146 lines
2.6 KiB
Text
146 lines
2.6 KiB
Text
{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {
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"autoscroll": false,
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"collapsed": false,
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"ein.tags": "worksheet-0",
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"slideshow": {
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"slide_type": "-"
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}
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},
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"outputs": [],
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"source": [
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"import numpy as np\n",
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"import pandas as pd\n",
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"import matplotlib.pyplot as plt\n",
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"%matplotlib inline"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {
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"autoscroll": false,
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"collapsed": false,
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"ein.tags": "worksheet-0",
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"slideshow": {
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"slide_type": "-"
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}
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},
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"outputs": [],
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"source": [
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"import igraph as ig\n",
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"import dionysus as d"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {},
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"outputs": [],
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"source": [
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"karate = ig.read(\"data/karate.gml\")"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 4,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"IGRAPH U--- 34 78 -- \n",
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"+ attr: id (v)\n"
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]
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}
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],
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"source": [
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"ig.summary(karate)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 5,
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"metadata": {},
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"outputs": [],
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"source": [
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"cl = karate.maximal_cliques()"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 6,
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"metadata": {},
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"outputs": [
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{
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"data": {
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"text/plain": [
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"5"
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]
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},
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"execution_count": 6,
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"metadata": {},
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"output_type": "execute_result"
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}
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],
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"source": [
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"max(map(len, cl))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 12,
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"metadata": {},
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"outputs": [],
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"source": [
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"from scipy.spatial.distance import squareform\n",
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"dists = np.array(karate.shortest_paths_dijkstra())\n",
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"dists = squareform(dists).astype('float64')"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 16,
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"metadata": {},
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"outputs": [],
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"source": [
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"f = d.fill_rips(dists, 2, 2)\n",
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"m = d.homology_persistence(f)\n",
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"dgms = d.init_diagrams(m, f)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.6.5"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 2
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}
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