|
a |
|
b/train_test.py |
|
|
1 |
""" Training and testing of the model |
|
|
2 |
""" |
|
|
3 |
import os |
|
|
4 |
import numpy as np |
|
|
5 |
from sklearn.metrics import accuracy_score, f1_score, roc_auc_score |
|
|
6 |
import torch |
|
|
7 |
import torch.nn.functional as F |
|
|
8 |
from models import init_model_dict, init_optim |
|
|
9 |
from utils import one_hot_tensor, cal_sample_weight, gen_adj_mat_tensor, gen_test_adj_mat_tensor, cal_adj_mat_parameter |
|
|
10 |
|
|
|
11 |
cuda = True if torch.cuda.is_available() else False |
|
|
12 |
|
|
|
13 |
|
|
|
14 |
def prepare_trte_data(data_folder, view_list): |
|
|
15 |
num_view = len(view_list) |
|
|
16 |
labels_tr = np.loadtxt(os.path.join(data_folder, "labels_tr.csv"), delimiter=',') |
|
|
17 |
labels_te = np.loadtxt(os.path.join(data_folder, "labels_te.csv"), delimiter=',') |
|
|
18 |
labels_tr = labels_tr.astype(int) |
|
|
19 |
labels_te = labels_te.astype(int) |
|
|
20 |
data_tr_list = [] |
|
|
21 |
data_te_list = [] |
|
|
22 |
for i in view_list: |
|
|
23 |
data_tr_list.append(np.loadtxt(os.path.join(data_folder, str(i)+"_tr.csv"), delimiter=',')) |
|
|
24 |
data_te_list.append(np.loadtxt(os.path.join(data_folder, str(i)+"_te.csv"), delimiter=',')) |
|
|
25 |
num_tr = data_tr_list[0].shape[0] |
|
|
26 |
num_te = data_te_list[0].shape[0] |
|
|
27 |
data_mat_list = [] |
|
|
28 |
for i in range(num_view): |
|
|
29 |
data_mat_list.append(np.concatenate((data_tr_list[i], data_te_list[i]), axis=0)) |
|
|
30 |
data_tensor_list = [] |
|
|
31 |
for i in range(len(data_mat_list)): |
|
|
32 |
data_tensor_list.append(torch.FloatTensor(data_mat_list[i])) |
|
|
33 |
if cuda: |
|
|
34 |
data_tensor_list[i] = data_tensor_list[i].cuda() |
|
|
35 |
idx_dict = {} |
|
|
36 |
idx_dict["tr"] = list(range(num_tr)) |
|
|
37 |
idx_dict["te"] = list(range(num_tr, (num_tr+num_te))) |
|
|
38 |
data_train_list = [] |
|
|
39 |
data_all_list = [] |
|
|
40 |
for i in range(len(data_tensor_list)): |
|
|
41 |
data_train_list.append(data_tensor_list[i][idx_dict["tr"]].clone()) |
|
|
42 |
data_all_list.append(torch.cat((data_tensor_list[i][idx_dict["tr"]].clone(), |
|
|
43 |
data_tensor_list[i][idx_dict["te"]].clone()),0)) |
|
|
44 |
labels = np.concatenate((labels_tr, labels_te)) |
|
|
45 |
|
|
|
46 |
return data_train_list, data_all_list, idx_dict, labels |
|
|
47 |
|
|
|
48 |
|
|
|
49 |
def gen_trte_adj_mat(data_tr_list, data_trte_list, trte_idx, adj_parameter): |
|
|
50 |
adj_metric = "cosine" # cosine distance |
|
|
51 |
adj_train_list = [] |
|
|
52 |
adj_test_list = [] |
|
|
53 |
for i in range(len(data_tr_list)): |
|
|
54 |
adj_parameter_adaptive = cal_adj_mat_parameter(adj_parameter, data_tr_list[i], adj_metric) |
|
|
55 |
adj_train_list.append(gen_adj_mat_tensor(data_tr_list[i], adj_parameter_adaptive, adj_metric)) |
|
|
56 |
adj_test_list.append(gen_test_adj_mat_tensor(data_trte_list[i], trte_idx, adj_parameter_adaptive, adj_metric)) |
|
|
57 |
|
|
|
58 |
return adj_train_list, adj_test_list |
|
|
59 |
|
|
|
60 |
|
|
|
61 |
def train_epoch(data_list, adj_list, label, one_hot_label, sample_weight, model_dict, optim_dict, train_VCDN=True): |
|
|
62 |
loss_dict = {} |
|
|
63 |
criterion = torch.nn.CrossEntropyLoss(reduction='none') |
|
|
64 |
for m in model_dict: |
|
|
65 |
model_dict[m].train() |
|
|
66 |
num_view = len(data_list) |
|
|
67 |
for i in range(num_view): |
|
|
68 |
optim_dict["C{:}".format(i+1)].zero_grad() |
|
|
69 |
ci_loss = 0 |
|
|
70 |
ci = model_dict["C{:}".format(i+1)](model_dict["E{:}".format(i+1)](data_list[i],adj_list[i])) |
|
|
71 |
ci_loss = torch.mean(torch.mul(criterion(ci, label),sample_weight)) |
|
|
72 |
ci_loss.backward() |
|
|
73 |
optim_dict["C{:}".format(i+1)].step() |
|
|
74 |
loss_dict["C{:}".format(i+1)] = ci_loss.detach().cpu().numpy().item() |
|
|
75 |
if train_VCDN and num_view >= 2: |
|
|
76 |
optim_dict["C"].zero_grad() |
|
|
77 |
c_loss = 0 |
|
|
78 |
ci_list = [] |
|
|
79 |
for i in range(num_view): |
|
|
80 |
ci_list.append(model_dict["C{:}".format(i+1)](model_dict["E{:}".format(i+1)](data_list[i],adj_list[i]))) |
|
|
81 |
c = model_dict["C"](ci_list) |
|
|
82 |
c_loss = torch.mean(torch.mul(criterion(c, label),sample_weight)) |
|
|
83 |
c_loss.backward() |
|
|
84 |
optim_dict["C"].step() |
|
|
85 |
loss_dict["C"] = c_loss.detach().cpu().numpy().item() |
|
|
86 |
|
|
|
87 |
return loss_dict |
|
|
88 |
|
|
|
89 |
|
|
|
90 |
def test_epoch(data_list, adj_list, te_idx, model_dict): |
|
|
91 |
for m in model_dict: |
|
|
92 |
model_dict[m].eval() |
|
|
93 |
num_view = len(data_list) |
|
|
94 |
ci_list = [] |
|
|
95 |
for i in range(num_view): |
|
|
96 |
ci_list.append(model_dict["C{:}".format(i+1)](model_dict["E{:}".format(i+1)](data_list[i],adj_list[i]))) |
|
|
97 |
if num_view >= 2: |
|
|
98 |
c = model_dict["C"](ci_list) |
|
|
99 |
else: |
|
|
100 |
c = ci_list[0] |
|
|
101 |
c = c[te_idx,:] |
|
|
102 |
prob = F.softmax(c, dim=1).data.cpu().numpy() |
|
|
103 |
|
|
|
104 |
return prob |
|
|
105 |
|
|
|
106 |
|
|
|
107 |
def train_test(data_folder, view_list, num_class, |
|
|
108 |
lr_e_pretrain, lr_e, lr_c, |
|
|
109 |
num_epoch_pretrain, num_epoch): |
|
|
110 |
test_inverval = 50 |
|
|
111 |
num_view = len(view_list) |
|
|
112 |
dim_hvcdn = pow(num_class,num_view) |
|
|
113 |
if data_folder == 'ROSMAP': |
|
|
114 |
adj_parameter = 2 |
|
|
115 |
dim_he_list = [200,200,100] |
|
|
116 |
if data_folder == 'BRCA': |
|
|
117 |
adj_parameter = 10 |
|
|
118 |
dim_he_list = [400,400,200] |
|
|
119 |
data_tr_list, data_trte_list, trte_idx, labels_trte = prepare_trte_data(data_folder, view_list) |
|
|
120 |
labels_tr_tensor = torch.LongTensor(labels_trte[trte_idx["tr"]]) |
|
|
121 |
onehot_labels_tr_tensor = one_hot_tensor(labels_tr_tensor, num_class) |
|
|
122 |
sample_weight_tr = cal_sample_weight(labels_trte[trte_idx["tr"]], num_class) |
|
|
123 |
sample_weight_tr = torch.FloatTensor(sample_weight_tr) |
|
|
124 |
if cuda: |
|
|
125 |
labels_tr_tensor = labels_tr_tensor.cuda() |
|
|
126 |
onehot_labels_tr_tensor = onehot_labels_tr_tensor.cuda() |
|
|
127 |
sample_weight_tr = sample_weight_tr.cuda() |
|
|
128 |
adj_tr_list, adj_te_list = gen_trte_adj_mat(data_tr_list, data_trte_list, trte_idx, adj_parameter) |
|
|
129 |
dim_list = [x.shape[1] for x in data_tr_list] |
|
|
130 |
model_dict = init_model_dict(num_view, num_class, dim_list, dim_he_list, dim_hvcdn) |
|
|
131 |
for m in model_dict: |
|
|
132 |
if cuda: |
|
|
133 |
model_dict[m].cuda() |
|
|
134 |
|
|
|
135 |
print("\nPretrain GCNs...") |
|
|
136 |
optim_dict = init_optim(num_view, model_dict, lr_e_pretrain, lr_c) |
|
|
137 |
for epoch in range(num_epoch_pretrain): |
|
|
138 |
train_epoch(data_tr_list, adj_tr_list, labels_tr_tensor, |
|
|
139 |
onehot_labels_tr_tensor, sample_weight_tr, model_dict, optim_dict, train_VCDN=False) |
|
|
140 |
print("\nTraining...") |
|
|
141 |
optim_dict = init_optim(num_view, model_dict, lr_e, lr_c) |
|
|
142 |
for epoch in range(num_epoch+1): |
|
|
143 |
train_epoch(data_tr_list, adj_tr_list, labels_tr_tensor, |
|
|
144 |
onehot_labels_tr_tensor, sample_weight_tr, model_dict, optim_dict) |
|
|
145 |
if epoch % test_inverval == 0: |
|
|
146 |
te_prob = test_epoch(data_trte_list, adj_te_list, trte_idx["te"], model_dict) |
|
|
147 |
print("\nTest: Epoch {:d}".format(epoch)) |
|
|
148 |
if num_class == 2: |
|
|
149 |
print("Test ACC: {:.3f}".format(accuracy_score(labels_trte[trte_idx["te"]], te_prob.argmax(1)))) |
|
|
150 |
print("Test F1: {:.3f}".format(f1_score(labels_trte[trte_idx["te"]], te_prob.argmax(1)))) |
|
|
151 |
print("Test AUC: {:.3f}".format(roc_auc_score(labels_trte[trte_idx["te"]], te_prob[:,1]))) |
|
|
152 |
else: |
|
|
153 |
print("Test ACC: {:.3f}".format(accuracy_score(labels_trte[trte_idx["te"]], te_prob.argmax(1)))) |
|
|
154 |
print("Test F1 weighted: {:.3f}".format(f1_score(labels_trte[trte_idx["te"]], te_prob.argmax(1), average='weighted'))) |
|
|
155 |
print("Test F1 macro: {:.3f}".format(f1_score(labels_trte[trte_idx["te"]], te_prob.argmax(1), average='macro'))) |
|
|
156 |
print() |