# -*- coding: utf-8 -*-
# Author: Zhi Qiao <mingshan_ai@163.com>
# License: BSD 2 clause
import os
import math
import torch
import torch.nn as nn
from torch.autograd import Variable
from torch.nn import Parameter
from torch import Tensor
import pickle
import warnings
from ._loss import callLoss
from ._dlbase import BaseControler
warnings.filterwarnings('ignore')
[docs]class tLSTMCell(nn.Module):
def __init__(self, input_size, hidden_size):
super(tLSTMCell, self).__init__()
self.input_size = input_size
self.hidden_size = hidden_size
self.x2h = nn.Linear(self.input_size, 4 * self.hidden_size)
self.h2h = nn.Linear(self.hidden_size, 4 * self.hidden_size)
self.c2h = nn.Linear(self.hidden_size, self.hidden_size)
self.activate_func_c = nn.Tanh()
self.activate_func_h = nn.Sigmoid()
self.activate_func_t = nn.Tanh()
self.reset_parameters()
[docs] def reset_parameters(self):
std = 1.0 / math.sqrt(self.hidden_size)
for w in self.parameters():
w.data.uniform_(-std, std)
[docs] def forward(self, data_x, data_t, h_t_1, c_t_1):
# print (data_x.shape)
# print (data_t.shape)
# print (h_t_1.shape)
# print (c_t_1.shape)
# shape of data_x : <n_batch, input_size>
# shape of data_t : <n_batch, 1>
# shape of data_h_t_1: <n_batch, hidden_size>
# shape of data_s_t_1: <n_batch, hidden_size>
# shape of gate_set : <n_batch, 4 * hidden_size>
gate_set = self.x2h(data_x) + self.h2h(h_t_1)
# shape of f_t : <n_batch, hidden_size>
# shape of i_t : <n_batch, hidden_size>
# shape of o_t : <n_batch, hidden_size>
# shape of c_hat : <n_batch, hidden_size>
_f_t, _i_t, _o_t, _c_hat = gate_set.chunk(4, -1)
f_t = self.activate_func_h(_f_t)
i_t = self.activate_func_h(_i_t)
o_t = self.activate_func_h(_o_t)
c_cur = self.activate_func_c(_c_hat)
# shape of c_s_t_1 : <n_batch, hidden_size>
c_s_t_1 = self.activate_func_c(self.c2h(c_t_1))
c_s_t_1_hat = c_s_t_1 * self.activate_func_t(data_t)
c_T_t_1 = c_t_1 - c_s_t_1
c_star_t_1 = c_T_t_1 + c_s_t_1_hat
# shape of c_t : <n_batch, hidden_size>
# shape of h_t : <n_batch, hidden_size>
c_t = f_t * c_star_t_1 + i_t * c_cur
h_t = o_t * self.activate_func_c(c_t)
return (h_t, c_t)
[docs]class callPredictor(nn.Module):
def __init__(self,
input_size = None,
hidden_size = 16,
output_size = 8,
batch_first = True,
dropout = 0.5,
label_size = 1,
device = None):
super(callPredictor, self).__init__()
assert input_size != None and isinstance(input_size, int), 'fill in correct input_size'
self.input_size = input_size
self.hidden_size = hidden_size
self.label_size = label_size
self.output_size = output_size
self.predict_func = nn.Linear(self.output_size, self.label_size)
self.rnn_unit = tLSTMCell(input_size, hidden_size)
self.device = device
[docs] def forward(self, input_data):
"""
Parameters
----------
input_data = {
'X': shape (batchsize, n_timestep, n_featdim)
'M': shape (batchsize, n_timestep)
'cur_M': shape (batchsize, n_timestep)
'T': shape (batchsize, n_timestep)
}
Return
----------
all_output, shape (batchsize, n_timestep, n_labels)
predict output of each time step
cur_output, shape (batchsize, n_labels)
predict output of last time step
"""
X = input_data['X']
M = input_data['M']
cur_M = input_data['cur_M']
T = input_data['T']
batchsize, n_timestep, _ = X.shape
h0 = Variable(torch.zeros(batchsize, self.hidden_size)).to(self.device)
c0 = Variable(torch.zeros(batchsize, self.hidden_size)).to(self.device)
outputs = []
h_t, c_t = h0, c0
for t in range(n_timestep):
h_t, c_t = self.rnn_unit(X[:,t,:], T[:, t].reshape(-1, 1), h_t, c_t)
outputs.append(h_t)
outputs = torch.stack(outputs, dim=1)
n_batchsize, n_timestep, n_featdim = outputs.shape
all_output = self.predict_func(outputs.reshape(n_batchsize*n_timestep, n_featdim)).\
reshape(n_batchsize, n_timestep, self.label_size) * M.unsqueeze(-1)
cur_output = (all_output * cur_M.unsqueeze(-1)).sum(dim=1)
return all_output, cur_output
[docs]class tLSTM(BaseControler):
"""
Time-Aware LSTM (T-LSTM), A kind of time-aware RNN neural network;
Used to handle irregular time intervals in longitudinal patient records.
"""
def __init__(self,
expmodel_id = 'test.new',
n_epoch = 100,
n_batchsize = 5,
learn_ratio = 1e-4,
weight_decay = 1e-4,
n_epoch_saved = 1,
hidden_size = 8,
output_size = 8,
bias = True,
dropout = 0.5,
batch_first = True,
loss_name = 'L1LossSigmoid',
target_repl = False,
target_repl_coef = 0.,
aggregate = 'sum',
optimizer_name = 'adam',
use_gpu = False,
gpu_ids = '0'
):
"""
Applies an Attention-based Bidirectional Recurrent Neural Networks for an healthcare data sequence
Parameters
----------
exp_id : str, optional (default='init.test')
name of current experiment
n_epoch : int, optional (default = 100)
number of epochs with the initial learning rate
n_batchsize : int, optional (default = 5)
batch size for model training
learn_ratio : float, optional (default = 1e-4)
initial learning rate for adam
weight_decay : float, optional (default = 1e-4)
weight decay (L2 penalty)
n_epoch_saved : int, optional (default = 1)
frequency of saving checkpoints at the end of epochs
hidden_size : int, optional (default = 8)
The number of features of the hidden state h
output_size: int, optional (default = 8)
The number of the embeded features of rnn output
bias : bool, optional (default = True)
If False, then the layer does not use bias weights b_ih and b_hh.
dropout : float, optional (default = 0.5)
If non-zero, introduces a Dropout layer on the outputs of each GRU layer except the last layer,
with dropout probability equal to dropout.
batch_first : bool, optional (default = False)
If True, then the input and output tensors are provided as (batch, seq, feature).
loss_name : str, optional (default='SigmoidCELoss')
Name or objective function.
use_gpu : bool, optional (default=False)
If yes, use GPU recources; else use CPU recources
gpu_ids : str, optional (default='')
If yes, assign concrete used gpu ids such as '0,2,6'; else use '0'
"""
super(tLSTM, self).__init__(expmodel_id)
self.n_batchsize = n_batchsize
self.n_epoch = n_epoch
self.learn_ratio = learn_ratio
self.weight_decay = weight_decay
self.n_epoch_saved = n_epoch_saved
self.hidden_size = hidden_size
self.output_size = output_size
self.bias = bias
self.dropout = dropout
self.batch_first = batch_first
self.loss_name = loss_name
self.target_repl = target_repl
self.target_repl_coef = target_repl_coef
self.aggregate = aggregate
self.optimizer_name = optimizer_name
self.use_gpu = use_gpu
self.gpu_ids = gpu_ids
self._args_check()
def _build_model(self):
"""
Build the crucial components for model training
"""
if self.is_loadmodel is False:
_config = {
'input_size': self.input_size,
'hidden_size': self.hidden_size,
'output_size': self.output_size,
'dropout': self.dropout,
'batch_first': self.batch_first,
'label_size': self.label_size,
'device': self.device
}
self.predictor = callPredictor(**_config).to(self.device)
self._save_predictor_config({key: value for key, value in _config.items() if key != 'device'})
if self.dataparallal:
self.predictor= torch.nn.DataParallel(self.predictor)
self.criterion = callLoss(task = self.task_type,
loss_name = self.loss_name,
target_repl = self.target_repl,
target_repl_coef = self.target_repl_coef,
aggregate = self.aggregate)
self.optimizer = self._get_optimizer(self.optimizer_name)
[docs] def fit(self, train_data, valid_data, assign_task_type = None):
"""
Parameters
----------
train_data : {
'x':list[episode_file_path],
'y':list[label],
'l':list[seq_len],
'feat_n': n of feature space,
'label_n': n of label space
}
The input train samples dict.
valid_data : {
'x':list[episode_file_path],
'y':list[label],
'l':list[seq_len],
'feat_n': n of feature space,
'label_n': n of label space
}
The input valid samples dict.
assign_task_type: str (default = None)
predifine task type to model mapping <feature, label>
current support ['binary','multiclass','multilabel','regression']
Returns
-------
self : object
Fitted estimator.
"""
self.task_type = assign_task_type
self._data_check([train_data, valid_data])
self._build_model()
train_reader = self._get_reader(train_data, 'train')
valid_reader = self._get_reader(valid_data, 'valid')
self._fit_model(train_reader, valid_reader)
[docs] def load_model(self,
loaded_epoch = '',
config_file_path = '',
model_file_path = ''):
"""
Parameters
----------
loaded_epoch : str, loaded model name
we save the model by <epoch_count>.epoch, latest.epoch, best.epoch
Returns
-------
self : object
loaded estimator.
"""
predictor_config = self._load_predictor_config(config_file_path)
predictor_config['device'] = self.device
self.predictor = callPredictor(**predictor_config).to(self.device)
self._load_model(loaded_epoch, model_file_path)
def _args_check(self):
"""
Check args whether valid/not and give tips
"""
assert isinstance(self.n_batchsize,int) and self.n_batchsize>0, \
'fill in correct n_batchsize (int, >0)'
assert isinstance(self.n_epoch,int) and self.n_epoch>0, \
'fill in correct n_epoch (int, >0)'
assert isinstance(self.learn_ratio,float) and self.learn_ratio>0., \
'fill in correct learn_ratio (float, >0.)'
assert isinstance(self.weight_decay,float) and self.weight_decay>=0., \
'fill in correct weight_decay (float, >=0.)'
assert isinstance(self.n_epoch_saved,int) and self.n_epoch_saved>0 and self.n_epoch_saved < self.n_epoch, \
'fill in correct n_epoch (int, >0 and <{0}).format(self.n_epoch)'
assert isinstance(self.hidden_size,int) and self.hidden_size>0, \
'fill in correct hidden_size (int, 8)'
assert isinstance(self.output_size,int) and self.output_size>0, \
'fill in correct output_size (int, >0)'
assert isinstance(self.bias,bool), \
'fill in correct bias (bool)'
assert isinstance(self.dropout,float) and self.dropout>0. and self.dropout<1., \
'fill in correct learn_ratio (float, >0 and <1.)'
assert isinstance(self.batch_first,bool), \
'fill in correct batch_first (bool)'
assert isinstance(self.target_repl,bool), \
'fill in correct target_repl (bool)'
assert isinstance(self.target_repl_coef,float) and self.target_repl_coef>=0. and self.target_repl_coef<=1., \
'fill in correct target_repl_coef (float, >=0 and <=1.)'
assert isinstance(self.aggregate,str) and self.aggregate in ['sum','avg'], \
'fill in correct aggregate (str, [\'sum\',\'avg\'])'
assert isinstance(self.optimizer_name,str) and self.optimizer_name in ['adam'], \
'fill in correct optimizer_name (str, [\'adam\'])'
assert isinstance(self.use_gpu,bool), \
'fill in correct use_gpu (bool)'
assert isinstance(self.loss_name,str), \
'fill in correct optimizer_name (str)'
assert isinstance(self.gpu_ids,str), \
'fill in correct use_gpu (str, \'0,2,7\')'
self.device = self._get_device()