Synthetic dataset of text attribute graph data, compiled by Du Enjun
Browse files- .gitattributes +5 -0
- .gitattributes copy +59 -0
- Children.json +3 -0
- History.json +3 -0
- README copy.md +3 -0
- SubChildren.json +0 -0
- SubCiteseer.json +0 -0
- SubCora.json +0 -0
- SubHistory.json +0 -0
- SubWikics.json +0 -0
- Subarxiv2023.json +0 -0
- arxiv2023.json +3 -0
- citeseer.json +0 -0
- cora.json +0 -0
- data_clear.py +52 -0
- data_statistics.py +67 -0
- few_shot.py +77 -0
- sample.py +396 -0
- wikics.json +3 -0
- wikics_cleaned.json +3 -0
.gitattributes
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@@ -57,3 +57,8 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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# Video files - compressed
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*.mp4 filter=lfs diff=lfs merge=lfs -text
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*.webm filter=lfs diff=lfs merge=lfs -text
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# Video files - compressed
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*.mp4 filter=lfs diff=lfs merge=lfs -text
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*.webm filter=lfs diff=lfs merge=lfs -text
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Children.json filter=lfs diff=lfs merge=lfs -text
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History.json filter=lfs diff=lfs merge=lfs -text
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arxiv2023.json filter=lfs diff=lfs merge=lfs -text
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wikics.json filter=lfs diff=lfs merge=lfs -text
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wikics_cleaned.json filter=lfs diff=lfs merge=lfs -text
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.gitattributes copy
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*.7z filter=lfs diff=lfs merge=lfs -text
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*.arrow filter=lfs diff=lfs merge=lfs -text
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*.bin filter=lfs diff=lfs merge=lfs -text
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*.bz2 filter=lfs diff=lfs merge=lfs -text
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*.ckpt filter=lfs diff=lfs merge=lfs -text
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*.ftz filter=lfs diff=lfs merge=lfs -text
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*.gz filter=lfs diff=lfs merge=lfs -text
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*.h5 filter=lfs diff=lfs merge=lfs -text
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*.joblib filter=lfs diff=lfs merge=lfs -text
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*.lfs.* filter=lfs diff=lfs merge=lfs -text
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*.lz4 filter=lfs diff=lfs merge=lfs -text
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*.mds filter=lfs diff=lfs merge=lfs -text
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*.mlmodel filter=lfs diff=lfs merge=lfs -text
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*.model filter=lfs diff=lfs merge=lfs -text
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*.msgpack filter=lfs diff=lfs merge=lfs -text
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*.npy filter=lfs diff=lfs merge=lfs -text
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*.npz filter=lfs diff=lfs merge=lfs -text
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*.onnx filter=lfs diff=lfs merge=lfs -text
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*.ot filter=lfs diff=lfs merge=lfs -text
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*.parquet filter=lfs diff=lfs merge=lfs -text
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*.pb filter=lfs diff=lfs merge=lfs -text
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*.pickle filter=lfs diff=lfs merge=lfs -text
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*.pkl filter=lfs diff=lfs merge=lfs -text
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*.pt filter=lfs diff=lfs merge=lfs -text
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*.pth filter=lfs diff=lfs merge=lfs -text
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*.rar filter=lfs diff=lfs merge=lfs -text
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*.safetensors filter=lfs diff=lfs merge=lfs -text
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saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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*.tar.* filter=lfs diff=lfs merge=lfs -text
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*.tar filter=lfs diff=lfs merge=lfs -text
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*.tflite filter=lfs diff=lfs merge=lfs -text
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*.tgz filter=lfs diff=lfs merge=lfs -text
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*.wasm filter=lfs diff=lfs merge=lfs -text
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*.xz filter=lfs diff=lfs merge=lfs -text
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*.zip filter=lfs diff=lfs merge=lfs -text
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*.zst filter=lfs diff=lfs merge=lfs -text
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*tfevents* filter=lfs diff=lfs merge=lfs -text
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# Audio files - uncompressed
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*.pcm filter=lfs diff=lfs merge=lfs -text
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*.sam filter=lfs diff=lfs merge=lfs -text
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*.raw filter=lfs diff=lfs merge=lfs -text
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# Audio files - compressed
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*.aac filter=lfs diff=lfs merge=lfs -text
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*.flac filter=lfs diff=lfs merge=lfs -text
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*.mp3 filter=lfs diff=lfs merge=lfs -text
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*.ogg filter=lfs diff=lfs merge=lfs -text
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*.wav filter=lfs diff=lfs merge=lfs -text
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# Image files - uncompressed
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*.bmp filter=lfs diff=lfs merge=lfs -text
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*.gif filter=lfs diff=lfs merge=lfs -text
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*.png filter=lfs diff=lfs merge=lfs -text
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*.tiff filter=lfs diff=lfs merge=lfs -text
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# Image files - compressed
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*.jpg filter=lfs diff=lfs merge=lfs -text
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*.jpeg filter=lfs diff=lfs merge=lfs -text
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*.webp filter=lfs diff=lfs merge=lfs -text
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# Video files - compressed
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*.mp4 filter=lfs diff=lfs merge=lfs -text
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*.webm filter=lfs diff=lfs merge=lfs -text
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Children.json
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version https://git-lfs.github.com/spec/v1
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oid sha256:3bbfa9e9ddf60d5bde95425c1713dde2087224bd1080e9e1b2c7a8087c286097
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size 125909900
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History.json
ADDED
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@@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:0226010aa829e8f2f723bc625920e92d7cd462d1a628f5479f0ea672f90531e8
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size 68660141
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README copy.md
ADDED
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---
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license: mit
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---
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SubChildren.json
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SubCiteseer.json
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SubCora.json
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SubHistory.json
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The diff for this file is too large to render.
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SubWikics.json
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The diff for this file is too large to render.
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Subarxiv2023.json
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arxiv2023.json
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version https://git-lfs.github.com/spec/v1
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oid sha256:ae1fb88d617182abedf2c8a01dd54288471499e0c2921a7c39981d86bafb31da
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size 66487587
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citeseer.json
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The diff for this file is too large to render.
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cora.json
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The diff for this file is too large to render.
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data_clear.py
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import json
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def clean_graph_data(input_file, output_file):
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"""
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Clean graph data by removing nodes with mask="None", ensuring sequential node_ids,
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and updating all neighbor references accordingly.
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"""
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# Load the JSON data
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with open(input_file, 'r', encoding='utf-8') as f:
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data = json.load(f)
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# Identify valid nodes (mask != "None") and their IDs
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valid_nodes = []
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valid_node_ids = set()
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for node in data:
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if 'mask' in node and node['mask'] != "None":
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valid_nodes.append(node)
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valid_node_ids.add(node['node_id'])
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# Create mapping from old node_id to new node_id
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old_to_new_mapping = {}
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new_id = 0
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for node in sorted(valid_nodes, key=lambda x: x['node_id']):
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old_to_new_mapping[node['node_id']] = new_id
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new_id += 1
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# Update node_ids and neighbors based on the mapping
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for node in valid_nodes:
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# Update neighbors first (while node_id is still the old one)
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new_neighbors = []
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for neighbor in node['neighbors']:
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if neighbor in valid_node_ids: # Only keep neighbors that weren't removed
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new_neighbors.append(old_to_new_mapping[neighbor])
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node['neighbors'] = new_neighbors
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# Update node_id
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node['node_id'] = old_to_new_mapping[node['node_id']]
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# Sort nodes by new node_id for better readability
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valid_nodes.sort(key=lambda x: x['node_id'])
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# Save the cleaned data
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with open(output_file, 'w') as f:
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json.dump(valid_nodes, f, indent=2)
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return f"Successfully cleaned the graph data. Removed {len(data) - len(valid_nodes)} nodes with mask='None'."
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# Usage
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| 51 |
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result = clean_graph_data('wikics.json', 'wikics_cleaned.json')
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print(result)
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data_statistics.py
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import json
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import networkx as nx
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import community as community_louvain # You may need to install this package using: pip install python-louvain
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def main():
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# Load the JSON file
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with open('arxiv2023_1624-10.json', 'r', encoding='utf-8') as f:
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data = json.load(f)
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# Initialize counters and sets
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nodes_count = len(data)
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classes = set()
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train_nodes_count = 0
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validation_nodes_count = 0
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test_nodes_count = 0
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# Build an undirected graph
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G = nx.Graph()
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# Iterate over each element in the dataset
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for entry in data:
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node_id = entry['node_id']
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label = entry['label']
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mask = entry['mask']
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# Add label to the classes set
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classes.add(label)
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# Add the node with its attributes to the graph
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G.add_node(node_id, label=label, mask=mask)
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# Count nodes by mask type
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if mask == 'Train':
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train_nodes_count += 1
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elif mask == 'Validation':
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validation_nodes_count += 1
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elif mask == 'Test':
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test_nodes_count += 1
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# Process neighbors and add edges (using set to remove duplicates)
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neighbors = set(entry['neighbors'])
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for neighbor in neighbors:
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# Avoid self-loop if desired (optional)
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if neighbor != node_id:
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G.add_edge(node_id, neighbor)
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# If you want to add self-loops, remove the above condition
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# Compute the number of edges in the graph
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edge_count = G.number_of_edges()
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classes_count = len(classes)
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# Perform Louvain community detection
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partition = community_louvain.best_partition(G)
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communities = set(partition.values())
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community_count = len(communities)
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# Print out the statistics
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| 58 |
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print("Nodes count:", nodes_count)
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print("Edges count:", edge_count)
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print("Classes count:", classes_count)
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print("Train nodes count:", train_nodes_count)
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print("Validation nodes count:", validation_nodes_count)
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print("Test nodes count:", test_nodes_count)
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print("Louvain community count:", community_count)
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if __name__ == '__main__':
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| 67 |
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main()
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few_shot.py
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| 1 |
+
import json
|
| 2 |
+
import random
|
| 3 |
+
|
| 4 |
+
path = r"C:\Code_Compiling\02_bit_Li\07_LLM4GDA\data\arxiv2023_label_16_10.json"
|
| 5 |
+
# 读取reddit.json
|
| 6 |
+
with open(path, 'r', encoding='utf-8') as f:
|
| 7 |
+
data = json.load(f)
|
| 8 |
+
|
| 9 |
+
# 统计每个label的节点个数
|
| 10 |
+
label_counts = {}
|
| 11 |
+
for node in data:
|
| 12 |
+
label = node['label']
|
| 13 |
+
if node['mask'] == 'Train':
|
| 14 |
+
if label not in label_counts:
|
| 15 |
+
label_counts[label] = 0
|
| 16 |
+
label_counts[label] += 1
|
| 17 |
+
|
| 18 |
+
# 输出每个label的节点个数
|
| 19 |
+
print("Train Label counts:", label_counts)
|
| 20 |
+
|
| 21 |
+
# 获取用户输入的x和y
|
| 22 |
+
x = int(input("Enter label value (x): "))
|
| 23 |
+
y = int(input("Enter number of nodes to keep (y): "))
|
| 24 |
+
|
| 25 |
+
# 先将所有mask为'train'且label为x的节点收集到一个列表中
|
| 26 |
+
train_x_nodes = [node for node in data if node['label'] == x and node['mask'] == 'Train']
|
| 27 |
+
|
| 28 |
+
# 确保train_x_nodes列表的长度至少为y
|
| 29 |
+
if len(train_x_nodes) < y:
|
| 30 |
+
print(f"Warning: There are fewer than {y} nodes with label {x} and mask 'train'. All {len(train_x_nodes)} nodes will be kept.")
|
| 31 |
+
selected_nodes = train_x_nodes # 如果不足y个节点,则保留所有该label和mask条件的节点
|
| 32 |
+
else:
|
| 33 |
+
# 随机选择y个节点
|
| 34 |
+
selected_nodes = random.sample(train_x_nodes, y)
|
| 35 |
+
|
| 36 |
+
# 创建一个删除节点的集合
|
| 37 |
+
deleted_nodes = set(node['node_id'] for node in train_x_nodes if node not in selected_nodes)
|
| 38 |
+
|
| 39 |
+
# 创建新数据列表,保留随机选择的label为x且mask为'train'的节点,其他节点不变
|
| 40 |
+
new_data = []
|
| 41 |
+
for node in data:
|
| 42 |
+
# 保留所有的节点,mask非'train'的节点不做任何更改
|
| 43 |
+
if node['label'] != x or (node['mask'] != 'Train' or node in selected_nodes):
|
| 44 |
+
new_data.append(node)
|
| 45 |
+
|
| 46 |
+
# 遍历所有节点的neighbors,删除已经删除的节点
|
| 47 |
+
for node in new_data:
|
| 48 |
+
if 'neighbors' in node:
|
| 49 |
+
# 过滤掉已经删除的节点
|
| 50 |
+
node['neighbors'] = [neighbor for neighbor in node['neighbors'] if neighbor not in deleted_nodes]
|
| 51 |
+
|
| 52 |
+
# 重新调整node_id,使其从0开始连续
|
| 53 |
+
id_mapping = {}
|
| 54 |
+
new_node_id = 0
|
| 55 |
+
|
| 56 |
+
# 对new_data中的所有节点进行重排
|
| 57 |
+
for node in new_data:
|
| 58 |
+
id_mapping[node['node_id']] = new_node_id
|
| 59 |
+
node['node_id'] = new_node_id
|
| 60 |
+
new_node_id += 1
|
| 61 |
+
|
| 62 |
+
# 更新所有节点的neighbors,使用新的node_id
|
| 63 |
+
for node in new_data:
|
| 64 |
+
if 'neighbors' in node:
|
| 65 |
+
# 使用id_mapping更新neighbors中的node_id
|
| 66 |
+
updated_neighbors = []
|
| 67 |
+
for neighbor in node['neighbors']:
|
| 68 |
+
if neighbor in id_mapping: # 只更新存在id_mapping中的邻居
|
| 69 |
+
updated_neighbors.append(id_mapping[neighbor])
|
| 70 |
+
node['neighbors'] = updated_neighbors
|
| 71 |
+
|
| 72 |
+
# 将修改后的数据保存为reddit_label:{x}_{y}.json
|
| 73 |
+
output_filename = f"arxiv2023_label_{x}_{y}.json"
|
| 74 |
+
with open(output_filename, 'w', encoding='utf-8') as f:
|
| 75 |
+
json.dump(new_data, f, indent=4)
|
| 76 |
+
|
| 77 |
+
print(f"Modified data saved to {output_filename}")
|
sample.py
ADDED
|
@@ -0,0 +1,396 @@
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|
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|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
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|
|
|
|
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|
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|
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|
|
|
|
|
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|
|
|
|
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|
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|
|
|
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|
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|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
import json
|
| 2 |
+
import numpy as np
|
| 3 |
+
import networkx as nx
|
| 4 |
+
from collections import Counter, defaultdict
|
| 5 |
+
import random
|
| 6 |
+
import scipy.sparse as sp
|
| 7 |
+
from scipy.sparse.linalg import eigsh
|
| 8 |
+
import sys
|
| 9 |
+
import os
|
| 10 |
+
|
| 11 |
+
try:
|
| 12 |
+
import community as community_louvain
|
| 13 |
+
except ImportError:
|
| 14 |
+
print("Warning: python-louvain package not found. Installing...")
|
| 15 |
+
import subprocess
|
| 16 |
+
subprocess.check_call([sys.executable, "-m", "pip", "install", "python-louvain"])
|
| 17 |
+
import community as community_louvain
|
| 18 |
+
|
| 19 |
+
def load_graph_from_json(json_file):
|
| 20 |
+
"""Load graph from a JSON file with nodes."""
|
| 21 |
+
nodes = []
|
| 22 |
+
|
| 23 |
+
try:
|
| 24 |
+
# First try to parse as a single JSON array or object
|
| 25 |
+
with open(json_file, 'r', encoding='utf-8') as f:
|
| 26 |
+
content = f.read().strip()
|
| 27 |
+
try:
|
| 28 |
+
data = json.loads(content)
|
| 29 |
+
if isinstance(data, list):
|
| 30 |
+
nodes = data
|
| 31 |
+
else:
|
| 32 |
+
nodes = [data]
|
| 33 |
+
except json.JSONDecodeError:
|
| 34 |
+
# Reset and try parsing line by line
|
| 35 |
+
nodes = []
|
| 36 |
+
with open(json_file, 'r') as f:
|
| 37 |
+
for line in f:
|
| 38 |
+
line = line.strip()
|
| 39 |
+
if line: # Skip empty lines
|
| 40 |
+
try:
|
| 41 |
+
node_data = json.loads(line)
|
| 42 |
+
nodes.append(node_data)
|
| 43 |
+
except json.JSONDecodeError:
|
| 44 |
+
continue
|
| 45 |
+
except Exception as e:
|
| 46 |
+
print(f"Error loading graph: {e}")
|
| 47 |
+
return []
|
| 48 |
+
|
| 49 |
+
return nodes
|
| 50 |
+
|
| 51 |
+
def build_networkx_graph(nodes):
|
| 52 |
+
"""Build a NetworkX graph from the loaded node data."""
|
| 53 |
+
G = nx.Graph()
|
| 54 |
+
|
| 55 |
+
# Add nodes with attributes
|
| 56 |
+
for node in nodes:
|
| 57 |
+
G.add_node(
|
| 58 |
+
node['node_id'],
|
| 59 |
+
label=node['label'],
|
| 60 |
+
text=node['text'],
|
| 61 |
+
mask=node['mask']
|
| 62 |
+
)
|
| 63 |
+
|
| 64 |
+
# Add edges
|
| 65 |
+
for node in nodes:
|
| 66 |
+
node_id = node['node_id']
|
| 67 |
+
for neighbor_id in node['neighbors']:
|
| 68 |
+
if G.has_node(neighbor_id): # Only add edge if both nodes exist
|
| 69 |
+
G.add_edge(node_id, neighbor_id)
|
| 70 |
+
|
| 71 |
+
return G
|
| 72 |
+
|
| 73 |
+
def analyze_graph_properties(G):
|
| 74 |
+
"""Analyze the properties of the graph as specified in the requirements."""
|
| 75 |
+
properties = {}
|
| 76 |
+
|
| 77 |
+
# Mask distribution (Train/Validation/Test)
|
| 78 |
+
masks = [G.nodes[n]['mask'] for n in G.nodes]
|
| 79 |
+
mask_distribution = Counter(masks)
|
| 80 |
+
properties['mask_distribution'] = {k: v/len(G.nodes) for k, v in mask_distribution.items()}
|
| 81 |
+
|
| 82 |
+
# Label distribution
|
| 83 |
+
labels = [G.nodes[n]['label'] for n in G.nodes]
|
| 84 |
+
label_distribution = Counter(labels)
|
| 85 |
+
properties['label_distribution'] = {k: v/len(G.nodes) for k, v in label_distribution.items()}
|
| 86 |
+
|
| 87 |
+
# Graph density
|
| 88 |
+
properties['density'] = nx.density(G)
|
| 89 |
+
|
| 90 |
+
# Degree distribution
|
| 91 |
+
degrees = [d for n, d in G.degree()]
|
| 92 |
+
degree_counts = Counter(degrees)
|
| 93 |
+
properties['degree_distribution'] = {k: v/len(G.nodes) for k, v in degree_counts.items()}
|
| 94 |
+
|
| 95 |
+
# Community structure (using Louvain algorithm)
|
| 96 |
+
try:
|
| 97 |
+
communities = community_louvain.best_partition(G)
|
| 98 |
+
community_counts = Counter(communities.values())
|
| 99 |
+
properties['community_distribution'] = {k: v/len(G.nodes) for k, v in community_counts.items()}
|
| 100 |
+
except:
|
| 101 |
+
properties['community_distribution'] = {}
|
| 102 |
+
|
| 103 |
+
# Spectral characteristics
|
| 104 |
+
if len(G) > 1:
|
| 105 |
+
try:
|
| 106 |
+
laplacian = nx.normalized_laplacian_matrix(G)
|
| 107 |
+
if sp.issparse(laplacian) and laplacian.shape[0] > 1:
|
| 108 |
+
try:
|
| 109 |
+
k = min(5, laplacian.shape[0]-1)
|
| 110 |
+
if k > 0:
|
| 111 |
+
eigenvalues = eigsh(laplacian, k=k, which='SM', return_eigenvectors=False)
|
| 112 |
+
properties['spectral_eigenvalues'] = sorted(eigenvalues.tolist())
|
| 113 |
+
else:
|
| 114 |
+
properties['spectral_eigenvalues'] = []
|
| 115 |
+
except:
|
| 116 |
+
properties['spectral_eigenvalues'] = []
|
| 117 |
+
else:
|
| 118 |
+
properties['spectral_eigenvalues'] = []
|
| 119 |
+
except:
|
| 120 |
+
properties['spectral_eigenvalues'] = []
|
| 121 |
+
else:
|
| 122 |
+
properties['spectral_eigenvalues'] = []
|
| 123 |
+
|
| 124 |
+
# Connectivity characteristics
|
| 125 |
+
properties['connected_components'] = nx.number_connected_components(G)
|
| 126 |
+
largest_cc = max(nx.connected_components(G), key=len)
|
| 127 |
+
properties['largest_cc_ratio'] = len(largest_cc) / len(G.nodes)
|
| 128 |
+
|
| 129 |
+
return properties
|
| 130 |
+
|
| 131 |
+
def sample_graph_preserving_properties(G, percentage, original_properties):
|
| 132 |
+
"""Sample a percentage of nodes while preserving graph properties."""
|
| 133 |
+
num_nodes = len(G.nodes)
|
| 134 |
+
num_nodes_to_sample = max(1, int(num_nodes * percentage / 100))
|
| 135 |
+
|
| 136 |
+
# If the graph is too small, just return it
|
| 137 |
+
if num_nodes <= num_nodes_to_sample:
|
| 138 |
+
return G, {n: n for n in G.nodes}
|
| 139 |
+
|
| 140 |
+
# 1. Preserve label and mask distribution (top priority per requirements)
|
| 141 |
+
mask_label_groups = defaultdict(list)
|
| 142 |
+
for node in G.nodes:
|
| 143 |
+
mask = G.nodes[node]['mask']
|
| 144 |
+
label = G.nodes[node]['label']
|
| 145 |
+
mask_label_groups[(mask, label)].append(node)
|
| 146 |
+
|
| 147 |
+
# Calculate how many nodes to sample from each mask-label group
|
| 148 |
+
group_counts = {}
|
| 149 |
+
for (mask, label), nodes in mask_label_groups.items():
|
| 150 |
+
mask_ratio = original_properties['mask_distribution'].get(mask, 0)
|
| 151 |
+
label_ratio = original_properties['label_distribution'].get(label, 0)
|
| 152 |
+
|
| 153 |
+
# Calculate joint probability
|
| 154 |
+
joint_ratio = mask_ratio * label_ratio / sum(
|
| 155 |
+
original_properties['mask_distribution'].get(m, 0) *
|
| 156 |
+
original_properties['label_distribution'].get(l, 0)
|
| 157 |
+
for m in original_properties['mask_distribution']
|
| 158 |
+
for l in original_properties['label_distribution']
|
| 159 |
+
)
|
| 160 |
+
|
| 161 |
+
target_count = int(num_nodes_to_sample * joint_ratio)
|
| 162 |
+
# Ensure at least one node from non-empty groups
|
| 163 |
+
group_counts[(mask, label)] = max(1, target_count) if nodes else 0
|
| 164 |
+
|
| 165 |
+
# Adjust to match the exact sample size
|
| 166 |
+
total_count = sum(group_counts.values())
|
| 167 |
+
if total_count != num_nodes_to_sample:
|
| 168 |
+
diff = num_nodes_to_sample - total_count
|
| 169 |
+
groups = list(group_counts.keys())
|
| 170 |
+
|
| 171 |
+
if diff > 0:
|
| 172 |
+
# Add nodes to groups proportionally to their size
|
| 173 |
+
group_sizes = [len(mask_label_groups[g]) for g in groups]
|
| 174 |
+
group_probs = [s/sum(group_sizes) for s in group_sizes]
|
| 175 |
+
|
| 176 |
+
for _ in range(diff):
|
| 177 |
+
group = random.choices(groups, weights=group_probs)[0]
|
| 178 |
+
if len(mask_label_groups[group]) > group_counts[group]:
|
| 179 |
+
group_counts[group] += 1
|
| 180 |
+
else:
|
| 181 |
+
# Remove nodes from groups with excess
|
| 182 |
+
groups_with_excess = [(g, c) for g, c in group_counts.items()
|
| 183 |
+
if c > 1 and c > len(mask_label_groups[g]) * 0.2]
|
| 184 |
+
groups_with_excess.sort(key=lambda x: x[1], reverse=True)
|
| 185 |
+
|
| 186 |
+
for i in range(min(-diff, len(groups_with_excess))):
|
| 187 |
+
group_counts[groups_with_excess[i][0]] -= 1
|
| 188 |
+
|
| 189 |
+
# 2. Sample nodes from each group, prioritizing connectivity and community structure
|
| 190 |
+
sampled_nodes = []
|
| 191 |
+
|
| 192 |
+
# First try to get community structure
|
| 193 |
+
try:
|
| 194 |
+
communities = community_louvain.best_partition(G)
|
| 195 |
+
except:
|
| 196 |
+
communities = {node: 0 for node in G.nodes} # Fallback if community detection fails
|
| 197 |
+
|
| 198 |
+
# Sample from each mask-label group
|
| 199 |
+
for (mask, label), count in group_counts.items():
|
| 200 |
+
candidates = mask_label_groups[(mask, label)]
|
| 201 |
+
|
| 202 |
+
if len(candidates) <= count:
|
| 203 |
+
# Take all nodes in this group
|
| 204 |
+
sampled_nodes.extend(candidates)
|
| 205 |
+
else:
|
| 206 |
+
# Score nodes based on degree and community representation
|
| 207 |
+
node_scores = {}
|
| 208 |
+
for node in candidates:
|
| 209 |
+
# Higher score for higher degree nodes (connectivity)
|
| 210 |
+
degree_score = G.degree(node) / max(1, max(d for n, d in G.degree()))
|
| 211 |
+
|
| 212 |
+
# Higher score for nodes in underrepresented communities
|
| 213 |
+
comm = communities.get(node, 0)
|
| 214 |
+
comm_sampled = sum(1 for n in sampled_nodes if communities.get(n, -1) == comm)
|
| 215 |
+
comm_total = sum(1 for n in G.nodes if communities.get(n, -1) == comm)
|
| 216 |
+
comm_score = 1 - (comm_sampled / max(1, comm_total))
|
| 217 |
+
|
| 218 |
+
# Combined score (prioritize connectivity slightly more)
|
| 219 |
+
node_scores[node] = 0.6 * degree_score + 0.4 * comm_score
|
| 220 |
+
|
| 221 |
+
# Sort candidates by score and select the top ones
|
| 222 |
+
sorted_candidates = sorted(candidates, key=lambda n: node_scores.get(n, 0), reverse=True)
|
| 223 |
+
sampled_nodes.extend(sorted_candidates[:count])
|
| 224 |
+
|
| 225 |
+
# 3. Create the sampled subgraph
|
| 226 |
+
sampled_G = G.subgraph(sampled_nodes).copy()
|
| 227 |
+
|
| 228 |
+
# 4. Improve connectivity if needed
|
| 229 |
+
if nx.number_connected_components(sampled_G) > original_properties['connected_components']:
|
| 230 |
+
# Try to improve connectivity by swapping nodes
|
| 231 |
+
non_sampled = [n for n in G.nodes if n not in sampled_nodes]
|
| 232 |
+
|
| 233 |
+
# Calculate betweenness centrality for non-sampled nodes
|
| 234 |
+
betweenness = {}
|
| 235 |
+
for node in non_sampled:
|
| 236 |
+
# Count how many different components this node would connect
|
| 237 |
+
neighbors = list(G.neighbors(node))
|
| 238 |
+
sampled_neighbors = [n for n in neighbors if n in sampled_nodes]
|
| 239 |
+
|
| 240 |
+
if not sampled_neighbors:
|
| 241 |
+
continue
|
| 242 |
+
|
| 243 |
+
components_connected = set()
|
| 244 |
+
for n in sampled_neighbors:
|
| 245 |
+
for comp_idx, comp in enumerate(nx.connected_components(sampled_G)):
|
| 246 |
+
if n in comp:
|
| 247 |
+
components_connected.add(comp_idx)
|
| 248 |
+
break
|
| 249 |
+
|
| 250 |
+
betweenness[node] = len(components_connected)
|
| 251 |
+
|
| 252 |
+
# Sort non-sampled nodes by how many components they would connect
|
| 253 |
+
connector_nodes = [(n, b) for n, b in betweenness.items() if b > 1]
|
| 254 |
+
connector_nodes.sort(key=lambda x: x[1], reverse=True)
|
| 255 |
+
|
| 256 |
+
# Try to improve connectivity by swapping nodes
|
| 257 |
+
for connector, _ in connector_nodes:
|
| 258 |
+
# Find a node to swap out (prefer low degree nodes from well-represented groups)
|
| 259 |
+
mask = G.nodes[connector]['mask']
|
| 260 |
+
label = G.nodes[connector]['label']
|
| 261 |
+
|
| 262 |
+
# Find nodes with the same mask and label
|
| 263 |
+
same_group = [n for n in sampled_nodes
|
| 264 |
+
if G.nodes[n]['mask'] == mask and G.nodes[n]['label'] == label]
|
| 265 |
+
|
| 266 |
+
if not same_group:
|
| 267 |
+
continue
|
| 268 |
+
|
| 269 |
+
# Sort by degree (ascending)
|
| 270 |
+
same_group.sort(key=lambda n: sampled_G.degree(n))
|
| 271 |
+
|
| 272 |
+
# Swap the node with lowest degree
|
| 273 |
+
to_remove = same_group[0]
|
| 274 |
+
sampled_nodes.remove(to_remove)
|
| 275 |
+
sampled_nodes.append(connector)
|
| 276 |
+
|
| 277 |
+
# Update the sampled subgraph
|
| 278 |
+
sampled_G = G.subgraph(sampled_nodes).copy()
|
| 279 |
+
|
| 280 |
+
# Stop if we've reached the desired connectivity
|
| 281 |
+
if nx.number_connected_components(sampled_G) <= original_properties['connected_components']:
|
| 282 |
+
break
|
| 283 |
+
|
| 284 |
+
# 5. Relabel nodes to have consecutive IDs starting from 0
|
| 285 |
+
node_mapping = {old_id: new_id for new_id, old_id in enumerate(sorted(sampled_nodes))}
|
| 286 |
+
relabeled_G = nx.relabel_nodes(sampled_G, node_mapping)
|
| 287 |
+
|
| 288 |
+
# Return the sampled graph and the inverse mapping (new_id -> original_id)
|
| 289 |
+
inverse_mapping = {new_id: old_id for old_id, new_id in node_mapping.items()}
|
| 290 |
+
return relabeled_G, inverse_mapping
|
| 291 |
+
|
| 292 |
+
def graph_to_json_format(G):
|
| 293 |
+
"""Convert a NetworkX graph to the required JSON format."""
|
| 294 |
+
result = []
|
| 295 |
+
|
| 296 |
+
for node_id in sorted(G.nodes):
|
| 297 |
+
node_data = {
|
| 298 |
+
"node_id": int(node_id),
|
| 299 |
+
"label": G.nodes[node_id]['label'],
|
| 300 |
+
"text": G.nodes[node_id]['text'],
|
| 301 |
+
"neighbors": sorted([int(n) for n in G.neighbors(node_id)]),
|
| 302 |
+
"mask": G.nodes[node_id]['mask']
|
| 303 |
+
}
|
| 304 |
+
|
| 305 |
+
result.append(node_data)
|
| 306 |
+
|
| 307 |
+
return result
|
| 308 |
+
|
| 309 |
+
def sample_text_attribute_graph(input_file, output_file, percentage):
|
| 310 |
+
"""Main function to sample a text attribute graph and preserve its properties."""
|
| 311 |
+
# Load the graph data
|
| 312 |
+
print(f"Loading graph from {input_file}...")
|
| 313 |
+
nodes = load_graph_from_json(input_file)
|
| 314 |
+
|
| 315 |
+
if not nodes:
|
| 316 |
+
print("Failed to load nodes from the input file.")
|
| 317 |
+
return None, None, None
|
| 318 |
+
|
| 319 |
+
print(f"Loaded {len(nodes)} nodes.")
|
| 320 |
+
|
| 321 |
+
# Build the NetworkX graph
|
| 322 |
+
print("Building graph...")
|
| 323 |
+
G = build_networkx_graph(nodes)
|
| 324 |
+
print(f"Built graph with {len(G.nodes)} nodes and {len(G.edges)} edges.")
|
| 325 |
+
|
| 326 |
+
# Analyze the original graph properties
|
| 327 |
+
print("Analyzing original graph properties...")
|
| 328 |
+
original_properties = analyze_graph_properties(G)
|
| 329 |
+
|
| 330 |
+
# Sample the graph
|
| 331 |
+
print(f"Sampling {percentage}% of the nodes...")
|
| 332 |
+
sampled_G, inverse_mapping = sample_graph_preserving_properties(G, percentage, original_properties)
|
| 333 |
+
print(f"Sampled graph has {len(sampled_G.nodes)} nodes and {len(sampled_G.edges)} edges.")
|
| 334 |
+
|
| 335 |
+
# Convert the sampled graph to JSON format
|
| 336 |
+
print("Converting sampled graph to JSON format...")
|
| 337 |
+
sampled_data = graph_to_json_format(sampled_G)
|
| 338 |
+
|
| 339 |
+
# Save the sampled graph
|
| 340 |
+
print(f"Saving sampled graph to {output_file}...")
|
| 341 |
+
with open(output_file, 'w') as f:
|
| 342 |
+
json.dump(sampled_data, f, indent=2)
|
| 343 |
+
|
| 344 |
+
# Analyze the sampled graph properties
|
| 345 |
+
print("Analyzing sampled graph properties...")
|
| 346 |
+
sampled_properties = analyze_graph_properties(sampled_G)
|
| 347 |
+
|
| 348 |
+
# Print comparison of original and sampled properties
|
| 349 |
+
print("\nComparison of Graph Properties:")
|
| 350 |
+
print(f"{'Property':<25} {'Original':<15} {'Sampled':<15}")
|
| 351 |
+
print("-" * 55)
|
| 352 |
+
print(f"{'Number of nodes':<25} {len(G.nodes):<15} {len(sampled_G.nodes):<15}")
|
| 353 |
+
print(f"{'Number of edges':<25} {len(G.edges):<15} {len(sampled_G.edges):<15}")
|
| 354 |
+
print(f"{'Density':<25} {original_properties['density']:.4f}{'':>10} {sampled_properties['density']:.4f}{'':>10}")
|
| 355 |
+
|
| 356 |
+
print("\nMask Distribution:")
|
| 357 |
+
print(f"{'Mask':<10} {'Original %':<15} {'Sampled %':<15}")
|
| 358 |
+
print("-" * 40)
|
| 359 |
+
for mask in sorted(set(original_properties['mask_distribution'].keys()) | set(sampled_properties['mask_distribution'].keys())):
|
| 360 |
+
orig_pct = original_properties['mask_distribution'].get(mask, 0) * 100
|
| 361 |
+
sampled_pct = sampled_properties['mask_distribution'].get(mask, 0) * 100
|
| 362 |
+
print(f"{mask:<10} {orig_pct:.2f}%{'':>9} {sampled_pct:.2f}%{'':>9}")
|
| 363 |
+
|
| 364 |
+
print("\nLabel Distribution:")
|
| 365 |
+
print(f"{'Label':<10} {'Original %':<15} {'Sampled %':<15}")
|
| 366 |
+
print("-" * 40)
|
| 367 |
+
for label in sorted(set(original_properties['label_distribution'].keys()) | set(sampled_properties['label_distribution'].keys())):
|
| 368 |
+
orig_pct = original_properties['label_distribution'].get(label, 0) * 100
|
| 369 |
+
sampled_pct = sampled_properties['label_distribution'].get(label, 0) * 100
|
| 370 |
+
print(f"{label:<10} {orig_pct:.2f}%{'':>9} {sampled_pct:.2f}%{'':>9}")
|
| 371 |
+
|
| 372 |
+
print("\nConnectivity:")
|
| 373 |
+
print(f"Connected components: {original_properties['connected_components']} (original) vs {sampled_properties['connected_components']} (sampled)")
|
| 374 |
+
|
| 375 |
+
return sampled_G, original_properties, sampled_properties
|
| 376 |
+
|
| 377 |
+
def main():
|
| 378 |
+
"""Command-line interface."""
|
| 379 |
+
if len(sys.argv) != 4:
|
| 380 |
+
print("Usage: python sample_graph.py input_file output_file percentage")
|
| 381 |
+
sys.exit(1)
|
| 382 |
+
|
| 383 |
+
input_file = sys.argv[1]
|
| 384 |
+
output_file = sys.argv[2]
|
| 385 |
+
try:
|
| 386 |
+
percentage = float(sys.argv[3])
|
| 387 |
+
if percentage <= 0 or percentage > 100:
|
| 388 |
+
raise ValueError("Percentage must be between 0 and 100")
|
| 389 |
+
except ValueError:
|
| 390 |
+
print("Error: Percentage must be a number between 0 and 100")
|
| 391 |
+
sys.exit(1)
|
| 392 |
+
|
| 393 |
+
sample_text_attribute_graph(input_file, output_file, percentage)
|
| 394 |
+
|
| 395 |
+
if __name__ == "__main__":
|
| 396 |
+
main()
|
wikics.json
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:ba9dd08bf0b5b50f3170d8e1ef794d1f6948d0a38be407a3217f3a830c483d65
|
| 3 |
+
size 44635743
|
wikics_cleaned.json
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:4567da141dd5c2f64e6b059bdc4db24bf974e655c803d3787ce3b569b392f406
|
| 3 |
+
size 29728898
|