tgb.linkproppred
LinkPropPredDataset
Bases: object
Source code in tgb/linkproppred/dataset.py
28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 |
|
edge_feat: Optional[np.ndarray]
property
Returns the edge features of the dataset with dim [E, feat_dim] Returns: edge_feat: np.ndarray, [E, feat_dim] or None if there is no edge feature
eval_metric: str
property
the official evaluation metric for the dataset, loaded from info.py Returns: eval_metric: str, the evaluation metric
full_data: Dict[str, Any]
property
the full data of the dataset as a dictionary with keys: 'sources', 'destinations', 'timestamps', 'edge_idxs', 'edge_feat', 'w', 'edge_label',
Returns:
Name | Type | Description |
---|---|---|
full_data |
Dict[str, Any]
|
Dict[str, Any] |
negative_sampler: NegativeEdgeSampler
property
Returns the negative sampler of the dataset, will load negative samples from disc Returns: negative_sampler: NegativeEdgeSampler
node_feat: Optional[np.ndarray]
property
Returns the node features of the dataset with dim [N, feat_dim] Returns: node_feat: np.ndarray, [N, feat_dim] or None if there is no node feature
test_mask: np.ndarray
property
Returns the test mask of the dataset: Returns: test_mask: Dict[str, Any]
train_mask: np.ndarray
property
Returns the train mask of the dataset Returns: train_mask: training masks
val_mask: np.ndarray
property
Returns the validation mask of the dataset Returns: val_mask: Dict[str, Any]
__init__(name, root='datasets', meta_dict=None, preprocess=True)
Dataset class for link prediction dataset. Stores meta information about each dataset such as evaluation metrics etc. also automatically pre-processes the dataset. Args: name: name of the dataset root: root directory to store the dataset folder meta_dict: dictionary containing meta information about the dataset, should contain key 'dir_name' which is the name of the dataset folder preprocess: whether to pre-process the dataset
Source code in tgb/linkproppred/dataset.py
download()
downloads this dataset from url check if files are already downloaded
Source code in tgb/linkproppred/dataset.py
generate_processed_files()
turns raw data .csv file into a pandas data frame, stored on disc if not already Returns: df: pandas data frame
Source code in tgb/linkproppred/dataset.py
generate_splits(full_data, val_ratio=0.15, test_ratio=0.15)
Generates train, validation, and test splits from the full dataset Args: full_data: dictionary containing the full dataset val_ratio: ratio of validation data test_ratio: ratio of test data Returns: train_data: dictionary containing the training dataset val_data: dictionary containing the validation dataset test_data: dictionary containing the test dataset
Source code in tgb/linkproppred/dataset.py
load_test_ns()
load_val_ns()
pre_process()
Pre-process the dataset and generates the splits, must be run before dataset properties can be accessed generates the edge data and different train, val, test splits
Source code in tgb/linkproppred/dataset.py
PyGLinkPropPredDataset
Bases: Dataset
Source code in tgb/linkproppred/dataset_pyg.py
10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 |
|
dst: torch.Tensor
property
Returns the destination nodes of the dataset Returns: dst: the idx of the destination nodes
edge_feat: torch.Tensor
property
Returns the edge features of the dataset Returns: edge_feat: the edge features
edge_label: torch.Tensor
property
Returns the edge labels of the dataset Returns: edge_label: the labels of the edges
eval_metric: str
property
the official evaluation metric for the dataset, loaded from info.py Returns: eval_metric: str, the evaluation metric
negative_sampler: NegativeEdgeSampler
property
Returns the negative sampler of the dataset, will load negative samples from disc Returns: negative_sampler: NegativeEdgeSampler
node_feat: torch.Tensor
property
Returns the node features of the dataset Returns: node_feat: the node features
src: torch.Tensor
property
Returns the source nodes of the dataset Returns: src: the idx of the source nodes
test_mask: torch.Tensor
property
Returns the test mask of the dataset: Returns: test_mask: the mask for edges in the test set
train_mask: torch.Tensor
property
Returns the train mask of the dataset Returns: train_mask: the mask for edges in the training set
ts: torch.Tensor
property
Returns the timestamps of the dataset Returns: ts: the timestamps of the edges
val_mask: torch.Tensor
property
Returns the validation mask of the dataset Returns: val_mask: the mask for edges in the validation set
__init__(name, root, transform=None, pre_transform=None)
PyG wrapper for the LinkPropPredDataset
can return pytorch tensors for src,dst,t,msg,label
can return Temporal Data object
Parameters:
name: name of the dataset, passed to LinkPropPredDataset
root (string): Root directory where the dataset should be saved, passed to LinkPropPredDataset
transform (callable, optional): A function/transform that takes in an, not used in this case
pre_transform (callable, optional): A function/transform that takes in, not used in this case
Source code in tgb/linkproppred/dataset_pyg.py
get(idx)
construct temporal data object for a single edge Parameters: idx: index of the edge Returns: data: TemporalData object
Source code in tgb/linkproppred/dataset_pyg.py
get_TemporalData()
return the TemporalData object for the entire dataset
Source code in tgb/linkproppred/dataset_pyg.py
len()
load_test_ns()
load_val_ns()
process_data()
convert the numpy arrays from dataset to pytorch tensors
Source code in tgb/linkproppred/dataset_pyg.py
Evaluator Module for Dynamic Link Prediction
Evaluator
Bases: object
Evaluator for Link Property Prediction
Source code in tgb/linkproppred/evaluate.py
18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 |
|
__init__(name, k_value=10)
Parameters:
Name | Type | Description | Default |
---|---|---|---|
name |
str
|
name of the dataset |
required |
k_value |
int
|
the desired 'k' value for calculating metric@k |
10
|
Source code in tgb/linkproppred/evaluate.py
eval(input_dict, verbose=False)
evaluate the link prediction task this method is callable through an instance of this object to compute the metric
Parameters:
Name | Type | Description | Default |
---|---|---|---|
input_dict |
dict
|
a dictionary containing "y_pred_pos", "y_pred_neg", and "eval_metric" the performance metric is calculated for the provided scores |
required |
verbose |
bool
|
whether to print out the computed metric |
False
|
Returns:
Name | Type | Description |
---|---|---|
perf_dict |
dict
|
a dictionary containing the computed performance metric |
Source code in tgb/linkproppred/evaluate.py
Sample negative edges for evaluation of dynamic link prediction Load already generated negative edges from file, batch them based on the positive edge, and return the evaluation set
NegativeEdgeSampler
Bases: object
Source code in tgb/linkproppred/negative_sampler.py
16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 |
|
__init__(dataset_name, strategy='hist_rnd')
Negative Edge Sampler Loads and query the negative batches based on the positive batches provided. constructor for the negative edge sampler class
Parameters:
Name | Type | Description | Default |
---|---|---|---|
dataset_name |
str
|
name of the dataset |
required |
strategy |
str
|
specifies which set of negatives should be loaded; can be 'rnd' or 'hist_rnd' |
'hist_rnd'
|
Returns:
Type | Description |
---|---|
None
|
None |
Source code in tgb/linkproppred/negative_sampler.py
load_eval_set(fname, split_mode='val')
Load the evaluation set from disk, can be either val or test set ns samples
Parameters:
fname: the file name of the evaluation ns on disk
split_mode: the split mode of the evaluation set, can be either val
or test
Returns:
Type | Description |
---|---|
None
|
None |
Source code in tgb/linkproppred/negative_sampler.py
query_batch(pos_src, pos_dst, pos_timestamp, split_mode='test')
For each positive edge in the pos_batch
, return a list of negative edges
split_mode
specifies whether the valiation or test evaluation set should be retrieved.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
pos_src |
Tensor
|
list of positive source nodes |
required |
pos_dst |
Tensor
|
list of positive destination nodes |
required |
pos_timestamp |
Tensor
|
list of timestamps of the positive edges |
required |
split_mode |
str
|
specifies whether to generate negative edges for 'validation' or 'test' splits |
'test'
|
Returns:
Name | Type | Description |
---|---|---|
neg_samples |
list
|
a list of list; each internal list contains the set of negative edges that should be evaluated against each positive edge. |
Source code in tgb/linkproppred/negative_sampler.py
reset_eval_set(split_mode='test')
Reset evaluation set
Parameters:
Name | Type | Description | Default |
---|---|---|---|
split_mode |
str
|
specifies whether to generate negative edges for 'validation' or 'test' splits |
'test'
|
Returns:
Type | Description |
---|---|
None
|
None |
Source code in tgb/linkproppred/negative_sampler.py
Sample and Generate negative edges that are going to be used for evaluation of a dynamic graph learning model
Negative samples are generated and saved to files ONLY once;
other times, they should be loaded from file with instances of the negative_sampler.py
.
NegativeEdgeGenerator
Bases: object
Source code in tgb/linkproppred/negative_generator.py
25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 |
|
__init__(dataset_name, first_dst_id, last_dst_id, num_neg_e=100, strategy='rnd', rnd_seed=123, hist_ratio=0.5, historical_data=None)
Negative Edge Sampler class this is a class for generating negative samples for a specific datasets the set of the positive samples are provided, the negative samples are generated with specific strategies and are saved for consistent evaluation across different methods negative edges are sampled with 'oen_vs_many' strategy. it is assumed that the destination nodes are indexed sequentially with 'first_dst_id' and 'last_dst_id' being the first and last index, respectively.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
dataset_name |
str
|
name of the dataset |
required |
first_dst_id |
int
|
identity of the first destination node |
required |
last_dst_id |
int
|
indentity of the last destination node |
required |
num_neg_e |
int
|
number of negative edges being generated per each positive edge |
100
|
strategy |
str
|
how to generate negative edges; can be 'rnd' or 'hist_rnd' |
'rnd'
|
rnd_seed |
int
|
random seed for consistency |
123
|
hist_ratio |
float
|
if the startegy is 'hist_rnd', how much of the negatives are historical |
0.5
|
historical_data |
TemporalData
|
previous records of the positive edges |
None
|
Returns:
Type | Description |
---|---|
None
|
None |
Source code in tgb/linkproppred/negative_generator.py
generate_historical_edge_set(historical_data)
Generate the set of edges seen durign training or validation
ONLY train_data
should be passed as historical data; i.e., the HISTORICAL negative edges should be selected from training data only.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
historical_data |
TemporalData
|
contains the positive edges observed previously |
required |
Returns:
Name | Type | Description |
---|---|---|
historical_edges |
tuple
|
distict historical positive edges |
hist_edge_set_per_node |
tuple
|
historical edges observed for each node |
Source code in tgb/linkproppred/negative_generator.py
generate_negative_samples(data, split_mode, partial_path)
Generate negative samples
Parameters:
Name | Type | Description | Default |
---|---|---|---|
data |
TemporalData
|
an object containing positive edges information |
required |
split_mode |
str
|
specifies whether to generate negative edges for 'validation' or 'test' splits |
required |
partial_path |
str
|
in which directory save the generated negatives |
required |
Source code in tgb/linkproppred/negative_generator.py
generate_negative_samples_hist_rnd(historical_data, data, split_mode, filename)
Generate negative samples based on the HIST-RND
strategy:
- up to 50% of the negative samples are selected from the set of edges seen during the training with the same source node.
- the rest of the negative edges are randomly sampled with the fixed source node.
Parameters:
Name | Type | Description | Default |
---|---|---|---|
historical_data |
TemporalData
|
contains the history of the observed positive edges including distinct positive edges and edges observed for each positive node |
required |
data |
TemporalData
|
an object containing positive edges information |
required |
split_mode |
str
|
specifies whether to generate negative edges for 'validation' or 'test' splits |
required |
filename |
str
|
name of the file to save generated negative edges |
required |
Returns:
Type | Description |
---|---|
None
|
None |
Source code in tgb/linkproppred/negative_generator.py
217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 |
|
generate_negative_samples_rnd(data, split_mode, filename)
Generate negative samples based on the HIST-RND
strategy:
- for each positive edge, sample a batch of negative edges from all possible edges with the same source node
- filter actual positive edges
Parameters:
Name | Type | Description | Default |
---|---|---|---|
data |
TemporalData
|
an object containing positive edges information |
required |
split_mode |
str
|
specifies whether to generate negative edges for 'validation' or 'test' splits |
required |
filename |
str
|
name of the file containing the generated negative edges |
required |