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ago109rxng8Alexander Ororbiawillgebhardt
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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>
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‎AUTHORS

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# The email address is not required for organizations.
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Core Team
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Alexander Ororbia <ago@cs.rit.edu>
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William Gebhardt <wdg1351@rit.edu>
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Viet Dung Nguyen <vn1747@rit.edu>
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Ankur Mali <aam35@psu.edu>
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Alexander Ororbia <agocse109@gmail.com>
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William Gebhardt <wdg1351@g.rit.edu>
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Viet Dung Nguyen <vn1747@g.rit.edu>
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Ankur Mali <ankurmali07@gmail.com>
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Faeze Habibi <habibifaeze.66@gmail.com>
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Contributors
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Maxbeth2 (Ohas)

‎README.md

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2) NumPy (>=1.26.0)
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3) SciPy (>=1.7.0)
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4) ngcsimlib (>=0.3.b4), (visit official page <a href="https://github.com/NACLab/ngc-sim-lib">here</a>)
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5) JAX (>= 0.4.18) (to enable GPU use, make sure to install one of the CUDA variants)
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5) JAX (>= 0.4.28) (to enable GPU use, make sure to install one of the CUDA variants)
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<!--
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5) scikit-learn (>=1.3.1) if using `ngclearn.utils.density`
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6) matplotlib (>=3.4.3) if using `ngclearn.utils.viz`
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Type "help", "copyright", "credits" or "license" for more information.
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>>> import ngclearn
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>>> ngclearn.__version__
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'1.2b3'
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'2.0.0'
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```
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<i>Note:</i> For access to the previous Tensorflow-2 version of ngc-learn (of
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</pre>
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**Version:**<br>
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1.2.3-Beta <!-- -Alpha -->
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2.0.0 <!--1.2.3-Beta--> <!-- -Alpha -->
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Author:
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Alexander G. Ororbia II<br>

‎docs/conf.py

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html_logo = "images/ngc-learn-logo.png"
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html_theme_options = {
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'logo_only': True,
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'display_version': True,
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#'display_version': True,
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}
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# def setup(app):

‎docs/modeling/input_encoders.md

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.. automethod:: reset
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:noindex:
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```
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### Phasor Cell
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This cell takes a real-valued pattern(s) and transforms it on-the-fly to
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a spike train composed of pulses emitted a regular interval.
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```{eval-rst}
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.. autoclass:: ngclearn.components.PhasorCell
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:noindex:
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.. automethod:: advance_state
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:noindex:
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.. automethod:: reset
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:noindex:
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```

‎docs/modeling/neurons.md

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.. automethod:: reset
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```
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### The Hodgkin-Huxley Cell
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This cell models dynamics over voltage `v` and three channels/gates (related to
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potassium and sodium activation/inactivation). This sophisticated cell system is,
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as a result, a set of four coupled differential equations and is driven by an appropriately configured set of biophysical constants/coefficients (default values of which have been set according to relevant source work).
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(Note that this cell supports either Euler or midpoint method / RK-2 integration.)
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```{eval-rst}
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.. autoclass:: ngclearn.components.HodgkinHuxleyCell
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:noindex:
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.. automethod:: advance_state
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:noindex:
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.. automethod:: reset
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:noindex:
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```

‎docs/modeling/synapses.md

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‎docs/museum/index.rst

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sparse_coding
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snn_dc
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snn_bfa
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sindy

‎docs/museum/sindy.md

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ẋ = 2.000 𝑦 -0.100 𝑥
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$[𝑦, 𝑦^2, 𝑥, 𝑥𝑦, 𝑥^2]$
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[𝑦, 𝑦^2, 𝑥, 𝑥𝑦, 𝑥^2]
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[[ 1.999 0. -0.100 0. 0.]
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[-0.099 0. -1.999 0. 0.]]
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```

‎docs/museum/snn_dc.md

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```console
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$ python analyze_dcsnn.py --dataX=../../data/mnist/testX.npy --sample_idx=0
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while will produce a visualization of your DC-SNN's receptive fields (the

‎docs/source/ngclearn.components.input_encoders.rst

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ngclearn.components.input\_encoders.phasorCell module
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-----------------------------------------------------
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ngclearn.components.input\_encoders.poissonCell module
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‎docs/source/ngclearn.components.neurons.graded.rst

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ngclearn.components.neurons.graded.bernoulliErrorCell module
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------------------------------------------------------------
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-----------------------------------------------------
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‎docs/source/ngclearn.components.neurons.spiking.rst

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ngclearn.components.neurons.spiking.IFCell module
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ngclearn.components.neurons.spiking.RAFCell module
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--------------------------------------------------
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ngclearn.components.neurons.spiking.hodgkinHuxleyCell module
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‎docs/source/ngclearn.components.synapses.hebbian.rst

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‎docs/source/ngclearn.components.synapses.modulated.rst

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‎docs/source/ngclearn.components.synapses.patched.rst

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ngclearn.components.synapses.patched package
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============================================
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Submodules
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----------------------------------------------------------------
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Module contents
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---------------
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:undoc-members:
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‎docs/source/ngclearn.components.synapses.rst

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‎docs/source/ngclearn.modules.regression.rst

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ngclearn.modules.regression package
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===================================
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-----------------------------------------------
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----------------------------------------
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----------------------------------------
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Module contents
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---------------
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:undoc-members:
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:show-inheritance:

‎docs/source/ngclearn.modules.rst

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ngclearn.modules package
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========================
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-----------
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---------------
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.. automodule:: ngclearn.modules
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:undoc-members:
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:show-inheritance:

‎docs/source/ngclearn.rst

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