|
a |
|
b/medicalbert/classifiers/standard/classifier.py |
|
|
1 |
import gcsfs,logging, os, torch |
|
|
2 |
import pandas as pd |
|
|
3 |
from statistics import mean |
|
|
4 |
from tqdm import trange, tqdm |
|
|
5 |
|
|
|
6 |
### |
|
|
7 |
# Base class for Bert classifiers. |
|
|
8 |
### |
|
|
9 |
class Classifier: |
|
|
10 |
|
|
|
11 |
def train(self, datareader): |
|
|
12 |
device = torch.device(self.config['device']) |
|
|
13 |
self.model.train() |
|
|
14 |
self.model.to(device) |
|
|
15 |
|
|
|
16 |
batch_losses = [] |
|
|
17 |
|
|
|
18 |
for _ in trange(self.epochs, int(self.config['epochs']), desc="Epoch"): |
|
|
19 |
tr_loss = 0 |
|
|
20 |
batche = [] |
|
|
21 |
with tqdm(datareader.get_train(), desc="Iteration") as t: |
|
|
22 |
for step, batch in enumerate(t): |
|
|
23 |
|
|
|
24 |
batch = tuple(t.to(device) for t in batch) |
|
|
25 |
input_ids, input_mask, segment_ids, label_ids = batch |
|
|
26 |
|
|
|
27 |
loss = self.model(input_ids, labels=label_ids)[0] |
|
|
28 |
|
|
|
29 |
# Statistics |
|
|
30 |
batche.append(loss.item()) |
|
|
31 |
|
|
|
32 |
loss = loss / self.config['gradient_accumulation_steps'] |
|
|
33 |
|
|
|
34 |
loss.backward() |
|
|
35 |
|
|
|
36 |
tr_loss += loss.item() |
|
|
37 |
|
|
|
38 |
if (step + 1) % self.config['gradient_accumulation_steps'] == 0: |
|
|
39 |
batch_losses.append(mean(batche)) |
|
|
40 |
# Update the model gradients |
|
|
41 |
#torch.nn.utils.clip_grad_norm_(self.model.parameters(), 1.0) |
|
|
42 |
self.optimizer.step() |
|
|
43 |
self.optimizer.zero_grad() |
|
|
44 |
|
|
|
45 |
# save a checkpoint here |
|
|
46 |
self.save() |
|
|
47 |
self.epochs = self.epochs+1 |
|
|
48 |
|
|
|
49 |
self.save_batch_losses(pd.DataFrame(batch_losses)) |
|
|
50 |
|
|
|
51 |
def save_batch_losses(self, losses): |
|
|
52 |
path = os.path.join(self.config['output_dir'], self.config['experiment_name']) |
|
|
53 |
if path[:2] != "gs": |
|
|
54 |
if not os.path.exists(path): |
|
|
55 |
os.makedirs(path) |
|
|
56 |
|
|
|
57 |
losses.to_csv(os.path.join(self.config['output_dir'], self.config['experiment_name'], "batch_loss.csv")) |
|
|
58 |
|
|
|
59 |
def set_eval_mode(self): |
|
|
60 |
self.model.eval() |
|
|
61 |
|
|
|
62 |
def load_from_checkpoint(self): |
|
|
63 |
|
|
|
64 |
if 'load_from_checkpoint' in self.config: |
|
|
65 |
file_path = os.path.join(self.config['output_dir'], "checkpoints", self.config['load_from_checkpoint']) |
|
|
66 |
|
|
|
67 |
checkpoint = torch.load(file_path) |
|
|
68 |
self.epochs = checkpoint['epoch'] |
|
|
69 |
self.model.load_state_dict(checkpoint['bert_dict']) |
|
|
70 |
self.optimizer.load_state_dict(checkpoint['optimizer']) |
|
|
71 |
|
|
|
72 |
# work around - for some reason reloading an optimizer that worked with CUDA tensors |
|
|
73 |
# causes an error - see https://github.com/pytorch/pytorch/issues/2830 |
|
|
74 |
for state in self.optimizer.state.values(): |
|
|
75 |
for k, v in state.items(): |
|
|
76 |
if isinstance(v, torch.Tensor): |
|
|
77 |
if self.config['device'] == 'gpu': |
|
|
78 |
state[k] = v.cuda() |
|
|
79 |
else: |
|
|
80 |
state[k] = v |
|
|
81 |
|
|
|
82 |
def load_object_from_location(self, checkpoint_file): |
|
|
83 |
if checkpoint_file[:2] != "gs": |
|
|
84 |
return torch.load(checkpoint_file) |
|
|
85 |
else: |
|
|
86 |
|
|
|
87 |
fs = gcsfs.GCSFileSystem() |
|
|
88 |
with fs.open(checkpoint_file, mode='rb') as f: |
|
|
89 |
return torch.load(f) |
|
|
90 |
|
|
|
91 |
def load_from_checkpoint(self, checkpoint_file): |
|
|
92 |
file_path = os.path.join(self.config['output_dir'], self.config['experiment_name'],"checkpoints", checkpoint_file) |
|
|
93 |
checkpoint = self.load_object_from_location(file_path) |
|
|
94 |
|
|
|
95 |
self.epochs = checkpoint['epoch'] |
|
|
96 |
self.model.load_state_dict(checkpoint['bert_dict']) |
|
|
97 |
self.optimizer.load_state_dict(checkpoint['optimizer']) |
|
|
98 |
|
|
|
99 |
# work around - for some reason reloading an optimizer that worked with CUDA tensors |
|
|
100 |
# causes an error - see https://github.com/pytorch/pytorch/issues/2830 |
|
|
101 |
for state in self.optimizer.state.values(): |
|
|
102 |
for k, v in state.items(): |
|
|
103 |
if isinstance(v, torch.Tensor): |
|
|
104 |
if self.config['device'] == 'gpu': |
|
|
105 |
state[k] = v.cuda() |
|
|
106 |
else: |
|
|
107 |
state[k] = v |
|
|
108 |
|
|
|
109 |
def save_object_to_location(self, object): |
|
|
110 |
|
|
|
111 |
if self.config['output_dir'][:2] != "gs": |
|
|
112 |
if not os.path.exists( |
|
|
113 |
os.path.join(self.config['output_dir'], self.config['experiment_name'], "checkpoints")): |
|
|
114 |
os.makedirs(os.path.join(self.config['output_dir'], self.config['experiment_name'], "checkpoints")) |
|
|
115 |
torch.save(object, |
|
|
116 |
os.path.join(self.config['output_dir'], self.config['experiment_name'], "checkpoints", |
|
|
117 |
str(self.epochs))) |
|
|
118 |
else: |
|
|
119 |
fs = gcsfs.GCSFileSystem() |
|
|
120 |
file_name = os.path.join(self.config['output_dir'], self.config['experiment_name'], "checkpoints", |
|
|
121 |
str(self.epochs)) |
|
|
122 |
with fs.open(file_name, mode='wb') as f: |
|
|
123 |
return torch.save(object, f) |
|
|
124 |
|
|
|
125 |
def save(self): |
|
|
126 |
checkpoint = { |
|
|
127 |
'epoch': self.epochs + 1, |
|
|
128 |
'bert_dict': self.model.state_dict(), |
|
|
129 |
'optimizer': self.optimizer.state_dict(), |
|
|
130 |
} |
|
|
131 |
self.save_object_to_location(checkpoint) |
|
|
132 |
logging.info("Saved model") |