def fit(self,
encoded_data: EncodedData,
label: Label,
cores_for_training: int = 2):
self.feature_names = encoded_data.feature_names
X = encoded_data.examples
assert X.shape[1] == 2, "ProbabilisticBinaryClassifier: the shape of the input is not compatible with the classifier. " \
"The classifier is defined when examples are encoded by two counts: the number of successful trials " \
"and the total number of trials. If this is not targeted use-case and the encoding, please consider using " \
"another classifier."
self.class_mapping = Util.make_binary_class_mapping(
encoded_data.labels[label.name])
self.label = label
self.N_0 = int(
np.sum(
np.array(encoded_data.labels[label.name]) ==
self.class_mapping[0]))
self.N_1 = int(
np.sum(
np.array(encoded_data.labels[label.name]) ==
self.class_mapping[1]))
self.alpha_0, self.beta_0 = self._find_beta_distribution_parameters(
X[np.nonzero(
np.array(encoded_data.labels[self.label.name]) ==
self.class_mapping[0])], self.N_0)
self.alpha_1, self.beta_1 = self._find_beta_distribution_parameters(
X[np.nonzero(
np.array(encoded_data.labels[self.label.name]) ==
self.class_mapping[1])], self.N_1)
def fit(self, encoded_data: EncodedData, label_name: str, cores_for_training: int = 2):
self.feature_names = encoded_data.feature_names
Util.setup_pytorch(self.number_of_threads, self.random_seed)
if "chain_names" in encoded_data.info and encoded_data.info["chain_names"] is not None and len(encoded_data.info["chain_names"]) == 2:
self.chain_names = encoded_data.info["chain_names"]
else:
self.chain_names = ["chain_1", "chain_2"]
self._make_CNN()
self.CNN.to(device=self.device)
self.class_mapping = Util.make_binary_class_mapping(encoded_data.labels[label_name])
self.label_name = label_name
self.CNN.train()
iteration = 0
loss_function = nn.BCEWithLogitsLoss().to(device=self.device)
optimizer = torch.optim.Adam(self.CNN.parameters(), lr=self.learning_rate, weight_decay=self.l2_weight_decay, eps=1e-4)
state = dict(model=copy.deepcopy(self.CNN).state_dict(), optimizer=optimizer, iteration=iteration, best_validation_loss=np.inf)
train_data, validation_data = self._prepare_and_split_data(encoded_data)
logging.info("ReceptorCNN: starting training.")
while iteration < self.iteration_count:
for examples, labels, example_ids in self._get_data_batch(train_data, self.label_name):
# Reset gradients
optimizer.zero_grad()
# Calculate predictions
logit_outputs = self.CNN(examples)
# Calculate losses
loss = self._compute_loss(loss_function, logit_outputs, labels)
# Perform update
loss.backward()
optimizer.step()
self.CNN.rescale_weights_for_IGM()
iteration += 1
# Calculate scores and loss on training set and validation set
if iteration % self.evaluate_at == 0 or iteration == self.iteration_count or iteration == 1:
logging.info(f"ReceptorCNN: training - iteration {iteration}.")
state = self._evaluate_state(state, iteration, loss_function, validation_data)
if iteration >= self.iteration_count:
self.CNN.load_state_dict(state["model"])
break
logging.info("ReceptorCNN: finished training.")
def fit(self,
encoded_data: EncodedData,
label: Label,
cores_for_training: int = 2):
self.feature_names = encoded_data.feature_names
Util.setup_pytorch(self.number_of_threads, self.random_seed)
self.input_size = encoded_data.examples.shape[1]
self._make_log_reg()
self.label = label
self.class_mapping = Util.make_binary_class_mapping(
encoded_data.labels[self.label.name])
loss = np.inf
state = {"loss": loss, "model": None}
loss_func = torch.nn.BCEWithLogitsLoss(reduction='mean')
optimizer = torch.optim.SGD(self.logistic_regression.parameters(),
lr=self.learning_rate)
for iteration in range(self.iteration_count):
# reset gradients
optimizer.zero_grad()
# compute predictions only for k-mers with max score
max_logit_indices = self._get_max_logits_indices(
encoded_data.examples)
example_count = encoded_data.examples.shape[0]
examples = torch.from_numpy(encoded_data.examples).float()[
torch.arange(example_count).long(), :, max_logit_indices]
logits = self.logistic_regression(examples)
# compute the loss
loss = loss_func(
logits,
torch.tensor(encoded_data.labels[self.label.name]).float())
# perform update
loss.backward()
optimizer.step()
# log current score and keep model for early stopping if specified
if iteration % self.evaluate_at == 0 or iteration == self.iteration_count - 1:
logging.info(
f"AtchleyKmerMILClassifier: log loss at iteration {iteration+1}/{self.iteration_count}: {loss}."
)
if state["loss"] < loss and self.use_early_stopping:
state = {
"loss": loss.numpy(),
"model": copy.deepcopy(self.logistic_regression)
}
if loss < self.threshold:
break
logging.warning(
f"AtchleyKmerMILClassifier: the logistic regression model did not converge."
)
if loss > state['loss'] and self.use_early_stopping:
self.logistic_regression.load_state_dict(state["model"])
