py │ └── tt_template.py │ ├── simulator │ ├── __init__.py │ └── neural_simulator.py │ ├── task_env │ ├── __init__.py │ ├── loss_func.py │ ├── multitask.py │ ├── old │ │ └── alternative_tasks.py.py │ ├── phase_coded_memory.py │ ├── random_target.py │ └── task_env.py │ ├── task_training.py │ ├── task_wrapper │ ├── __init__.py │ └── task_wrapper.py │ └── utils.py ├── examples ├── compare_dd_tt_models.ipynb ├── figures │ ├── Embedding │ │ ├── Figure4_NBFF_TTNODE_DTGRU_LatSweeps.ipynb │ │ └── Figure4_NBFF_TTNODE_DTNODE_LatSweeps.ipynb │ ├── Fig1PerfCriteria │ │ ├── Fig1OneBitFlipFlopGen.ipynb │ │ └── old │ │ │ ├── Fig8Gen.ipynb │ │ │ └── lorenz.ipynb │ ├── Fig3TaskPerformance │ │ ├── Figure3AllTasks.ipynb │ │ ├── Figure3MultiTask.ipynb │ │ ├── Figure3NBFF.ipynb │ │ ├── Figure3RandomTarget.ipynb │ │ ├── FigurePhaseCodedMemory.ipynb │ │ ├── MemoryPro_MemoryProPCs_combined_video.gif │ │ └── bumpMove.ipynb │ ├── Fig4Canonical │ │ ├── CanonicalDatasetPerf.ipynb │ │ ├── LearningProgress.ipynb │ │ └── NBFF_Exploration.ipynb │ ├── Fig5Metrics │ │ ├── Figure1_MultiTask_TTGRULyap.ipynb │ │ ├── Figure1_MultiTask_TTGRUSweep.ipynb │ │ ├── Figure1_NBFF_TTGRULyap.ipynb │ │ ├── Figure1_NBFF_TTGRUSweep.ipynb │ │ ├── Figure1_RandomTarget_TTGRULyap.ipynb │ │ └── SLDS │ │ │ └── slds.ipynb │ ├── Fig6InputInf │ │ ├── FigInputInf.ipynb │ │ └── FigInputInfFPFinding.ipynb │ ├── HPSweeping │ │ ├── Figure3_NBFF_TTGRU_DTNODE_LatSweeps.ipynb │ │ └── Figure3_NBFF_TTNODE_DTGRU_LatSweeps.ipynb │ ├── TaskPerformance │ │ └── Figure3MultiTask.ipynb │ └── websiteVids │ │ └── videoGen.ipynb ├── gen_datasets.py ├── notebooks │ ├── old │ │ ├── CtDTutorial.ipynb │ │ ├── NeuroMatchNotebook.ipynb │ │ └── WorkshopNotebook.ipynb │ └── png │ │ ├── AnalysisStructure-01.png │ │ ├── BenchmarkFlow2-01.png │ │ ├── BenchmarkFlowTTDT-01-01.png │ │ ├── BenchmarkGrey-01.png │ │ ├── BenchmarkSchematicSimple_steps.png │ │ ├── DSAPic.png │ │ ├── FinalGif.gif │ │ ├── Hourglass.png │ │ ├── MemoryPro_MemoryProPCs_combined_video.gif │ │ ├── MotorNet Illustration-01.png │ │ ├── MotorNetGif.gif │ │ ├── NoteBookQR.png │ │ ├── Problem.png │ │ ├── SAE.png │ │ ├── SimulationDiagram.png │ │ ├── StateR2-01.png │ │ ├── Step1-01.png │ │ ├── Step2-01.png │ │ ├── Step3-01.png │ │ ├── Step4-01.png │ │ ├── SussilloBarack.png │ │ ├── TTModelExample-01.png │ │ ├── TaskComplexity-01.png │ │ ├── TaskEnvs-01.png │ │ ├── TaskTrained-01.png │ │ ├── TaskTraininSchematic-01.png │ │ ├── Template.png │ │ ├── TutorialTT-01.png │ │ ├── TutorialTT0-01.png │ │ ├── TutorialTTComp-01.png │ │ ├── TutorialTT_model-01.png │ │ ├── lfads_fps.png │ │ └── loopingMultiTask.gif ├── run_data_training.py └── run_task_training.py ├── pretrained ├── .gitattributes ├── 20241017_NBFF_NoisyGRU_NewFinal │ ├── .gitattributes │ ├── datamodule_sim.pkl │ ├── datamodule_train.pkl │ ├── model.pkl │ └── simulator.pkl ├── 20241113_MultiTask_NoisyGRU_Final2 │ ├── datamodule_sim.pkl │ ├── datamodule_train.pkl │ ├── model.pkl │ └── simulator.pkl └── 20241113_RandomTarget_NoisyGRU_Final2 │ ├── datamodule_sim.pkl │ ├── datamodule_train.pkl │ ├── model.pkl │ └── simulator.pkl ├── requirements.txt ├── 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