In [5]:

    

!pip install .


    

    




Processing /Users/tracyx/Desktop/Stat663-Final-Project/GBW
  Requirement already satisfied (use --upgrade to upgrade): GBW==0.1 from file:///Users/tracyx/Desktop/Stat663-Final-Project/GBW in /anaconda/lib/python3.5/site-packages

In [1]:

    

import GBW


    

In [2]:

    

import numpy as np
from scipy import stats
import scipy.io
from matplotlib import pyplot as plt
import time
import pstats

## Load synthesized data
Y = scipy.io.loadmat('Y.mat')['Y'] # Graph information of contacts each timestamp, dim=(84,84,107)
X = scipy.io.loadmat('X.mat')['X'] # Hidden(infection) states, dim=(84,108), including X(0)
G = scipy.io.loadmat('G.mat')['G'] # Observed(symptom) states, dim=(84,6,107)
C = scipy.io.loadmat('C.mat')['C']

sC = [np.sum(c[0], 1) for c in C]


    

In [3]:

    

[XBELEM, paraAEM] = GBW.AEMBP_GCHMM(G,Y,C, sC, 'f', 5, 0.0001,X)


    

In [4]:

    

plt.imshow(XBELEM[:,1,:], cmap='seismic')
plt.savefig("predicted_AEM.png", dpi = 300, bbox_inches ="tight")
plt.show()


    

In [6]:

    

plt.imshow(X, cmap='seismic')
plt.savefig("true.png", dpi = 300, bbox_inches ="tight")
plt.show()


    

In [ ]:

    

def work(G,Y,C, sC, initial, MaxIter, tol,X):
     GBW.AEMBP_GCHMM(G,Y,C, sC, initial, MaxIter, tol,X)


    

In [ ]:

    

%prun -q -D GBW.AEMBP_GCHMM.prof  GBW.AEMBP_GCHMM(G, Y, C, sC,'f', 5, 0.0001, X)


    

In [ ]:

    

p = pstats.Stats('AEMBP_GCHMM.prof')
p.sort_stats('time','cumulative').print_stats(15)
pass