
In this tutorial we will consider colorectal histology tissues classification using ResNet architecture and PyTorch framework.

## Introduction

Recently machine learning (ML) applications became widespread in the healthcare industry: omics field (genomics, transcriptomics, proteomics), drug investigation, radiology and digital histology. Deep learning based image analysis studies in histopathology include different tasks (e.g., classification, semantic segmentation, detection, and instance segmentation). The main goal of ML in this field is automatic detection, grading and prognosis of cancer.

However, there are several challenges in digital pathology. Usually histology slides are large sized hematoxylin and eosin (H&E) stained images with color variations and artifacts; different levels of magnification result in different levels of information extraction. One Whole Slide Image (WSI) is a multi-gigabyte image with typical resolution **100,000 × 100,000** pixels.

In a supervised classification scenario, WSIs are divided into patches with some stride, then a CNN architecture extracts feature vectors from patches which can be passed into traditional ML algorithms (SVM, gradient boosting) for further operations.

![Typical steps for ML in digital pathological image analysis.](/images/2020-10-26-colorectal-tissue-classification/introduction-pic.jpg)

In this article we apply CNN **ResNet** architecture to classify tissue types of colon. We won't use transfer learning — weights from ImageNet are not related to histology and won't help convergence.

---

## Dataset

The collection of textures in colorectal cancer histology — a "MNIST for biologists". Available at:
- [Zenodo](https://zenodo.org/record/53169#.X5XO59AzbIV)
- [Kaggle](https://www.kaggle.com/kmader/colorectal-histology-mnist)

Two folders:
- **5000 image tiles**: 150 × 150 px each (74 × 74 µm). Eight tissue categories.
- **10 larger images**: 5000 × 5000 px each. Multiple tissue types per image.

All images are RGB, 0.495 µm/pixel, digitized with Aperio ScanScope, magnification 20×. Histological samples are fully anonymized images of formalin-fixed paraffin-embedded human colorectal adenocarcinomas from the University Medical Center Mannheim, Germany.

---

## Colorectal MNIST Classification with ResNet

[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/MariaZork/my-machine-learning-tutorials/blob/master/colorectal-cancer-classification.ipynb)

### Setup

<CodeCell language="python">
{`import os
import random
import itertools

import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
from sklearn.model_selection import train_test_split
from PIL import Image
from sklearn.metrics import confusion_matrix, classification_report
import torch
import torch.nn as nn
import torch.utils.data as D
import torch.nn.functional as F
from torchvision import transforms, models
from tqdm import tqdm

import warnings
warnings.filterwarnings('ignore')

torch.cuda.empty_cache()`}
</CodeCell>

<CodeCell language="python">
{`DATA_DIR = '/kaggle/input/colorectal-histology-mnist/'
SMALL_IMG_DATA_DIR = os.path.join(DATA_DIR,
    'kather_texture_2016_image_tiles_5000/Kather_texture_2016_image_tiles_5000')

IMAGE_SIZE = 224
SEED = 2000
BATCH_SIZE = 64
NUM_EPOCHS = 15

random.seed(SEED)
np.random.seed(SEED)
torch.manual_seed(SEED)
torch.cuda.manual_seed(SEED)
torch.backends.cudnn.deterministic = True

device = torch.device("cuda:0" if torch.cuda.is_available() else "cpu")`}
</CodeCell>

---

### Data Exploration

<CodeCell language="python" output={`['03_COMPLEX', '08_EMPTY', '04_LYMPHO', '01_TUMOR',
 '02_STROMA', '06_MUCOSA', '05_DEBRIS', '07_ADIPOSE']`}>
{`classes = os.listdir(SMALL_IMG_DATA_DIR)
classes`}
</CodeCell>

<CodeCell language="python" output={`03_COMPLEX  625
08_EMPTY    625
04_LYMPHO   625
01_TUMOR    625
02_STROMA   625
06_MUCOSA   625
05_DEBRIS   625
07_ADIPOSE  625`}>
{`for label in classes:
    num_samples = len(os.listdir(os.path.join(SMALL_IMG_DATA_DIR, label)))
    print(label + '\t' + str(num_samples))`}
</CodeCell>

Sample tiles from each class:

![Sample tiles from each tissue class](/images/nb_images/colorectal-tissue-classification_files/colorectal-tissue-classification_9_0.png)

---

### PyTorch Dataset and DataLoaders

<CodeCell language="python">
{`class HistologyMnistDS(D.Dataset):
    def __init__(self, df, transforms, mode='train'):
        self.records = df.to_records(index=False)
        self.transforms = transforms
        self.mode = mode
        self.len = df.shape[0]

    @staticmethod
    def _load_image_pil(path):
        return Image.open(path)

    def __getitem__(self, index):
        path = self.records[index].img_path
        img = self._load_image_pil(path)
        if self.transforms:
            img = self.transforms(img)
        if self.mode in ['train', 'val', 'test']:
            return img, torch.from_numpy(np.array(self.records[index].label_num))
        return img

    def __len__(self):
        return self.len`}
</CodeCell>

<CodeCell language="python">
{`train_transforms = transforms.Compose([
    transforms.Resize((IMAGE_SIZE, IMAGE_SIZE)),
    transforms.ToTensor(),
    transforms.Normalize([0.485, 0.456, 0.406], [0.229, 0.224, 0.225])
])

val_transforms = transforms.Compose([
    transforms.Resize((IMAGE_SIZE, IMAGE_SIZE)),
    transforms.ToTensor(),
    transforms.Normalize([0.485, 0.456, 0.406], [0.229, 0.224, 0.225])
])`}
</CodeCell>

<CodeCell language="python" output={`Train DF shape: (4000, 3)
Valid DF shape: (200, 3)
Test DF shape:  (800, 3)`}>
{`train_df, tmp_df = train_test_split(df, test_size=0.2,
                                    random_state=SEED, stratify=df['label'])
valid_df, test_df = train_test_split(tmp_df, test_size=0.8,
                                     random_state=SEED, stratify=tmp_df['label'])

print("Train DF shape:", train_df.shape)
print("Valid DF shape:", valid_df.shape)
print("Test DF shape:", test_df.shape)`}
</CodeCell>

<CodeCell language="python">
{`ds_train = HistologyMnistDS(train_df, train_transforms)
ds_val   = HistologyMnistDS(valid_df, val_transforms, mode='val')
ds_test  = HistologyMnistDS(test_df,  val_transforms, mode='test')

train_loader = D.DataLoader(ds_train, batch_size=BATCH_SIZE, shuffle=True,  num_workers=4)
val_loader   = D.DataLoader(ds_val,   batch_size=BATCH_SIZE, shuffle=False, num_workers=4)
test_loader  = D.DataLoader(ds_test,  batch_size=BATCH_SIZE, shuffle=False, num_workers=4)`}
</CodeCell>

Example batch image (denormalised):

![Example batch image](/images/nb_images/colorectal-tissue-classification_files/colorectal-tissue-classification_20_0.png)

---

### Train Loop

<CodeCell language="python">
{`import copy

checkpoints_dir = '/kaggle/working/'
history_train_loss, history_val_loss = [], []

def train_model(model, loss, optimizer, scheduler, num_epochs):
    best_model_wts = copy.deepcopy(model.state_dict())
    best_loss = 10e10
    best_acc_score = 0.0

    for epoch in range(num_epochs):
        print('Epoch {}/{}:'.format(epoch, num_epochs - 1), flush=True)

        for phase in ['train', 'val']:
            dataloader = train_loader if phase == 'train' else val_loader
            if phase == 'train':
                scheduler.step()
                model.train()
            else:
                model.eval()

            running_loss = running_acc = 0.

            for inputs, labels in tqdm(dataloader):
                inputs = inputs.to(device)
                labels = labels.to(device)
                optimizer.zero_grad()

                with torch.set_grad_enabled(phase == 'train'):
                    preds = model(inputs)
                    loss_value = loss(preds, labels)
                    preds_class = preds.argmax(dim=1)
                    if phase == 'train':
                        loss_value.backward()
                        optimizer.step()

                running_loss += loss_value.item()
                running_acc  += (preds_class == labels.data).float().mean()

            epoch_loss = running_loss / len(dataloader)
            epoch_acc  = running_acc  / len(dataloader)
            print(f'{phase} Loss: {epoch_loss:.4f}  Acc: {epoch_acc:.4f}', flush=True)

            if phase == 'train':
                history_train_loss.append(epoch_loss)
            else:
                history_val_loss.append(epoch_loss)
                if epoch_loss < best_loss:
                    best_loss = epoch_loss
                    best_model_wts = copy.deepcopy(model.state_dict())
                    print("Saving model for best loss")
                    os.makedirs(checkpoints_dir, exist_ok=True)
                    torch.save({'state_dict': best_model_wts},
                               checkpoints_dir + 'best_model.pth.tar')
                if epoch_acc > best_acc_score:
                    best_acc_score = epoch_acc
                print(f'Best loss: {best_loss:.4f}  Best acc: {best_acc_score:.4f}')

    return model`}
</CodeCell>

---

### Model Setup and Training

ResNet-50 with the final linear layer replaced to output 8 classes. StepLR reduces the Adam learning rate by 10× every 7 epochs.

<CodeCell language="python">
{`model = models.resnet50(pretrained=False)
model.fc = torch.nn.Linear(model.fc.in_features, len(classes))
model = model.to(device)

loss      = torch.nn.CrossEntropyLoss()
optimizer = torch.optim.Adam(model.parameters(), lr=1e-3)
scheduler = torch.optim.lr_scheduler.StepLR(optimizer, step_size=7, gamma=0.1)`}
</CodeCell>

<CodeCell language="python" output={`Epoch 0/14:  val Loss: 0.7102  Acc: 0.7578  → Saving
Epoch 2/14:  val Loss: 0.4103  Acc: 0.8477  → Saving
Epoch 6/14:  val Loss: 0.1979  Acc: 0.9414  → Saving
Epoch 9/14:  val Loss: 0.1765  Acc: 0.9414  → Saving`}>
{`train_model(model, loss, optimizer, scheduler, num_epochs=NUM_EPOCHS);`}
</CodeCell>

---

### Results

Train/validation loss curves:

![Train and validation loss curves](/images/nb_images/colorectal-tissue-classification_files/colorectal-tissue-classification_24_1.png)

<CodeCell language="python">
{`model.load_state_dict(
    torch.load(os.path.join(checkpoints_dir, 'best_model.pth.tar'))['state_dict']
)
model.eval()

y_preds = []
for inputs, labels in tqdm(test_loader):
    inputs = inputs.to(device)
    with torch.set_grad_enabled(False):
        preds = model(inputs)
    y_preds.append(preds.argmax(dim=1).data.cpu().numpy())

y_preds = np.concatenate(y_preds)`}
</CodeCell>

<CodeCell language="python" output={`Confusion matrix, without normalization:
[[98  0  1  0  0  1  0  0]
 [ 0 88  5  0  7  0  0  0]
 [ 2 11 83  3  0  1  0  0]
 [ 0  0  5 95  0  0  0  0]
 [ 0  4  2  0 89  1  4  0]
 [ 1  0  2  4  2 91  0  0]
 [ 0  0  0  0  1  0 96  3]
 [ 0  0  0  0  0  0  1 99]]`}>
{`cm = confusion_matrix(test_df.label_num.values, y_preds)
plot_confusion_matrix(cm, label_num)`}
</CodeCell>

![Confusion matrix](/images/nb_images/colorectal-tissue-classification_files/colorectal-tissue-classification_28_1.png)

<CodeCell language="python" output={`              precision  recall  f1-score  support
01_TUMOR           0.97    0.98      0.98      100
02_STROMA          0.85    0.88      0.87      100
03_COMPLEX         0.85    0.83      0.84      100
04_LYMPHO          0.93    0.95      0.94      100
05_DEBRIS          0.90    0.89      0.89      100
06_MUCOSA          0.97    0.91      0.94      100
07_ADIPOSE         0.95    0.96      0.96      100
08_EMPTY           0.97    0.99      0.98      100

accuracy                             0.92      800`}>
{`print(classification_report(
    test_df.label_num.values,
    y_preds,
    target_names=list(label_num.keys())
))`}
</CodeCell>

---

## Conclusion

We trained ResNet-50 for 15 epochs achieving **92% accuracy** on the test set. **Tumor** and **Empty** classes are the most recognisable (F1 = 0.98). The most confusable label is **Complex**, which likely represents combinations of other tissue types.

#pytorch

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