def splitData(X,y,portion,seed):
startLog(__name__)
logger = logging.getLogger(__name__)
records = {'portion':portion, 'seed':seed}
logger.info('split data into train and test %s',records)
if not isinstance(X, np.ndarray):
logger.debug('X is not a nparray, converted')
X = np.array(X)
y = np.array(y)
(rows, cols) = np.shape(X)
size_data = rows
index = np.random.permutation(size_data)
Ntr = math.floor(portion*size_data)
idx_test = index[0:Ntr]
idx_train = index[Ntr:]
X_test = X[idx_test,:]
X_train = X[idx_train,:]
y_test = y[idx_test]
y_train = y[idx_train]
logger.info('split done check split')
# check split
(rows_test, cols_test) = np.shape(X_test)
(rows_train, cols_train) = np.shape(X_train)
if rows_train < rows_train:
logger.warning('test set larger than training set')
logger.info('size of X_test is %d and X_train %d, #fts %d',rows_test,rows_train,cols_train)
return X_test, X_train, y_train, y_test
def kmeansClustering(X, k, maxIters = 10):
"""
X: data in shape N X D
k: number of cluster
"""
my_io.startLog(__name__)
logger = logging.getLogger(__name__)
X = normalize(X)
#X = np.transpose(X)
(N, D) = np.shape(X)
ax = plt.gca()
# colors = ['r' if i==0 else 'g' for i in ?]
colors = 'r'
ax.scatter(X[:,0], X[:,1], c=colors,alpha=0.8)
# plt.show()
# initialize
# D = np.zeros((0,1))
min_x = np.amin(X)
max_x = np.amax(X)
# shape of mu: K X D
mu_old = np.zeros((k, D))
# mu_old = [ randomInit(max_x, min_x, D) for idk in range(k)]
# mu_old = np.array(mu_old)
mu_old = np.array(random.sample(X,k))
logger.info('randomly initialize mean vector, check dimension: ')
logger.info('pass' if ((k, D) == np.array(mu_old)).all
else logger.error('failed'))
logger.info('maximum iteration: %s start iteration',
str(maxIters))
loss = np.zeros((N,1))
for i in range(maxIters):
(Ln, r, Mu) = kmeans_update(X, mu_old)
loss[i] = Ln
logger.info('iteration %d, loss %4f \n', i, Ln)
mu_old = Mu
logger.info('done loss %3f', Ln)
ax = plt.gca()
colors_list = ['r','g','b','y']
colors = [colors_list[int(r[i])] for i in range(N)]
# colors = 'r'
ax.scatter(X[:,0], X[:,1], c=colors,alpha=0.8)
# plt.show()
return X, r
def gmmClustering(X, k = 2, maxiter = 3):
my_io.startLog(__name__)
logger = logging.getLogger(__name__)
X, r = kmeans.kmeansClustering(X, 2, 1)
(N, D) = np.shape(X)
pi_k_old = [np.divide(len(np.where(r==kth)[0]), float(N))
for kth in range(k) ]
# mu_old = compute_muk(X, k, r)
cova_old, mu_old = compute_cova(k, X, r)
for i in range(maxiter):
#if i==1:
# pdb.set_trace()
logger.info('ite: %d loss: %f',i,
loss(X, mu_old, pi_k_old, cova_old) )
p = gmm_Esteps(X, pi_k_old, k, cova_old, mu_old)
mu_new, cova_new, pi_k_new = gmm_Msteps(mu_old, X, p)
pi_k_old = pi_k_new
mu_old = mu_new
cova_old = cova_new
#matplotlib.cm=get_cmap("jet")
cm = plt.get_cmap('jet')
ax = plt.gca()
# colors = ['r' if i==0 else 'g' for i in ?]
#colors = 'r'
#ax.scatter(X[:,0], X[:,1], c=colors,alpha=0.8)
# plt.show()
for j in range(N):
likehood = p[1][j]
color = cm(likehood)
plt.plot(X[j,0], X[j,1] ,"o", color=color)
plt.show()
for j in range(N):
likehood = p[0][j]
color = cm(likehood)
plt.plot(X[j,0], X[j,1] ,"o", color=color)
plt.show()
# svm_bench.py
import logging
import my_io
import classification_baseline
from sklearn import svm
import numpy as np
from sklearn.metrics import classification
from numpy import linalg as LA
my_io.setUp('./biological_response/')
my_io.startLog(__name__)
logger = logging.getLogger(__name__)
y,X,trainData,testData = my_io.readCsv()
portion = 0.2
seed = 1
X_test, X_train, y_train, y_test = classification_baseline.splitData(X,y,portion,seed)
logger.info('init svm classifier')
svc = svm.SVC(probability = True)
logger.info('fitting svc')
svc.fit(X_train, y_train)
logger.info('start predict')
predict_probs = svc.predict_proba(X_test)
predict = my_io.toZeroOne(predict_probs)
# error = classification.zero_one_loss(y_test, predict)
loss = np.subtract(predict,y_test)
error = LA.norm(loss)
def kmeans_update(X, Mu):
"""update r and Mu given X and Mu
X is [N D]data
Mu is [K D] mean vector
r is 1xN responsibility vector,
e.g. r = [1,2,1] for 2 clusters 3 data points
Ln is 1xN minimum distance to its center for each point n
"""
my_io.startLog(__name__)
logger = logging.getLogger(__name__)
# initialize
(K, D1) = np.shape(Mu)
(N, D) = np.shape(X)
logger.info('check shape mu: %s X: %s',
str(np.shape(Mu)),str(np.shape(X)))
logger.info('pass' if D1==D else logger.error('failed'))
r = np.zeros((1, N))
# Mu = zeros(D,K)
Ln = np.zeros((N,1))
r = np.zeros((N,1))
dis2Muk = np.zeros((K,1))
for n in range(0, N):
"""for each point
assign x_n to the nearest group
"""
xn = X[n,:]
# for each cluster, compute the error
for k in range(0, K):
"""for each group
calculate the distane from point x_n to mu_k
"""
dis2Muk[k] = LA.norm(np.subtract(xn, Mu[k,:]))
# print('dis to cluster %d is %.2f \n',k,dis2Muk(k))
# np.amin(a, axis=1) return Minima along the second axis
# (i,j)=np.unravel_index(dis2Muk.argmin(), dis2Muk.shape)
""" find the minimum distance, ie. the nearest group
assigh r_n
"""
indexk = np.argmin(dis2Muk)
# (minVal, indexK) = min(dis2Muk)
# assigh cluster
# compute r
try:
r[n] = indexk
except Exception as err:
logger.exception('distance to mean vector should be 1D array,'
' now ', np.shape(dis2Muk))
# fprintf('assign to cluster: %d \n',r(n))
# compute Mu for each k
"""
for each group:
update mean vector
"""
# r is assighment of xk
# pdb.set_trace()
for k in range(0, K):
# indexArray = r == k
xk = [X[idx,:] for idx in range(len(r)) if r[idx] == k]
# xk: Nk x D
logger.info(' in group %d, num of points %s', k, str(np.shape(xk)))
Mu[k,:] = np.mean(xk, 0) # 0: cal mean along each column
"""for each point,
cal the distance to new mean vector u_k, k = r[n]
"""
Ln = [LA.norm(np.subtract(X[n, :], Mu[int(r[n]), :])) for n in range(0, N)]
logging.info('cal disortion measurement for each x,'
' check dimension OK' if len(Ln) == n else 'error here')
# Ln[n] = norm(X[:, n]-Mu[:, r(n)])
# print Ln
Ln_mean = np.mean(Ln)
return Ln_mean, r, Mu