Merge pull request #1256 from NLGithubWP/diabetic_training

Support Diabetic readmission training

examples/healthcare/application/Diabetic_Readmission_Prediction/train.py

@@ -0,0 +1,265 @@
+#
+# Licensed to the Apache Software Foundation (ASF) under one
+# or more contributor license agreements.  See the NOTICE file
+# distributed with this work for additional information
+# regarding copyright ownership.  The ASF licenses this file
+# to you under the Apache License, Version 2.0 (the
+# "License"); you may not use this file except in compliance
+# with the License.  You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing,
+# software distributed under the License is distributed on an
+# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
+# KIND, either express or implied.  See the License for the
+# specific language governing permissions and limitations
+# under the License.
+#
+
+from singa import device
+from singa import tensor
+from singa import opt
+import numpy as np
+import time
+import argparse
+from healthcare.data import diabetic
+from healthcare.models import diabetic_net
+
+np_dtype = {"float16": np.float16, "float32": np.float32}
+
+singa_dtype = {"float16": tensor.float16, "float32": tensor.float32}
+
+
+# Calculate accuracy
+def accuracy(pred, target):
+    # y is network output to be compared with ground truth (int)
+    y = np.argmax(pred, axis=1)
+    a = y == target
+    correct = np.array(a, "int").sum()
+    return correct
+
+
+# Data partition according to the rank
+def partition(global_rank, world_size, train_x, train_y, val_x, val_y):
+    # Partition training data
+    data_per_rank = train_x.shape[0] // world_size
+    idx_start = global_rank * data_per_rank
+    idx_end = (global_rank + 1) * data_per_rank
+    train_x = train_x[idx_start:idx_end]
+    train_y = train_y[idx_start:idx_end]
+
+    # Partition evaluation data
+    data_per_rank = val_x.shape[0] // world_size
+    idx_start = global_rank * data_per_rank
+    idx_end = (global_rank + 1) * data_per_rank
+    val_x = val_x[idx_start:idx_end]
+    val_y = val_y[idx_start:idx_end]
+    return train_x, train_y, val_x, val_y
+
+
+# Function to all reduce NUMPY accuracy and loss from multiple devices
+def reduce_variable(variable, dist_opt, reducer):
+    reducer.copy_from_numpy(variable)
+    dist_opt.all_reduce(reducer.data)
+    dist_opt.wait()
+    output = tensor.to_numpy(reducer)
+    return output
+
+
+def run(global_rank,
+        world_size,
+        local_rank,
+        max_epoch,
+        batch_size,
+        model,
+        data,
+        sgd,
+        graph,
+        verbosity,
+        dist_option='plain',
+        spars=None,
+        precision='float32'):
+    dev = device.create_cpu_device()  # now CPU version only, could change to GPU device for GPU-support machines
+    dev.SetRandSeed(0)
+    np.random.seed(0)
+
+    # Load data based on specified dataset
+    if data == 'diabetic':
+        train_x, train_y, val_x, val_y = diabetic.load()
+    elif data == 'mnist' or data == 'cifar10' or data == 'cifar100':
+        raise ValueError("Only 'diabetic' dataset (2D table data) is supported with MLP model.")
+
+    # Ensure the data is already 2D (train_x.shape[1:] should have only one dimension)
+    data_size = train_x.shape[1]
+    num_classes = int(np.max(train_y) + 1)
+
+    # Initialize MLP model
+    if model == 'mlp':
+        model = diabetic_net.create_model(data_size=data_size,
+                                          num_classes=num_classes)
+    else:
+        print(
+            'Wrong model!'
+        )
+        sys.exit(0)
+    # Setup distributed training flags
+    if hasattr(sgd, "communicator"):
+        DIST = True
+        sequential = True
+    else:
+        DIST = False
+        sequential = False
+
+    # Partition data if distributed training is used
+    if DIST:
+        train_x, train_y, val_x, val_y = partition(global_rank, world_size,
+                                                   train_x, train_y, val_x,
+                                                   val_y)
+
+    # Define tensors for inputs and labels
+    tx = tensor.Tensor((batch_size, data_size), dev, singa_dtype[precision])
+    ty = tensor.Tensor((batch_size,), dev, tensor.int32)
+
+    num_train_batch = train_x.shape[0] // batch_size
+    num_val_batch = val_x.shape[0] // batch_size
+    idx = np.arange(train_x.shape[0], dtype=np.int32)
+
+    # Attach optimizer to model
+    model.set_optimizer(sgd)
+    model.compile([tx], is_train=True, use_graph=graph, sequential=sequential)
+    dev.SetVerbosity(verbosity)
+
+    # Training and evaluation loop
+    for epoch in range(max_epoch):
+        start_time = time.time()
+        np.random.shuffle(idx)
+
+        if global_rank == 0:
+            print('Starting Epoch %d:' % epoch)
+
+        # Training phase
+        train_correct = np.zeros(shape=[1], dtype=np.float32)
+        test_correct = np.zeros(shape=[1], dtype=np.float32)
+        train_loss = np.zeros(shape=[1], dtype=np.float32)
+
+        model.train()
+        for b in range(num_train_batch):
+            x = train_x[idx[b * batch_size:(b + 1) * batch_size]]
+            y = train_y[idx[b * batch_size:(b + 1) * batch_size]]
+
+            x = x.astype(np_dtype[precision])  # Ensure correct precision
+            tx.copy_from_numpy(x)
+            ty.copy_from_numpy(y)
+
+            # Train the model
+            out, loss = model(tx, ty, dist_option, spars)
+            train_correct += accuracy(tensor.to_numpy(out), y)
+            train_loss += tensor.to_numpy(loss)[0]
+
+        if DIST:
+            # Reduce training stats across distributed devices
+            reducer = tensor.Tensor((1,), dev, tensor.float32)
+            train_correct = reduce_variable(train_correct, sgd, reducer)
+            train_loss = reduce_variable(train_loss, sgd, reducer)
+
+        if global_rank == 0:
+            print('Training loss = %f, training accuracy = %f' %
+                  (train_loss, train_correct /
+                   (num_train_batch * batch_size * world_size)),
+                  flush=True)
+
+        # Evaluation phase
+        model.eval()
+        for b in range(num_val_batch):
+            x = val_x[b * batch_size:(b + 1) * batch_size]
+            y = val_y[b * batch_size:(b + 1) * batch_size]
+
+            x = x.astype(np_dtype[precision])
+            tx.copy_from_numpy(x)
+            ty.copy_from_numpy(y)
+
+            out_test = model(tx)
+            test_correct += accuracy(tensor.to_numpy(out_test), y)
+
+        if DIST:
+            # Reduce evaluation stats across distributed devices
+            test_correct = reduce_variable(test_correct, sgd, reducer)
+
+        if global_rank == 0:
+            print('Evaluation accuracy = %f, Elapsed Time = %fs' %
+                  (test_correct / (num_val_batch * batch_size * world_size),
+                   time.time() - start_time),
+                  flush=True)
+
+    dev.PrintTimeProfiling()
+
+
+
+if __name__ == '__main__':
+    # Use argparse to get command config: max_epoch, model, data, etc., for single gpu training
+    parser = argparse.ArgumentParser(
+        description='Training using the autograd and graph.')
+    parser.add_argument(
+        'model',
+        choices=['cnn', 'resnet', 'xceptionnet', 'mlp', 'alexnet'],
+        default='mlp')
+    parser.add_argument('data',
+                        choices=['mnist', 'cifar10', 'cifar100', 'diabetic'],
+                        default='mnist')
+    parser.add_argument('-p',
+                        choices=['float32', 'float16'],
+                        default='float32',
+                        dest='precision')
+    parser.add_argument('-m',
+                        '--max-epoch',
+                        default=100,
+                        type=int,
+                        help='maximum epochs',
+                        dest='max_epoch')
+    parser.add_argument('-b',
+                        '--batch-size',
+                        default=64,
+                        type=int,
+                        help='batch size',
+                        dest='batch_size')
+    parser.add_argument('-l',
+                        '--learning-rate',
+                        default=0.005,
+                        type=float,
+                        help='initial learning rate',
+                        dest='lr')
+    # Determine which gpu to use
+    parser.add_argument('-i',
+                        '--device-id',
+                        default=0,
+                        type=int,
+                        help='which GPU to use',
+                        dest='device_id')
+    parser.add_argument('-g',
+                        '--disable-graph',
+                        default='True',
+                        action='store_false',
+                        help='disable graph',
+                        dest='graph')
+    parser.add_argument('-v',
+                        '--log-verbosity',
+                        default=0,
+                        type=int,
+                        help='logging verbosity',
+                        dest='verbosity')
+
+    args = parser.parse_args()
+
+    sgd = opt.SGD(lr=args.lr, momentum=0.9, weight_decay=1e-5, dtype=singa_dtype[args.precision])
+    run(0,
+        1,
+        args.device_id,
+        args.max_epoch,
+        args.batch_size,
+        args.model,
+        args.data,
+        sgd,
+        args.graph,
+        args.verbosity,
+        precision=args.precision)