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README.md
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@@ -48,6 +48,39 @@ wsi_dataset = load_dataset("Lab-Rasool/TCGA", "wsi", split="train")
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molecular_dataset = load_dataset("Lab-Rasool/TCGA", "molecular", split="train")
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```
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## Dataset Creation
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#### Data Collection and Processing
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molecular_dataset = load_dataset("Lab-Rasool/TCGA", "molecular", split="train")
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```
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Example code for loading HF dataset into a PyTorch Dataloader.
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**Note**: Some embeddings are stored as buffers due to their multi-dimensional shape.
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```python
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from datasets import load_dataset
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import os
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from torch.utils.data import Dataset
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import numpy as np
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class CustomDataset(Dataset):
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def __init__(self, hf_dataset):
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self.hf_dataset = hf_dataset
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def __len__(self):
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return len(self.hf_dataset)
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def __getitem__(self, idx):
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hf_item = self.hf_dataset[idx]
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embedding = np.frombuffer(hf_item["embedding"], dtype=np.float32)
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embedding_shape = hf_item["embedding_shape"]
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embedding = embedding.reshape(embedding_shape)
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return embedding
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if __name__ == "__main__":
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clinical_dataset = load_dataset("Lab-Rasool/TCGA", "clinical", split="train")
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wsi_dataset = load_dataset("Lab-Rasool/TCGA", "wsi", split="train")
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for index, item in enumerate(clinical_dataset):
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print(np.frombuffer(item.get("embedding"), dtype=np.float32).reshape(item.get("embedding_shape")).shape)
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break
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```
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## Dataset Creation
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#### Data Collection and Processing
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