def compress(self, X):
n = X.shape[0]
# Compute Euclidean distances
D = utils.euclidean_dist_squared(X, X)
D = np.sqrt(D)
# D is symmetric matrix
geoD = np.zeros((n, n))
# find nn-neighbours
for i in range(n):
sort = np.argsort(D[:, i])
neigh = np.setdiff1d(sort[0:self.nn + 1], i)
# find the nn+1 smallest indexes that are not i
for j in range(len(neigh)):
t = neigh[j]
geoD[i, t] = D[i, t]
geoD[t, i] = D[t, i]
D = utils.dijkstra(geoD)
# for disconnected vertices (distance is Inf)
# set their dist = max_dist(graph)
# to encourage they are far away from each other
D[np.isinf(D)] = D[~np.isinf(D)].max()
# Initialize low-dimensional representation with PCA
pca = PCA(self.k)
pca.fit(X)
Z = pca.compress(X)
# Solve for the minimizer
z, f = findMin(self._fun_obj_z, Z.flatten(), 500, D)
Z = z.reshape(n, self.k)
return Z
def compress(self, X):
n = X.shape[0]
# Compute Euclidean distances
D = utils.euclidean_dist_squared(X, X)
D = np.sqrt(D)
# Construct nearest neighbour graph
G = np.zeros([n, n])
for i in range(n):
neighbours = np.argsort(D[i])[:self.nn + 1]
for j in neighbours:
G[i, j] = D[i, j]
G[j, i] = D[j, i]
# Compute ISOMAP distances
D = utils.dijkstra(G)
# If two points are disconnected (distance is Inf)
# then set their distance to the maximum
# distance in the graph, to encourage them to be far apart.
D[np.isinf(D)] = D[~np.isinf(D)].max()
# Initialize low-dimensional representation with PCA
pca = PCA(self.k)
pca.fit(X)
Z = pca.compress(X)
# Solve for the minimizer
z, f = findMin(self._fun_obj_z, Z.flatten(), 500, D)
Z = z.reshape(n, self.k)
return Z
def compress(self, X):
n = X.shape[0]
# Compute Euclidean distances
D = utils.euclidean_dist_squared(X, X)
D = np.sqrt(D)
sorted_indices = np.argsort(D)
G = np.zeros((n, n))
for i in range(D.shape[0]):
for j in range(self.nn + 1):
G[i, sorted_indices[i, j]] = D[i, sorted_indices[i, j]]
G[sorted_indices[i, j], i] = D[sorted_indices[i, j], i]
dist = utils.dijkstra(G)
dist[np.isinf(dist)] = dist[~np.isinf(dist)].max()
# Initialize low-dimensional representation with PCA
pca = PCA(self.k)
pca.fit(X)
Z = pca.compress(X)
# Solve for the minimizer
z, f = findMin(self._fun_obj_z, Z.flatten(), 500, dist)
Z = z.reshape(n, self.k)
return Z
def compress(self, X):
n = X.shape[0]
# Compute Euclidean distances
D = utils.euclidean_dist_squared(X,X)
D = np.sqrt(D)
#TODO:
D = self.construct_dist_graph(X , D)
# If two points are disconnected (distance is Inf)
# then set their distance to the maximum
# distance in the graph, to encourage them to be far apart.
D[np.isinf(D)] = D[~np.isinf(D)].max()
# Initialize low-dimensional representation with PCA
pca = PCA(self.k)
pca.fit(X)
Z = pca.compress(X)
# Solve for the minimizer
z,f = findMin(self._fun_obj_z, Z.flatten(), 500, D)
Z = z.reshape(n, self.k)
return Z
def compress(self, X):
n = X.shape[0]
k = self.k
# Compute Euclidean distances
D = utils.euclidean_dist_squared(X, X)
D = np.sqrt(D)
# Initialize low-dimensional representation with PCA
pca = PCA(k)
pca.fit(X)
Z = pca.compress(X)
# Solve for the minimizer
z, f = findMin(self._fun_obj_z, Z.flatten(), 500, D)
Z = z.reshape(n, k)
return Z
def compress(self, X):
n = X.shape[0]
# Compute Euclidean distances
D = utils.euclidean_dist_squared(X, X)
D = np.sqrt(D)
np.fill_diagonal(D, np.inf)
########
#"finding the neighbor at each point"
G = np.matrix(np.ones((n, n)) * 0)
for i in range(n):
neighbours = np.argsort(D[:, i])
#want only the k nearest
for j in neighbours[1:self.nn + 1]:
G[i, j] = D[i, j]
G[j, i] = D[j, i]
#weighted shortest path between points (dijksta's)
D = np.zeros((n, n))
for i in range(n):
for j in range(i + 1, n):
D[i, j] = utils.dijkstra(G, i, j)
########
# If two points are disconnected (distance is Inf)
# then set their distance to the maximum
# distance in the graph, to encourage them to be far apart.
D[np.isinf(D)] = D[~np.isinf(D)].max()
# Initialize low-dimensional representation with PCA
pca = PCA(self.k)
pca.fit(X)
Z = pca.compress(X)
# Solve for the minimizer
z, f = findMin(self._fun_obj_z, Z.flatten(), 500, D)
Z = z.reshape(n, self.k)
return Z
def compress(self, X):
n = X.shape[0]
# Compute Euclidean distances
D = utils.euclidean_dist_squared(X, X)
D = np.sqrt(D)
########
# TODO #
G = np.full((n, n), np.inf)
for i in range(n):
for j in range(n):
#temp = np.list(D[i]).sort
temp = sorted(D[i])
#print(self.nn+1)
if D[i][j] in temp[:(self.nn + 1)]:
G[i][j] = D[i][j]
for i in range(n):
for j in range(n):
D[i][j] = utils.dijkstra(G, i, j)
########
# If two points are disconnected (distance is Inf)
# then set their distance to the maximum
# distance in the graph, to encourage them to be far apart.
D[np.isinf(D)] = D[~np.isinf(D)].max()
#G[np.isinf(G)] = G[~np.isinf(G)].max()
# Initialize low-dimensional representation with PCA
pca = PCA(self.k)
pca.fit(X)
Z = pca.compress(X)
# Solve for the minimizer
z, f = findMin(self._fun_obj_z, Z.flatten(), 500, D)
Z = z.reshape(n, self.k)
return Z
for i in range(n):
plt.annotate(animals[i], (X[i, f1], X[i, f2]))
utils.savefig('two_random_features.png')
elif question == '2.2':
dataset = load_dataset('animals.pkl')
X = dataset['X'].astype(float)
animals = dataset['animals']
n, d = X.shape
# standardize columns
X = utils.standardize_cols(X)
model = PCA(k=2)
model.fit(X)
Z = model.compress(X)
fig, ax = plt.subplots()
plt.ylabel('z2')
plt.xlabel('z1')
ax.scatter(Z[:, 0], Z[:, 1])
for i in range(n):
ax.annotate(animals[i], (Z[i, 0], Z[i, 1]))
utils.savefig('q2_2_PCA_animals.png')
elif question == '3.1':
X = load_dataset('highway.pkl')['X'].astype(float) / 255
n, d = X.shape
print(n, d)
h, w = 64, 64 # height and width of each image
choices=['1.2', '2.1', '3', '3.1', '3.2'])
io_args = parser.parse_args()
question = io_args.question
if question == '1.2':
dataset = utils.load_dataset('animals')
X = dataset['X'].astype(float)
animals = dataset['animals']
n, d = X.shape
k = 5
X = utils.standardize_cols(X) # standardize columns
model = PCA(k=2)
model.fit(X)
Z = model.compress(X)
# Plot the matrix
plt.imshow(Z)
utils.savefig('q1_unsatisfying_visualization_1.png')
## Randomly plot two features, and label all points
fig, ax = plt.subplots()
ax.scatter(Z[:, 0], Z[:, 1])
for i in range(n):
ax.annotate(animals[i], (Z[i, 0], Z[i, 1]))
utils.savefig('q1_unsatisfying_visualization_2.png')
v = 1 - norm(np.dot(Z, model.W) - X, 'fro')**2 / norm(X, 'fro')**2
print v #The variance
print("[+] Processing data...")
X = (data[:, 1:].astype(np.int) - 127.5) / 127.5
y = data[:, 0].astype(np.int)
print("[+] Running PCA...")
pca = PCA()
X = pca.fit_compress(X, 500)
print("[+] Fitting neural net...")
model = NeuralNetwork((500, 300, 100, 10), alpha=8e-2, reg=1e-3, batch_size=60, epochs=3, momentum = 0.8)
model.fit(X, y)
print("[+] Loading test data...")
reader = csv.reader(open("mnist_test.csv", "r"))
data = np.array(list(reader))
print("[+] Processing data...")
X = (data[:, 1:].astype(np.int) - 127.5) / 127.5
y = data[:, 0].astype(np.int)
print("[+] Compressing data...")
X = pca.compress(X)
print("[+] Making predictions...")
predictions = np.array(model.predict(X))
print("[+] Calculating accuracy...")
accuracy = sum(predictions == y) / len(y)
print(accuracy)
fig = pyplot.figure()
ax = fig.add_subplot(1, 1, 1)
sns.scatterplot(features_tsne[:, 0],
features_tsne[:, 1],
hue=labels,
legend='full')
ax.set_title("T-SNE on Iris Data-Set", fontsize=16)
##################################################
print("Plotting PCA projection of data-set and classifier.")
pca = PCA()
pca.analyze(features)
pca.save("iris_results/iris")
features_compressed = pca.compress(features, 2)
fig = pyplot.figure()
ax = fig.add_subplot(1, 1, 1)
ax.set_title('MLP-Classification of the Iris Data-Set', fontsize=16)
ax.set_xlim([-4.0, 4.0])
ax.set_xlabel("PCA Component 0", fontsize=12)
ax.set_ylim([-1.5, 1.5])
ax.set_ylabel("PCA Component 1", fontsize=12)
XX, YY = np.meshgrid(np.arange(*ax.get_xlim(), 0.005),
np.arange(*ax.get_ylim(), 0.005))
XY = np.vstack((XX.ravel(), YY.ravel())).T
ZZ = np.argmax(model.predict(pca.decompress(XY)), axis=1).reshape(XX.shape)
ax.contourf(XX, YY, ZZ + 1e-6, levels=3, colors=['g', 'b', 'r'], alpha=0.2)
for d in dimensions[:-1]:
name += '_' + str(d)
print(name)
##################################################
pca = PCA()
new_pca = False
if new_pca:
eigs = pca.analyze(samples_train)
pca.save("faces_results/faces")
else:
pca.load("faces_results/faces")
samples_train_compressed = pca.compress(samples_train, dimensionality=dimensions[0])
samples_test_compressed = pca.compress(samples_test, dimensionality=dimensions[0])
##################################################
mlp = MLP(dimensions)
new_mlp = False
if new_mlp:
mlp.train(samples_train_compressed,
targets_train,
max_epochs=200,
step=0.1,
gain=0.9)
mlp.save(name)
else: