WIP GraphSpace integration.

data-raw/wip-graphspace.Rmd

@@ -0,0 +1,274 @@
+---
+title: "Untitled"
+output: html_document
+---
+
+```{r setup, include=FALSE}
+library(reticulate)
+virtualenv_create("graph-space")
+py_install("~/Softs/GraphSpace/", envname = "graph-space")
+use_virtualenv("graph-space")
+```
+
+```{python}
+import os
+import sys
+#sys.path.append("C:\\Users\\Anna\\OneDrive - Politecnico di Milano\\Windows\\Polimi\\Ricerca\\Regression\\GraphSpace\\")
+
+from core import Graph, GraphSet, Mean, MeanIterative
+from distance import euclidean
+from matcher import GA, ID
+from AlignCompute import mean_aac, gpc_aac, mean_aac_pred, ggr_aac
+
+from core import Graph
+from core import GraphSet
+from core import Mean
+from core import MeanIterative
+from matcher import Matcher, alignment, GA, ID, GAS, GAS1
+from distance import euclidean, hamming, sqeuclidean
+
+import math
+import numpy as np
+import pandas as pd
+from scipy.sparse import lil_matrix, vstack
+```
+
+## 1) Binary graphs
+
+Define the graphs:
+
+```{python}
+x1 = {}
+x1[0, 0] = [1]
+x1[1, 1] = [1]
+x1[2, 2] = [1]
+x1[3, 3] = [1]
+x1[4, 4] = [1]
+x1[5, 5] = [1]
+x1[0, 1] = [1]
+x1[1, 0] = [1]
+x1[1, 2] = [1]
+x1[2, 1] = [1]
+x1[2, 5] = [1]
+x1[3, 4] = [1]
+x1[4, 3] = [1]
+x1[5, 2] = [1]
+x2 = {}
+x2[0, 0] = [1]
+x2[1, 1] = [1]
+x2[2, 2] = [1]
+x2[3, 3] = [1]
+x2[4, 4] = [1]
+x2[5, 5] = [1]
+x2[0, 1] = [1]
+x2[1, 0] = [1]
+x2[1, 2] = [1]
+x2[2, 1] = [1]
+x2[3, 4] = [1]
+x2[4, 3] = [1]
+```
+
+Create Graph set:
+
+```{python}
+G = GraphSet(graph_type='directed')
+G.add(Graph(x=x1, s=[1,2], adj=None))
+G.add(Graph(x=x2, s=[2,3], adj=None))
+```
+
+Compute a distance with euclidean distance without matching the graphs
+
+```{python}
+match=ID(hamming())
+match.dis(G.X[0],G.X[1])
+```
+
+## 2) GRAPHS with Euclidean scalar and vector attributes on both nodes and edges
+
+Define the graphs:
+
+```{python}
+x1 = {}
+x1[0, 0] = [0.813, 0.630]
+x1[1, 1] = [1.606, 2.488]
+x1[2, 2] = [2.300, 0.710]
+x1[3, 3] = [0.950, 1.616]
+x1[4, 4] = [2.046, 1.560]
+x1[5, 5] = [2.959, 2.387]
+x1[0, 1] = [1]
+x1[1, 0] = [1]
+x1[1, 2] = [1]
+x1[2, 1] = [1]
+x1[2, 5] = [1]
+x1[3, 4] = [1]
+x1[4, 3] = [1]
+x1[5, 2] = [1]
+x2 = {}
+x2[0, 0] = [0.810, 0.701]
+x2[1, 1] = [1.440, 2.437]
+x2[2, 2] = [2.358, 0.645]
+x2[3, 3] = [0.786, 1.535]
+x2[4, 4] = [2.093, 1.591]
+x2[5, 5] = [3.3, 2.2]
+x2[0, 1] = [1]
+x2[1, 0] = [1]
+x2[1, 2] = [1]
+x2[2, 1] = [1]
+x2[3, 4] = [1]
+x2[4, 3] = [1]
+x3 = {}
+x3[0, 0] = [0.71, 0.72]
+x3[1, 1] = [1.45532, 2.45648]
+x3[2, 2] = [2.21121, 0.757368]
+x3[3, 3] = [0.796224, 1.53137]
+x3[4, 4] = [2.06496, 1.5699]
+x3[5, 5] = [2.75535, 0.194153]
+x3[0, 1] = [1]
+x3[1, 0] = [1]
+x3[0, 5] = [1]
+x3[5, 0] = [1]
+x3[1, 2] = [1]
+x3[2, 1] = [1]
+x3[3, 4] = [1]
+x3[4, 3] = [1]
+```
+
+Create Graph set:
+
+```{python}
+G = GraphSet(graph_type='directed')
+G.add(Graph(x=x1, s=None, adj=None))
+G.add(Graph(x=x2, s=None, adj=None))
+G.add(Graph(x=x3, s=None, adj=None))
+```
+
+or import a GraphSet
+
+```{python}
+X = GraphSet()
+X.read_from_text("Dataset.txt")
+```
+
+Compute the euclidean distance with or without matching between two graphs
+
+- Identity matching
+```{python}
+match = ID(sqeuclidean())
+match.dis(G.X[0], G.X[1])
+print(match.f)
+# the identity permutation as expected!
+```
+- Matching Function - GA or GAS:
+```{python}
+match = GAS(sqeuclidean())
+match.dis(G.X[1], G.X[2])
+# to see the matching transformation:
+print(match.f)
+del match
+```
+
+Compute the mean with the identity matcher
+```{python}
+match = ID(sqeuclidean())
+mu = Mean(G, match)
+MU = mu.mean()
+# to see the result:
+print(MU.x)
+
+del match, mu, MU
+```
+
+Align All and Compute Mean with GA matcher
+```{python}
+match = GA(sqeuclidean())
+mu = mean_aac(G, match)
+mu.align_and_est()
+MU = mu.mean
+print(MU.x)
+
+del match, mu, MU
+```
+
+Align All and Compute Mean with GAS matcher
+```{python}
+match = GAS(sqeuclidean())
+# or equivalently:
+# GAS(euclidean())
+# GAS('euclidean')
+# GAS('euclidean','euclidean')
+mu = mean_aac(G, match)
+mu.align_and_est()
+MU = mu.mean
+print(MU.x)
+
+del match, mu, MU
+```
+
+Align All and Compute GPC
+```{python}
+n_comp=2
+p=gpc_aac(G,GA(sqeuclidean()))
+p.align_and_est(n_comp,scale=False,s=[0,10])
+```
+
+To project the data along the i-th GPC you need to:
+- create the geodesic by interpolation the two points barycenter and p.e_vec.X[i]
+- save the graphs along the geodesic that correspond to the scores (p.scores[:,i])
+For example the first GPC:
+```{python}
+n_gpc=0
+Vector=p.e_vec.X[n_gpc]
+Bar=p.barycenter_net
+l=list(np.sort(p.scores[:,n_gpc]))
+G_along_GPC=GraphSet()
+for i in range(len(l)):
+    G_along_GPC.add(p.add(1,Bar,l[i],Vector,range(Vector.n_nodes)))
+    print(G_along_GPC.X[i].x)
+```
+
+Align All and Compute GGR regression scalar on graph
+```{python}
+G=GraphSet()
+G.read_from_text("ErdosReny_100.txt")
+# Training and Test set
+n_train=10
+X_train=G.sublist(list(range(0,n_train)))
+
+# Run GGR:
+r=ggr_aac(X_train,GAS(sqeuclidean()),distance=sqeuclidean())
+r.align_and_est()
+
+# Proportion of variance explained
+r.R2
+
+# Network Coefficient
+print(r.network_coef.x)
+
+# Prediction:
+Y_test=G.X[1]
+x_new=pd.DataFrame(data=[float(Y_test.s)])
+r.predict(x_new)
+
+# Conformal Prediction Bands:
+
+Y = GraphSet(graph_type='directed')
+for j in range(190):
+    x0 = {}
+    i0 = np.random.binomial(n=1,p=0.4)
+    x0[0,0] = [1]
+    x0[1,1] = [1]
+    x0[i0,(1-i0)] = [np.random.normal(loc=20, scale=3)]
+    Y.add(Graph(x=x0, y=None, adj=None))
+for j in range(10):
+    x0 = {}
+    x0[0,0] = [1]
+    x0[1,1] = [1]
+    x0[0,1] = [np.random.normal(loc=20, scale=3)]
+    x0[1,0] = [np.random.normal(loc=2, scale=0.1)]
+    Y.add(Graph(x=x0, y=None, adj=None))
+
+match = GAS()
+mu_pred = mean_aac_pred(Y, match)
+mu_pred.align_est_and_predRegions()
+mu_pred.conformal_matrix
+```