networkx-to-lava-nc

This module compares SNN algorithms to their default/Neumann implementations. The user can specify an SNN and "normal" algorithm which take as input a networkx graph, and compute some graph property as output. The output of the SNN is then compared to the "normal" algorithm as "ground truth", in terms of:

• Score: How many results the SNN algorithm computed correctly (from a set of input graphs).
• Runtime In theory, the score should always be 100% for the SNN, as it should be an exact SNN implementation of the ground truth algorithm. This comparison is mainly relevant for the additions of brain adaptation and simulated radiation.

Brain adaptation

For each SNN algorithm that the user specifies, the user can also specify a form of brain-inspired adaptation. This serves to increase the robustness of the SNN against radiation effects. The brain adaptation can be called from a separate pip package called: adaptivesnn.

Radiation

A basic form of radiation effects is modelled on the SNNs. For example, radiation is modelled as yielding permanent activity termination for random neurons.

It is noted that the accuracy of the modelling of the neuronal effects induced by the radiation is a function of the underlying hardware platforms. For example, on the Intel Loihi chips, the memory/routing and computations are somewhat intertwined from what I understood. This would suggest that radiation effects may yield errors that prevent a computation being executed at all, instead of a computation being corrupted, if for example a memory address is corrupted. (If that memory, for example, were to orchestrate some group of neurons to do something, but instead orchestrates an inactive set of neurons to perform some computation). In such cases, "neuronal- & synaptic" adaptation could be the best in the world, but nothing would happen with it if the neurons don't get the right input/send the output to the wrong place.

In hardware platforms where neurons and synapses have a more physical implementation on chip, the adaptation may be more effective to increase the radiation robustness.

Backends

Since the effectiveness of the adaptation mechanisms, in terms of radiation robustness, is a function of neuromorphic hardware platform, multiple backends are supported. These backends also allow for different neuronal and synaptic models. Currently the following backends are supported:

• A self-made networkx SNN simulator (LIF-neurons)
• Lava-nc simulator v0.5.0 (LIF-neurons)

Algorithms

Different SNN implementations may use different encoding schemes, such as sparse coding, population coding and/or rate coding. In population coding, adaptation may be realised in the form of larger populations, whereas in rate coding, adaptation may be realised through varying the spike-rate. This implies that different algorithms may benefit from different types of adaptation. Hence, an overview is included of the implemented SNN algorithms and their respective compatibilities with adaptation and radiation implementations:

Algorithm	Encoding	Adaptation	Radiation
Minimum Dominating Set Approximation	Sparse	Redundancy	Neuron Death

Minimum Dominating Set Approximation

This is an implementation of the distributed algorithm presented by Alipour et al.

• Input: Non-triangle, planar Networkx graph. (Non triangle means there should not be any 3 nodes that are all connected with each other (forming a triangle)). Planar means that if you lay-out the graph on a piece of paper, no lines intersect (that you can roll it out on a 2D plane).
• Output: A set of nodes that form a dominating set in the graph.

Description: The algorithm basically consists of k rounds, where you can choose k based on how accurate you want the approximation to be, more rounds (generally) means more accuracy. At the start each node i gets 1 random number r_i. This is kept constant throughout the entire algorithm. Then for the first round:

• Each node i computes how many neighbours (degree) d_i it has.
• Then it adds r_i+d_i=w_i. In all consecutive rounds:
• Each node i "computes" which neighbour has the highest weight w_j, and gives that node 1 mark/point. Then each node i has some mark/score m_i. Next, the weight w_i=r_i+m_i is computed (again) and the next round starts. This last round is repeated until k rounds are completed. At the end, the nodes with a non-zero mark/score m_i are selected to form the dominating set.

Experiment Stages

The experiment generates some input graphs, the SNN algorithm, a copied SNN with some form of adaptation, and two copies with radiation (one with-/out adaptation). Then it simulates those SNNs for "as long as it takes" (=implicit in the algorithm specification), and computes the results of these 4 SNNs based on the "ground truth" Neumann/default algorithm.

This experiment is executed in 4 stages:

Input: Experiment configuration. Which consists of: SubInput: Run configuration within an experiment. Stage 1: Create networkx graphs that will be propagated. Stage 2: Create propagated networkx graphs (at least one per timestep). Stage 3: Visaualisation of the networkx graphs over time. Stage 4: Post-processed performance data of algorithm and adaptation mechanism.

Running Experiment

You can run the experiment with command (to run the experiment using the networkx backend):

pip install snncompare
pip install https://github.com/a-t-0/lava/archive/refs/tags/v0.5.1.tar.gz
ulimit -n 800000
python -m src

And run tests with:

python -m pytest

Get help with:

python -m src --halp

This generates the graphs from the default experiment configurations, and outputs the graphs in json format to the results/ directory, and outputs the graph behaviour to: latex/Images/graphs/.

Test Coverage

Developers can use:

conda env create --file environment.yml
conda activate snncompare
ulimit -n 800000
python -m pytest

And the respective output is listed below, with a test coverage of 65%:

============================ test session starts ==============================
platform linux -- Python 3.8.13, pytest-7.2.0, pluggy-1.0.0
rootdir: /home/name/git/snncompare, configfile: pyproject.toml, testpaths: tests
plugins: cov-4.0.0
collected 82 items

experiment_settings/test_generic_experiment_settings.py ....           \[ 4%\]
experiment_settings/test_generic_run_settings.py ....                  \[ 9%\]
experiment_settings/test_supported_settings_adaptation.py ......       \[17%\]
experiment_settings/test_supported_settings_iteration.py .....         \[23%\]
experiment_settings/test_supported_settings_m_vals.py .....            \[29%\]
experiment_settings/test_supported_settings_max_graph_size.py .....    \[35%\]
experiment_settings/test_supported_settings_max_max_graphs.py .....    \[41%\]
experiment_settings/test_supported_settings_min_graph_size.py ....     \[46%\]
experiment_settings/test_supported_settings_min_max_graphs.py ....     \[51%\]
experiment_settings/test_supported_settings_overwrite_sim_results.py ..\[53%\]
experiment_settings/test_supported_settings_overwrite_visualisation.py \[56%\]
experiment_settings/test_supported_settings_radiation.py ......        \[63%\]
experiment_settings/test_supported_settings_seed.py ..                 \[65%\]
experiment_settings/test_supported_settings_simulators.py ....         \[70%\]
experiment_settings/test_supported_settings_size_and_max_graphs.py ....\[76%\]
export_results/performed_stage/test_performed_stage_TFFF.py .          \[78%\]
export_results/performed_stage/test_performed_stage_TTFF.py .          \[79%\]
export_results/performed_stage/test_performed_stage_TTTF.py .          \[80%\]
export_results/performed_stage/test_performed_stage_TTTT.py .          \[81%\]
graph_generation/test_get_graph.py .                                   \[82%\]
graph_generation/test_rand_network_generation.py ..                    \[85%\]
simulation/test_cyclic_graph_propagation.py .                          \[86%\]
simulation/test_has_recurrent_edge_lava.py .....                       \[92%\]
simulation/test_has_recurrent_edge_networkx.py .....                   \[98%\]
simulation/test_rand_network_propagation.py .                          \[00%\]

## ---------- coverage: platform linux, python 3.8.13-final-0 -----------
Name                                                       Stmts   Miss  Cover

## src/__init__.py                                                0    0  100%

src/snncompare/__init__.py                                        2    0  100%
src/snncompare/__main__.py                                       13   13    0%
src/snncompare/exp_setts/Adaptation_Rad_settings.py              16    0  100%
src/snncompare/exp_setts/Experiment_runner.py                   110    9   92%
src/snncompare/exp_setts/Scope_of_tests.py                       39   17   56%
src/snncompare/exp_setts/Supported_algorithms.py                  5    0  100%
src/snncompare/exp_setts/Supported_experiment_settings.py        57    4   93%
src/snncompare/exp_setts/Supported_run_settings.py               18    2   89%
src/snncompare/exp_setts/__init__.py                              0    0  100%
src/snncompare/exp_setts/create_testobject.py                    61   45   26%
src/snncompare/exp_setts/verify_experiment_settings.py          123   12   90%
src/snncompare/exp_setts/verify_run_completion.py                 4    1   75%
src/snncompare/exp_setts/verify_run_settings.py                  31    8   74%
src/snncompare/export_results/Output.py                         114   80   30%
src/snncompare/export_results/Output_stage_12.py                  5    0  100%
src/snncompare/export_results/Output_stage_34.py                 13    5   62%
src/snncompare/export_results/Plot_to_tex.py                     75   59   21%
src/snncompare/export_results/__init__.py                         0    0  100%
src/snncompare/export_results/check_json_graphs.py               12   12    0%
src/snncompare/export_results/check_nx_graphs.py                  9    7   22%
src/snncompare/export_results/export_json_results.py             37   21   43%
src/snncompare/export_results/export_nx_graph_to_json.py         42    8   81%
src/snncompare/export_results/helper.py                          39    2   95%
src/snncompare/export_results/load_json_to_nx_graph.py           64   31   52%
src/snncompare/export_results/load_pickles_get_results.py        22   18   18%
src/snncompare/export_results/plot_graphs.py                     36    9   75%
src/snncompare/export_results/verify_json_graphs.py              21    5   76%
src/snncompare/export_results/verify_nx_graphs.py                42   10   76%
src/snncompare/export_results/verify_stage_1_graphs.py           23   10   57%
src/snncompare/export_results/verify_stage_2_graphs.py            1    0  100%
src/snncompare/export_results/verify_stage_3_graphs.py            1    0  100%
src/snncompare/export_results/verify_stage_4_graphs.py            1    0  100%
src/snncompare/graph_generation/Used_graphs.py                   95   25   74%
src/snncompare/graph_generation/__init__.py                       0    0  100%
src/snncompare/graph_generation/adaptation/__init__.py            0    0  100%
src/snncompare/graph_generation/adaptation/redundancy.py         59    5   92%
src/snncompare/graph_generation/brain_adaptation.py              78   78    0%
src/snncompare/graph_generation/convert_networkx_to_lava.py     117    9   92%
src/snncompare/graph_generation/get_graph.py                     76    3   96%
src/snncompare/graph_generation/helper_network_structure.py     144  114   21%
src/snncompare/graph_generation/radiation/Radiation_damage.py    71   28   61%
src/snncompare/graph_generation/radiation/__init__.py             0    0  100%
src/snncompare/graph_generation/snn_algo/__init__.py              0    0  100%
src/snncompare/graph_generation/snn_algo/mdsa_snn_algo.py       110    1   99%
src/snncompare/graph_generation/stage_1_get_input_graphs.py      85   14   84%
src/snncompare/helper.py                                        276  167   39%
src/snncompare/import_results/__init__.py                         0    0  100%
src/snncompare/import_results/check_completed_stages.py          77   21   73%
src/snncompare/import_results/read_json.py                       37    4   89%
src/snncompare/import_results/stage_1_load_input_graphs.py       28   20   29%
src/snncompare/old_conversion.py                                 59   49   17%
src/snncompare/process_results/__init__.py                        0    0  100%
src/snncompare/process_results/get_alipour_nodes.py              17    0  100%
src/snncompare/process_results/get_mdsa_results.py               54    3   94%
src/snncompare/process_results/process_results.py                36    3   92%
src/snncompare/process_results/stage_2_propagate_graphs.py        0    0  100%
src/snncompare/simulation/LIF_neuron.py                         120   11   91%
src/snncompare/simulation/__init__.py                             0    0  100%
src/snncompare/simulation/run_on_lava.py                         24    2   92%
src/snncompare/simulation/run_on_networkx.py                     51    3   94%
src/snncompare/simulation/stage2_sim.py                          25    3   88%
src/snncompare/simulation/verify_graph_is_lava_snn.py            14    4   71%
src/snncompare/simulation/verify_graph_is_networkx_snn.py        31    7   77%
src/snncompare/simulation/verify_graph_is_snn.py                 12    0  100%
src/snncompare/verification_generic.py                           10    2   80%

TOTAL                                                            2742    964    65%
Coverage XML written to file cov.xml

=================== 82 passed, 1 warning in 415.57s (0:06:55) =======================

And for type checking:

mypy --disallow-untyped-calls --disallow-untyped-defs tests/export_results/performed_stage/test_performed_stage_TTFF.py

Releasing pip package update

To udate the Python pip package, one can first satisfy the following requirements:

pip install --upgrade pip setuptools wheel
pip install twine

Followed by updating the package with:

python3 setup.py sdist bdist_wheel
python -m twine upload dist/*