Merge Dev branch into master

examples/healthcare/application/Diabetic_Readmission_Prediction/README.md

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+<!--
+    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.
+-->
+
+# Singa for Diabetic Readmission Prediction task
+
+## Diabetic Readmission
+
+Diabetic readmission is a significant concern in healthcare, with a substantial number of patients being readmitted to the hospital within a short period after discharge. This not only leads to increased healthcare costs but also poses a risk to patient well-being.
+
+Although diabetes is a manageable condition, early identification of patients at high risk of readmission remains a challenge. A reliable and efficient predictive model can help identify these patients, enabling healthcare providers to intervene early and prevent unnecessary readmissions.
+
+To address this issue, we use Singa to implement a machine learning model for predicting diabetic readmission. The dataset is from [BMC Medical Informatics and Decision-Making](https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-021-01423-y). Please download the dataset before running the scripts.
+
+
+## Structure
+
+* `data` includes the scripts for preprocessing Diabetic Readmission datasets.
+
+* `model` includes the MLP model construction codes by creating
+  a subclass of `Module` to wrap the neural network operations 
+  of each model.
+
+* `train_mlp.py` is the training script, which controls the training flow by
+  doing BackPropagation and SGD update.
+
+## Command
+```bash
+python train.py mlp diabetic
+```

examples/healthcare/application/Diabetic_Retinopathy_Classification/README.md

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+<!--
+    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.
+-->
+
+# Singa for Diabetic Retinopathy Classification
+
+## Diabetic Retinopathy
+
+Diabetic Retinopathy (DR) is a progressive eye disease caused by long-term diabetes, which damages the blood vessels in the retina, the light-sensitive tissue at the back of the eye. It typically develops in stages, starting with non-proliferative diabetic retinopathy (NPDR), where weakened blood vessels leak fluid or blood, causing swelling or the formation of deposits. If untreated, it can progress to proliferative diabetic retinopathy (PDR), characterized by the growth of abnormal blood vessels that can lead to severe vision loss or blindness. Symptoms may include blurred vision, dark spots, or difficulty seeing at night, although it is often asymptomatic in the early stages. Early diagnosis through regular eye exams and timely treatment, such as laser therapy or anti-VEGF injections, can help manage the condition and prevent vision impairment.
+
+The dataset has 5 groups characterized by the severity of Diabetic Retinopathy (DR).
+
+- 0: No DR
+- 1: Mild Non-Proliferative DR
+- 2: Moderate Non-Proliferative DR
+- 3: Severe Non-Proliferative DR
+- 4: Proliferative DR
+
+
+To mitigate the problem, we use Singa to implement a machine learning model to help with Diabetic Retinopathy  diagnosis. The dataset is from Kaggle https://www.kaggle.com/datasets/mohammadasimbluemoon/diabeticretinopathy-messidor-eyepac-preprocessed. Please download the dataset before running the scripts.
+
+## Structure
+
+* `data` includes the scripts for preprocessing DR image datasets.
+
+* `model` includes the CNN model construction codes by creating
+  a subclass of `Module` to wrap the neural network operations 
+  of each model.
+
+* `train_cnn.py` is the training script, which controls the training flow by
+  doing BackPropagation and SGD update.
+
+## Command
+```bash
+python train_cnn.py cnn diaret -dir pathToDataset
+```

examples/healthcare/application/Diabetic_Retinopathy_Classification/train.py

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+from singa import singa_wrap as singa
+from singa import device
+from singa import tensor
+from singa import opt
+import numpy as np
+import time
+import argparse
+import sys
+sys.path.append("../../..")
+
+from PIL import Image
+
+from healthcare.data import diaret
+from healthcare.models import diabetic_retinopthy_net
+
+np_dtype = {"float16": np.float16, "float32": np.float32}
+
+singa_dtype = {"float16": tensor.float16, "float32": tensor.float32}
+
+
+# Data augmentation
+def augmentation(x, batch_size):
+    xpad = np.pad(x, [[0, 0], [0, 0], [4, 4], [4, 4]], 'symmetric')
+    for data_num in range(0, batch_size):
+        offset = np.random.randint(8, size=2)
+        x[data_num, :, :, :] = xpad[data_num, :,
+                               offset[0]:offset[0] + x.shape[2],
+                               offset[1]:offset[1] + x.shape[2]]
+        if_flip = np.random.randint(2)
+        if (if_flip):
+            x[data_num, :, :, :] = x[data_num, :, :, ::-1]
+    return x
+
+
+# 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 resize_dataset(x, image_size):
+    num_data = x.shape[0]
+    dim = x.shape[1]
+    X = np.zeros(shape=(num_data, dim, image_size, image_size),
+                 dtype=np.float32)
+    for n in range(0, num_data):
+        for d in range(0, dim):
+            X[n, d, :, :] = np.array(Image.fromarray(x[n, d, :, :]).resize(
+                (image_size, image_size), Image.BILINEAR),
+                dtype=np.float32)
+    return X
+
+
+def run(global_rank,
+        world_size,
+        dir_path,
+        max_epoch,
+        batch_size,
+        model,
+        data,
+        sgd,
+        graph,
+        verbosity,
+        dist_option='plain',
+        spars=None,
+        precision='float32'):
+    # now CPU version only, could change to GPU device for GPU-support machines
+    dev = device.get_default_device()
+    dev.SetRandSeed(0)
+    np.random.seed(0)
+    if data == 'diaret':
+        train_x, train_y, val_x, val_y = diaret.load(dir_path=dir_path)
+    else:
+        print(
+            'Wrong dataset!'
+        )
+        sys.exit(0)
+
+    num_channels = train_x.shape[1]
+    image_size = train_x.shape[2]
+    data_size = np.prod(train_x.shape[1:train_x.ndim]).item()
+    num_classes = (np.max(train_y) + 1).item()
+
+    if model == 'cnn':
+        model = diabetic_retinopthy_net.create_model(num_channels=num_channels,
+                                                     num_classes=num_classes)
+    else:
+        print(
+            'Wrong model!'
+        )
+        sys.exit(0)
+
+    # For distributed training, sequential has better performance
+    if hasattr(sgd, "communicator"):
+        DIST = True
+        sequential = True
+    else:
+        DIST = False
+        sequential = False
+
+    if DIST:
+        train_x, train_y, val_x, val_y = partition(global_rank, world_size,
+                                                   train_x, train_y, val_x,
+                                                   val_y)
+
+    if model.dimension == 4:
+        tx = tensor.Tensor(
+            (batch_size, num_channels, model.input_size, model.input_size), dev,
+            singa_dtype[precision])
+    elif model.dimension == 2:
+        tx = tensor.Tensor((batch_size, data_size),
+                           dev, singa_dtype[precision])
+        np.reshape(train_x, (train_x.shape[0], -1))
+        np.reshape(val_x, (val_x.shape[0], -1))
+
+    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 model to graph
+    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):
+            # if b % 100 == 0:
+            #     print ("b: \n", b)
+            # Generate the patch data in this iteration
+            x = train_x[idx[b * batch_size:(b + 1) * batch_size]]
+            if model.dimension == 4:
+                x = augmentation(x, batch_size)
+                if (image_size != model.input_size):
+                    x = resize_dataset(x, model.input_size)
+            x = x.astype(np_dtype[precision])
+            y = train_y[idx[b * batch_size:(b + 1) * batch_size]]
+
+            # Copy the patch data into input tensors
+            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 the evaluation accuracy and loss from multiple 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]
+            if model.dimension == 4:
+                if (image_size != model.input_size):
+                    x = resize_dataset(x, model.input_size)
+            x = x.astype(np_dtype[precision])
+            y = val_y[b * batch_size:(b + 1) * batch_size]
+            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 the evaulation accuracy from multiple devices
+            test_correct = reduce_variable(test_correct, sgd, reducer)
+
+        # Output the evaluation accuracy
+        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'],
+        default='cnn')
+    parser.add_argument('data',
+                        choices=['diaret'],
+                        default='diaret')
+    parser.add_argument('-p',
+                        choices=['float32', 'float16'],
+                        default='float32',
+                        dest='precision')
+    parser.add_argument('-dir',
+                        '--dir-path',
+                        default="/tmp/diaret",
+                        type=str,
+                        help='the directory to store the Diabetic Retinopathy dataset',
+                        dest='dir_path')
+    parser.add_argument('-m',
+                        '--max-epoch',
+                        default=300,
+                        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')
+    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.dir_path,
+        args.max_epoch,
+        args.batch_size,
+        args.model,
+        args.data,
+        sgd,
+        args.graph,
+        args.verbosity,
+        precision=args.precision)