update on machine learning

2017-12-06 14:13:28 +01:00
parent 2111fd0fbc
commit 3eaf9e4578
70 changed files with 7950 additions and 551 deletions
@@ -0,0 +1,27 @@
+import numpy as np
+
+# Estimate r
+data = np.loadtxt('ecoli.csv', delimiter=',')
+t_e = data[:,0]
+N_e = data[:,1]
+i = 2  # Data point (i,i+1) used to estimate r
+r = (N_e[i+1] - N_e[i])/(N_e[i]*(t_e[i+1] - t_e[i]))
+print 'Estimated r=%.5f' % r
+# Can experiment with r values and see if the model can
+# match the data better
+
+T = 1200     # cell can divide after T sec
+t_max = 5*T  # 5 generations in experiment
+t = np.linspace(0, t_max, 1000)
+dt = t[1] - t[0]
+N = np.zeros(t.size)
+
+N[0] = 100
+for n in range(0, len(t)-1, 1):
+    N[n+1] = N[n] + r*dt*N[n]
+
+import matplotlib.pyplot as plt
+plt.plot(t, N, 'r-', t_e, N_e, 'bo')
+plt.xlabel('time [s]');  plt.ylabel('N')
+plt.legend(['model', 'experiment'], loc='upper left')
+plt.show()