Tags: NACLab/ngc-learn
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Minor mods in release sync'd up back to main (#106) * further nudge from main to release (#104) * generalized rate-cell a bit * touched up rate-cell further * minor mod to lif * updated lif-cell to use units/tags and minor cleanup and edits * Monitor plot (#66) * Update base_monitor.py * added plotting viewed compartments * added meta-data to rate-cell, input encoders, adex * fixed minor saving/loading in rate-cell w/ vectorized compartments * Added auto resolving for monitors (#67) * fixed surr arg in lif-cell * modded bernoulli-cell to include max-frequency constraint * added warning check to bernoulli, some cleanup * integrated if-cell, cleaned up lif and inits * mod to latency-cell * updated the poissonCell to be a true poisson * fixed minor bug in deprecation for poiss/bern * fixed minor bug in deprecation for poiss/bern * fixed validation fun in bern/poiss * moved back and cleaned up bernoulli and poisson cells * added threshold-clipping to latency cell * updates to if/lif * added batch-size arg to slif * fixed minor load bug in lif-cell * fixed a blocking jit-partial call in lif update_theta method; when loading * minor edit to dim-reduce * Patched synapses added (#68) * Patched synapses added * Update __init__.py * Update patch_utils.py patch_with_stride & patch_with_overlap functions + Create_Patches class added * Update patchedSynapse.py * Update hebbianPatchedSynapse.py * Update synapse_plot.py order added * updated monitor plot code * update to dim-reduce * integrated phasor-cell, minor cleanup of latency * tweak to adex thr arg * tweak to adex thr arg * integrated resonate-and-fire neuronal cell * mod to raf-cell * cleaned up raf * cleaned up raf * cleaned up raf-cell * cleaned up raf-cell * cleaned up raf-cell * minor tweak to dim-reduce in utils * Fix typo in pcn_discrim.md (#69) * model_utils and rate cell (#70) * Patched synapses added * Update __init__.py * Update patch_utils.py patch_with_stride & patch_with_overlap functions + Create_Patches class added * Update patchedSynapse.py * Update hebbianPatchedSynapse.py * Update synapse_plot.py order added * Create hierarchical_sc.md 1 * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update sparse_coding.md * Update sparse_coding.md * Update sparse_coding.md * Update sparse_coding.md * Update hierarchical_sc.md * Update sparse_coding.md * Update sparse_coding.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Add files via upload * Delete docs/images/hgpc_network.pdf * Add files via upload * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Create hgpc * Delete docs/images/museum/hgpc * Create d * Add files via upload * Delete docs/images/hgpc_model.png * Delete docs/images/museum/hgpc/d * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Add files via upload * Update hierarchical_sc.md * Update hierarchical_sc.md * Delete docs/images/museum/hgpc/Input_layer.png * Add files via upload * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Create Generative_PC.md * Update and rename Generative_PC.md to generative_pc.md * Update generative_pc.md * Update generative_pc.md * Update model_utils.py * Update model_utils.py * Update model_utils.py * Update model_utils.py * Update rateCell.py * Update generative_pc.md * Create pc-sindy.md * Update pc-sindy.md * Update model_utils.py sine activation function added * Update model_utils.py * Update ode_utils.py jitified * Delete docs/museum/hierarchical_sc.md * Delete docs/museum/generative_pc.md * Delete ngclearn/components/synapses/patched directory * Update __init__.py * Add files via upload ode with scanner added * Update ode_solver.py _ removed * Fix/reorganize feature library (#74) * Update ode_utils.py * Update ode_solver.py rk4 revised and __main__ added * Delete ngclearn/utils/diffeq/ode_functions.py * Create odes.py odes name and structure changed * Update __init__.py * Create feature_library.py * Create __init__.py * Create base.py * Delete docs/museum/pc-sindy.md * Create m.md * Add files via upload * Delete docs/images/museum/sindy/m.md * Add files via upload * Create sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * fix: correct feature library path and directory name * Delete ngclearn/utils/dymbolic_dictionary directory * Update model_utils.py (#78) * Additions for inhibition stuff * add sindy documentation for exhibits (#81) * Add files via upload * Add files via upload * Update ode_utils.py (#79) refactor: delete @partial(jit, static_argnums=(2, )) lines Co-authored-by: Will Gebhardt <[email protected]> * Add patched synapse (#80) * Update __init__.py Add point to patched components * Add patched in __init__.py Add patched synapses importing * Add patched synaptic components * Delete ngclearn/components/synapses/patched/__pycache__ directory * Update __init__.py new line characters added * Update hebbianPatchedSynapse.py * Update patchedSynapse.py new line characters added * Update staticPatchedSynapse.py new line characters added * Update staticPatchedSynapse.py New line characters + comments for describing each input vars * Update patchedSynapse.py Removed a comment line * Update hebbianPatchedSynapse.py remove unused arguments * Update hebbianPatchedSynapse.py * Update hebbianPatchedSynapse.py add description for w_mask * Update hebbianPatchedSynapse.py * Update hebbianPatchedSynapse.py * Update patchedSynapse.py * Update patchedSynapse.py * Update hebbianPatchedSynapse.py * Update __init__.py (#83) * Update __init__.py typo fixed * Update staticPatchedSynapse.py a typo fixed * Update hebbianPatchedSynapse.py typo foxed * Add l1 decay term to update calculation (#84) * Update hebbianSynapse.py * update main update main at the end * Update hebbianSynapse.py add regularization argument and w_decay is deprecated. * Update hebbianSynapse.py add elastic_net * Update hebbianSynapse.py * Update hebbianSynapse.py * feat NGC module regression (#86) * feat npc module regression * Update __init__.py * Update __init__.py * Update elastic_net.py * Update lasso.py * Update ridge.py * Update elastic_net.py * Update ridge.py * Update lasso.py * Update odes.py removed @partial(jit, static_argnums=(0,)) * Update odes.py (#87) removed @partial(jit, static_argnums=(0,)) * Update odes.py typo fixed in __main__ * Update __init__.py add dot * Update __init__.py add dot * Add attribute 'lr' (#90) * Update elastic_net.py * add lr as attribute to lasso.py * add lr as attribute to ridge.py * refactor w_bound=0. for weights elastic_net.py deactivated w_bound for weights elastic_net.py * Update lasso.py * deactivated w_bound for weights ridge.py * commit probes/mods to utils to analysis_tools branch * commit probes/mods to utils to analysis_tools branch * update documentation * cleaned up probes/docs for probes * change heads_dim to attn_dim, and modify the mlp to be as similar as possible to the attentive probing pattern * in layer normalization or any other Gaussian, standardeviation can never be zero. Additionally, if the subtraction inside the square root goes to zero, the gradient will become NaN. Therefore, adding a clipping is necessary. * update attentive probe code * minor tweak to attentive prob code comments * cleaned up probe parent fit routine * cleaned up probe parent fit routine * cleaned up probe parent fit routine * cleaned up probe parent fit routine * minor edits to attn probe * update attentive probe with input layer norm * update input layer normalization * update code to fix nan bug * minor tweak to attn probe * cleaned up probes * cleaned up probes * cleaned up probes * cleaned up probes * generalized dropout in terms of shape * tweak to atten probe * tweak to atten probe * added silu/swish/elu to model_utils * cleaned up model_utils * fix bug in attention probe dropout, fix bug in None noise_key passed in the probing jit function, add the spliting of noise_keys to two dropout in two cross attention * hyperparameter tunning arguments added * Merging over Dynamics feature branch to main (#92) * modded bernoulli-cell to include max-frequency constraint * added warning check to bernoulli, some cleanup * integrated if-cell, cleaned up lif and inits * mod to latency-cell * updated the poissonCell to be a true poisson * fixed minor bug in deprecation for poiss/bern * fixed minor bug in deprecation for poiss/bern * fixed validation fun in bern/poiss * moved back and cleaned up bernoulli and poisson cells * added threshold-clipping to latency cell * updates to if/lif * added batch-size arg to slif * fixed minor load bug in lif-cell * fixed a blocking jit-partial call in lif update_theta method; when loading * minor edit to dim-reduce * updated monitor plot code * update to dim-reduce * integrated phasor-cell, minor cleanup of latency * tweak to adex thr arg * tweak to adex thr arg * integrated resonate-and-fire neuronal cell * mod to raf-cell * cleaned up raf * cleaned up raf * cleaned up raf-cell * cleaned up raf-cell * cleaned up raf-cell * minor tweak to dim-reduce in utils * Additions for inhibition stuff * update to API modeling docs to reflect RAF neuronal cell --------- Co-authored-by: Alexander Ororbia <[email protected]> Co-authored-by: Will Gebhardt <[email protected]> * remove unused local variables * update note * update model utils * remove notes * Update ode utils (#94) * Update ode_utils.py merge ode_solver into ide_utils * Delete ngclearn/utils/diffeq/ode_solver.py * Update ode_utils.py refactor doc-string * minor fix to header in diffeq * Update files with ode_solver (#95) * Update ode_utils.py merge ode_solver into ide_utils * Delete ngclearn/utils/diffeq/ode_solver.py * Update ode_utils.py refactor doc-string * Update odes.py * Update sindy.md ode_solver to ode_utils * revised/cleaned up sindy tutorial doc/imgs * add prior for hebbian patched synapse (#96) * prior replaced w_decay hebbianPatchedSynapse.py remove w_decay add prior_type and prior_lmbda * revised typo hebbianSynapse.py dWweight was typo * cleaned up doc-strings in odes.py to comply w/ ngc-learn format * minor tweak to sig-figs printing in probe utils * add-sigma-to-gaussianErrorCell (#97) * add-sigma-to-gaussianErrorCell add not updating scalar variance for gaussian errors * Update gaussianErrorCell.py * cleaned up ode_utils, cleaned up gaussian/laplacian cell * Update gaussianErrorCell.py (#98) added `and not isinstance(sigma, int)` * cleaned up gauss/laplace error cells * integrated bernoulli err-cell * Major release update merge to main (in prep for 2.0.0 release on release branch/pip) (#99) * add initial patch mask features * minor edit to bern-cell * fixed bernoulli error cell * example rate cell test * made some corrections to bern err-cell and heb syn * made some corrections to bern err-cell and heb syn * cleaned up bern-cell, hebb-syn * minor mod to model-utils * attempted rewrite of bernoulli-cell * got bernoulli-cell rewritten and unit-tested * edit to bern-cell * bernoulli and poisson cells revised, unit-tested * latency-cell refactored and unit-tested * refactored Rate Cell * minor revisions to input-encoders, revised phasor-cell w/ unit-test * revised and add unit-test for varTrace * revised and added unit-test for exp-kernel * revised and added unit-test for exp-kernel * revised slif cell w/ unit-test; needed mod to diffeq * revised slif-cell w/ unit-test; cleaned up ode_utils to play nicer w/ new sim-lib * revised lif-cell w/ unit-test * revised unit-tests to pass globally; some minor patches to phasor-cell and lif * minor cleanup of unit-test for phasor * revised if-cell w/ unit-test * revised if-cell w/ unit-test * revised quad-lif w/ unit-test * revised adex-cell w/ unit test, minor cleanup of quad-lif * minor edit to adex unit-test * refactor bernoulli, laplacian, and rewarderror cells * revised raf-cell w/ unit test; fixed typos/mistakes in all spiking cells * revised wtas-cell w/ unit test * revised fh-cell w/ unit test * revised izh-cell w/ unit test * patched ode_utils backend wrt jax, cleaned up unit-tests, added disable flag for phasor-cell * update rate cell * fix test rate cell * update test for bernoulli cell * update refactoring for gaussian error cell * update unit testing for all graded neurons * wrote+unit-test of hodgkin-huxley spike cell, minor tweaks/clean-up elsewhere * added rk2 support for H-H cell * update rate cell and fix bug of passing a tuple of (jax Array -- not hashable) to jax jit functions. Basically, simplify the codebase by using a hashmap of functions * update test rate cell * refactored dense and trace-stdp syn w/ unit-test * refactored exp-stdp syn w/ unit-test * refactored event-stdp w/ unit-test * cleanup of stdp-syn * refactored bcm syn w/ unit-test * refactored stp-syn with unit-test * cleaned up modulated * refactored mstdp-et syn w/ unit-test * refactored lava components to new sim-lib * refactored conv/hebb-conv syn w/ unit-test * refactored/revised hebb-deconv syn w/ unit-test * revised/refactored hebb/stdp conv/deconv syn w/ unit-tests * updated modeling doc to point to hodgkin-huxley cell * updated modeling docs * fixed typo in adex-cell tutorial doc * revised tutorials to reflect new sim-lib config/syntax * revised tutorials to reflect new sim-lib config/syntax * patched docs to reflect revisions/refactor * tweaked requirements in prep for major release * cleaned up a few unit tests to use deterministic syn init vals * mod to requirements * nudge toml to upcoming 2.0.0 * update to support docs in prep for 2.0.0 * update patched synapses and their test cases * cleaned up syn modeling doc * push hebbian synapse * push reinforce synapse * push np seed * patched minor prior None arg issue in hebb-syn * moved reinforce-syn to right spot * update reinforce synapse and testing * tweaked trace-stdp and mstdpet * patched mstdpet unit-test * update reinforce synapse and test cases * add reinforce synapse fix * minor mod to mstdpet * update test code for more than 1 steps * Updated monitors * patched tests to use process naming * Added wrapper for reset and advance_state * Added a JaxProcess Added Jax Process to allow for scanning over the process. * update the old rate cell * update old hebbian synapse * minor edit to if-cell * ported over adex tutorial to new ngclearn format * hh-cell supports rk4 integration * clean up and integrated hodgkin-huxley mini lesson in neurocog tutorials * Update jaxProcess.py Updated the jax process to allow for more configurations of inputs. * update working reinforce synapse * update correct reinforce and testing * update documentation * update features, documentation, and testing * update testing for REINFORCE cell * update code and test * update code * add clipping gradient to model utils * update reinforce cell to the new model utils clip * update test cases --------- Co-authored-by: Viet Dung Nguyen <[email protected]> Co-authored-by: Alexander Ororbia <[email protected]> Co-authored-by: Will Gebhardt <[email protected]> * Major release update (to 2.0.0) (#100) * add initial patch mask features * minor edit to bern-cell * fixed bernoulli error cell * example rate cell test * made some corrections to bern err-cell and heb syn * made some corrections to bern err-cell and heb syn * cleaned up bern-cell, hebb-syn * minor mod to model-utils * attempted rewrite of bernoulli-cell * got bernoulli-cell rewritten and unit-tested * edit to bern-cell * bernoulli and poisson cells revised, unit-tested * latency-cell refactored and unit-tested * refactored Rate Cell * minor revisions to input-encoders, revised phasor-cell w/ unit-test * revised and add unit-test for varTrace * revised and added unit-test for exp-kernel * revised and added unit-test for exp-kernel * revised slif cell w/ unit-test; needed mod to diffeq * revised slif-cell w/ unit-test; cleaned up ode_utils to play nicer w/ new sim-lib * revised lif-cell w/ unit-test * revised unit-tests to pass globally; some minor patches to phasor-cell and lif * minor cleanup of unit-test for phasor * revised if-cell w/ unit-test * revised if-cell w/ unit-test * revised quad-lif w/ unit-test * revised adex-cell w/ unit test, minor cleanup of quad-lif * minor edit to adex unit-test * refactor bernoulli, laplacian, and rewarderror cells * revised raf-cell w/ unit test; fixed typos/mistakes in all spiking cells * revised wtas-cell w/ unit test * revised fh-cell w/ unit test * revised izh-cell w/ unit test * patched ode_utils backend wrt jax, cleaned up unit-tests, added disable flag for phasor-cell * update rate cell * fix test rate cell * update test for bernoulli cell * update refactoring for gaussian error cell * update unit testing for all graded neurons * wrote+unit-test of hodgkin-huxley spike cell, minor tweaks/clean-up elsewhere * added rk2 support for H-H cell * update rate cell and fix bug of passing a tuple of (jax Array -- not hashable) to jax jit functions. Basically, simplify the codebase by using a hashmap of functions * update test rate cell * refactored dense and trace-stdp syn w/ unit-test * refactored exp-stdp syn w/ unit-test * refactored event-stdp w/ unit-test * cleanup of stdp-syn * refactored bcm syn w/ unit-test * refactored stp-syn with unit-test * cleaned up modulated * refactored mstdp-et syn w/ unit-test * refactored lava components to new sim-lib * refactored conv/hebb-conv syn w/ unit-test * refactored/revised hebb-deconv syn w/ unit-test * revised/refactored hebb/stdp conv/deconv syn w/ unit-tests * updated modeling doc to point to hodgkin-huxley cell * updated modeling docs * fixed typo in adex-cell tutorial doc * revised tutorials to reflect new sim-lib config/syntax * revised tutorials to reflect new sim-lib config/syntax * patched docs to reflect revisions/refactor * tweaked requirements in prep for major release * cleaned up a few unit tests to use deterministic syn init vals * mod to requirements * nudge toml to upcoming 2.0.0 * update to support docs in prep for 2.0.0 * update patched synapses and their test cases * cleaned up syn modeling doc * push hebbian synapse * push reinforce synapse * push np seed * patched minor prior None arg issue in hebb-syn * moved reinforce-syn to right spot * update reinforce synapse and testing * tweaked trace-stdp and mstdpet * patched mstdpet unit-test * update reinforce synapse and test cases * add reinforce synapse fix * minor mod to mstdpet * update test code for more than 1 steps * Updated monitors * patched tests to use process naming * Added wrapper for reset and advance_state * Added a JaxProcess Added Jax Process to allow for scanning over the process. * update the old rate cell * update old hebbian synapse * minor edit to if-cell * ported over adex tutorial to new ngclearn format * hh-cell supports rk4 integration * clean up and integrated hodgkin-huxley mini lesson in neurocog tutorials * Update jaxProcess.py Updated the jax process to allow for more configurations of inputs. * update working reinforce synapse * update correct reinforce and testing * update documentation * update features, documentation, and testing * update testing for REINFORCE cell * update code and test * update code * add clipping gradient to model utils * update reinforce cell to the new model utils clip * major cleanup in prep for merge over to main/prep for major release * update test cases * update to require file in docs --------- Co-authored-by: Viet Dung Nguyen <[email protected]> Co-authored-by: Alexander Ororbia <[email protected]> Co-authored-by: Will Gebhardt <[email protected]> * Major release update merge to main (sync up) (#101) * add initial patch mask features * minor edit to bern-cell * fixed bernoulli error cell * example rate cell test * made some corrections to bern err-cell and heb syn * made some corrections to bern err-cell and heb syn * cleaned up bern-cell, hebb-syn * minor mod to model-utils * attempted rewrite of bernoulli-cell * got bernoulli-cell rewritten and unit-tested * edit to bern-cell * bernoulli and poisson cells revised, unit-tested * latency-cell refactored and unit-tested * refactored Rate Cell * minor revisions to input-encoders, revised phasor-cell w/ unit-test * revised and add unit-test for varTrace * revised and added unit-test for exp-kernel * revised and added unit-test for exp-kernel * revised slif cell w/ unit-test; needed mod to diffeq * revised slif-cell w/ unit-test; cleaned up ode_utils to play nicer w/ new sim-lib * revised lif-cell w/ unit-test * revised unit-tests to pass globally; some minor patches to phasor-cell and lif * minor cleanup of unit-test for phasor * revised if-cell w/ unit-test * revised if-cell w/ unit-test * revised quad-lif w/ unit-test * revised adex-cell w/ unit test, minor cleanup of quad-lif * minor edit to adex unit-test * refactor bernoulli, laplacian, and rewarderror cells * revised raf-cell w/ unit test; fixed typos/mistakes in all spiking cells * revised wtas-cell w/ unit test * revised fh-cell w/ unit test * revised izh-cell w/ unit test * patched ode_utils backend wrt jax, cleaned up unit-tests, added disable flag for phasor-cell * update rate cell * fix test rate cell * update test for bernoulli cell * update refactoring for gaussian error cell * update unit testing for all graded neurons * wrote+unit-test of hodgkin-huxley spike cell, minor tweaks/clean-up elsewhere * added rk2 support for H-H cell * update rate cell and fix bug of passing a tuple of (jax Array -- not hashable) to jax jit functions. Basically, simplify the codebase by using a hashmap of functions * update test rate cell * refactored dense and trace-stdp syn w/ unit-test * refactored exp-stdp syn w/ unit-test * refactored event-stdp w/ unit-test * cleanup of stdp-syn * refactored bcm syn w/ unit-test * refactored stp-syn with unit-test * cleaned up modulated * refactored mstdp-et syn w/ unit-test * refactored lava components to new sim-lib * refactored conv/hebb-conv syn w/ unit-test * refactored/revised hebb-deconv syn w/ unit-test * revised/refactored hebb/stdp conv/deconv syn w/ unit-tests * updated modeling doc to point to hodgkin-huxley cell * updated modeling docs * fixed typo in adex-cell tutorial doc * revised tutorials to reflect new sim-lib config/syntax * revised tutorials to reflect new sim-lib config/syntax * patched docs to reflect revisions/refactor * tweaked requirements in prep for major release * cleaned up a few unit tests to use deterministic syn init vals * mod to requirements * nudge toml to upcoming 2.0.0 * update to support docs in prep for 2.0.0 * update patched synapses and their test cases * cleaned up syn modeling doc * push hebbian synapse * push reinforce synapse * push np seed * patched minor prior None arg issue in hebb-syn * moved reinforce-syn to right spot * update reinforce synapse and testing * tweaked trace-stdp and mstdpet * patched mstdpet unit-test * update reinforce synapse and test cases * add reinforce synapse fix * minor mod to mstdpet * update test code for more than 1 steps * Updated monitors * patched tests to use process naming * Added wrapper for reset and advance_state * Added a JaxProcess Added Jax Process to allow for scanning over the process. * update the old rate cell * update old hebbian synapse * minor edit to if-cell * ported over adex tutorial to new ngclearn format * hh-cell supports rk4 integration * clean up and integrated hodgkin-huxley mini lesson in neurocog tutorials * Update jaxProcess.py Updated the jax process to allow for more configurations of inputs. * update working reinforce synapse * update correct reinforce and testing * update documentation * update features, documentation, and testing * update testing for REINFORCE cell * update code and test * update code * add clipping gradient to model utils * update reinforce cell to the new model utils clip * major cleanup in prep for merge over to main/prep for major release * update test cases * update to require file in docs --------- Co-authored-by: Viet Dung Nguyen <[email protected]> Co-authored-by: Alexander Ororbia <[email protected]> Co-authored-by: Will Gebhardt <[email protected]> * update test cases * added hh-plot for hh tutorial * tweak to img folder for sindy --------- Co-authored-by: Will Gebhardt <[email protected]> Co-authored-by: Alexander Ororbia <[email protected]> Co-authored-by: Faezeh Habibi <[email protected]> Co-authored-by: Sonny George <[email protected]> Co-authored-by: Viet Dung Nguyen <[email protected]> Co-authored-by: Alexander Ororbia <[email protected]> Co-authored-by: Viet Dung Nguyen <[email protected]> Co-authored-by: Viet Nguyen <[email protected]> Co-authored-by: Alexander Ororbia <[email protected]> * nudge from main to release (update to sindy tutorial) (#105) * generalized rate-cell a bit * touched up rate-cell further * minor mod to lif * updated lif-cell to use units/tags and minor cleanup and edits * Monitor plot (#66) * Update base_monitor.py * added plotting viewed compartments * added meta-data to rate-cell, input encoders, adex * fixed minor saving/loading in rate-cell w/ vectorized compartments * Added auto resolving for monitors (#67) * fixed surr arg in lif-cell * modded bernoulli-cell to include max-frequency constraint * added warning check to bernoulli, some cleanup * integrated if-cell, cleaned up lif and inits * mod to latency-cell * updated the poissonCell to be a true poisson * fixed minor bug in deprecation for poiss/bern * fixed minor bug in deprecation for poiss/bern * fixed validation fun in bern/poiss * moved back and cleaned up bernoulli and poisson cells * added threshold-clipping to latency cell * updates to if/lif * added batch-size arg to slif * fixed minor load bug in lif-cell * fixed a blocking jit-partial call in lif update_theta method; when loading * minor edit to dim-reduce * Patched synapses added (#68) * Patched synapses added * Update __init__.py * Update patch_utils.py patch_with_stride & patch_with_overlap functions + Create_Patches class added * Update patchedSynapse.py * Update hebbianPatchedSynapse.py * Update synapse_plot.py order added * updated monitor plot code * update to dim-reduce * integrated phasor-cell, minor cleanup of latency * tweak to adex thr arg * tweak to adex thr arg * integrated resonate-and-fire neuronal cell * mod to raf-cell * cleaned up raf * cleaned up raf * cleaned up raf-cell * cleaned up raf-cell * cleaned up raf-cell * minor tweak to dim-reduce in utils * Fix typo in pcn_discrim.md (#69) * model_utils and rate cell (#70) * Patched synapses added * Update __init__.py * Update patch_utils.py patch_with_stride & patch_with_overlap functions + Create_Patches class added * Update patchedSynapse.py * Update hebbianPatchedSynapse.py * Update synapse_plot.py order added * Create hierarchical_sc.md 1 * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update sparse_coding.md * Update sparse_coding.md * Update sparse_coding.md * Update sparse_coding.md * Update hierarchical_sc.md * Update sparse_coding.md * Update sparse_coding.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Add files via upload * Delete docs/images/hgpc_network.pdf * Add files via upload * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Create hgpc * Delete docs/images/museum/hgpc * Create d * Add files via upload * Delete docs/images/hgpc_model.png * Delete docs/images/museum/hgpc/d * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Add files via upload * Update hierarchical_sc.md * Update hierarchical_sc.md * Delete docs/images/museum/hgpc/Input_layer.png * Add files via upload * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Update hierarchical_sc.md * Create Generative_PC.md * Update and rename Generative_PC.md to generative_pc.md * Update generative_pc.md * Update generative_pc.md * Update model_utils.py * Update model_utils.py * Update model_utils.py * Update model_utils.py * Update rateCell.py * Update generative_pc.md * Create pc-sindy.md * Update pc-sindy.md * Update model_utils.py sine activation function added * Update model_utils.py * Update ode_utils.py jitified * Delete docs/museum/hierarchical_sc.md * Delete docs/museum/generative_pc.md * Delete ngclearn/components/synapses/patched directory * Update __init__.py * Add files via upload ode with scanner added * Update ode_solver.py _ removed * Fix/reorganize feature library (#74) * Update ode_utils.py * Update ode_solver.py rk4 revised and __main__ added * Delete ngclearn/utils/diffeq/ode_functions.py * Create odes.py odes name and structure changed * Update __init__.py * Create feature_library.py * Create __init__.py * Create base.py * Delete docs/museum/pc-sindy.md * Create m.md * Add files via upload * Delete docs/images/museum/sindy/m.md * Add files via upload * Create sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * Update sindy.md * fix: correct feature library path and directory name * Delete ngclearn/utils/dymbolic_dictionary directory * Update model_utils.py (#78) * Additions for inhibition stuff * add sindy documentation for exhibits (#81) * Add files via upload * Add files via upload * Update ode_utils.py (#79) refactor: delete @partial(jit, static_argnums=(2, )) lines Co-authored-by: Will Gebhardt <[email protected]> * Add patched synapse (#80) * Update __init__.py Add point to patched components * Add patched in __init__.py Add patched synapses importing * Add patched synaptic components * Delete ngclearn/components/synapses/patched/__pycache__ directory * Update __init__.py new line characters added * Update hebbianPatchedSynapse.py * Update patchedSynapse.py new line characters added * Update staticPatchedSynapse.py new line characters added * Update staticPatchedSynapse.py New line characters + comments for describing each input vars * Update patchedSynapse.py Removed a comment line * Update hebbianPatchedSynapse.py remove unused arguments * Update hebbianPatchedSynapse.py * Update hebbianPatchedSynapse.py add description for w_mask * Update hebbianPatchedSynapse.py * Update hebbianPatchedSynapse.py * Update patchedSynapse.py * Update patchedSynapse.py * Update hebbianPatchedSynapse.py * Update __init__.py (#83) * Update __init__.py typo fixed * Update staticPatchedSynapse.py a typo fixed * Update hebbianPatchedSynapse.py typo foxed * Add l1 decay term to update calculation (#84) * Update hebbianSynapse.py * update main update main at the end * Update hebbianSynapse.py add regularization argument and w_decay is deprecated. * Update hebbianSynapse.py add elastic_net * Update hebbianSynapse.py * Update hebbianSynapse.py * feat NGC module regression (#86) * feat npc module regression * Update __init__.py * Update __init__.py * Update elastic_net.py * Update lasso.py * Update ridge.py * Update elastic_net.py * Update ridge.py * Update lasso.py * Update odes.py removed @partial(jit, static_argnums=(0,)) * Update odes.py (#87) removed @partial(jit, static_argnums=(0,)) * Update odes.py typo fixed in __main__ * Update __init__.py add dot * Update __init__.py add dot * Add attribute 'lr' (#90) * Update elastic_net.py * add lr as attribute to lasso.py * add lr as attribute to ridge.py * refactor w_bound=0. for weights elastic_net.py deactivated w_bound for weights elastic_net.py * Update lasso.py * deactivated w_bound for weights ridge.py * commit probes/mods to utils to analysis_tools branch * commit probes/mods to utils to analysis_tools branch * update documentation * cleaned up probes/docs for probes * change heads_dim to attn_dim, and modify the mlp to be as similar as possible to the attentive probing pattern * in layer normalization or any other Gaussian, standardeviation can never be zero. Additionally, if the subtraction inside the square root goes to zero, the gradient will become NaN. Therefore, adding a clipping is necessary. * update attentive probe code * minor tweak to attentive prob code comments * cleaned up probe parent fit routine * cleaned up probe parent fit routine * cleaned up probe parent fit routine * cleaned up probe parent fit routine * minor edits to attn probe * update attentive probe with input layer norm * update input layer normalization * update code to fix nan bug * minor tweak to attn probe * cleaned up probes * cleaned up probes * cleaned up probes * cleaned up probes * generalized dropout in terms of shape * tweak to atten probe * tweak to atten probe * added silu/swish/elu to model_utils * cleaned up model_utils * fix bug in attention probe dropout, fix bug in None noise_key passed in the probing jit function, add the spliting of noise_keys to two dropout in two cross attention * hyperparameter tunning arguments added * Merging over Dynamics feature branch to main (#92) * modded bernoulli-cell to include max-frequency constraint * added warning check to bernoulli, some cleanup * integrated if-cell, cleaned up lif and inits * mod to latency-cell * updated the poissonCell to be a true poisson * fixed minor bug in deprecation for poiss/bern * fixed minor bug in deprecation for poiss/bern * fixed validation fun in bern/poiss * moved back and cleaned up bernoulli and poisson cells * added threshold-clipping to latency cell * updates to if/lif * added batch-size arg to slif * fixed minor load bug in lif-cell * fixed a blocking jit-partial call in lif update_theta method; when loading * minor edit to dim-reduce * updated monitor plot code * update to dim-reduce * integrated phasor-cell, minor cleanup of latency * tweak to adex thr arg * tweak to adex thr arg * integrated resonate-and-fire neuronal cell * mod to raf-cell * cleaned up raf * cleaned up raf * cleaned up raf-cell * cleaned up raf-cell * cleaned up raf-cell * minor tweak to dim-reduce in utils * Additions for inhibition stuff * update to API modeling docs to reflect RAF neuronal cell --------- Co-authored-by: Alexander Ororbia <[email protected]> Co-authored-by: Will Gebhardt <[email protected]> * remove unused local variables * update note * update model utils * remove notes * Update ode utils (#94) * Update ode_utils.py merge ode_solver into ide_utils * Delete ngclearn/utils/diffeq/ode_solver.py * Update ode_utils.py refactor doc-string * minor fix to header in diffeq * Update files with ode_solver (#95) * Update ode_utils.py merge ode_solver into ide_utils * Delete ngclearn/utils/diffeq/ode_solver.py * Update ode_utils.py refactor doc-string * Update odes.py * Update sindy.md ode_solver to ode_utils * revised/cleaned up sindy tutorial doc/imgs * add prior for hebbian patched synapse (#96) * prior replaced w_decay hebbianPatchedSynapse.py remove w_decay add prior_type and prior_lmbda * revised typo hebbianSynapse.py dWweight was typo * cleaned up doc-strings in odes.py to comply w/ ngc-learn format * minor tweak to sig-figs printing in probe utils * add-sigma-to-gaussianErrorCell (#97) * add-sigma-to-gaussianErrorCell add not updating scalar variance for gaussian errors * Update gaussianErrorCell.py * cleaned up ode_utils, cleaned up gaussian/laplacian cell * Update gaussianErrorCell.py (#98) added `and not isinstance(sigma, int)` * cleaned up gauss/laplace error cells * integrated bernoulli err-cell * Major release update merge to main (in prep for 2.0.0 release on release branch/pip) (#99) * add initial patch mask features * minor edit to bern-cell * fixed bernoulli error cell * example rate cell test * made some corrections to bern err-cell and heb syn * made some corrections to bern err-cell and heb syn * cleaned up bern-cell, hebb-syn * minor mod to model-utils * attempted rewrite of bernoulli-cell * got bernoulli-cell rewritten and unit-tested * edit to bern-cell * bernoulli and poisson cells revised, unit-tested * latency-cell refactored and unit-tested * refactored Rate Cell * minor revisions to input-encoders, revised phasor-cell w/ unit-test * revised and add unit-test for varTrace * revised and added unit-test for exp-kernel * revised and added unit-test for exp-kernel * revised slif cell w/ unit-test; needed mod to diffeq * revised slif-cell w/ unit-test; cleaned up ode_utils to play nicer w/ new sim-lib * revised lif-cell w/ unit-test * revised unit-tests to pass globally; some minor patches to phasor-cell and lif * minor cleanup of unit-test for phasor * revised if-cell w/ unit-test * revised if-cell w/ unit-test * revised quad-lif w/ unit-test * revised adex-cell w/ unit test, minor cleanup of quad-lif * minor edit to adex unit-test * refactor bernoulli, laplacian, and rewarderror cells * revised raf-cell w/ unit test; fixed typos/mistakes in all spiking cells * revised wtas-cell w/ unit test * revised fh-cell w/ unit test * revised izh-cell w/ unit test * patched ode_utils backend wrt jax, cleaned up unit-tests, added disable flag for phasor-cell * update rate cell * fix test rate cell * update test for bernoulli cell * update refactoring for gaussian error cell * update unit testing for all graded neurons * wrote+unit-test of hodgkin-huxley spike cell, minor tweaks/clean-up elsewhere * added rk2 support for H-H cell * update rate cell and fix bug of passing a tuple of (jax Array -- not hashable) to jax jit functions. Basically, simplify the codebase by using a hashmap of functions * update test rate cell * refactored dense and trace-stdp syn w/ unit-test * refactored exp-stdp syn w/ unit-test * refactored event-stdp w/ unit-test * cleanup of stdp-syn * refactored bcm syn w/ unit-test * refactored stp-syn with unit-test * cleaned up modulated * refactored mstdp-et syn w/ unit-test * refactored lava components to new sim-lib * refactored conv/hebb-conv syn w/ unit-test * refactored/revised hebb-deconv syn w/ unit-test * revised/refactored hebb/stdp conv/deconv syn w/ unit-tests * updated modeling doc to point to hodgkin-huxley cell * updated modeling docs * fixed typo in adex-cell tutorial doc * revised tutorials to reflect new sim-lib config/syntax * revised tutorials to reflect new sim-lib config/syntax * patched docs to reflect revisions/refactor * tweaked requirements in prep for major release * cleaned up a few unit tests to use deterministic syn init vals * mod to requirements * nudge toml to upcoming 2.0.0 * update to support docs in prep for 2.0.0 * update patched synapses and their test cases * cleaned up syn modeling doc * push hebbian synapse * push reinforce synapse * push np seed * patched minor prior None arg issue in hebb-syn * moved reinforce-syn to right spot * update reinforce synapse and testing * tweaked trace-stdp and mstdpet * patched mstdpet unit-test * update reinforce synapse and test cases * add reinforce synapse fix * minor mod to mstdpet * update test code for more than 1 steps * Updated monitors * patched tests to use process naming * Added wrapper for reset and advance_state * Added a JaxProcess Added Jax Process to allow for scanning over the process. * update the old rate cell * update old hebbian synapse * minor edit to if-cell * ported over adex tutorial to new ngclearn format * hh-cell supports rk4 integration * clean up and integrated hodgkin-huxley mini lesson in neurocog tutorials * Update jaxProcess.py Updated the jax process to allow for more configurations of inputs. * update working reinforce synapse * update correct reinforce and testing * update documentation * update features, documentation, and testing * update testing for REINFORCE cell * update code and test * update code * add clipping gradient to model utils * update reinforce cell to the new model utils clip * update test cases --------- Co-authored-by: Viet Dung Nguyen <[email protected]> Co-authored-by: Alexander Ororbia <[email protected]> Co-authored-by: Will Gebhardt <[email protected]> * Major release update (to 2.0.0) (#100) * add initial patch mask features * minor edit to bern-cell * fixed bernoulli error cell * example rate cell test * made some corrections to bern err-cell and heb syn * made some corrections to bern err-cell and heb syn * cleaned up bern-cell, hebb-syn * minor mod to model-utils * attempted rewrite of bernoulli-cell * got bernoulli-cell rewritten and unit-tested * edit to bern-cell * bernoulli and poisson cells revised, unit-tested * latency-cell refactored and unit-tested * refactored Rate Cell * minor revisions to input-encoders, revised phasor-cell w/ unit-test * revised and add unit-test for varTrace * revised and added unit-test for exp-kernel * revised and added unit-test for exp-kernel * revised slif cell w/ unit-test; needed mod to diffeq * revised slif-cell w/ unit-test; cleaned up ode_utils to play nicer w/ new sim-lib * revised lif-cell w/ unit-test * revised unit-tests to pass globally; some minor patches to phasor-cell and lif * minor cleanup of unit-test for phasor * revised if-cell w/ unit-test * revised if-cell w/ unit-test * revised quad-lif w/ unit-test * revised adex-cell w/ unit test, minor cleanup of quad-lif * minor edit to adex unit-test * refactor bernoulli, laplacian, and rewarderror cells * revised raf-cell w/ unit test; fixed typos/mistakes in all spiking cells * revised wtas-cell w/ unit test * revised fh-cell w/ unit test * revised izh-cell w/ unit test * patched ode_utils backend wrt jax, cleaned up unit-tests, added disable flag for phasor-cell * update rate cell * fix test rate cell * update test for bernoulli cell * update refactoring for gaussian error cell * update unit testing for all graded neurons * wrote+unit-test of hodgkin-huxley spike cell, minor tweaks/clean-up elsewhere * added rk2 support for H-H cell * update rate cell and fix bug of passing a tuple of (jax Array -- not hashable) to jax jit functions. Basically, simplify the codebase by using a hashmap of functions * update test rate cell * refactored dense and trace-stdp syn w/ unit-test * refactored exp-stdp syn w/ unit-test * refactored event-stdp w/ unit-test * cleanup of stdp-syn * refactored bcm syn w/ unit-test * refactored stp-syn with unit-test * cleaned up modulated * refactored mstdp-et syn w/ unit-test * refactored lava components to new sim-lib * refactored conv/hebb-conv syn w/ unit-test * refactored/revised hebb-deconv syn w/ unit-test * revised/refactored hebb/stdp conv/deconv syn w/ unit-tests * updated modeling doc to point to hodgkin-huxley cell * updated modeling docs * fixed typo in adex-cell tutorial doc * revised tutorials to reflect new sim-lib config/syntax * revised tutorials to reflect new sim-lib config/syntax * patched docs to reflect revisions/refactor * tweaked requirements in prep for major release * cleaned up a few unit tests to use deterministic syn init vals * mod to requirements * nudge toml to upcoming 2.0.0 * update to support docs in prep for 2.0.0 * update patched synapses and their test cases * cleaned up syn modeling doc * push hebbian synapse * push reinforce synapse * push np seed * patched minor prior None arg issue in hebb-syn * moved reinforce-syn to right spot * update reinforce synapse and testing * tweaked trace-stdp and mstdpet * patched mstdpet unit-test * update reinforce synapse and test cases * add reinforce synapse fix * minor mod to mstdpet * update test code for more than 1 steps * Updated monitors * patched tests to use process naming * Added wrapper for reset and advance_state * Added a JaxProcess Added Jax Process to allow for scanning over the process. * update the old rate cell * update old hebbian synapse * minor edit to if-cell * ported over adex tutorial to new ngclearn format * hh-cell supports rk4 integration * clean up and integrated hodgkin-huxley mini lesson in neurocog tutorials * Update jaxProcess.py Updated the jax process to allow for more configurations of inputs. * update working reinforce synapse * update correct reinforce and testing * update documentation * update features, documentation, and testing * update testing for REINFORCE cell * update code and test * update code * add clipping gradient to model utils * update reinforce cell to the new model utils clip * major cleanup in prep for merge over to main/prep for major release * update test cases * update to require file in docs --------- Co-authored-by: Viet Dung Nguyen <[email protected]> Co-authored-by: Alexander Ororbia <[email protected]> Co-authored-by: Will Gebhardt <[email protected]> * Major release update merge to main (sync up) (#101) * add initial patch mask features * minor edit to bern-cell * fixed bernoulli error cell * example rate cell test * made some corrections to bern err-cell and heb syn * made some corrections to bern err-cell and heb syn * cleaned up bern-cell, hebb-syn * minor mod to model-utils * attempted rewrite of bernoulli-cell * got bernoulli-cell rewritten and unit-tested * edit to bern-cell * bernoulli and poisson cells revised, unit-tested * latency-cell refactored and unit-tested * refactored Rate Cell * minor revisions to input-encoders, revised phasor-cell w/ unit-test * revised and add unit-test for varTrace * revised and added unit-test for exp-kernel * revised and added unit-test for exp-kernel * revised slif cell w/ unit-test; needed mod to diffeq * revised slif-cell w/ unit-test; cleaned up ode_utils to play nicer w/ new sim-lib * revised lif-cell w/ unit-test * revised unit-tests to pass globally; some minor patches to phasor-cell and lif * minor cleanup of unit-test for phasor * revised if-cell w/ unit-test * revised if-cell w/ unit-test * revised quad-lif w/ unit-test * revised adex-cell w/ unit test, minor cleanup of quad-lif * minor edit to adex unit-test * refactor bernoulli, laplacian, and rewarderror cells * revised raf-cell w/ unit test; fixed typos/mistakes in all spiking cells * revised wtas-cell w/ unit test * revised fh-cell w/ unit test * revised izh-cell w/ unit test * patched ode_utils backend wrt jax, cleaned up unit-tests, added disable flag for phasor-cell * update rate cell * fix test rate cell * update test for bernoulli cell * update refactoring for gaussian error cell * update unit testing for all graded neurons * wrote+unit-test of hodgkin-huxley spike cell, minor tweaks/clean-up elsewhere * added rk2 support for H-H cell * update rate cell and fix bug of passing a tuple of (jax Array -- not hashable) to jax jit functions. Basically, simplify the codebase by using a hashmap of functions * update test rate cell * refactored dense and trace-stdp syn w/ unit-test * refactored exp-stdp syn w/ unit-test * refactored event-stdp w/ unit-test * cleanup of stdp-syn * refactored bcm syn w/ unit-test * refactored stp-syn with unit-test * cleaned up modulated * refactored mstdp-et syn w/ unit-test * refactored lava components to new sim-lib * refactored conv/hebb-conv syn w/ unit-test * refactored/revised hebb-deconv syn w/ unit-test * revised/refactored hebb/stdp conv/deconv syn w/ unit-tests * updated modeling doc to point to hodgkin-huxley cell * updated modeling docs * fixed typo in adex-cell tutorial doc * revised tutorials to reflect new sim-lib config/syntax * revised tutorials to reflect new sim-lib config/syntax * patched docs to reflect revisions/refactor * tweaked requirements in prep for major release * cleaned up a few unit tests to use deterministic syn init vals * mod to requirements * nudge toml to upcoming 2.0.0 * update to support docs in prep for 2.0.0 * update patched synapses and their test cases * cleaned up syn modeling doc * push hebbian synapse * push reinforce synapse * push np seed * patched minor prior None arg issue in hebb-syn * moved reinforce-syn to right spot * update reinforce synapse and testing * tweaked trace-stdp and mstdpet * patched mstdpet unit-test * update reinforce synapse and test cases * add reinforce synapse fix * minor mod to mstdpet * update test code for more than 1 steps * Updated monitors * patched tests to use process naming * Added wrapper for reset and advance_state * Added a JaxProcess Added Jax Process to allow for scanning over the process. * update the old rate cell * update old hebbian synapse * minor edit to if-cell * ported over adex tutorial to new ngclearn format * hh-cell supports rk4 integration * clean up and integrated hodgkin-huxley mini lesson in neurocog tutorials * Update jaxProcess.py Updated the jax process to allow for more configurations of inputs. * update working reinforce synapse * update correct reinforce and testing * update documentation * update features, documentation, and testing * update testing for REINFORCE cell * update code and test * update code * add clipping gradient to model utils * update reinforce cell to the new model utils clip * major cleanup in prep for merge over to main/prep for major release * update test cases * update to require file in docs --------- Co-authored-by: Viet Dung Nguyen <[email protected]> Co-authored-by: Alexander Ororbia <[email protected]> Co-authored-by: Will Gebhardt <[email protected]> * update test cases * added hh-plot for hh tutorial * tweak to img folder for sindy * update to sindy tutorial to adhere to readthedocs formatting --------- Co-authored-by: Will Gebhardt <[email protected]> Co-authored-by: Alexander Ororbia <[email protected]> Co-authored-by: Faezeh Habibi <[email protected]> Co-authored-by: Sonny George <[email protected]> Co-authored-by: Viet Dung Nguyen <[email protected]> Co-authored-by: Alexander Ororbia <[email protected]> Co-authored-by: Viet Dung Nguyen <[email protected]> Co-authored-by: Viet Nguyen <[email protected]> Co-authored-by: Alexander Ororbia <[email protected]> * removed some clutter - old files * minor update to installation doc --------- Co-authored-by: Will Gebhardt <[email protected]> Co-authored-by: Alexander Ororbia <[email protected]> Co-authored-by: Faezeh Habibi <[email protected]> Co-authored-by: Sonny George <[email protected]> Co-authored-by: Viet Dung Nguyen <[email protected]> Co-authored-by: Alexander Ororbia <[email protected]> Co-authored-by: Viet Dung Nguyen <[email protected]> Co-authored-by: Viet Nguyen <[email protected]> Co-authored-by: Alexander Ororbia <[email protected]>
Merge branch 'main' of github.com:NACLab/ngc-learn into main