{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "%matplotlib inline" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "import pandas as pd\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", "import seaborn as sns\n", "from sklearn.metrics.pairwise import pairwise_distances" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## References\n", "http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.0020095\n", "https://people.ece.cornell.edu/atang/pub/15/PLOS_One.pdf" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "# Load Global network of 277 neurons (zip) dataset from [[kraiser et al. 2006]](http://www.biological-networks.org/pubs/suppl/Kaiser2006.html)" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "nodes_labels = pd.read_csv(\"celegans277labels.csv\", header=None) \n", "adjacency = pd.read_csv(\"celegans277matrix.csv\", header=None)\n", "locations = pd.read_csv(\"celegans277positions.csv\", header=None)\n", "adjacency.index = nodes_labels[0] \n", "adjacency.columns = nodes_labels[0]\n", "locations.index = nodes_labels[0]\n", "inter_neuron_dist = pd.DataFrame(pairwise_distances(locations))\n", "inter_neuron_dist.columns = nodes_labels[0]\n", "inter_neuron_dist.index = nodes_labels[0]" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | ADAL | \n", "ADAR | \n", "ADEL | \n", "ADER | \n", "ADFL | \n", "ADFR | \n", "ADLL | \n", "ADLR | \n", "AFDL | \n", "AFDR | \n", "... | \n", "VD12 | \n", "VD13 | \n", "VD2 | \n", "VD3 | \n", "VD4 | \n", "VD5 | \n", "VD6 | \n", "VD7 | \n", "VD8 | \n", "VD9 | \n", "
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0 | \n", "\n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " | \n", " |
ADAL | \n", "0.000000 | \n", "0.004850 | \n", "0.005171 | \n", "0.005157 | \n", "0.071657 | \n", "0.072781 | \n", "0.074034 | \n", "0.074281 | \n", "0.075752 | \n", "0.075708 | \n", "... | \n", "0.879595 | \n", "0.925826 | \n", "0.045768 | \n", "0.148903 | \n", "0.233522 | \n", "0.327535 | \n", "0.418788 | \n", "0.500684 | \n", "0.608913 | \n", "0.700111 | \n", "
ADAR | \n", "0.004850 | \n", "0.000000 | \n", "0.004004 | \n", "0.007141 | \n", "0.068261 | \n", "0.069283 | \n", "0.070109 | \n", "0.070422 | \n", "0.072290 | \n", "0.072327 | \n", "... | \n", "0.882789 | \n", "0.928948 | \n", "0.050171 | \n", "0.152795 | \n", "0.237204 | \n", "0.331086 | \n", "0.422265 | \n", "0.504087 | \n", "0.612279 | \n", "0.703425 | \n", "
ADEL | \n", "0.005171 | \n", "0.004004 | \n", "0.000000 | \n", "0.003873 | \n", "0.066492 | \n", "0.067626 | \n", "0.068987 | \n", "0.069209 | \n", "0.070593 | \n", "0.070543 | \n", "... | \n", "0.884763 | \n", "0.930989 | \n", "0.050632 | \n", "0.154001 | \n", "0.238665 | \n", "0.332695 | \n", "0.423954 | \n", "0.505854 | \n", "0.614083 | \n", "0.705282 | \n", "
ADER | \n", "0.005157 | \n", "0.007141 | \n", "0.003873 | \n", "0.000000 | \n", "0.068233 | \n", "0.069470 | \n", "0.071290 | \n", "0.071439 | \n", "0.072392 | \n", "0.072258 | \n", "... | \n", "0.883429 | \n", "0.929726 | \n", "0.048178 | \n", "0.152003 | \n", "0.236869 | \n", "0.331023 | \n", "0.422350 | \n", "0.504321 | \n", "0.612584 | \n", "0.703832 | \n", "
ADFL | \n", "0.071657 | \n", "0.068261 | \n", "0.066492 | \n", "0.068233 | \n", "0.000000 | \n", "0.002372 | \n", "0.012054 | \n", "0.010565 | \n", "0.004296 | \n", "0.004070 | \n", "... | \n", "0.951023 | \n", "0.997134 | \n", "0.116032 | \n", "0.220199 | \n", "0.305094 | \n", "0.399184 | \n", "0.490444 | \n", "0.572320 | \n", "0.680529 | \n", "0.771686 | \n", "
5 rows × 277 columns
\n", "\n", " | 0 | \n", "1 | \n", "
---|---|---|
0 | \n", "\n", " | \n", " |
ADAL | \n", "0.011068 | \n", "0.005903 | \n", "
ADAR | \n", "0.014206 | \n", "0.002204 | \n", "
ADEL | \n", "0.016233 | \n", "0.005657 | \n", "
ADER | \n", "0.014941 | \n", "0.009308 | \n", "
ADFL | \n", "0.082393 | \n", "-0.000984 | \n", "
\n", " | ADAL | \n", "ADAR | \n", "ADEL | \n", "ADER | \n", "ADFL | \n", "ADFR | \n", "ADLL | \n", "ADLR | \n", "AFDL | \n", "AFDR | \n", "... | \n", "VD12 | \n", "VD13 | \n", "VD2 | \n", "VD3 | \n", "VD4 | \n", "VD5 | \n", "VD6 | \n", "VD7 | \n", "VD8 | \n", "VD9 | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ADAL | \n", "0 | \n", "0 | \n", "1 | \n", "0 | \n", "1 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "... | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "
ADAR | \n", "0 | \n", "0 | \n", "0 | \n", "1 | \n", "0 | \n", "1 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "... | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "
ADEL | \n", "0 | \n", "0 | \n", "0 | \n", "1 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "... | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "
ADER | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "... | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "
ADFL | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "... | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "0 | \n", "
5 rows × 277 columns
\n", "\n", " | input | \n", "output | \n", "weight | \n", "
---|---|---|---|
0 | \n", "ADAL | \n", "ADEL | \n", "0.005171 | \n", "
1 | \n", "ADAL | \n", "ADFL | \n", "0.071657 | \n", "
2 | \n", "ADAL | \n", "AIAL | \n", "0.054218 | \n", "
3 | \n", "ADAL | \n", "AWAL | \n", "0.067481 | \n", "
4 | \n", "ADAL | \n", "PVPL | \n", "0.906806 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "
2100 | \n", "VD9 | \n", "DB6 | \n", "0.030530 | \n", "
2101 | \n", "VD9 | \n", "DB7 | \n", "0.139014 | \n", "
2102 | \n", "VD9 | \n", "DD5 | \n", "0.079375 | \n", "
2103 | \n", "VD9 | \n", "VA9 | \n", "0.025985 | \n", "
2104 | \n", "VD9 | \n", "VC6 | \n", "0.035242 | \n", "
2105 rows × 3 columns
\n", "