Fix typo in pcn_discrim.md #69
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
ago109
added a commit
that referenced
this pull request
Apr 12, 2025
* 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 <will@gebhardts.net> * 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 <agocse109@gmail.com> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * update test cases --------- Co-authored-by: Will Gebhardt <will@gebhardts.net> Co-authored-by: Alexander Ororbia <ago@skynet02.cs.rit.edu> Co-authored-by: Faezeh Habibi <155960330+Faezehabibi@users.noreply.github.com> Co-authored-by: Sonny George <56851635+sonnygeorge@users.noreply.github.com> Co-authored-by: Viet Dung Nguyen <60036798+rxng8@users.noreply.github.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Viet Dung Nguyen <vietdungnguyen233@gmail.com> Co-authored-by: Viet Nguyen <alexvn.edu@gmail.com> Co-authored-by: Alexander Ororbia <ago@skynet01.cs.rit.edu>
ago109
added a commit
that referenced
this pull request
Apr 12, 2025
* 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 <will@gebhardts.net> * 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 <agocse109@gmail.com> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * update test cases * added hh-plot for hh tutorial --------- Co-authored-by: Will Gebhardt <will@gebhardts.net> Co-authored-by: Alexander Ororbia <ago@skynet02.cs.rit.edu> Co-authored-by: Faezeh Habibi <155960330+Faezehabibi@users.noreply.github.com> Co-authored-by: Sonny George <56851635+sonnygeorge@users.noreply.github.com> Co-authored-by: Viet Dung Nguyen <60036798+rxng8@users.noreply.github.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Viet Dung Nguyen <vietdungnguyen233@gmail.com> Co-authored-by: Viet Nguyen <alexvn.edu@gmail.com> Co-authored-by: Alexander Ororbia <ago@skynet01.cs.rit.edu>
ago109
added a commit
that referenced
this pull request
Apr 12, 2025
* 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 <will@gebhardts.net> * 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 <agocse109@gmail.com> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * update test cases * added hh-plot for hh tutorial * tweak to img folder for sindy --------- Co-authored-by: Will Gebhardt <will@gebhardts.net> Co-authored-by: Alexander Ororbia <ago@skynet02.cs.rit.edu> Co-authored-by: Faezeh Habibi <155960330+Faezehabibi@users.noreply.github.com> Co-authored-by: Sonny George <56851635+sonnygeorge@users.noreply.github.com> Co-authored-by: Viet Dung Nguyen <60036798+rxng8@users.noreply.github.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Viet Dung Nguyen <vietdungnguyen233@gmail.com> Co-authored-by: Viet Nguyen <alexvn.edu@gmail.com> Co-authored-by: Alexander Ororbia <ago@skynet01.cs.rit.edu>
ago109
added a commit
that referenced
this pull request
Apr 13, 2025
* 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 <will@gebhardts.net> * 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 <agocse109@gmail.com> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <will@gebhardts.net> Co-authored-by: Alexander Ororbia <ago@skynet02.cs.rit.edu> Co-authored-by: Faezeh Habibi <155960330+Faezehabibi@users.noreply.github.com> Co-authored-by: Sonny George <56851635+sonnygeorge@users.noreply.github.com> Co-authored-by: Viet Dung Nguyen <60036798+rxng8@users.noreply.github.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Viet Dung Nguyen <vietdungnguyen233@gmail.com> Co-authored-by: Viet Nguyen <alexvn.edu@gmail.com> Co-authored-by: Alexander Ororbia <ago@skynet01.cs.rit.edu>
ago109
added a commit
that referenced
this pull request
Apr 13, 2025
* 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 <will@gebhardts.net> * 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 <agocse109@gmail.com> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * update test cases * added hh-plot for hh tutorial * tweak to img folder for sindy --------- Co-authored-by: Will Gebhardt <will@gebhardts.net> Co-authored-by: Alexander Ororbia <ago@skynet02.cs.rit.edu> Co-authored-by: Faezeh Habibi <155960330+Faezehabibi@users.noreply.github.com> Co-authored-by: Sonny George <56851635+sonnygeorge@users.noreply.github.com> Co-authored-by: Viet Dung Nguyen <60036798+rxng8@users.noreply.github.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Viet Dung Nguyen <vietdungnguyen233@gmail.com> Co-authored-by: Viet Nguyen <alexvn.edu@gmail.com> Co-authored-by: Alexander Ororbia <ago@skynet01.cs.rit.edu> * 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 <will@gebhardts.net> * 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 <agocse109@gmail.com> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <vietdungnguyen233@gmail.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Will Gebhardt <will@gebhardts.net> * 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 <will@gebhardts.net> Co-authored-by: Alexander Ororbia <ago@skynet02.cs.rit.edu> Co-authored-by: Faezeh Habibi <155960330+Faezehabibi@users.noreply.github.com> Co-authored-by: Sonny George <56851635+sonnygeorge@users.noreply.github.com> Co-authored-by: Viet Dung Nguyen <60036798+rxng8@users.noreply.github.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Viet Dung Nguyen <vietdungnguyen233@gmail.com> Co-authored-by: Viet Nguyen <alexvn.edu@gmail.com> Co-authored-by: Alexander Ororbia <ago@skynet01.cs.rit.edu> * removed some clutter - old files * minor update to installation doc --------- Co-authored-by: Will Gebhardt <will@gebhardts.net> Co-authored-by: Alexander Ororbia <ago@skynet02.cs.rit.edu> Co-authored-by: Faezeh Habibi <155960330+Faezehabibi@users.noreply.github.com> Co-authored-by: Sonny George <56851635+sonnygeorge@users.noreply.github.com> Co-authored-by: Viet Dung Nguyen <60036798+rxng8@users.noreply.github.com> Co-authored-by: Alexander Ororbia <ago@hal3.cs.rit.edu> Co-authored-by: Viet Dung Nguyen <vietdungnguyen233@gmail.com> Co-authored-by: Viet Nguyen <alexvn.edu@gmail.com> Co-authored-by: Alexander Ororbia <ago@skynet01.cs.rit.edu>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.