![](\"../figures/validation_environment.png\")
\n",
+ "\n",
+ "System of interest: an entity, situation, or system which has been selected for analysis
Mathematical model: an abstract description formed by analysis and observation of the system of interest.
Executable model: an implementation of the mathematical model
Confirmation: attributing credibility to the mathematical model as a useful description of the system of interest.
Verification: evaluation whether the executable model is a correct realization of the mathematical model
Validation: a quantitative evaluation of usefulness and accuracy
![](\"../figures/NetworkUnit_Flowchart_X2M_M2M.png\")
\n",
+ "\"A model, like a novel, may resonate with nature, but it is not a 'real' thing. Like novel, a model may be convinving - it may 'ring true' if it is consistent with our experience of the natural world. But just as we may wonder how much the characters in a novel are drawn from real life and how much is artifice, we might ask the same of a model: How much is based on observation and measurement of accesssible phenomena, how much is based on informed judgment, and how much is convencience?\"
\n", + "Orsekes, 1994
\n" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### References\n", + "\n", + "- Trensch et al. (2018) Rigorous neural network simulations: model cross-validation665for boosting the correctness of simulation results, Frontiers in Neuroinformatics 12:81, doi: 10.3389/fninf.2018.00081 \n", + "\n", + "- Gutzen et al. (2018) Reproducible neural network simulations: model validation on the level of network activity data, Frontiers in Neuroinformatics 12:90, doi: 10.3389/fninf.2018.00090 \n", + "\n", + "- Schlesinger, S. (1979). Terminology for model credibility, Simulation 32, 103-104. doi: 10.1177/003754977903200304 \n", + "\n", + "- Izhikevich, E. M. (2006). Polychronization: Computation with spikes, Neural Computation 18, 245–282. doi: 10.1162/089976606775093882 \n", + "\n", + "- Brochier et al. (2018) Massively parallel recordings in macaque motor cortex during an instructed delayed reach-to-grasp task, Scientific Data, 5, pp. 1–23. doi: 10.1038/sdata.2018.55. \n", + "\n", + "- Riehle et al. (2013) Mapping the spatio-temporal structure of motor cortical LFP and spiking activities during reach-to-grasp movements, Frontiers in Neural Circuits, 7(48). doi: 10.3389/fncir.2013.00048. \n", + "\n" + ] + } + ], + "metadata": { + "celltoolbar": "Slideshow", + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.7.3" + }, + "livereveal": { + "autolaunch": true, + "scroll": true + }, + "rise": { + "autolaunch": true + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/examples/joint_test.ipynb b/examples/joint_test.ipynb new file mode 100644 index 0000000..8a55c69 --- /dev/null +++ b/examples/joint_test.ipynb @@ -0,0 +1,136 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "import sys\n", + "sys.path.insert(0, '../')\n", + "from networkunit import models, tests, scores\n", + "import quantities as pq\n", + "import sciunit" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [], + "source": [ + "# Define models\n", + "model_A = models.stochastic_activity('model A', rate=5*pq.Hz)\n", + "model_B = models.stochastic_activity('model B', rate=15*pq.Hz)\n", + "\n", + "# Define test\n", + "class fr_lv_jtest(tests.TestM2M, tests.joint_test):\n", + " score_type = scores.ks_distance # <- define score statistic\n", + "# score_type = scores.kl_divergence\n", + " params = {}\n", + " test_list = [tests.firing_rate_test, tests.isi_variation_test, tests.isi_variation_test]\n", + " test_params = [{}, {'variation_measure': 'lv'}, {'variation_measure': 'cv'}]" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [], + "source": [ + "jtest_inst = fr_lv_jtest()" + ] + }, + { + "cell_type": "code", + "execution_count": 22, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "(3, 100)" + ] + }, + "execution_count": 22, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "pred = jtest_inst.generate_prediction(model_A)\n", + "pred.shape" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "True" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "isinstance(fr_lv_jtest, type)" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [], + "source": [ + "score = jtest_inst.judge([model_A, model_B])" + ] + }, + { + "cell_type": "code", + "execution_count": 21, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "sciunit.scores.collections_m2m.ScoreMatrixM2M" + ] + }, + "execution_count": 21, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "type(score)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.7.3" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +} diff --git a/readthedocs.yml b/readthedocs.yml new file mode 100644 index 0000000..54dc860 --- /dev/null +++ b/readthedocs.yml @@ -0,0 +1,19 @@ +# readthedocs version +version: 2 + +build: + os: ubuntu-22.04 + tools: + python: "3.9" + +sphinx: + builder: html + configuration: doc/conf.py + + +python: + install: + - method: pip + path: . + extra_requirements: + - docs \ No newline at end of file diff --git a/requirements-docs.txt b/requirements-docs.txt new file mode 100644 index 0000000..818bdca --- /dev/null +++ b/requirements-docs.txt @@ -0,0 +1,5 @@ +# Packages required to build docs (in addition to requirements-tutorials.rst) + +jupyter>=1.0.0 +sphinx>=7.2.5 +nbsphinx>=0.9.3 diff --git a/setup.py b/setup.py index 9366684..94a248f 100644 --- a/setup.py +++ b/setup.py @@ -8,6 +8,9 @@ with open('requirements.txt', 'r') as fp: install_requires = fp.read() extras_require = {} +for extra in ['docs']: + with open('requirements-{0}.txt'.format(extra)) as fp: + extras_require[extra] = fp.read() setup( name="networkunit",