update readme with lightning

Update pytorch_inceptionet.py

.github/FUNDING.yml

@@ -1,12 +0,0 @@
-# These are supported funding model platforms
-
-github: # Replace with up to 4 GitHub Sponsors-enabled usernames e.g., [user1, user2]
-patreon: aladdinpersson # Replace with a single Patreon username
-open_collective: # Replace with a single Open Collective username
-ko_fi: # Replace with a single Ko-fi username
-tidelift: # Replace with a single Tidelift platform-name/package-name e.g., npm/babel
-community_bridge: # Replace with a single Community Bridge project-name e.g., cloud-foundry
-liberapay: # Replace with a single Liberapay username
-issuehunt: # Replace with a single IssueHunt username
-otechie: # Replace with a single Otechie username
-custom: # Replace with up to 4 custom sponsorship URLs e.g., ['link1', 'link2']

.gitignore

@@ -1,3 +1,12 @@
 .idea/
 ML/Pytorch/more_advanced/image_captioning/flickr8k/
 ML/algorithms/svm/__pycache__/utils.cpython-38.pyc
+__pycache__/
+*.pth.tar
+*.DS_STORE
+ML/Pytorch/huggingface/train.csv
+ML/Pytorch/huggingface/validation.csv
+ML/Pytorch/huggingface/test.csv
+ML/Pytorch/huggingface/tb_logs/
+ML/Pytorch/huggingface/checkpoints/
+ML/Pytorch/huggingface/notebooks/

ML/Kaggles/DiabeticRetinopathy/config.py

@@ -0,0 +1,48 @@
+import torch
+import albumentations as A
+from albumentations.pytorch import ToTensorV2
+
+DEVICE = "cuda" if torch.cuda.is_available() else "cpu"
+LEARNING_RATE = 3e-5
+WEIGHT_DECAY = 5e-4
+BATCH_SIZE = 20
+NUM_EPOCHS = 100
+NUM_WORKERS = 6
+CHECKPOINT_FILE = "b3.pth.tar"
+PIN_MEMORY = True
+SAVE_MODEL = True
+LOAD_MODEL = True
+
+# Data augmentation for images
+train_transforms = A.Compose(
+    [
+        A.Resize(width=760, height=760),
+        A.RandomCrop(height=728, width=728),
+        A.HorizontalFlip(p=0.5),
+        A.VerticalFlip(p=0.5),
+        A.RandomRotate90(p=0.5),
+        A.Blur(p=0.3),
+        A.CLAHE(p=0.3),
+        A.ColorJitter(p=0.3),
+        A.CoarseDropout(max_holes=12, max_height=20, max_width=20, p=0.3),
+        A.IAAAffine(shear=30, rotate=0, p=0.2, mode="constant"),
+        A.Normalize(
+            mean=[0.3199, 0.2240, 0.1609],
+            std=[0.3020, 0.2183, 0.1741],
+            max_pixel_value=255.0,
+        ),
+        ToTensorV2(),
+    ]
+)
+
+val_transforms = A.Compose(
+    [
+        A.Resize(height=728, width=728),
+        A.Normalize(
+            mean=[0.3199, 0.2240, 0.1609],
+            std=[0.3020, 0.2183, 0.1741],
+            max_pixel_value=255.0,
+        ),
+        ToTensorV2(),
+    ]
+)

ML/Kaggles/DiabeticRetinopathy/dataset.py

@@ -0,0 +1,56 @@
+import config
+import os
+import pandas as pd
+import numpy as np
+from torch.utils.data import Dataset, DataLoader
+from PIL import Image
+from tqdm import tqdm
+
+
+class DRDataset(Dataset):
+    def __init__(self, images_folder, path_to_csv, train=True, transform=None):
+        super().__init__()
+        self.data = pd.read_csv(path_to_csv)
+        self.images_folder = images_folder
+        self.image_files = os.listdir(images_folder)
+        self.transform = transform
+        self.train = train
+
+    def __len__(self):
+        return self.data.shape[0] if self.train else len(self.image_files)
+
+    def __getitem__(self, index):
+        if self.train:
+            image_file, label = self.data.iloc[index]
+        else:
+            # if test simply return -1 for label, I do this in order to
+            # re-use same dataset class for test set submission later on
+            image_file, label = self.image_files[index], -1
+            image_file = image_file.replace(".jpeg", "")
+
+        image = np.array(Image.open(os.path.join(self.images_folder, image_file+".jpeg")))
+
+        if self.transform:
+            image = self.transform(image=image)["image"]
+
+        return image, label, image_file
+
+
+if __name__ == "__main__":
+    """
+    Test if everything works ok
+    """
+    dataset = DRDataset(
+        images_folder="../train/images_resized_650/",
+        path_to_csv="../train/trainLabels.csv",
+        transform=config.val_transforms,
+    )
+    loader = DataLoader(
+        dataset=dataset, batch_size=32, num_workers=2, shuffle=True, pin_memory=True
+    )
+
+    for x, label, file in tqdm(loader):
+        print(x.shape)
+        print(label.shape)
+        import sys
+        sys.exit()

ML/Kaggles/DiabeticRetinopathy/preprocess_images.py

@@ -0,0 +1,82 @@
+"""
+Tries to remove unnecessary black borders around the images, and
+"trim" the images to they take up the entirety of the image.
+It's hacky & not very nice but it works :))
+"""
+
+import os
+import numpy as np
+from PIL import Image
+import warnings
+from multiprocessing import Pool
+from tqdm import tqdm
+import cv2
+
+
+def trim(im):
+    """
+    Converts image to grayscale using cv2, then computes binary matrix
+    of the pixels that are above a certain threshold, then takes out
+    the first row where a certain percetage of the pixels are above the
+    threshold will be the first clip point. Same idea for col, max row, max col.
+    """
+    percentage = 0.02
+
+    img = np.array(im)
+    img_gray = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
+    im = img_gray > 0.1 * np.mean(img_gray[img_gray != 0])
+    row_sums = np.sum(im, axis=1)
+    col_sums = np.sum(im, axis=0)
+    rows = np.where(row_sums > img.shape[1] * percentage)[0]
+    cols = np.where(col_sums > img.shape[0] * percentage)[0]
+    min_row, min_col = np.min(rows), np.min(cols)
+    max_row, max_col = np.max(rows), np.max(cols)
+    im_crop = img[min_row : max_row + 1, min_col : max_col + 1]
+    return Image.fromarray(im_crop)
+
+
+def resize_maintain_aspect(image, desired_size):
+    """
+    Stole this from some stackoverflow post but can't remember which,
+    this will add padding to maintain the aspect ratio.
+    """
+    old_size = image.size  # old_size[0] is in (width, height) format
+    ratio = float(desired_size) / max(old_size)
+    new_size = tuple([int(x * ratio) for x in old_size])
+    im = image.resize(new_size, Image.ANTIALIAS)
+    new_im = Image.new("RGB", (desired_size, desired_size))
+    new_im.paste(im, ((desired_size - new_size[0]) // 2, (desired_size - new_size[1]) // 2))
+    return new_im
+
+
+def save_single(args):
+    img_file, input_path_folder, output_path_folder, output_size = args
+    image_original = Image.open(os.path.join(input_path_folder, img_file))
+    image = trim(image_original)
+    image = resize_maintain_aspect(image, desired_size=output_size[0])
+    image.save(os.path.join(output_path_folder + img_file))
+
+
+def fast_image_resize(input_path_folder, output_path_folder, output_size=None):
+    """
+    Uses multiprocessing to make it fast
+    """
+    if not output_size:
+        warnings.warn("Need to specify output_size! For example: output_size=100")
+        exit()
+
+    if not os.path.exists(output_path_folder):
+        os.makedirs(output_path_folder)
+
+    jobs = [
+        (file, input_path_folder, output_path_folder, output_size)
+        for file in os.listdir(input_path_folder)
+    ]
+
+    with Pool() as p:
+        list(tqdm(p.imap_unordered(save_single, jobs), total=len(jobs)))
+
+
+if __name__ == "__main__":
+    fast_image_resize("../train/images/", "../train/images_resized_150/", output_size=(150, 150))
+    fast_image_resize("../test/images/", "../test/images_resized_150/", output_size=(150, 150))

ML/Kaggles/DiabeticRetinopathy/train.py

@@ -0,0 +1,125 @@
+import torch
+from torch import nn, optim
+import os
+import config
+from torch.utils.data import DataLoader
+from tqdm import tqdm
+from sklearn.metrics import cohen_kappa_score
+from efficientnet_pytorch import EfficientNet
+from dataset import DRDataset
+from torchvision.utils import save_image
+from utils import (
+    load_checkpoint,
+    save_checkpoint,
+    check_accuracy,
+    make_prediction,
+    get_csv_for_blend,
+)
+
+
+def train_one_epoch(loader, model, optimizer, loss_fn, scaler, device):
+    losses = []
+    loop = tqdm(loader)
+    for batch_idx, (data, targets, _) in enumerate(loop):
+        # save examples and make sure they look ok with the data augmentation,
+        # tip is to first set mean=[0,0,0], std=[1,1,1] so they look "normal"
+        #save_image(data, f"hi_{batch_idx}.png")
+
+        data = data.to(device=device)
+        targets = targets.to(device=device)
+
+        # forward
+        with torch.cuda.amp.autocast():
+            scores = model(data)
+            loss = loss_fn(scores, targets.unsqueeze(1).float())
+
+        losses.append(loss.item())
+
+        # backward
+        optimizer.zero_grad()
+        scaler.scale(loss).backward()
+        scaler.step(optimizer)
+        scaler.update()
+        loop.set_postfix(loss=loss.item())
+
+    print(f"Loss average over epoch: {sum(losses)/len(losses)}")
+
+
+def main():
+    train_ds = DRDataset(
+        images_folder="train/images_preprocessed_1000/",
+        path_to_csv="train/trainLabels.csv",
+        transform=config.val_transforms,
+    )
+    val_ds = DRDataset(
+        images_folder="train/images_preprocessed_1000/",
+        path_to_csv="train/valLabels.csv",
+        transform=config.val_transforms,
+    )
+    test_ds = DRDataset(
+        images_folder="test/images_preprocessed_1000",
+        path_to_csv="train/trainLabels.csv",
+        transform=config.val_transforms,
+        train=False,
+    )
+    test_loader = DataLoader(
+        test_ds, batch_size=config.BATCH_SIZE, num_workers=6, shuffle=False
+    )
+    train_loader = DataLoader(
+        train_ds,
+        batch_size=config.BATCH_SIZE,
+        num_workers=config.NUM_WORKERS,
+        pin_memory=config.PIN_MEMORY,
+        shuffle=False,
+    )
+    val_loader = DataLoader(
+        val_ds,
+        batch_size=config.BATCH_SIZE,
+        num_workers=2,
+        pin_memory=config.PIN_MEMORY,
+        shuffle=False,
+    )
+    loss_fn = nn.MSELoss()
+
+    model = EfficientNet.from_pretrained("efficientnet-b3")
+    model._fc = nn.Linear(1536, 1)
+    model = model.to(config.DEVICE)
+    optimizer = optim.Adam(model.parameters(), lr=config.LEARNING_RATE, weight_decay=config.WEIGHT_DECAY)
+    scaler = torch.cuda.amp.GradScaler()
+
+    if config.LOAD_MODEL and config.CHECKPOINT_FILE in os.listdir():
+        load_checkpoint(torch.load(config.CHECKPOINT_FILE), model, optimizer, config.LEARNING_RATE)
+
+    # Run after training is done and you've achieved good result
+    # on validation set, then run train_blend.py file to use information
+    # about both eyes concatenated
+    get_csv_for_blend(val_loader, model, "../train/val_blend.csv")
+    get_csv_for_blend(train_loader, model, "../train/train_blend.csv")
+    get_csv_for_blend(test_loader, model, "../train/test_blend.csv")
+    make_prediction(model, test_loader, "submission_.csv")
+    import sys
+    sys.exit()
+    #make_prediction(model, test_loader)
+
+    for epoch in range(config.NUM_EPOCHS):
+        train_one_epoch(train_loader, model, optimizer, loss_fn, scaler, config.DEVICE)
+
+        # get on validation
+        preds, labels = check_accuracy(val_loader, model, config.DEVICE)
+        print(f"QuadraticWeightedKappa (Validation): {cohen_kappa_score(labels, preds, weights='quadratic')}")
+
+        # get on train
+        #preds, labels = check_accuracy(train_loader, model, config.DEVICE)
+        #print(f"QuadraticWeightedKappa (Training): {cohen_kappa_score(labels, preds, weights='quadratic')}")
+
+        if config.SAVE_MODEL:
+            checkpoint = {
+                "state_dict": model.state_dict(),
+                "optimizer": optimizer.state_dict(),
+            }
+            save_checkpoint(checkpoint, filename=f"b3_{epoch}.pth.tar")
+
+
+
+if __name__ == "__main__":
+    main()

ML/Kaggles/DiabeticRetinopathy/train_blend.py

@@ -0,0 +1,126 @@
+import torch
+from tqdm import tqdm
+import numpy as np
+from torch import nn
+from torch import optim
+from torch.utils.data import DataLoader, Dataset
+from utils import save_checkpoint, load_checkpoint, check_accuracy
+from sklearn.metrics import cohen_kappa_score
+import config
+import os
+import pandas as pd
+
+
+def make_prediction(model, loader, file):
+    preds = []
+    filenames = []
+    model.eval()
+
+    for x, y, files in tqdm(loader):
+        x = x.to(config.DEVICE)
+        with torch.no_grad():
+            predictions = model(x)
+            # Convert MSE floats to integer predictions
+            predictions[predictions < 0.5] = 0
+            predictions[(predictions >= 0.5) & (predictions < 1.5)] = 1
+            predictions[(predictions >= 1.5) & (predictions < 2.5)] = 2
+            predictions[(predictions >= 2.5) & (predictions < 3.5)] = 3
+            predictions[(predictions >= 3.5) & (predictions < 1000000000000)] = 4
+            predictions = predictions.long().view(-1)
+            y = y.view(-1)
+
+            preds.append(predictions.cpu().numpy())
+            filenames += map(list, zip(files[0], files[1]))
+
+    filenames = [item for sublist in filenames for item in sublist]
+    df = pd.DataFrame({"image": filenames, "level": np.concatenate(preds, axis=0)})
+    df.to_csv(file, index=False)
+    model.train()
+    print("Done with predictions")
+
+
+class MyDataset(Dataset):
+    def __init__(self, csv_file):
+        self.csv = pd.read_csv(csv_file)
+
+    def __len__(self):
+        return self.csv.shape[0]
+
+    def __getitem__(self, index):
+        example = self.csv.iloc[index, :]
+        features = example.iloc[: example.shape[0] - 4].to_numpy().astype(np.float32)
+        labels = example.iloc[-4:-2].to_numpy().astype(np.int64)
+        filenames = example.iloc[-2:].values.tolist()
+        return features, labels, filenames
+
+
+class MyModel(nn.Module):
+    def __init__(self):
+        super().__init__()
+        self.model = nn.Sequential(
+            nn.BatchNorm1d((1536 + 1) * 2),
+            nn.Linear((1536+1) * 2, 500),
+            nn.BatchNorm1d(500),
+            nn.ReLU(),
+            nn.Dropout(0.2),
+            nn.Linear(500, 100),
+            nn.BatchNorm1d(100),
+            nn.ReLU(),
+            nn.Dropout(0.2),
+            nn.Linear(100, 2),
+        )
+
+    def forward(self, x):
+        return self.model(x)
+
+
+if __name__ == "__main__":
+    model = MyModel().to(config.DEVICE)
+    ds = MyDataset(csv_file="train/train_blend.csv")
+    loader = DataLoader(ds, batch_size=256, num_workers=3, pin_memory=True, shuffle=True)
+    ds_val = MyDataset(csv_file="train/val_blend.csv")
+    loader_val = DataLoader(
+        ds_val, batch_size=256, num_workers=3, pin_memory=True, shuffle=True
+    )
+    ds_test = MyDataset(csv_file="train/test_blend.csv")
+    loader_test = DataLoader(
+        ds_test, batch_size=256, num_workers=2, pin_memory=True, shuffle=False
+    )
+    optimizer = optim.Adam(model.parameters(), lr=1e-4, weight_decay=1e-5)
+    loss_fn = nn.MSELoss()
+
+    if config.LOAD_MODEL and "linear.pth.tar" in os.listdir():
+        load_checkpoint(torch.load("linear.pth.tar"), model, optimizer, lr=1e-4)
+        model.train()
+
+    for _ in range(5):
+        losses = []
+        for x, y, files in tqdm(loader_val):
+            x = x.to(config.DEVICE).float()
+            y = y.to(config.DEVICE).view(-1).float()
+
+            # forward
+            scores = model(x).view(-1)
+            loss = loss_fn(scores, y)
+            losses.append(loss.item())
+
+            # backward
+            optimizer.zero_grad()
+            loss.backward()
+
+            # gradient descent or adam step
+            optimizer.step()
+
+        print(f"Loss: {sum(losses)/len(losses)}")
+
+    if config.SAVE_MODEL:
+        checkpoint = {"state_dict": model.state_dict(), "optimizer": optimizer.state_dict()}
+        save_checkpoint(checkpoint, filename="linear.pth.tar")
+
+    preds, labels = check_accuracy(loader_val, model)
+    print(cohen_kappa_score(labels, preds, weights="quadratic"))
+
+    preds, labels = check_accuracy(loader, model)
+    print(cohen_kappa_score(labels, preds, weights="quadratic"))
+
+    make_prediction(model, loader_test, "test_preds.csv")

ML/Kaggles/DiabeticRetinopathy/utils.py

@@ -0,0 +1,128 @@
+import torch
+import pandas as pd
+import numpy as np
+import config
+from tqdm import tqdm
+import warnings
+import torch.nn.functional as F
+
+
+def make_prediction(model, loader, output_csv="submission.csv"):
+    preds = []
+    filenames = []
+    model.eval()
+
+    for x, y, files in tqdm(loader):
+        x = x.to(config.DEVICE)
+        with torch.no_grad():
+            predictions = model(x)
+            # Convert MSE floats to integer predictions
+            predictions[predictions < 0.5] = 0
+            predictions[(predictions >= 0.5) & (predictions < 1.5)] = 1
+            predictions[(predictions >= 1.5) & (predictions < 2.5)] = 2
+            predictions[(predictions >= 2.5) & (predictions < 3.5)] = 3
+            predictions[(predictions >= 3.5) & (predictions < 10000000)] = 4
+            predictions = predictions.long().squeeze(1)
+            preds.append(predictions.cpu().numpy())
+            filenames += files
+
+    df = pd.DataFrame({"image": filenames, "level": np.concatenate(preds, axis=0)})
+    df.to_csv(output_csv, index=False)
+    model.train()
+    print("Done with predictions")
+
+
+def check_accuracy(loader, model, device="cuda"):
+    model.eval()
+    all_preds, all_labels = [], []
+    num_correct = 0
+    num_samples = 0
+
+    for x, y, filename in tqdm(loader):
+        x = x.to(device=device)
+        y = y.to(device=device)
+
+        with torch.no_grad():
+            predictions = model(x)
+
+        # Convert MSE floats to integer predictions
+        predictions[predictions < 0.5] = 0
+        predictions[(predictions >= 0.5) & (predictions < 1.5)] = 1
+        predictions[(predictions >= 1.5) & (predictions < 2.5)] = 2
+        predictions[(predictions >= 2.5) & (predictions < 3.5)] = 3
+        predictions[(predictions >= 3.5) & (predictions < 100)] = 4
+        predictions = predictions.long().view(-1)
+        y = y.view(-1)
+
+        num_correct += (predictions == y).sum()
+        num_samples += predictions.shape[0]
+
+        # add to lists
+        all_preds.append(predictions.detach().cpu().numpy())
+        all_labels.append(y.detach().cpu().numpy())
+
+    print(
+        f"Got {num_correct} / {num_samples} with accuracy {float(num_correct) / float(num_samples) * 100:.2f}"
+    )
+    model.train()
+    return np.concatenate(all_preds, axis=0, dtype=np.int64), np.concatenate(
+        all_labels, axis=0, dtype=np.int64
+    )
+
+
+def save_checkpoint(state, filename="my_checkpoint.pth.tar"):
+    print("=> Saving checkpoint")
+    torch.save(state, filename)
+
+
+def load_checkpoint(checkpoint, model, optimizer, lr):
+    print("=> Loading checkpoint")
+    model.load_state_dict(checkpoint["state_dict"])
+    #optimizer.load_state_dict(checkpoint["optimizer"])
+
+    # If we don't do this then it will just have learning rate of old checkpoint
+    # and it will lead to many hours of debugging \:
+    for param_group in optimizer.param_groups:
+        param_group["lr"] = lr
+
+
+def get_csv_for_blend(loader, model, output_csv_file):
+    warnings.warn("Important to have shuffle=False (and to ensure batch size is even size) when running get_csv_for_blend also set val_transforms to train_loader!")
+    model.eval()
+    filename_first = []
+    filename_second = []
+    labels_first = []
+    labels_second = []
+    all_features = []
+
+    for idx, (images, y, image_files) in enumerate(tqdm(loader)):
+        images = images.to(config.DEVICE)
+
+        with torch.no_grad():
+            features = F.adaptive_avg_pool2d(
+                model.extract_features(images), output_size=1
+            )
+            features_logits = features.reshape(features.shape[0] // 2, 2, features.shape[1])
+            preds = model(images).reshape(images.shape[0] // 2, 2, 1)
+            new_features = (
+                torch.cat([features_logits, preds], dim=2)
+                .view(preds.shape[0], -1)
+                .cpu()
+                .numpy()
+            )
+            all_features.append(new_features)
+            filename_first += image_files[::2]
+            filename_second += image_files[1::2]
+            labels_first.append(y[::2].cpu().numpy())
+            labels_second.append(y[1::2].cpu().numpy())
+
+    all_features = np.concatenate(all_features, axis=0)
+    df = pd.DataFrame(
+        data=all_features, columns=[f"f_{idx}" for idx in range(all_features.shape[1])]
+    )
+    df["label_first"] = np.concatenate(labels_first, axis=0)
+    df["label_second"] = np.concatenate(labels_second, axis=0)
+    df["file_first"] = filename_first
+    df["file_second"] = filename_second
+    df.to_csv(output_csv_file, index=False)
+    model.train()

ML/Kaggles/Dog vs Cat Competition/Logistic Regression on EfficientNet Features.ipynb

@@ -0,0 +1,119 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "51c78b68",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import sklearn\n",
+    "import pandas as pd\n",
+    "import numpy as np\n",
+    "from sklearn.linear_model import LogisticRegression\n",
+    "from sklearn.model_selection import train_test_split\n",
+    "from sklearn.metrics import log_loss"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "4421a043",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Training data shape: (25000, 2560), labels shape: (25000,)\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "LogisticRegression(max_iter=2000)"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "X = np.load(f'data_features/X_train_b7.npy')\n",
+    "y = np.load(f'data_features/y_train_b7.npy')\n",
+    "\n",
+    "# Split data and train classifier\n",
+    "print(f\"Training data shape: {X.shape}, labels shape: {y.shape}\")\n",
+    "X_train, X_val, y_train, y_val = train_test_split(X, y, test_size=0.001, random_state=1337)\n",
+    "clf = LogisticRegression(max_iter=2000)\n",
+    "clf.fit(X_train, y_train)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "d5cfc5b0",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "On validation set:\n",
+      "Accuracy: 1.0\n",
+      "LOG LOSS: 7.980845755748817e-05 \n",
+      "%--------------------------------------------------%\n",
+      "Getting predictions for test set\n",
+      "Done getting predictions!\n"
+     ]
+    }
+   ],
+   "source": [
+    "# Check on validation\n",
+    "val_preds= clf.predict_proba(X_val)[:,1]\n",
+    "print(f\"On validation set:\")\n",
+    "print(f\"Accuracy: {clf.score(X_val, y_val)}\")\n",
+    "print(f\"LOG LOSS: {log_loss(y_val, val_preds)} \")\n",
+    "print(\"%--------------------------------------------------%\")\n",
+    "\n",
+    "# Get predictions on test set\n",
+    "print(\"Getting predictions for test set\")\n",
+    "X_test = np.load(f'data_features/X_test_b7.npy')\n",
+    "X_test_preds = clf.predict_proba(X_test)[:,1]\n",
+    "df = pd.DataFrame({'id': np.arange(1, 12501), 'label': np.clip(X_test_preds, 0.005, 0.995)})\n",
+    "df.to_csv(f\"submissions/mysubmission.csv\", index=False)\n",
+    "print(\"Done getting predictions!\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "a9cce7af",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

ML/Kaggles/Dog vs Cat Competition/competition.txt

@@ -0,0 +1 @@
+https://www.kaggle.com/c/dogs-vs-cats-redux-kernels-edition

ML/Kaggles/Dog vs Cat Competition/config.py

@@ -0,0 +1,26 @@
+import torch
+import albumentations as A
+from albumentations.pytorch import ToTensorV2
+
+DEVICE = "cuda" if torch.cuda.is_available() else "cpu"
+NUM_WORKERS = 4
+BATCH_SIZE = 20
+PIN_MEMORY = True
+LOAD_MODEL = True
+SAVE_MODEL = True
+CHECKPOINT_FILE = "b7.pth.tar"
+WEIGHT_DECAY = 1e-4
+LEARNING_RATE = 1e-4
+NUM_EPOCHS = 1
+
+basic_transform = A.Compose(
+    [
+        A.Resize(height=448, width=448),
+        A.Normalize(
+            mean=[0.485, 0.456, 0.406],
+            std=[0.229, 0.224, 0.225],
+            max_pixel_value=255.0,
+        ),
+        ToTensorV2(),
+    ]
+)

ML/Kaggles/Dog vs Cat Competition/dataset.py

@@ -0,0 +1,32 @@
+import os
+import re
+import numpy as np
+from torch.utils.data import Dataset
+from PIL import Image
+
+
+class CatDog(Dataset):
+    def __init__(self, root, transform=None):
+        self.images = os.listdir(root)
+        self.images.sort(key=lambda x: int(re.findall(r"\d+", x)[0]))
+        self.root = root
+        self.transform = transform
+
+    def __len__(self):
+        return len(self.images)
+
+    def __getitem__(self, index):
+        file = self.images[index]
+        img = np.array(Image.open(os.path.join(self.root, file)))
+
+        if self.transform is not None:
+            img = self.transform(image=img)["image"]
+
+        if "dog" in file:
+            label = 1
+        elif "cat" in file:
+            label = 0
+        else:
+            label = -1
+
+        return img, label

ML/Kaggles/Dog vs Cat Competition/train.py

@@ -0,0 +1,93 @@
+# Imports
+import os
+import torch
+import torch.nn.functional as F
+import numpy as np
+import config
+from torch import nn, optim
+from torch.utils.data import DataLoader
+from tqdm import tqdm
+from dataset import CatDog
+from efficientnet_pytorch import EfficientNet
+from utils import check_accuracy, load_checkpoint, save_checkpoint
+
+
+def save_feature_vectors(model, loader, output_size=(1, 1), file="trainb7"):
+    model.eval()
+    images, labels = [], []
+
+    for idx, (x, y) in enumerate(tqdm(loader)):
+        x = x.to(config.DEVICE)
+
+        with torch.no_grad():
+            features = model.extract_features(x)
+            features = F.adaptive_avg_pool2d(features, output_size=output_size)
+        images.append(features.reshape(x.shape[0], -1).detach().cpu().numpy())
+        labels.append(y.numpy())
+
+    np.save(f"data_features/X_{file}.npy", np.concatenate(images, axis=0))
+    np.save(f"data_features/y_{file}.npy", np.concatenate(labels, axis=0))
+    model.train()
+
+
+def train_one_epoch(loader, model, loss_fn, optimizer, scaler):
+    loop = tqdm(loader)
+
+    for batch_idx, (data, targets) in enumerate(loop):
+        data = data.to(config.DEVICE)
+        targets = targets.to(config.DEVICE).unsqueeze(1).float()
+
+        with torch.cuda.amp.autocast():
+            scores = model(data)
+            loss = loss_fn(scores, targets)
+
+        optimizer.zero_grad()
+        scaler.scale(loss).backward()
+        scaler.step(optimizer)
+        scaler.update()
+        loop.set_postfix(loss=loss.item())
+
+
+def main():
+    model = EfficientNet.from_pretrained("efficientnet-b7")
+    model._fc = nn.Linear(2560, 1)
+    train_dataset = CatDog(root="data/train/", transform=config.basic_transform)
+    test_dataset = CatDog(root="data/test/", transform=config.basic_transform)
+    train_loader = DataLoader(
+        train_dataset,
+        shuffle=True,
+        batch_size=config.BATCH_SIZE,
+        num_workers=config.NUM_WORKERS,
+        pin_memory=True,
+    )
+    test_loader = DataLoader(
+        test_dataset,
+        shuffle=False,
+        batch_size=config.BATCH_SIZE,
+        num_workers=config.NUM_WORKERS,
+    )
+    model = model.to(config.DEVICE)
+
+    scaler = torch.cuda.amp.GradScaler()
+    loss_fn = nn.BCEWithLogitsLoss()
+    optimizer = optim.Adam(
+        model.parameters(), lr=config.LEARNING_RATE, weight_decay=config.WEIGHT_DECAY
+    )
+
+    if config.LOAD_MODEL and config.CHECKPOINT_FILE in os.listdir():
+        load_checkpoint(torch.load(config.CHECKPOINT_FILE), model)
+
+    for epoch in range(config.NUM_EPOCHS):
+        train_one_epoch(train_loader, model, loss_fn, optimizer, scaler)
+        check_accuracy(train_loader, model, loss_fn)
+
+    if config.SAVE_MODEL:
+        checkpoint = {"state_dict": model.state_dict(), "optimizer": optimizer.state_dict()}
+        save_checkpoint(checkpoint, filename=config.CHECKPOINT_FILE)
+
+    save_feature_vectors(model, train_loader, output_size=(1, 1), file="train_b7")
+    save_feature_vectors(model, test_loader, output_size=(1, 1), file="test_b7")
+
+
+if __name__ == "__main__":
+    main()

ML/Kaggles/Dog vs Cat Competition/utils.py

@@ -0,0 +1,192 @@
+import torch
+import os
+import pandas as pd
+import numpy as np
+import albumentations as A
+from albumentations.pytorch import ToTensorV2
+import config
+from tqdm import tqdm
+from dataset import CatDog
+from torch.utils.data import DataLoader
+from sklearn.metrics import log_loss
+
+
+def check_accuracy(
+    loader, model, loss_fn, input_shape=None, toggle_eval=True, print_accuracy=True
+):
+    """
+    Check accuracy of model on data from loader
+    """
+    if toggle_eval:
+        model.eval()
+    device = next(model.parameters()).device
+    num_correct = 0
+    num_samples = 0
+
+    y_preds = []
+    y_true = []
+
+    with torch.no_grad():
+        for x, y in loader:
+            x = x.to(device=device)
+            y = y.to(device=device)
+            if input_shape:
+                x = x.reshape(x.shape[0], *input_shape)
+            scores = model(x)
+            predictions = torch.sigmoid(scores) > 0.5
+            y_preds.append(torch.clip(torch.sigmoid(scores), 0.005, 0.995).cpu().numpy())
+            y_true.append(y.cpu().numpy())
+            num_correct += (predictions.squeeze(1) == y).sum()
+            num_samples += predictions.size(0)
+
+    accuracy = num_correct / num_samples
+
+    if toggle_eval:
+        model.train()
+
+    if print_accuracy:
+        print(f"Accuracy: {accuracy * 100:.2f}%")
+        print(log_loss(np.concatenate(y_true, axis=0), np.concatenate(y_preds, axis=0)))
+
+    return accuracy
+
+
+def save_checkpoint(state, filename="my_checkpoint.pth.tar"):
+    print("=> Saving checkpoint")
+    torch.save(state, filename)
+
+
+def load_checkpoint(checkpoint, model):
+    print("=> Loading checkpoint")
+    model.load_state_dict(checkpoint["state_dict"])
+
+
+def create_submission(model, model_name, files_dir):
+    my_transforms = {
+        "base": A.Compose(
+            [
+                A.Resize(height=240, width=240),
+                A.Normalize(
+                    mean=[0.485, 0.456, 0.406],
+                    std=[0.229, 0.224, 0.225],
+                    max_pixel_value=255.0,
+                ),
+                ToTensorV2(),
+            ]
+        ),
+        "horizontal_flip": A.Compose(
+            [
+                A.Resize(height=240, width=240),
+                A.HorizontalFlip(p=1.0),
+                A.Normalize(
+                    mean=[0.485, 0.456, 0.406],
+                    std=[0.229, 0.224, 0.225],
+                    max_pixel_value=255.0,
+                ),
+                ToTensorV2(),
+            ]
+        ),
+        "vertical_flip": A.Compose(
+            [
+                A.Resize(height=240, width=240),
+                A.VerticalFlip(p=1.0),
+                A.Normalize(
+                    mean=[0.485, 0.456, 0.406],
+                    std=[0.229, 0.224, 0.225],
+                    max_pixel_value=255.0,
+                ),
+                ToTensorV2(),
+            ]
+        ),
+        "coloring": A.Compose(
+            [
+                A.Resize(height=240, width=240),
+                A.ColorJitter(p=1.0),
+                A.Normalize(
+                    mean=[0.485, 0.456, 0.406],
+                    std=[0.229, 0.224, 0.225],
+                    max_pixel_value=255.0,
+                ),
+                ToTensorV2(),
+            ]
+        ),
+        "rotate": A.Compose(
+            [
+                A.Resize(height=240, width=240),
+                A.Rotate(p=1.0, limit=45),
+                A.Normalize(
+                    mean=[0.485, 0.456, 0.406],
+                    std=[0.229, 0.224, 0.225],
+                    max_pixel_value=255.0,
+                ),
+                ToTensorV2(),
+            ]
+        ),
+        "shear": A.Compose(
+            [
+                A.Resize(height=240, width=240),
+                A.IAAAffine(p=1.0),
+                A.Normalize(
+                    mean=[0.485, 0.456, 0.406],
+                    std=[0.229, 0.224, 0.225],
+                    max_pixel_value=255.0,
+                ),
+                ToTensorV2(),
+            ]
+        ),
+    }
+
+    for t in ["base", "horizontal_flip", "vertical_flip", "coloring", "rotate", "shear"]:
+        predictions = []
+        labels = []
+        all_files = []
+        test_dataset = MyDataset(root=files_dir, transform=my_transforms[t])
+        test_loader = DataLoader(
+            test_dataset, batch_size=32, num_workers=4, shuffle=False, pin_memory=True
+        )
+        model.eval()
+
+        for idx, (x, y, filenames) in enumerate(tqdm(test_loader)):
+            x = x.to(config.DEVICE)
+            with torch.no_grad():
+                outputs = (
+                    torch.clip(torch.sigmoid(model(x)), 0.005, 0.995).squeeze(1).cpu().numpy()
+                )
+                predictions.append(outputs)
+                labels += y.numpy().tolist()
+                all_files += filenames
+
+        df = pd.DataFrame(
+            {
+                "id": np.arange(
+                    1,
+                    (len(predictions) - 1) * predictions[0].shape[0]
+                    + predictions[-1].shape[0]
+                    + 1,
+                ),
+                "label": np.concatenate(predictions, axis=0),
+            }
+        )
+        df.to_csv(f"predictions_test/submission_{model_name}_{t}.csv", index=False)
+
+        model.train()
+        print(f"Created submission file for model {model_name} and transform {t}")
+
+
+def blending_ensemble_data():
+    pred_csvs = []
+    root_dir = "predictions_validation/"
+
+    for file in os.listdir(root_dir):
+        if "label" not in file:
+            df = pd.read_csv(root_dir + "/" + file)
+            pred_csvs.append(df)
+        else:
+            label_csv = pd.read_csv(root_dir + "/" + file)
+
+    all_preds = pd.concat(pred_csvs, axis=1)
+    print(all_preds)
+
+
+if __name__ == "__main__":
+    blending_ensemble_data()

ML/Kaggles/Facial Keypoint Detection Competition/config.py

@@ -0,0 +1,61 @@
+import torch
+import albumentations as A
+from albumentations.pytorch import ToTensorV2
+import cv2
+
+DEVICE = "cuda" if torch.cuda.is_available() else "cpu"
+LEARNING_RATE = 1e-4
+WEIGHT_DECAY = 5e-4
+BATCH_SIZE = 64
+NUM_EPOCHS = 100
+NUM_WORKERS = 4
+CHECKPOINT_FILE = "b0_4.pth.tar"
+PIN_MEMORY = True
+SAVE_MODEL = True
+LOAD_MODEL = True
+
+# Data augmentation for images
+train_transforms = A.Compose(
+    [
+        A.Resize(width=96, height=96),
+        A.Rotate(limit=15, border_mode=cv2.BORDER_CONSTANT, p=0.8),
+        A.IAAAffine(shear=15, scale=1.0, mode="constant", p=0.2),
+        A.RandomBrightnessContrast(contrast_limit=0.5, brightness_limit=0.5, p=0.2),
+        A.OneOf([
+            A.GaussNoise(p=0.8),
+            A.CLAHE(p=0.8),
+            A.ImageCompression(p=0.8),
+            A.RandomGamma(p=0.8),
+            A.Posterize(p=0.8),
+            A.Blur(p=0.8),
+        ], p=1.0),
+        A.OneOf([
+            A.GaussNoise(p=0.8),
+            A.CLAHE(p=0.8),
+            A.ImageCompression(p=0.8),
+            A.RandomGamma(p=0.8),
+            A.Posterize(p=0.8),
+            A.Blur(p=0.8),
+        ], p=1.0),
+        A.ShiftScaleRotate(shift_limit=0.1, scale_limit=0.1, rotate_limit=0, p=0.2, border_mode=cv2.BORDER_CONSTANT),
+        A.Normalize(
+            mean=[0.4897, 0.4897, 0.4897],
+            std=[0.2330, 0.2330, 0.2330],
+            max_pixel_value=255.0,
+        ),
+        ToTensorV2(),
+    ], keypoint_params=A.KeypointParams(format="xy", remove_invisible=False),
+)
+
+
+val_transforms = A.Compose(
+    [
+        A.Resize(height=96, width=96),
+        A.Normalize(
+            mean=[0.4897, 0.4897, 0.4897],
+            std=[0.2330, 0.2330, 0.2330],
+            max_pixel_value=255.0,
+        ),
+        ToTensorV2(),
+    ], keypoint_params=A.KeypointParams(format="xy", remove_invisible=False),
+)

ML/Kaggles/Facial Keypoint Detection Competition/dataset.py

@@ -0,0 +1,50 @@
+import pandas as pd
+import numpy as np
+import config
+import matplotlib.pyplot as plt
+from torch.utils.data import DataLoader, Dataset
+
+
+class FacialKeypointDataset(Dataset):
+    def __init__(self, csv_file, train=True, transform=None):
+        super().__init__()
+        self.data = pd.read_csv(csv_file)
+        self.category_names = ['left_eye_center_x', 'left_eye_center_y', 'right_eye_center_x', 'right_eye_center_y', 'left_eye_inner_corner_x', 'left_eye_inner_corner_y', 'left_eye_outer_corner_x', 'left_eye_outer_corner_y', 'right_eye_inner_corner_x', 'right_eye_inner_corner_y', 'right_eye_outer_corner_x', 'right_eye_outer_corner_y', 'left_eyebrow_inner_end_x', 'left_eyebrow_inner_end_y', 'left_eyebrow_outer_end_x', 'left_eyebrow_outer_end_y', 'right_eyebrow_inner_end_x', 'right_eyebrow_inner_end_y', 'right_eyebrow_outer_end_x', 'right_eyebrow_outer_end_y', 'nose_tip_x', 'nose_tip_y', 'mouth_left_corner_x', 'mouth_left_corner_y', 'mouth_right_corner_x', 'mouth_right_corner_y', 'mouth_center_top_lip_x', 'mouth_center_top_lip_y', 'mouth_center_bottom_lip_x', 'mouth_center_bottom_lip_y']
+        self.transform = transform
+        self.train = train
+
+    def __len__(self):
+        return self.data.shape[0]
+
+    def __getitem__(self, index):
+        if self.train:
+            image = np.array(self.data.iloc[index, 30].split()).astype(np.float32)
+            labels = np.array(self.data.iloc[index, :30].tolist())
+            labels[np.isnan(labels)] = -1
+        else:
+            image = np.array(self.data.iloc[index, 1].split()).astype(np.float32)
+            labels = np.zeros(30)
+
+        ignore_indices = labels == -1
+        labels = labels.reshape(15, 2)
+
+        if self.transform:
+            image = np.repeat(image.reshape(96, 96, 1), 3, 2).astype(np.uint8)
+            augmentations = self.transform(image=image, keypoints=labels)
+            image = augmentations["image"]
+            labels = augmentations["keypoints"]
+
+        labels = np.array(labels).reshape(-1)
+        labels[ignore_indices] = -1
+
+        return image, labels.astype(np.float32)
+
+
+if __name__ == "__main__":
+    ds = FacialKeypointDataset(csv_file="data/train_4.csv", train=True, transform=config.train_transforms)
+    loader = DataLoader(ds, batch_size=1, shuffle=True, num_workers=0)
+
+    for idx, (x, y) in enumerate(loader):
+        plt.imshow(x[0][0].detach().cpu().numpy(), cmap='gray')
+        plt.plot(y[0][0::2].detach().cpu().numpy(), y[0][1::2].detach().cpu().numpy(), "go")
+        plt.show()

ML/Kaggles/Facial Keypoint Detection Competition/extract_images_from_csv.py

@@ -0,0 +1,19 @@
+import numpy as np
+import pandas as pd
+import os
+from PIL import Image
+
+
+def extract_images_from_csv(csv, column, save_folder, resize=(96, 96)):
+    if not os.path.exists(save_folder):
+        os.makedirs(save_folder)
+
+    for idx, image in enumerate(csv[column]):
+        image = np.array(image.split()).astype(np.uint8)
+        image = image.reshape(resize[0], resize[1])
+        img = Image.fromarray(image, 'L')
+        img.save(save_folder+f"img_{idx}.png")
+
+
+csv = pd.read_csv("test.csv")
+extract_images_from_csv(csv, "Image", "data/test/")

ML/Kaggles/Facial Keypoint Detection Competition/train.py

@@ -0,0 +1,111 @@
+import torch
+from dataset import FacialKeypointDataset
+from torch import nn, optim
+import os
+import config
+from torch.utils.data import DataLoader
+from tqdm import tqdm
+from efficientnet_pytorch import EfficientNet
+from utils import (
+    load_checkpoint,
+    save_checkpoint,
+    get_rmse,
+    get_submission
+)
+
+
+def train_one_epoch(loader, model, optimizer, loss_fn, scaler, device):
+    losses = []
+    loop = tqdm(loader)
+    num_examples = 0
+    for batch_idx, (data, targets) in enumerate(loop):
+        data = data.to(device=device)
+        targets = targets.to(device=device)
+
+        # forward
+        scores = model(data)
+        scores[targets == -1] = -1
+        loss = loss_fn(scores, targets)
+        num_examples += torch.numel(scores[targets != -1])
+        losses.append(loss.item())
+
+        # backward
+        optimizer.zero_grad()
+        loss.backward()
+        optimizer.step()
+
+    print(f"Loss average over epoch: {(sum(losses)/num_examples)**0.5}")
+
+
+def main():
+    train_ds = FacialKeypointDataset(
+        csv_file="data/train_4.csv",
+        transform=config.train_transforms,
+    )
+    train_loader = DataLoader(
+        train_ds,
+        batch_size=config.BATCH_SIZE,
+        num_workers=config.NUM_WORKERS,
+        pin_memory=config.PIN_MEMORY,
+        shuffle=True,
+    )
+    val_ds = FacialKeypointDataset(
+        transform=config.val_transforms,
+        csv_file="data/val_4.csv",
+    )
+    val_loader = DataLoader(
+        val_ds,
+        batch_size=config.BATCH_SIZE,
+        num_workers=config.NUM_WORKERS,
+        pin_memory=config.PIN_MEMORY,
+        shuffle=False,
+    )
+
+    test_ds = FacialKeypointDataset(
+        csv_file="data/test.csv",
+        transform=config.val_transforms,
+        train=False,
+    )
+
+    test_loader = DataLoader(
+        test_ds,
+        batch_size=1,
+        num_workers=config.NUM_WORKERS,
+        pin_memory=config.PIN_MEMORY,
+        shuffle=False,
+    )
+    loss_fn = nn.MSELoss(reduction="sum")
+    model = EfficientNet.from_pretrained("efficientnet-b0")
+    model._fc = nn.Linear(1280, 30)
+    model = model.to(config.DEVICE)
+    optimizer = optim.Adam(model.parameters(), lr=config.LEARNING_RATE, weight_decay=config.WEIGHT_DECAY)
+    scaler = torch.cuda.amp.GradScaler()
+
+    model_4 = EfficientNet.from_pretrained("efficientnet-b0")
+    model_4._fc = nn.Linear(1280, 30)
+    model_15 = EfficientNet.from_pretrained("efficientnet-b0")
+    model_15._fc = nn.Linear(1280, 30)
+    model_4 = model_4.to(config.DEVICE)
+    model_15 = model_15.to(config.DEVICE)
+
+    if config.LOAD_MODEL and config.CHECKPOINT_FILE in os.listdir():
+        load_checkpoint(torch.load(config.CHECKPOINT_FILE), model, optimizer, config.LEARNING_RATE)
+        load_checkpoint(torch.load("b0_4.pth.tar"), model_4, optimizer, config.LEARNING_RATE)
+        load_checkpoint(torch.load("b0_15.pth.tar"), model_15, optimizer, config.LEARNING_RATE)
+
+    get_submission(test_loader, test_ds, model_15, model_4)
+
+    for epoch in range(config.NUM_EPOCHS):
+        get_rmse(val_loader, model, loss_fn, config.DEVICE)
+        train_one_epoch(train_loader, model, optimizer, loss_fn, scaler, config.DEVICE)
+
+        # get on validation
+        if config.SAVE_MODEL:
+            checkpoint = {
+                "state_dict": model.state_dict(),
+                "optimizer": optimizer.state_dict(),
+            }
+            save_checkpoint(checkpoint, filename=config.CHECKPOINT_FILE)
+
+if __name__ == "__main__":
+    main()

ML/Kaggles/Facial Keypoint Detection Competition/utils.py

@@ -0,0 +1,71 @@
+import torch
+import numpy as np
+import config
+import pandas as pd
+from tqdm import tqdm
+
+
+def get_submission(loader, dataset, model_15, model_4):
+    """
+    This can be done a lot faster.. but it didn't take
+    too much time to do it in this inefficient way
+    """
+    model_15.eval()
+    model_4.eval()
+    id_lookup = pd.read_csv("data/IdLookupTable.csv")
+    predictions = []
+    image_id = 1
+
+    for image, label in tqdm(loader):
+        image = image.to(config.DEVICE)
+        preds_15 = torch.clip(model_15(image).squeeze(0), 0.0, 96.0)
+        preds_4 = torch.clip(model_4(image).squeeze(0), 0.0, 96.0)
+        feature_names = id_lookup.loc[id_lookup["ImageId"] == image_id]["FeatureName"]
+
+        for feature_name in feature_names:
+            feature_index = dataset.category_names.index(feature_name)
+            if feature_names.shape[0] < 10:
+                predictions.append(preds_4[feature_index].item())
+            else:
+                predictions.append(preds_15[feature_index].item())
+
+        image_id += 1
+
+    df = pd.DataFrame({"RowId": np.arange(1, len(predictions)+1), "Location": predictions})
+    df.to_csv("submission.csv", index=False)
+    model_15.train()
+    model_4.train()
+
+
+def get_rmse(loader, model, loss_fn, device):
+    model.eval()
+    num_examples = 0
+    losses = []
+    for batch_idx, (data, targets) in enumerate(loader):
+        data = data.to(device=device)
+        targets = targets.to(device=device)
+
+        # forward
+        scores = model(data)
+        loss = loss_fn(scores[targets != -1], targets[targets != -1])
+        num_examples += scores[targets != -1].shape[0]
+        losses.append(loss.item())
+
+    model.train()
+    print(f"Loss on val: {(sum(losses)/num_examples)**0.5}")
+
+
+def save_checkpoint(state, filename="my_checkpoint.pth.tar"):
+    print("=> Saving checkpoint")
+    torch.save(state, filename)
+
+
+def load_checkpoint(checkpoint, model, optimizer, lr):
+    print("=> Loading checkpoint")
+    model.load_state_dict(checkpoint["state_dict"])
+    optimizer.load_state_dict(checkpoint["optimizer"])
+
+    # If we don't do this then it will just have learning rate of old checkpoint
+    # and it will lead to many hours of debugging \:
+    for param_group in optimizer.param_groups:
+        param_group["lr"] = lr

ML/Pytorch/Basics/Imbalanced_classes/main.py

@@ -0,0 +1,93 @@
+"""
+This code is for dealing with imbalanced datasets in PyTorch. Imbalanced datasets 
+are those where the number of samples in one or more classes is significantly lower 
+than the number of samples in the other classes. This can be a problem because it 
+can lead to a model that is biased towards the more common classes, which can result 
+in poor performance on the less common classes.
+
+To deal with imbalanced datasets, this code implements two methods: oversampling and 
+class weighting.
+
+Oversampling involves generating additional samples for the underrepresented classes, 
+while class weighting involves assigning higher weights to the loss of samples in the 
+underrepresented classes, so that the model pays more attention to them.
+
+In this code, the get_loader function takes a root directory for a dataset and a batch 
+size, and returns a PyTorch data loader. The data loader is used to iterate over the 
+dataset in batches. The get_loader function first applies some transformations to the 
+images in the dataset using the transforms module from torchvision. Then it calculates 
+the class weights based on the number of samples in each class. It then creates a 
+WeightedRandomSampler object, which is used to randomly select a batch of samples with a 
+probability proportional to their weights. Finally, it creates the data loader using the 
+dataset and the weighted random sampler.
+
+The main function then uses the data loader to iterate over the dataset for 10 epochs, 
+and counts the number of samples in each class. Finally, it prints the counts for each class.
+
+Programmed by Aladdin Persson <aladdin.persson at hotmail dot com>
+* 2020-04-08: Initial coding
+* 2021-03-24: Added more detailed comments also removed part of
+              check_accuracy which would only work specifically on MNIST.
+* 2022-12-19: Updated detailed comments, small code revision, checked code still works with latest PyTorch. 
+"""
+
+import torch
+import torchvision.datasets as datasets
+import os
+from torch.utils.data import WeightedRandomSampler, DataLoader
+import torchvision.transforms as transforms
+import torch.nn as nn
+
+# Methods for dealing with imbalanced datasets:
+# 1. Oversampling (probably preferable)
+# 2. Class weighting
+
+
+def get_loader(root_dir, batch_size):
+    my_transforms = transforms.Compose(
+        [
+            transforms.Resize((224, 224)),
+            transforms.ToTensor(),
+        ]
+    )
+
+    dataset = datasets.ImageFolder(root=root_dir, transform=my_transforms)
+    subdirectories = dataset.classes
+    class_weights = []
+
+    # loop through each subdirectory and calculate the class weight
+    # that is 1 / len(files) in that subdirectory
+    for subdir in subdirectories:
+        files = os.listdir(os.path.join(root_dir, subdir))
+        class_weights.append(1 / len(files))
+
+    sample_weights = [0] * len(dataset)
+
+    for idx, (data, label) in enumerate(dataset):
+        class_weight = class_weights[label]
+        sample_weights[idx] = class_weight
+
+    sampler = WeightedRandomSampler(
+        sample_weights, num_samples=len(sample_weights), replacement=True
+    )
+
+    loader = DataLoader(dataset, batch_size=batch_size, sampler=sampler)
+    return loader
+
+
+def main():
+    loader = get_loader(root_dir="dataset", batch_size=8)
+
+    num_retrievers = 0
+    num_elkhounds = 0
+    for epoch in range(10):
+        for data, labels in loader:
+            num_retrievers += torch.sum(labels == 0)
+            num_elkhounds += torch.sum(labels == 1)
+
+    print(num_retrievers.item())
+    print(num_elkhounds.item())
+
+
+if __name__ == "__main__":
+    main()

ML/Pytorch/Basics/albumentations_tutorial/classification.py

@@ -3,6 +3,7 @@ import albumentations as A
 import numpy as np
 from utils import plot_examples
 from PIL import Image
+from tqdm import tqdm
 
 image = Image.open("images/elon.jpeg")
 
@@ -14,18 +15,20 @@ transform = A.Compose(
         A.HorizontalFlip(p=0.5),
         A.VerticalFlip(p=0.1),
         A.RGBShift(r_shift_limit=25, g_shift_limit=25, b_shift_limit=25, p=0.9),
-        A.OneOf([
+        A.OneOf(
-            A.Blur(blur_limit=3, p=0.5),
+            [
-            A.ColorJitter(p=0.5),
+                A.Blur(blur_limit=3, p=0.5),
-        ], p=1.0),
+                A.ColorJitter(p=0.5),
+            ],
+            p=1.0,
+        ),
     ]
 )
 
 images_list = [image]
 image = np.array(image)
-for i in range(15):
+for i in tqdm(range(15)):
     augmentations = transform(image=image)
     augmented_img = augmentations["image"]
     images_list.append(augmented_img)
 plot_examples(images_list)
-

ML/Pytorch/Basics/albumentations_tutorial/full_pytorch_example.py

@@ -8,6 +8,7 @@ from albumentations.pytorch import ToTensorV2
 from torch.utils.data import Dataset
 import os
 
+
 class ImageFolder(Dataset):
     def __init__(self, root_dir, transform=None):
         super(ImageFolder, self).__init__()
@@ -18,7 +19,7 @@ class ImageFolder(Dataset):
 
         for index, name in enumerate(self.class_names):
             files = os.listdir(os.path.join(root_dir, name))
-            self.data += list(zip(files, [index]*len(files)))
+            self.data += list(zip(files, [index] * len(files)))
 
     def __len__(self):
         return len(self.data)
@@ -43,10 +44,13 @@ transform = A.Compose(
         A.HorizontalFlip(p=0.5),
         A.VerticalFlip(p=0.1),
         A.RGBShift(r_shift_limit=25, g_shift_limit=25, b_shift_limit=25, p=0.9),
-        A.OneOf([
+        A.OneOf(
-            A.Blur(blur_limit=3, p=0.5),
+            [
-            A.ColorJitter(p=0.5),
+                A.Blur(blur_limit=3, p=0.5),
-        ], p=1.0),
+                A.ColorJitter(p=0.5),
+            ],
+            p=1.0,
+        ),
         A.Normalize(
             mean=[0, 0, 0],
             std=[1, 1, 1],
@@ -58,5 +62,5 @@ transform = A.Compose(
 
 dataset = ImageFolder(root_dir="cat_dogs", transform=transform)
 
-for x,y in dataset:
+for x, y in dataset:
     print(x.shape)

ML/Pytorch/Basics/albumentations_tutorial/utils.py

@@ -8,7 +8,7 @@ import albumentations as A
 
 def visualize(image):
     plt.figure(figsize=(10, 10))
-    plt.axis('off')
+    plt.axis("off")
     plt.imshow(image)
     plt.show()
 
@@ -22,7 +22,7 @@ def plot_examples(images, bboxes=None):
         if bboxes is not None:
             img = visualize_bbox(images[i - 1], bboxes[i - 1], class_name="Elon")
         else:
-            img = images[i-1]
+            img = images[i - 1]
         fig.add_subplot(rows, columns, i)
         plt.imshow(img)
     plt.show()

ML/Pytorch/Basics/custom_dataset/custom_FCNN.py

@@ -1,131 +0,0 @@
-# Imports
-import os
-from typing import Union
-
-import torch.nn.functional as F  # All functions that don't have any parameters
-import pandas as pd
-import torch
-import torch.nn as nn  # All neural network modules, nn.Linear, nn.Conv2d, BatchNorm, Loss functions
-import torch.optim as optim  # For all Optimization algorithms, SGD, Adam, etc.
-import torchvision
-import torchvision.transforms as transforms  # Transformations we can perform on our dataset
-from pandas import io
-
-# from skimage import io
-from torch.utils.data import (
-    Dataset,
-    DataLoader,
-)  # Gives easier dataset managment and creates mini batches
-import torch.nn as nn  # All neural network modules, nn.Linear, nn.Conv2d, BatchNorm, Loss functions
-
-
-# Create Fully Connected Network
-class NN(nn.Module):
-    def __init__(self, input_size, num_classes):
-        super(NN, self).__init__()
-        self.fc1 = nn.Linear(input_size, 50)
-        self.fc2 = nn.Linear(50, num_classes)
-
-    def forward(self, x):
-        x = F.relu(self.fc1(x))
-        x = self.fc2(x)
-        return x
-
-
-class SoloDataset(Dataset):
-    def __init__(self, csv_file, root_dir, transform=None):
-        self.annotations = pd.read_csv(csv_file)
-        self.root_dir = root_dir
-        self.transform = transform
-
-    def __len__(self):
-        return len(self.annotations)
-
-    def __getitem__(self, index):
-        x_data = self.annotations.iloc[index, 0:11]
-        x_data = torch.tensor(x_data)
-        y_label = torch.tensor(int(self.annotations.iloc[index, 11]))
-
-        return (x_data.float(), y_label)
-
-
-# Set device
-device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
-
-# Hyperparameters
-num_classes = 26
-learning_rate = 1e-3
-batch_size = 5
-num_epochs = 30
-input_size = 11
-
-# Load Data
-dataset = SoloDataset(
-    csv_file="power.csv", root_dir="test123", transform=transforms.ToTensor()
-)
-train_set, test_set = torch.utils.data.random_split(dataset, [2900, 57])
-train_loader = DataLoader(dataset=train_set, batch_size=batch_size, shuffle=True)
-test_loader = DataLoader(dataset=test_set, batch_size=batch_size, shuffle=True)
-
-# Model
-model = NN(input_size=input_size, num_classes=num_classes).to(device)
-
-# Loss and optimizer
-criterion = nn.CrossEntropyLoss()
-optimizer = optim.Adam(model.parameters(), lr=learning_rate)
-
-print(len(train_set))
-print(len(test_set))
-# Train Network
-for epoch in range(num_epochs):
-    losses = []
-
-    for batch_idx, (data, targets) in enumerate(train_loader):
-        # Get data to cuda if possible
-        data = data.to(device=device)
-        targets = targets.to(device=device)
-
-        # forward
-        scores = model(data)
-        loss = criterion(scores, targets)
-
-        losses.append(loss.item())
-
-        # backward
-        optimizer.zero_grad()
-        loss.backward()
-
-        # gradient descent or adam step
-        optimizer.step()
-
-    print(f"Cost at epoch {epoch} is {sum(losses) / len(losses)}")
-
-
-# Check accuracy on training to see how good our model is
-def check_accuracy(loader, model):
-    num_correct = 0
-    num_samples = 0
-    model.eval()
-
-    with torch.no_grad():
-        for x, y in loader:
-            x = x.to(device=device)
-            y = y.to(device=device)
-
-            scores = model(x)
-            _, predictions = scores.max(1)
-            num_correct += (predictions == y).sum()
-            num_samples += predictions.size(0)
-
-        print(
-            f"Got {num_correct} / {num_samples} with accuracy {float(num_correct) / float(num_samples) * 100:.2f}"
-        )
-
-    model.train()
-
-
-print("Checking accuracy on Training Set")
-check_accuracy(train_loader, model)
-
-print("Checking accuracy on Test Set")
-check_accuracy(test_loader, model)

ML/Pytorch/Basics/custom_dataset/custom_dataset.py

@@ -6,7 +6,7 @@ label (0 for cat, 1 for dog).
 
 Programmed by Aladdin Persson <aladdin.persson at hotmail dot com>
 *    2020-04-03 Initial coding
-
+*    2022-12-19 Updated with better comments, improved code using PIL, and checked code still functions as intended.
 """
 
 # Imports
@@ -17,7 +17,7 @@ import torchvision.transforms as transforms  # Transformations we can perform on
 import torchvision
 import os
 import pandas as pd
-from skimage import io
+from PIL import Image
 from torch.utils.data import (
     Dataset,
     DataLoader,
@@ -35,7 +35,7 @@ class CatsAndDogsDataset(Dataset):
 
     def __getitem__(self, index):
         img_path = os.path.join(self.root_dir, self.annotations.iloc[index, 0])
-        image = io.imread(img_path)
+        image = Image.open(img_path)
         y_label = torch.tensor(int(self.annotations.iloc[index, 1]))
 
         if self.transform:
@@ -50,7 +50,7 @@ device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
 # Hyperparameters
 in_channel = 3
 num_classes = 2
-learning_rate = 1e-3
+learning_rate = 3e-4
 batch_size = 32
 num_epochs = 10
 
@@ -69,12 +69,19 @@ train_loader = DataLoader(dataset=train_set, batch_size=batch_size, shuffle=True
 test_loader = DataLoader(dataset=test_set, batch_size=batch_size, shuffle=True)
 
 # Model
-model = torchvision.models.googlenet(pretrained=True)
+model = torchvision.models.googlenet(weights="DEFAULT")
+
+# freeze all layers, change final linear layer with num_classes
+for param in model.parameters():
+    param.requires_grad = False
+
+# final layer is not frozen
+model.fc = nn.Linear(in_features=1024, out_features=num_classes)
 model.to(device)
 
 # Loss and optimizer
 criterion = nn.CrossEntropyLoss()
-optimizer = optim.Adam(model.parameters(), lr=learning_rate)
+optimizer = optim.Adam(model.parameters(), lr=learning_rate, weight_decay=1e-5)
 
 # Train Network
 for epoch in range(num_epochs):

ML/Pytorch/Basics/custom_dataset_txt/get_data.sh

@@ -0,0 +1,3 @@
+#!/bin/sh
+
+wget https://www.kaggle.com/datasets/e1cd22253a9b23b073794872bf565648ddbe4f17e7fa9e74766ad3707141adeb/download?datasetVersionNumber=1

ML/Pytorch/Basics/custom_dataset_txt/loader_customtext.py

@@ -1,3 +1,15 @@
+"""
+Introductory tutorial on how to deal with custom text datasets in PyTorch.
+Note that there are better ways to do this when dealing with huge text datasets.
+But this is a good way of understanding how it works and can be used as a starting 
+point, particularly for smaller/medium datasets.
+
+Programmed by Aladdin Persson <aladdin.persson at hotmail dot com>
+*    2020-04-09 Initial coding
+*    2022-12-19 Updated comments, minor code revision, and checked code still works with latest PyTorch.
+"""
+
+
 import os  # when loading file paths
 import pandas as pd  # for lookup in annotation file
 import spacy  # for tokenizer
@@ -15,8 +27,8 @@ import torchvision.transforms as transforms
 #    of same seq_len and setup dataloader)
 # Note that loading the image is very easy compared to the text!
 
-# Download with: python -m spacy download en
+# Download with: python -m spacy download en_core_web_sm
-spacy_eng = spacy.load("en")
+spacy_eng = spacy.load("en_core_web_sm")
 
 
 class Vocabulary:
@@ -130,7 +142,10 @@ def get_loader(
 
 if __name__ == "__main__":
     transform = transforms.Compose(
-        [transforms.Resize((224, 224)), transforms.ToTensor(),]
+        [
+            transforms.Resize((224, 224)),
+            transforms.ToTensor(),
+        ]
     )
 
     loader, dataset = get_loader(

ML/Pytorch/Basics/lightning_simple_CNN.py

@@ -0,0 +1,190 @@
+"""
+Simple pytorch lightning example
+"""
+
+# Imports
+import torch
+import torch.nn.functional as F  # Parameterless functions, like (some) activation functions
+import torchvision.datasets as datasets  # Standard datasets
+import torchvision.transforms as transforms  # Transformations we can perform on our dataset for augmentation
+from torch import optim  # For optimizers like SGD, Adam, etc.
+from torch import nn  # All neural network modules
+from torch.utils.data import (
+    DataLoader,
+)  # Gives easier dataset managment by creating mini batches etc.
+from tqdm import tqdm  # For nice progress bar!
+import pytorch_lightning as pl
+import torchmetrics
+from pytorch_lightning.callbacks import Callback, EarlyStopping
+
+
+precision = "medium"
+torch.set_float32_matmul_precision(precision)
+criterion = nn.CrossEntropyLoss()
+
+
+## use 20% of training data for validation
+# train_set_size = int(len(train_dataset) * 0.8)
+# valid_set_size = len(train_dataset) - train_set_size
+#
+## split the train set into two
+# seed = torch.Generator().manual_seed(42)
+# train_dataset, val_dataset = torch.utils.data.random_split(
+#    train_dataset, [train_set_size, valid_set_size], generator=seed
+# )
+
+
+class CNNLightning(pl.LightningModule):
+    def __init__(self, lr=3e-4, in_channels=1, num_classes=10):
+        super().__init__()
+        self.lr = lr
+        self.train_acc = torchmetrics.Accuracy(task="multiclass", num_classes=10)
+        self.test_acc = torchmetrics.Accuracy(task="multiclass", num_classes=10)
+        self.conv1 = nn.Conv2d(
+            in_channels=in_channels,
+            out_channels=8,
+            kernel_size=3,
+            stride=1,
+            padding=1,
+        )
+        self.pool = nn.MaxPool2d(kernel_size=2, stride=2)
+        self.conv2 = nn.Conv2d(
+            in_channels=8,
+            out_channels=16,
+            kernel_size=3,
+            stride=1,
+            padding=1,
+        )
+        self.fc1 = nn.Linear(16 * 7 * 7, num_classes)
+        self.lr = lr
+
+    def training_step(self, batch, batch_idx):
+        x, y = batch
+        y_hat = self._common_step(x, batch_idx)
+        loss = criterion(y_hat, y)
+        accuracy = self.train_acc(y_hat, y)
+        self.log(
+            "train_acc_step",
+            self.train_acc,
+            on_step=True,
+            on_epoch=False,
+            prog_bar=True,
+        )
+        return loss
+
+    def training_epoch_end(self, outputs):
+        self.train_acc.reset()
+
+    def test_step(self, batch, batch_idx):
+        x, y = batch
+        y_hat = self._common_step(x, batch_idx)
+        loss = F.cross_entropy(y_hat, y)
+        accuracy = self.test_acc(y_hat, y)
+        self.log("test_loss", loss, on_step=True)
+        self.log("test_acc", accuracy, on_step=True)
+
+    def validation_step(self, batch, batch_idx):
+        x, y = batch
+        y_hat = self._common_step(x, batch_idx)
+        loss = F.cross_entropy(y_hat, y)
+        accuracy = self.test_acc(y_hat, y)
+        self.log("val_loss", loss, on_step=True)
+        self.log("val_acc", accuracy, on_step=True)
+
+    def predict_step(self, batch, batch_idx):
+        x, y = batch
+        y_hat = self._common_step(x)
+        return y_hat
+
+    def _common_step(self, x, batch_idx):
+        x = self.pool(F.relu(self.conv1(x)))
+        x = self.pool(F.relu(self.conv2(x)))
+        x = x.reshape(x.shape[0], -1)
+        y_hat = self.fc1(x)
+        return y_hat
+
+    def configure_optimizers(self):
+        optimizer = optim.Adam(self.parameters(), lr=self.lr)
+        return optimizer
+
+
+class MNISTDataModule(pl.LightningDataModule):
+    def __init__(self, batch_size=512):
+        super().__init__()
+        self.batch_size = batch_size
+
+    def setup(self, stage):
+        mnist_full = train_dataset = datasets.MNIST(
+            root="dataset/", train=True, transform=transforms.ToTensor(), download=True
+        )
+        self.mnist_test = datasets.MNIST(
+            root="dataset/", train=False, transform=transforms.ToTensor(), download=True
+        )
+        self.mnist_train, self.mnist_val = torch.utils.data.random_split(
+            mnist_full, [55000, 5000]
+        )
+
+    def train_dataloader(self):
+        return DataLoader(
+            self.mnist_train,
+            batch_size=self.batch_size,
+            num_workers=6,
+            shuffle=True,
+        )
+
+    def val_dataloader(self):
+        return DataLoader(
+            self.mnist_val, batch_size=self.batch_size, num_workers=2, shuffle=False
+        )
+
+    def test_dataloader(self):
+        return DataLoader(
+            self.mnist_test, batch_size=self.batch_size, num_workers=2, shuffle=False
+        )
+
+
+class MyPrintingCallback(Callback):
+    def on_train_start(self, trainer, pl_module):
+        print("Training is starting")
+
+    def on_train_end(self, trainer, pl_module):
+        print("Training is ending")
+
+
+# Set device
+device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+
+# Load Data
+if __name__ == "__main__":
+    # Initialize network
+    model_lightning = CNNLightning()
+
+    trainer = pl.Trainer(
+        #fast_dev_run=True,
+        # overfit_batches=3,
+        max_epochs=5,
+        precision=16,
+        accelerator="gpu",
+        devices=[0,1],
+        callbacks=[EarlyStopping(monitor="val_loss", mode="min")],
+        auto_lr_find=True,
+        enable_model_summary=True,
+        profiler="simple",
+        strategy="deepspeed_stage_1",
+        # accumulate_grad_batches=2,
+        # auto_scale_batch_size="binsearch",
+        # log_every_n_steps=1,
+    )
+
+    dm = MNISTDataModule()
+
+    # trainer tune first to find best batch size and lr
+    trainer.tune(model_lightning, dm)
+
+    trainer.fit(
+        model=model_lightning,
+        datamodule=dm,
+    )
+
+    # test model on test loader from LightningDataModule
+    trainer.test(model=model_lightning, datamodule=dm)

ML/Pytorch/Basics/pytorch_bidirectional_lstm.py

@@ -1,15 +1,17 @@
 """
 Example code of a simple bidirectional LSTM on the MNIST dataset.
+Note that using RNNs on image data is not the best idea, but it is a 
+good example to show how to use RNNs that still generalizes to other tasks.
 
 Programmed by Aladdin Persson <aladdin.persson at hotmail dot com>
 *    2020-05-09 Initial coding
+*    2022-12-16 Updated with more detailed comments, docstrings to functions, and checked code still functions as intended.
 
 """
 
 
 # Imports
 import torch
-import torchvision
 import torch.nn as nn  # All neural network modules, nn.Linear, nn.Conv2d, BatchNorm, Loss functions
 import torch.optim as optim  # For all Optimization algorithms, SGD, Adam, etc.
 import torch.nn.functional as F  # All functions that don't have any parameters
@@ -18,9 +20,10 @@ from torch.utils.data import (
 )  # Gives easier dataset managment and creates mini batches
 import torchvision.datasets as datasets  # Has standard datasets we can import in a nice way
 import torchvision.transforms as transforms  # Transformations we can perform on our dataset
+from tqdm import tqdm  # progress bar
 
 # Set device
-device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+device = "cuda" if torch.cuda.is_available() else "cpu"
 
 # Hyperparameters
 input_size = 28
@@ -28,7 +31,7 @@ sequence_length = 28
 num_layers = 2
 hidden_size = 256
 num_classes = 10
-learning_rate = 0.001
+learning_rate = 3e-4
 batch_size = 64
 num_epochs = 2
 
@@ -47,7 +50,7 @@ class BRNN(nn.Module):
         h0 = torch.zeros(self.num_layers * 2, x.size(0), self.hidden_size).to(device)
         c0 = torch.zeros(self.num_layers * 2, x.size(0), self.hidden_size).to(device)
 
-        out, _ = self.lstm(x, (h0, c0))
+        out, _ = self.lstm(x)
         out = self.fc(out[:, -1, :])
 
         return out
@@ -74,7 +77,7 @@ optimizer = optim.Adam(model.parameters(), lr=learning_rate)
 
 # Train Network
 for epoch in range(num_epochs):
-    for batch_idx, (data, targets) in enumerate(train_loader):
+    for batch_idx, (data, targets) in enumerate(tqdm(train_loader)):
         # Get data to cuda if possible
         data = data.to(device=device).squeeze(1)
         targets = targets.to(device=device)
@@ -90,9 +93,8 @@ for epoch in range(num_epochs):
         # gradient descent or adam step
         optimizer.step()
 
+
 # Check accuracy on training & test to see how good our model
-
-
 def check_accuracy(loader, model):
     if loader.dataset.train:
         print("Checking accuracy on training data")

ML/Pytorch/Basics/pytorch_init_weights.py

@@ -1,12 +1,16 @@
 """
 Example code of how to initialize weights for a simple CNN network.
+Usually this is not needed as default initialization is usually good,
+but sometimes it can be useful to initialize weights in a specific way.
+This way of doing it should generalize to other network types just make 
+sure to specify and change the modules you wish to modify.
 
 Video explanation: https://youtu.be/xWQ-p_o0Uik
 Got any questions leave a comment on youtube :)
 
 Programmed by Aladdin Persson <aladdin.persson at hotmail dot com>
 *    2020-04-10 Initial coding
-
+*    2022-12-16 Updated with more detailed comments, and checked code still functions as intended.
 """
 
 # Imports
@@ -20,17 +24,17 @@ class CNN(nn.Module):
         self.conv1 = nn.Conv2d(
             in_channels=in_channels,
             out_channels=6,
-            kernel_size=(3, 3),
+            kernel_size=3,
-            stride=(1, 1),
+            stride=1,
-            padding=(1, 1),
+            padding=1,
         )
         self.pool = nn.MaxPool2d(kernel_size=(2, 2), stride=(2, 2))
         self.conv2 = nn.Conv2d(
             in_channels=6,
             out_channels=16,
-            kernel_size=(3, 3),
+            kernel_size=3,
-            stride=(1, 1),
+            stride=1,
-            padding=(1, 1),
+            padding=1,
         )
         self.fc1 = nn.Linear(16 * 7 * 7, num_classes)
         self.initialize_weights()

ML/Pytorch/Basics/pytorch_loadsave.py

@@ -9,7 +9,8 @@ Video explanation of code & how to save and load model: https://youtu.be/g6kQl_E
 Got any questions leave a comment on youtube :)
 
 Coded by Aladdin Persson <aladdin dot person at hotmail dot com>
--   2020-04-07 Initial programming
+*   2020-04-07 Initial programming
+*   2022-12-16 Updated with more detailed comments, and checked code still functions as intended.
 
 """
 
@@ -39,7 +40,9 @@ def load_checkpoint(checkpoint, model, optimizer):
 
 def main():
     # Initialize network
-    model = torchvision.models.vgg16(pretrained=False)
+    model = torchvision.models.vgg16(
+        weights=None
+    )  # pretrained=False deprecated, use weights instead
     optimizer = optim.Adam(model.parameters())
 
     checkpoint = {"state_dict": model.state_dict(), "optimizer": optimizer.state_dict()}

ML/Pytorch/Basics/pytorch_lr_ratescheduler.py

@@ -3,13 +3,12 @@ Example code of how to use a learning rate scheduler simple, in this
 case with a (very) small and simple Feedforward Network training on MNIST
 dataset with a learning rate scheduler. In this case ReduceLROnPlateau
 scheduler is used, but can easily be changed to any of the other schedulers
-available.
+available. I think simply reducing LR by 1/10 or so, when loss plateaus is 
-
+a good default. 
-Video explanation: https://youtu.be/P31hB37g4Ak
-Got any questions leave a comment on youtube :)
 
 Programmed by Aladdin Persson <aladdin.persson at hotmail dot com>
 *    2020-04-10 Initial programming
+*    2022-12-19 Updated comments, made sure it works with latest PyTorch
 
 """
 
@@ -28,7 +27,9 @@ device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
 
 # Hyperparameters
 num_classes = 10
-learning_rate = 0.1
+learning_rate = (
+    0.1  # way too high learning rate, but we want to see the scheduler in action
+)
 batch_size = 128
 num_epochs = 100
 
@@ -47,7 +48,7 @@ optimizer = optim.Adam(model.parameters(), lr=learning_rate)
 
 # Define Scheduler
 scheduler = torch.optim.lr_scheduler.ReduceLROnPlateau(
-    optimizer, factor=0.1, patience=5, verbose=True
+    optimizer, factor=0.1, patience=10, verbose=True
 )
 
 # Train Network
@@ -67,19 +68,19 @@ for epoch in range(1, num_epochs):
         losses.append(loss.item())
 
         # backward
-        loss.backward()
-
-        # gradient descent or adam step
-        # scheduler.step(loss)
-        optimizer.step()
         optimizer.zero_grad()
+        loss.backward()
+        optimizer.step()
 
     mean_loss = sum(losses) / len(losses)
+    mean_loss = round(mean_loss, 2)  # we should see difference in loss at 2 decimals
 
     # After each epoch do scheduler.step, note in this scheduler we need to send
-    # in loss for that epoch!
+    # in loss for that epoch! This can also be set using validation loss, and also
+    # in the forward loop we can do on our batch but then we might need to modify
+    # the patience parameter
     scheduler.step(mean_loss)
-    print(f"Cost at epoch {epoch} is {mean_loss}")
+    print(f"Average loss for epoch {epoch} was {mean_loss}")
 
 # Check accuracy on training & test to see how good our model
 def check_accuracy(loader, model):
@@ -90,6 +91,7 @@ def check_accuracy(loader, model):
     with torch.no_grad():
         for x, y in loader:
             x = x.to(device=device)
+            x = x.reshape(x.shape[0], -1)
             y = y.to(device=device)
 
             scores = model(x)

ML/Pytorch/Basics/pytorch_mixed_precision_example.py

@@ -1,9 +1,23 @@
+"""
+Example code of how to use mixed precision training with PyTorch. In this
+case with a (very) small and simple CNN training on MNIST dataset. This
+example is based on the official PyTorch documentation on mixed precision 
+training.
+
+Programmed by Aladdin Persson <aladdin.persson at hotmail dot com>
+*    2020-04-10 Initial programming
+*    2022-12-19 Updated comments, made sure it works with latest PyTorch
+
+"""
+
 # Imports
 import torch
 import torch.nn as nn  # All neural network modules, nn.Linear, nn.Conv2d, BatchNorm, Loss functions
 import torch.optim as optim  # For all Optimization algorithms, SGD, Adam, etc.
 import torch.nn.functional as F  # All functions that don't have any parameters
-from torch.utils.data import DataLoader  # Gives easier dataset managment and creates mini batches
+from torch.utils.data import (
+    DataLoader,
+)  # Gives easier dataset managment and creates mini batches
 import torchvision.datasets as datasets  # Has standard datasets we can import in a nice way
 import torchvision.transforms as transforms  # Transformations we can perform on our dataset
 
@@ -12,9 +26,21 @@ import torchvision.transforms as transforms  # Transformations we can perform on
 class CNN(nn.Module):
     def __init__(self, in_channels=1, num_classes=10):
         super(CNN, self).__init__()
-        self.conv1 = nn.Conv2d(in_channels=1, out_channels=420, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))
+        self.conv1 = nn.Conv2d(
+            in_channels=1,
+            out_channels=420,
+            kernel_size=(3, 3),
+            stride=(1, 1),
+            padding=(1, 1),
+        )
         self.pool = nn.MaxPool2d(kernel_size=(2, 2), stride=(2, 2))
-        self.conv2 = nn.Conv2d(in_channels=420, out_channels=1000, kernel_size=(3, 3), stride=(1, 1), padding=(1, 1))
+        self.conv2 = nn.Conv2d(
+            in_channels=420,
+            out_channels=1000,
+            kernel_size=(3, 3),
+            stride=(1, 1),
+            padding=(1, 1),
+        )
         self.fc1 = nn.Linear(1000 * 7 * 7, num_classes)
 
     def forward(self, x):
@@ -29,19 +55,24 @@ class CNN(nn.Module):
 
 
 # Set device
-device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')
+device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+assert device == "cuda", "GPU not available"
 
 # Hyperparameters
 in_channel = 1
 num_classes = 10
-learning_rate = 0.001
+learning_rate = 3e-4
 batch_size = 100
 num_epochs = 5
 
 # Load Data
-train_dataset = datasets.MNIST(root='dataset/', train=True, transform=transforms.ToTensor(), download=True)
+train_dataset = datasets.MNIST(
+    root="dataset/", train=True, transform=transforms.ToTensor(), download=True
+)
 train_loader = DataLoader(dataset=train_dataset, batch_size=batch_size, shuffle=True)
-test_dataset = datasets.MNIST(root='dataset/', train=False, transform=transforms.ToTensor(), download=True)
+test_dataset = datasets.MNIST(
+    root="dataset/", train=False, transform=transforms.ToTensor(), download=True
+)
 test_loader = DataLoader(dataset=test_dataset, batch_size=batch_size, shuffle=True)
 
 # Initialize network
@@ -74,7 +105,6 @@ for epoch in range(num_epochs):
 
 
 # Check accuracy on training & test to see how good our model
-
 def check_accuracy(loader, model):
     num_correct = 0
     num_samples = 0
@@ -90,10 +120,12 @@ def check_accuracy(loader, model):
             num_correct += (predictions == y).sum()
             num_samples += predictions.size(0)
 
-        print(f'Got {num_correct} / {num_samples} with accuracy {float(num_correct) / float(num_samples) * 100:.2f}')
+        print(
+            f"Got {num_correct} / {num_samples} with accuracy {float(num_correct) / float(num_samples) * 100:.2f}"
+        )
 
     model.train()
 
 
 check_accuracy(train_loader, model)
-check_accuracy(test_loader, model)
+check_accuracy(test_loader, model)

ML/Pytorch/Basics/pytorch_pretrain_finetune.py

@@ -3,11 +3,9 @@ Shows a small example of how to load a pretrain model (VGG16) from PyTorch,
 and modifies this to train on the CIFAR10 dataset. The same method generalizes
 well to other datasets, but the modifications to the network may need to be changed.
 
-Video explanation: https://youtu.be/U4bHxEhMGNk
-Got any questions leave a comment on youtube :)
-
 Programmed by Aladdin Persson <aladdin.persson at hotmail dot com>
 *    2020-04-08 Initial coding
+*    2022-12-19 Updated comments, minor code changes, made sure it works with latest PyTorch
 
 """
 
@@ -22,8 +20,8 @@ from torch.utils.data import (
 )  # Gives easier dataset managment and creates mini batches
 import torchvision.datasets as datasets  # Has standard datasets we can import in a nice way
 import torchvision.transforms as transforms  # Transformations we can perform on our dataset
+from tqdm import tqdm
 
-# Set device
 device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
 
 # Hyperparameters
@@ -32,17 +30,8 @@ learning_rate = 1e-3
 batch_size = 1024
 num_epochs = 5
 
-# Simple Identity class that let's input pass without changes
-class Identity(nn.Module):
-    def __init__(self):
-        super(Identity, self).__init__()
-
-    def forward(self, x):
-        return x
-
-
 # Load pretrain model & modify it
-model = torchvision.models.vgg16(pretrained=True)
+model = torchvision.models.vgg16(weights="DEFAULT")
 
 # If you want to do finetuning then set requires_grad = False
 # Remove these two lines if you want to train entire model,
@@ -50,7 +39,7 @@ model = torchvision.models.vgg16(pretrained=True)
 for param in model.parameters():
     param.requires_grad = False
 
-model.avgpool = Identity()
+model.avgpool = nn.Identity()
 model.classifier = nn.Sequential(
     nn.Linear(512, 100), nn.ReLU(), nn.Linear(100, num_classes)
 )
@@ -71,7 +60,7 @@ optimizer = optim.Adam(model.parameters(), lr=learning_rate)
 for epoch in range(num_epochs):
     losses = []
 
-    for batch_idx, (data, targets) in enumerate(train_loader):
+    for batch_idx, (data, targets) in enumerate(tqdm(train_loader)):
         # Get data to cuda if possible
         data = data.to(device=device)
         targets = targets.to(device=device)

ML/Pytorch/Basics/pytorch_progress_bar.py

@@ -1,11 +1,18 @@
+"""
+Example code of how to set progress bar using tqdm that is very efficient and nicely looking.
+
+Programmed by Aladdin Persson <aladdin.persson at hotmail dot com>
+*    2020-05-09 Initial coding
+*    2022-12-19 Updated with more detailed comments, and checked code works with latest PyTorch.
+
+"""
+
 import torch
 import torch.nn as nn
 from tqdm import tqdm
 from torch.utils.data import TensorDataset, DataLoader
 
-# Create a simple toy dataset example, normally this
+# Create a simple toy dataset
-# would be doing custom class with __getitem__ etc,
-# which we have done in custom dataset tutorials
 x = torch.randn((1000, 3, 224, 224))
 y = torch.randint(low=0, high=10, size=(1000, 1))
 ds = TensorDataset(x, y)
@@ -13,12 +20,12 @@ loader = DataLoader(ds, batch_size=8)
 
 
 model = nn.Sequential(
-    nn.Conv2d(3, 10, kernel_size=3, padding=1, stride=1),
+    nn.Conv2d(in_channels=3, out_channels=10, kernel_size=3, padding=1, stride=1),
     nn.Flatten(),
-    nn.Linear(10*224*224, 10),
+    nn.Linear(10 * 224 * 224, 10),
 )
 
-NUM_EPOCHS = 100
+NUM_EPOCHS = 10
 for epoch in range(NUM_EPOCHS):
     loop = tqdm(loader)
     for idx, (x, y) in enumerate(loop):
@@ -35,7 +42,3 @@ for epoch in range(NUM_EPOCHS):
         loop.set_postfix(loss=torch.rand(1).item(), acc=torch.rand(1).item())
 
 # There you go. Hope it was useful :)
-
-
-
-

ML/Pytorch/Basics/pytorch_rnn_gru_lstm.py

@@ -3,23 +3,24 @@ Example code of a simple RNN, GRU, LSTM on the MNIST dataset.
 
 Programmed by Aladdin Persson <aladdin.persson at hotmail dot com>
 *    2020-05-09 Initial coding
+*    2022-12-16 Updated with more detailed comments, docstrings to functions, and checked code still functions as intended.
 
 """
 
 # Imports
 import torch
-import torchvision
+import torch.nn.functional as F  # Parameterless functions, like (some) activation functions
-import torch.nn as nn  # All neural network modules, nn.Linear, nn.Conv2d, BatchNorm, Loss functions
+import torchvision.datasets as datasets  # Standard datasets
-import torch.optim as optim  # For all Optimization algorithms, SGD, Adam, etc.
+import torchvision.transforms as transforms  # Transformations we can perform on our dataset for augmentation
-import torch.nn.functional as F  # All functions that don't have any parameters
+from torch import optim  # For optimizers like SGD, Adam, etc.
+from torch import nn  # All neural network modules
 from torch.utils.data import (
     DataLoader,
-)  # Gives easier dataset managment and creates mini batches
+)  # Gives easier dataset managment by creating mini batches etc.
-import torchvision.datasets as datasets  # Has standard datasets we can import in a nice way
+from tqdm import tqdm  # For a nice progress bar!
-import torchvision.transforms as transforms  # Transformations we can perform on our dataset
 
 # Set device
-device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
+device = "cuda" if torch.cuda.is_available() else "cpu"
 
 # Hyperparameters
 input_size = 28
@@ -29,7 +30,7 @@ num_classes = 10
 sequence_length = 28
 learning_rate = 0.005
 batch_size = 64
-num_epochs = 2
+num_epochs = 3
 
 # Recurrent neural network (many-to-one)
 class RNN(nn.Module):
@@ -104,15 +105,13 @@ class RNN_LSTM(nn.Module):
 train_dataset = datasets.MNIST(
     root="dataset/", train=True, transform=transforms.ToTensor(), download=True
 )
-
 test_dataset = datasets.MNIST(
     root="dataset/", train=False, transform=transforms.ToTensor(), download=True
 )
-
 train_loader = DataLoader(dataset=train_dataset, batch_size=batch_size, shuffle=True)
 test_loader = DataLoader(dataset=test_dataset, batch_size=batch_size, shuffle=True)
 
-# Initialize network
+# Initialize network (try out just using simple RNN, or GRU, and then compare with LSTM)
 model = RNN_LSTM(input_size, hidden_size, num_layers, num_classes).to(device)
 
 # Loss and optimizer
@@ -121,7 +120,7 @@ optimizer = optim.Adam(model.parameters(), lr=learning_rate)
 
 # Train Network
 for epoch in range(num_epochs):
-    for batch_idx, (data, targets) in enumerate(train_loader):
+    for batch_idx, (data, targets) in enumerate(tqdm(train_loader)):
         # Get data to cuda if possible
         data = data.to(device=device).squeeze(1)
         targets = targets.to(device=device)
@@ -134,16 +133,11 @@ for epoch in range(num_epochs):
         optimizer.zero_grad()
         loss.backward()
 
-        # gradient descent or adam step
+        # gradient descent update step/adam step
         optimizer.step()
 
 # Check accuracy on training & test to see how good our model
 def check_accuracy(loader, model):
-    if loader.dataset.train:
-        print("Checking accuracy on training data")
-    else:
-        print("Checking accuracy on test data")
-
     num_correct = 0
     num_samples = 0
 
@@ -160,13 +154,10 @@ def check_accuracy(loader, model):
             num_correct += (predictions == y).sum()
             num_samples += predictions.size(0)
 
-        print(
+    # Toggle model back to train
-            f"Got {num_correct} / {num_samples} with \
-              accuracy {float(num_correct)/float(num_samples)*100:.2f}"
-        )
-    # Set model back to train
     model.train()
+    return num_correct / num_samples
 
 
-check_accuracy(train_loader, model)
+print(f"Accuracy on training set: {check_accuracy(train_loader, model)*100:2f}")
-check_accuracy(test_loader, model)
+print(f"Accuracy on test set: {check_accuracy(test_loader, model)*100:.2f}")

ML/Pytorch/Basics/pytorch_simple_CNN.py

@@ -1,46 +1,47 @@
 """
-Example code of a simple CNN network training on MNIST dataset.
+A simple walkthrough of how to code a convolutional neural network (CNN)
-The code is intended to show how to create a CNN network as well
+using the PyTorch library. For demonstration we train it on the very
-as how to initialize loss, optimizer, etc. in a simple way to get
+common MNIST dataset of handwritten digits. In this code we go through
-training to work with function that checks accuracy as well.
+how to create the network as well as initialize a loss function, optimizer,
+check accuracy and more.
 
-Video explanation: https://youtu.be/wnK3uWv_WkU
+Programmed by Aladdin Persson
-Got any questions leave a comment on youtube :)
+* 2020-04-08: Initial coding
-
+* 2021-03-24: More detailed comments and small revision of the code
-Programmed by Aladdin Persson <aladdin.persson at hotmail dot com>
+* 2022-12-19: Small revision of code, checked that it works with latest PyTorch version
-*    2020-04-08 Initial coding
 
 """
 
 # Imports
 import torch
-import torch.nn as nn  # All neural network modules, nn.Linear, nn.Conv2d, BatchNorm, Loss functions
+import torch.nn.functional as F  # Parameterless functions, like (some) activation functions
-import torch.optim as optim  # For all Optimization algorithms, SGD, Adam, etc.
+import torchvision.datasets as datasets  # Standard datasets
-import torch.nn.functional as F  # All functions that don't have any parameters
+import torchvision.transforms as transforms  # Transformations we can perform on our dataset for augmentation
+from torch import optim  # For optimizers like SGD, Adam, etc.
+from torch import nn  # All neural network modules
 from torch.utils.data import (
     DataLoader,
-)  # Gives easier dataset managment and creates mini batches
+)  # Gives easier dataset managment by creating mini batches etc.
-import torchvision.datasets as datasets  # Has standard datasets we can import in a nice way
+from tqdm import tqdm  # For nice progress bar!
-import torchvision.transforms as transforms  # Transformations we can perform on our dataset
 
 # Simple CNN
 class CNN(nn.Module):
     def __init__(self, in_channels=1, num_classes=10):
         super(CNN, self).__init__()
         self.conv1 = nn.Conv2d(
-            in_channels=1,
+            in_channels=in_channels,
             out_channels=8,
-            kernel_size=(3, 3),
+            kernel_size=3,
-            stride=(1, 1),
+            stride=1,
-            padding=(1, 1),
+            padding=1,
         )
-        self.pool = nn.MaxPool2d(kernel_size=(2, 2), stride=(2, 2))
+        self.pool = nn.MaxPool2d(kernel_size=2, stride=2)
         self.conv2 = nn.Conv2d(
             in_channels=8,
             out_channels=16,
-            kernel_size=(3, 3),
+            kernel_size=3,
-            stride=(1, 1),
+            stride=1,
-            padding=(1, 1),
+            padding=1,
         )
         self.fc1 = nn.Linear(16 * 7 * 7, num_classes)
 
@@ -51,7 +52,6 @@ class CNN(nn.Module):
         x = self.pool(x)
         x = x.reshape(x.shape[0], -1)
         x = self.fc1(x)
-
         return x
 
 
@@ -59,24 +59,24 @@ class CNN(nn.Module):
 device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
 
 # Hyperparameters
-in_channel = 1
+in_channels = 1
 num_classes = 10
-learning_rate = 0.001
+learning_rate = 3e-4 # karpathy's constant
 batch_size = 64
-num_epochs = 5
+num_epochs = 3
 
 # Load Data
 train_dataset = datasets.MNIST(
     root="dataset/", train=True, transform=transforms.ToTensor(), download=True
 )
-train_loader = DataLoader(dataset=train_dataset, batch_size=batch_size, shuffle=True)
 test_dataset = datasets.MNIST(
     root="dataset/", train=False, transform=transforms.ToTensor(), download=True
 )
+train_loader = DataLoader(dataset=train_dataset, batch_size=batch_size, shuffle=True)
 test_loader = DataLoader(dataset=test_dataset, batch_size=batch_size, shuffle=True)
 
 # Initialize network
-model = CNN().to(device)
+model = CNN(in_channels=in_channels, num_classes=num_classes).to(device)
 
 # Loss and optimizer
 criterion = nn.CrossEntropyLoss()
@@ -84,7 +84,7 @@ optimizer = optim.Adam(model.parameters(), lr=learning_rate)
 
 # Train Network
 for epoch in range(num_epochs):
-    for batch_idx, (data, targets) in enumerate(train_loader):
+    for batch_idx, (data, targets) in enumerate(tqdm(train_loader)):
         # Get data to cuda if possible
         data = data.to(device=device)
         targets = targets.to(device=device)
@@ -101,14 +101,7 @@ for epoch in range(num_epochs):
         optimizer.step()
 
 # Check accuracy on training & test to see how good our model
-
-
 def check_accuracy(loader, model):
-    if loader.dataset.train:
-        print("Checking accuracy on training data")
-    else:
-        print("Checking accuracy on test data")
-
     num_correct = 0
     num_samples = 0
     model.eval()
@@ -123,12 +116,9 @@ def check_accuracy(loader, model):
             num_correct += (predictions == y).sum()
             num_samples += predictions.size(0)
 
-        print(
-            f"Got {num_correct} / {num_samples} with accuracy {float(num_correct)/float(num_samples)*100:.2f}"
-        )
-
     model.train()
+    return num_correct / num_samples
 
 
-check_accuracy(train_loader, model)
+print(f"Accuracy on training set: {check_accuracy(train_loader, model)*100:.2f}")
-check_accuracy(test_loader, model)
+print(f"Accuracy on test set: {check_accuracy(test_loader, model)*100:.2f}")

ML/Pytorch/Basics/pytorch_simple_fullynet.py

@@ -1,43 +1,70 @@
 """
-Working code of a simple Fully Connected (FC) network training on MNIST dataset.
+A simple walkthrough of how to code a fully connected neural network
-The code is intended to show how to create a FC network as well
+using the PyTorch library. For demonstration we train it on the very
-as how to initialize loss, optimizer, etc. in a simple way to get
+common MNIST dataset of handwritten digits. In this code we go through
-training to work with function that checks accuracy as well.
+how to create the network as well as initialize a loss function, optimizer,
-
+check accuracy and more.
-Video explanation: https://youtu.be/Jy4wM2X21u0
-Got any questions leave a comment on youtube :)
-
-Programmed by Aladdin Persson <aladdin.persson at hotmail dot com>
-*    2020-04-08 Initial coding
 
+Programmed by Aladdin Persson
+* 2020-04-08: Initial coding
+* 2021-03-24: Added more detailed comments also removed part of
+              check_accuracy which would only work specifically on MNIST.
+* 2022-09-23: Updated with more detailed comments, docstrings to functions, and checked code still functions as intended.
 """
 
 # Imports
 import torch
-import torchvision
+import torch.nn.functional as F  # Parameterless functions, like (some) activation functions
-import torch.nn as nn  # All neural network modules, nn.Linear, nn.Conv2d, BatchNorm, Loss functions
+import torchvision.datasets as datasets  # Standard datasets
-import torch.optim as optim  # For all Optimization algorithms, SGD, Adam, etc.
+import torchvision.transforms as transforms  # Transformations we can perform on our dataset for augmentation
-import torch.nn.functional as F  # All functions that don't have any parameters
+from torch import optim  # For optimizers like SGD, Adam, etc.
+from torch import nn  # All neural network modules
 from torch.utils.data import (
     DataLoader,
-)  # Gives easier dataset managment and creates mini batches
+)  # Gives easier dataset managment by creating mini batches etc.
-import torchvision.datasets as datasets  # Has standard datasets we can import in a nice way
+from tqdm import tqdm  # For nice progress bar!
-import torchvision.transforms as transforms  # Transformations we can perform on our dataset
 
-# Create Fully Connected Network
+# Here we create our simple neural network. For more details here we are subclassing and
+# inheriting from nn.Module, this is the most general way to create your networks and
+# allows for more flexibility. I encourage you to also check out nn.Sequential which
+# would be easier to use in this scenario but I wanted to show you something that
+# "always" works and is a general approach.
 class NN(nn.Module):
     def __init__(self, input_size, num_classes):
+        """
+        Here we define the layers of the network. We create two fully connected layers
+
+        Parameters:
+            input_size: the size of the input, in this case 784 (28x28)
+            num_classes: the number of classes we want to predict, in this case 10 (0-9)
+
+        """
         super(NN, self).__init__()
+        # Our first linear layer take input_size, in this case 784 nodes to 50
+        # and our second linear layer takes 50 to the num_classes we have, in
+        # this case 10.
         self.fc1 = nn.Linear(input_size, 50)
         self.fc2 = nn.Linear(50, num_classes)
 
     def forward(self, x):
+        """
+        x here is the mnist images and we run it through fc1, fc2 that we created above.
+        we also add a ReLU activation function in between and for that (since it has no parameters)
+        I recommend using nn.functional (F)
+
+        Parameters:
+            x: mnist images
+
+        Returns:
+            out: the output of the network
+        """
+
         x = F.relu(self.fc1(x))
         x = self.fc2(x)
         return x
 
 
-# Set device
+# Set device cuda for GPU if it's available otherwise run on the CPU
 device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
 
 # Hyperparameters
@@ -45,16 +72,16 @@ input_size = 784
 num_classes = 10
 learning_rate = 0.001
 batch_size = 64
-num_epochs = 1
+num_epochs = 3
 
 # Load Data
 train_dataset = datasets.MNIST(
     root="dataset/", train=True, transform=transforms.ToTensor(), download=True
 )
-train_loader = DataLoader(dataset=train_dataset, batch_size=batch_size, shuffle=True)
 test_dataset = datasets.MNIST(
     root="dataset/", train=False, transform=transforms.ToTensor(), download=True
 )
+train_loader = DataLoader(dataset=train_dataset, batch_size=batch_size, shuffle=True)
 test_loader = DataLoader(dataset=test_dataset, batch_size=batch_size, shuffle=True)
 
 # Initialize network
@@ -66,7 +93,7 @@ optimizer = optim.Adam(model.parameters(), lr=learning_rate)
 
 # Train Network
 for epoch in range(num_epochs):
-    for batch_idx, (data, targets) in enumerate(train_loader):
+    for batch_idx, (data, targets) in enumerate(tqdm(train_loader)):
         # Get data to cuda if possible
         data = data.to(device=device)
         targets = targets.to(device=device)
@@ -74,47 +101,64 @@ for epoch in range(num_epochs):
         # Get to correct shape
         data = data.reshape(data.shape[0], -1)
 
-        # forward
+        # Forward
         scores = model(data)
         loss = criterion(scores, targets)
 
-        # backward
+        # Backward
         optimizer.zero_grad()
         loss.backward()
 
-        # gradient descent or adam step
+        # Gradient descent or adam step
         optimizer.step()
 
+
 # Check accuracy on training & test to see how good our model
-
-
 def check_accuracy(loader, model):
-    if loader.dataset.train:
+    """
-        print("Checking accuracy on training data")
+    Check accuracy of our trained model given a loader and a model
-    else:
+
-        print("Checking accuracy on test data")
+    Parameters:
+        loader: torch.utils.data.DataLoader
+            A loader for the dataset you want to check accuracy on
+        model: nn.Module
+            The model you want to check accuracy on
+
+    Returns:
+        acc: float
+            The accuracy of the model on the dataset given by the loader
+    """
 
     num_correct = 0
     num_samples = 0
     model.eval()
 
+    # We don't need to keep track of gradients here so we wrap it in torch.no_grad()
     with torch.no_grad():
+        # Loop through the data
         for x, y in loader:
+
+            # Move data to device
             x = x.to(device=device)
             y = y.to(device=device)
+
+            # Get to correct shape
             x = x.reshape(x.shape[0], -1)
 
+            # Forward pass
             scores = model(x)
             _, predictions = scores.max(1)
+
+            # Check how many we got correct
             num_correct += (predictions == y).sum()
+
+            # Keep track of number of samples
             num_samples += predictions.size(0)
 
-        print(
-            f"Got {num_correct} / {num_samples} with accuracy {float(num_correct)/float(num_samples)*100:.2f}"
-        )
-
     model.train()
+    return num_correct / num_samples
 
 
-check_accuracy(train_loader, model)
+# Check accuracy on training & test to see how good our model
-check_accuracy(test_loader, model)
+print(f"Accuracy on training set: {check_accuracy(train_loader, model)*100:.2f}")
+print(f"Accuracy on test set: {check_accuracy(test_loader, model)*100:.2f}")

ML/Pytorch/Basics/pytorch_std_mean.py

@@ -1,3 +1,13 @@
+"""
+Code for calculating the mean and standard deviation of a dataset.
+This is useful for normalizing the dataset to obtain mean 0, std 1. 
+
+Programmed by Aladdin Persson <aladdin.persson at hotmail dot com>
+*    2020-05-09 Initial coding
+*    2022-12-16 Updated comments, code revision, and checked code still works with latest PyTorch.
+
+"""
+
 import torch
 import torchvision.transforms as transforms
 from torch.utils.data import DataLoader
@@ -5,20 +15,23 @@ import torchvision.datasets as datasets
 from tqdm import tqdm
 
 device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
-train_set = datasets.CIFAR10(root="ds/", transform=transforms.ToTensor(), download=True)
+train_set = datasets.CIFAR10(
+    root="dataset/", transform=transforms.ToTensor(), download=True
+)
 train_loader = DataLoader(dataset=train_set, batch_size=64, shuffle=True)
 
+
 def get_mean_std(loader):
     # var[X] = E[X**2] - E[X]**2
     channels_sum, channels_sqrd_sum, num_batches = 0, 0, 0
 
     for data, _ in tqdm(loader):
         channels_sum += torch.mean(data, dim=[0, 2, 3])
-        channels_sqrd_sum += torch.mean(data ** 2, dim=[0, 2, 3])
+        channels_sqrd_sum += torch.mean(data**2, dim=[0, 2, 3])
         num_batches += 1
 
     mean = channels_sum / num_batches
-    std = (channels_sqrd_sum / num_batches - mean ** 2) ** 0.5
+    std = (channels_sqrd_sum / num_batches - mean**2) ** 0.5
 
     return mean, std
 

ML/Pytorch/Basics/pytorch_tensorbasics.py

@@ -11,9 +11,13 @@ But also other things such as setting the device (GPU/CPU) and converting
 between different types (int, float etc) and how to convert a tensor to an
 numpy array and vice-versa.
 
+Programmed by Aladdin Persson
+* 2020-06-27: Initial coding
+* 2022-12-19: Small revision of code, checked that it works with latest PyTorch version
 """
 
 import torch
+import numpy as np
 
 # ================================================================= #
 #                        Initializing Tensor                        #
@@ -74,8 +78,6 @@ print(
 print(f"Converted float64 {tensor.double()}")  # Converted to float64
 
 # Array to Tensor conversion and vice-versa
-import numpy as np
-
 np_array = np.zeros((5, 5))
 tensor = torch.from_numpy(np_array)
 np_array_again = (
@@ -109,7 +111,7 @@ t += x  # Also inplace: t = t + x is not inplace, bit confusing.
 
 # -- Exponentiation (Element wise if vector or matrices) --
 z = x.pow(2)  # z = [1, 4, 9]
-z = x ** 2  # z = [1, 4, 9]
+z = x**2  # z = [1, 4, 9]
 
 
 # -- Simple Comparison --
@@ -150,7 +152,7 @@ z = (
     x1 - x2
 )  # Shape of z is 5x5: How? The 1x5 vector (x2) is subtracted for each row in the 5x5 (x1)
 z = (
-    x1 ** x2
+    x1**x2
 )  # Shape of z is 5x5: How? Broadcasting! Element wise exponentiation for every row
 
 # Other useful tensor operations