Merge branch 'master' into moshiko

README.md

@@ -223,7 +223,7 @@ $ pip install fuse-med-ml[all,examples]
 # Examples
 
 * Easy access "Hello World" [colab notebook](https://colab.research.google.com/github/BiomedSciAI/fuse-med-ml/blob/master/fuse_examples/imaging/hello_world/hello_world.ipynb)
-* classification
+* Classification
     * [**MNIST**](./fuse_examples/imaging/classification/mnist/)  - a simple example, including training, inference and evaluation over [MNIST dataset](http://yann.lecun.com/exdb/mnist/)
     * [**STOIC**](./fuse_examples/imaging/classification/stoic21/) - severe COVID-19 classifier baseline given a Computed-Tomography (CT), age group and gender. [Challenge description](https://stoic2021.grand-challenge.org/)
 
@@ -232,6 +232,9 @@ $ pip install fuse-med-ml[all,examples]
     * [**Skin Lesion**](./fuse_examples/imaging/classification/isic/) - skin lesion classification , including training, inference and evaluation over the public dataset introduced in [ISIC challenge](https://challenge.isic-archive.com/landing/2019)
     * [**Breast Cancer Lesion Classification**](./fuse_examples/imaging/classification/cmmd) - lesions classification of tumor ( benign, malignant) in breast mammography over the public dataset introduced in [The Chinese Mammography Database (CMMD)](https://wiki.cancerimagingarchive.net/pages/viewpage.action?pageId=70230508)
     * [**Mortality prediction for ICU patients**](./fuse_examples/multimodality/ehr_transformer) - Example of EHR transformer applied to the data of Intensive Care Units patients for in-hospital mortality prediction. The dataset is from [PhysioNet Computing in Cardiology Challenge (2012)](https://physionet.org/content/challenge-2012/1.0.0/)
+* Pre-training
+    * [**Medical Imaging Pre-training and Downstream Task Validation**](./fuse_examples/imaging/oai_example) - pre-training a model on 3D MRI medical imaging and then using it for classification and segmentation downstream tasks.
+
 
 ## Walkthrough template
 * [**Walkthrough Template**](./fuse/dl/templates/walkthrough_template.py) - includes several TODO notes, marking the minimal scope of code required to get your pipeline up and running. The template also includes useful explanations and tips.

fuse/dl/models/backbones/backbone_unet3d.py

@@ -0,0 +1,153 @@
+import torch
+import torch.nn as nn
+import torch.nn.functional as F
+from typing import Tuple
+
+# Based on the architecture from https://github.com/MrGiovanni/ModelsGenesis
+torch.use_deterministic_algorithms(False)
+
+
+class ContBatchNorm3d(nn.modules.batchnorm._BatchNorm):
+    def _check_input_dim(self, input: torch.Tensor) -> None:
+
+        if input.dim() != 5:
+            raise ValueError("expected 5D input (got {}D input)".format(input.dim()))
+        # super(ContBatchNorm3d, self)._check_input_dim(input)
+
+    def forward(self, input: torch.Tensor) -> torch.Tensor:
+        self._check_input_dim(input)
+        return F.batch_norm(
+            input,
+            self.running_mean,
+            self.running_var,
+            self.weight,
+            self.bias,
+            True,
+            self.momentum,
+            self.eps,
+        )
+
+
+class LUConv(nn.Module):
+    def __init__(self, in_chan: int, out_chan: int, act: str):
+        super(LUConv, self).__init__()
+        self.conv1 = nn.Conv3d(in_chan, out_chan, kernel_size=3, padding=1)
+        self.bn1 = ContBatchNorm3d(out_chan)
+
+        if act == "relu":
+            self.activation = nn.ReLU(out_chan)
+        elif act == "prelu":
+            self.activation = nn.PReLU(out_chan)
+        elif act == "elu":
+            self.activation = nn.ELU(inplace=True)
+        else:
+            raise
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        out = self.activation(self.bn1(self.conv1(x)))
+        return out
+
+
+def _make_nConv(
+    in_channel: int, depth: int, act: str, double_chnnel: bool = False
+) -> nn.Module:
+    if double_chnnel:
+        layer1 = LUConv(in_channel, 32 * (2 ** (depth + 1)), act)
+        layer2 = LUConv(32 * (2 ** (depth + 1)), 32 * (2 ** (depth + 1)), act)
+    else:
+        layer1 = LUConv(in_channel, 32 * (2**depth), act)
+        layer2 = LUConv(32 * (2**depth), 32 * (2**depth) * 2, act)
+
+    return nn.Sequential(layer1, layer2)
+
+
+# class InputTransition(nn.Module):
+#     def __init__(self, outChans, elu):
+#         super(InputTransition, self).__init__()
+#         self.conv1 = nn.Conv3d(1, 16, kernel_size=5, padding=2)
+#         self.bn1 = ContBatchNorm3d(16)
+#         self.relu1 = ELUCons(elu, 16)
+#
+#     def forward(self, x):
+#         # do we want a PRELU here as well?
+#         out = self.bn1(self.conv1(x))
+#         # split input in to 16 channels
+#         x16 = torch.cat((x, x, x, x, x, x, x, x,
+#                          x, x, x, x, x, x, x, x), 1)
+#         out = self.relu1(torch.add(out, x16))
+#         return out
+
+
+class DownTransition(nn.Module):
+    def __init__(self, in_channel: int, depth: int, act: str):
+        super(DownTransition, self).__init__()
+        self.ops = _make_nConv(in_channel, depth, act)
+        self.maxpool = nn.MaxPool3d(2)
+        self.current_depth = depth
+
+    def forward(self, x: torch.Tensor) -> Tuple[torch.Tensor, torch.Tensor]:
+        if self.current_depth == 3:
+            out = self.ops(x)
+            out_before_pool = out
+        else:
+            out_before_pool = self.ops(x)
+            out = self.maxpool(out_before_pool)
+        return out, out_before_pool
+
+
+class UpTransition(nn.Module):
+    def __init__(self, inChans: int, outChans: int, depth: int, act: str):
+        super(UpTransition, self).__init__()
+        self.depth = depth
+        self.up_conv = nn.ConvTranspose3d(inChans, outChans, kernel_size=2, stride=2)
+        self.ops = _make_nConv(inChans + outChans // 2, depth, act, double_chnnel=True)
+
+    def forward(self, x: torch.Tensor, skip_x: torch.Tensor) -> torch.Tensor:
+        out_up_conv = self.up_conv(x)
+        concat = torch.cat((out_up_conv, skip_x), 1)
+        out = self.ops(concat)
+        return out
+
+
+class OutputTransition(nn.Module):
+    def __init__(self, inChans: int, n_labels: int):
+
+        super(OutputTransition, self).__init__()
+        self.final_conv = nn.Conv3d(inChans, n_labels, kernel_size=1)
+        self.sigmoid = nn.Sigmoid()
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        out = self.sigmoid(self.final_conv(x))
+        return out
+
+
+class UNet3D(nn.Module):
+    # the number of convolutions in each layer corresponds
+    # to what is in the actual prototxt, not the intent
+    def __init__(self, n_class: int = 1, act: str = "relu", for_cls: bool = False):
+        super(UNet3D, self).__init__()
+        self.for_cls = for_cls
+        self.down_tr64 = DownTransition(1, 0, act)
+        self.down_tr128 = DownTransition(64, 1, act)
+        self.down_tr256 = DownTransition(128, 2, act)
+        self.down_tr512 = DownTransition(256, 3, act)
+        if not for_cls:
+            self.up_tr256 = UpTransition(512, 512, 2, act)
+            self.up_tr128 = UpTransition(256, 256, 1, act)
+            self.up_tr64 = UpTransition(128, 128, 0, act)
+            # self.out_tr = OutputTransition(64, n_class)
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        self.out64, self.skip_out64 = self.down_tr64(x)
+        self.out128, self.skip_out128 = self.down_tr128(self.out64)
+        self.out256, self.skip_out256 = self.down_tr256(self.out128)
+        self.out512, self.skip_out512 = self.down_tr512(self.out256)
+        if self.for_cls:
+            return self.out512
+
+        self.out_up_256 = self.up_tr256(self.out512, self.skip_out256)
+        self.out_up_128 = self.up_tr128(self.out_up_256, self.skip_out128)
+        self.out_up_64 = self.up_tr64(self.out_up_128, self.skip_out64)
+        # self.out = self.out_tr(self.out_up_64)
+
+        return self.out_up_64

fuse/eval/metrics/libs/classification.py

@@ -268,7 +268,7 @@ def confusion_metrics(
             if metric in ["sensitivity", "recall", "tpr"]:
                 res[metric] = tp / (tp + fn)
             elif metric in ["specificity", "selectivity", "tnr"]:
-                res[metric] = tp / (tn + fp)
+                res[metric] = tn / (tn + fp)
             elif metric in ["precision", "ppv"]:
                 if tp + fp != 0:
                     res[metric] = tp / (tp + fp)

fuse_examples/imaging/oai_example/README.md

@@ -0,0 +1,98 @@
+# 3D Medical Imaging Pre-training and Downstream Task Validation
+
+Self-supervision is employed to learn meaningful representations from unlabeled medical imaging data. By pre-training the model on this vast source of information, we equip it with a strong foundation of understanding the underlying data structure. This leads to significantly improved performance and faster convergence when fine-tuning on downstream tasks like classification and segmentation, compared to training from scratch.
+
+This example demonstrates how to pre-train a model on 3D MRI medical imaging using self-supervised learning techniques, specifically DINO, on large datasets. The pre-trained model can then be fine-tuned for downstream tasks such as classification and segmentation. The fine-tuning process is adaptable to various medical imaging tasks, even when working with small datasets.
+We use the NIH Osteoarthritis Initiative (OAI) dataset for this example which can be downloaded from https://nda.nih.gov/oai
+## Data Preparation
+
+For each training type (self-supervised, classification, segmentation), prepare a CSV file with the following structure:
+
+### Self-Supervised and Classification CSV
+
+| PatientID | path | fold |
+|-----------|------|------|
+| ID1       | /path/to/dicom/folder1 | 0 |
+| ID2       | /path/to/dicom/folder2 | 1 |
+
+For classification, you can add multiple categorical columns to predict and add them as "cls_targets" in the  `classification_config.yaml`.
+For example, you can classify the disease status (Progression, Non-exposed control group) using the V00COHORT label in the OAI dataset.
+
+### Segmentation CSV
+
+| PatientID | img_path | seg_path | fold |
+|-----------|----------|----------|------|
+| ID1       | /path/to/image1.nii.gz | /path/to/segmentation1.nii.gz | train |
+| ID2       | /path/to/image2.nii.gz | /path/to/segmentation2.nii.gz | val |
+
+For example, you can segment the knee parts using the OAI iMorphics Segmentation.
+The "fold" column can be used for cross-validation and can contain any value. The values should be added to the "train/val/test_folds" in the config.yaml files.
+
+## Configuration
+
+Each training type has its own `config.yaml` file. Make sure to set the following parameters:
+
+- `results_dir`: Path to save results and checkpoints
+- `csv_path`: Path to the CSV file for the respective training type
+- `experiment`: Name of the experiment and also the name of the results folder
+- `train_folds`: List of fold values to use for training (e.g., [0, 1, 2])
+- `val_folds`: List of fold values to use for validation (e.g., [3])
+- `test_folds`: List of fold values to use for testing (e.g., [4])
+- `test_ckpt`: Path to the checkpoint for testing. If set to "null", the model will train using the train and validation sets. If a path is provided, it will perform evaluation on the test set using the given checkpoint.
+
+To load pretrained weights or start from certain checkpoint you need to set only <b>one</b> of the following:
+- `suprem_weights`: Path to the backbone pretrained weights from SuPreM (download from https://github.com/MrGiovanni/SuPreM)
+- `dino_weights`: Path to the backbone pretrained weights from Dino
+- `resume_training_from`: Path to training checkpoint
+- `test_ckpt`: If set, the test set as defined in `test_folds` will be evaluated using this checkpoint
+If none of them are set you will train from scratch
+
+Pretrained weights can be downloaded from [SuPreM GitHub repository](https://github.com/MrGiovanni/SuPreM).
+
+## Training
+
+The training process involves three main steps:
+
+1. Self-supervised pre-training with DINO
+2. Fine-tuning for classification
+3. Fine-tuning for segmentation
+
+### 1. Self-Supervised Pre-training
+
+Run DINO pre-training:
+
+```bash
+python fuse_examples/imaging/oai_example/self_supervised/dino.py
+```
+
+### 2. Classification Fine-tuning
+
+Set dino_weights in classification_config.yaml to the path of the best DINO checkpoint.
+Run classification training:
+
+```bash
+python fuse_examples/imaging/oai_example/downstream/classification.py
+```
+
+### 3. Segmentation Fine-tuning
+
+Set dino_weights in segmentation_config.yaml to the same DINO checkpoint path.
+Run segmentation training:
+```bash
+python fuse_examples/imaging/oai_example/downstream/segmentation.py
+```
+This process leverages transfer learning, using DINO pre-trained weights to improve performance on downstream tasks.
+
+### Monitoring Results
+
+You can track the progress of your training/testing using one of the following methods:
+
+1. TensorBoard:
+   To view losses and metrics, run:
+   ```
+   tensorboard --logdir=<path_to_experiments_directory>
+   ```
+2. ClearML:
+    If ClearML is installed and enabled in your config file (`clearml : True`), you can use it to monitor your results.
+
+    Choose the method that best suits your workflow and preferences.