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
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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
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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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SubWikics.json
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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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cora.json
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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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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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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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main()
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few_shot.py
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import json
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import random
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path = r"C:\Code_Compiling\02_bit_Li\07_LLM4GDA\data\arxiv2023_label_16_10.json"
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# 读取reddit.json
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with open(path, 'r', encoding='utf-8') as f:
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data = json.load(f)
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# 统计每个label的节点个数
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label_counts = {}
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for node in data:
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label = node['label']
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if node['mask'] == 'Train':
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if label not in label_counts:
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label_counts[label] = 0
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label_counts[label] += 1
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# 输出每个label的节点个数
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print("Train Label counts:", label_counts)
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# 获取用户输入的x和y
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x = int(input("Enter label value (x): "))
|
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y = int(input("Enter number of nodes to keep (y): "))
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# 先将所有mask为'train'且label为x的节点收集到一个列表中
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train_x_nodes = [node for node in data if node['label'] == x and node['mask'] == 'Train']
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# 确保train_x_nodes列表的长度至少为y
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29 |
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if len(train_x_nodes) < y:
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print(f"Warning: There are fewer than {y} nodes with label {x} and mask 'train'. All {len(train_x_nodes)} nodes will be kept.")
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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
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else:
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# 随机选择y个节点
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selected_nodes = random.sample(train_x_nodes, y)
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# 创建一个删除节点的集合
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deleted_nodes = set(node['node_id'] for node in train_x_nodes if node not in selected_nodes)
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# 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
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new_data = []
|
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for node in data:
|
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# 保留所有的节点,mask非'train'的节点不做任何更改
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if node['label'] != x or (node['mask'] != 'Train' or node in selected_nodes):
|
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new_data.append(node)
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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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|
|
|
|
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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
|