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"])