benchtemp 1.1.1

BenchTemp: A General Benchmark for Evaluating Temporal Graph Neural Networks

BenchTemp: A General Benchmark for Evaluating Temporal Graph Neural Networks

Overview

BenchTemp is a general Benchmark Python Library for users to evaluate Temporal Graph Neural Networks (TGNNs) quickly and efficiently on various workloads. BenchTemp provides Benchmark Datasets, and unified pipelines (DataPreprocessor, DataLoader EdgeSampler, Evaluator, EarlyStopMonitor, BCELoss, Optimizer,and Leaderboard ) for evaluating Temporal Graph Neural Networks on both link prediction and node classification tasks.

• The BenchTemp PyPI Website is Here.

• The GitHub of BenchTemp project is Here.

• The datasets are Here.

• The leaderboards website for Temporal Graph Neural Networks on both Link Prediction and Node Classification tasks is Here.

• The source codes for evaluating existing Temporal Graph Neural Networks based on BenchTemp are coming soon.

Installation

Requirements

Please ensure that you have installed the following dependencies:

• numpy >= 1.18.0
• pandas >= 1.2.0
• sklearn >= 0.20.0

BenchTemp PyPI install

pip install benchtemp 

Package Usage

Datasets

The datasets that have been preprocessed by BenchTemp are Here. You can directly download the datasets and then put them into the directory './data'.

In addition, BenchTemp provides data processing functions for you to preprocess yours TGNNs datasets.

Function: benchtemp.preprocessing.data.data_preprocess(data_name : str, bipartite : bool=True)

Parameters:

• data_name : str - the name of the dataset.
• bipartite : bool - Whether the Temporal Graph is bipartite graph.

Returns:

• ml_{data_name}.csv - the csv file of the Temporal Graph.
• ml_{data_name}.npy - the edge features of the Temporal Graph.
• ml_{data_name}_node.npy - the node features of the Temporal Graph.

Example:

import benchtemp as bt

processor = bt.DataPreprocessor(data_path="./data/", data_name="mooc")
# If the dataset is bipartite graph, i.e. the user (source nodes) and the item (destination nodes) are of the same type.
processor.data_preprocess(bipartite=True)

# non-bipartite graph.
processor.data_preprocess(bipartite=False)

Notes:

For bipartite graph, BenchTemp will factorize the source node index and the destination node index, respectively.

import pandas as pd

assert len(sources) == len(destinations)

# bipartite graph
sources, _ = pd.factorize(sources)
destinations, _ = pd.factorize(destinations)

upper_u = sources.max + 1
destinations = destinations + upper_u

For non-bipartite graph, BenchTemp will factorize the concatenation of source node array and the destination node array.

import pandas as pd
import numpy as np

assert len(sources) == len(destinations)
interaction_num = len(sources)

# non-bipartite graph
node_index, _ = pd.factorize(np.concatenate((sources, destinations), axis=0))

sources = node_index[[0:interaction_num]]
destinations = node_index[[interaction_num:interaction_num + interaction_num]]

TemporalData Class

Class:

Data(sources : numpy.ndarray, destinations : numpy.ndarray, timestamps : numpy.ndarray, edge_idxs : numpy.ndarray, labels : numpy.ndarray)

Parameters:

• sources : numpy.ndarray - Array of sources of Temporal Graph edges.
• destinations : numpy.ndarray - Array of destinations of Temporal Graph edges.
• timestamps : numpy.ndarray - Array of timestamps of Temporal Graph edges.
• edge_idxs : numpy.ndarray - Array of edge IDs of Temporal Graph edges.
• labels : numpy.ndarray - Array of labels of Temporal Graphe dges.

Returns:

• benchtemp.Data. A Temporal Graph.

Example:

import pandas as pd
import numpy as np
import benchtemp as bt


graph_df = pd.read_csv("dataset_path")

sources = graph_df.u.values
destinations = graph_df.i.values
edge_idxs = graph_df.idx.values
labels = graph_df.label.values
timestamps = graph_df.ts.values

# For example, the full Temporal Graph of the dataset is full_data.
full_data = bt.Data(sources, destinations, timestamps, edge_idxs, labels)

DataLoader

(1) Link Prediction task

Function:

benchtemp.lp.readers.get_data(dataset_name : str, different_new_nodes_between_val_and_test=False, randomize_features=False)

Parameters:

• dataset_name : str - The name of the dataset. The dataset file (.csv file of the Temporal Graph, .npy file of the node features and .npy file of the edge features) should be in "./data" directory.
• different_new_nodes_between_val_and_test : bool - Different new nodes between the validation and test dataset.
• randomize_features : bool - Random initialization of node Features.

Returns:

• node_features : numpy.ndarray - Array of the Node Features of the Temporal Graph.
• edge_features : numpy.ndarray - Array of the Edge Features of the Temporal Graph.
• full_data : benchtemp.Data - Full Temporal Graph dataset.
• train_data : benchtemp.Data - The training Temporal Graph dataset.
• val_data : benchtemp.Data - The validation Temporal Graph dataset.
• test_data : benchtemp.Data - The transductive test Temporal Graph dataset.
• new_node_val_data : benchtemp.Data - The inductive [new-] setting validation Temporal Graph dataset.
• new_node_test_data : benchtemp.Data - The inductive [new-] setting test Temporal Graph dataset.
• new_old_node_val_data : benchtemp.Data - The inductive [new-old] setting validation Temporal Graph dataset.
• new_old_node_test_data : benchtemp.Data - The inductive [new-old] setting test Temporal Graph dataset.
• new_new_node_val_data : benchtemp.Data - The inductive [new-new] setting validation Temporal Graph dataset.
• new_new_node_test_data : benchtemp.Data - The inductive [new-new] setting test Temporal Graph dataset.
• unseen_nodes_num : int - The number of unseen nodes of inductive setting.

Example:

import benchtemp as bt

data = bt.lp.DataLoader(dataset_path="./data/", dataset_name='mooc')

node_features, edge_features, full_data, train_data, val_data, test_data, new_node_val_data, new_node_test_data, new_old_node_val_data, new_old_node_test_data, new_new_node_val_data, new_new_node_test_data, unseen_nodes_num = data.load()

EdgeSampler

BenchTemp provides the unified negative edge sampler with seed for Link Prediction task to sample an equal amount of negatives to the positive interactions.

Class:

RandEdgeSampler(src_list : numpy.ndarray, dst_list : numpy.ndarray, seed : int =None)

Parameters:

• src_list : numpy.ndarray - the list of source nodes.
• dst_list : numpy.ndarray - the list of destination nodes.
• seed : numpy.ndarray - seed of random.

Returns:

• benchtemp.RandEdgeSampler

Example:

import benchtemp as bt

# For example, if you are training , you should create a training  RandEdgeSampler based on the training dataset.
train_rand_sampler = bt.lp.RandEdgeSampler(train_data.sources, train_data.destinations)

...
for epoch in range(args.epochs):
    ...
    # sample an equal amount of negatives to the positive interactions.
    _, negatives_batch = train_rand_sampler.sample(size)
    ...
...

(2) Node Classification task

Function:

benchtemp.nc.readers.get_data_node_classification((dataset_name : str, use_validation : bool=False))

Parameters:

• dataset_name : str - The name of the dataset. The dataset file (.csv file of the Temporal Graph, .npy file of the node features and .npy file of the edge features) should be in "./data" directory.
• use_validation : bool - Whether use validation dataset or not.

Returns:

• node_features : numpy.ndarray - Array of the Node Features of the Temporal Graph.
• edge_features : numpy.ndarray - Array of the Edge Features of the Temporal Graph.
• full_data : benchtemp.Data - Full Temporal Graph dataset for Node Classification task.
• train_data : benchtemp.Data - The training Temporal Graph dataset for Node Classification task.
• val_data : benchtemp.Data - The validation Temporal Graph dataset for Node Classification task.
• test_data : benchtemp.Data - The test Temporal Graph dataset for Node Classification task.

EarlyStopMonitor

Class:

EarlyStopMonitor(max_round=3, higher_better=True, tolerance=1e-10)

Parameters:

• max_round : int - the maximum number of rounds of EarlyStopMonitor.
• higher_better : bool - better the performance.
• tolerance : float - the tolerance of the EarlyStopMonitor.

Returns:

• benchtemp.EarlyStopMonitor

Example:

import benchtemp as bt

...
early_stopper = bt.EarlyStopMonitor(max_round=args.patience)
for epoch in range(args.epochs):
    ...
    val_ap = model(val_datasets)
    if early_stopper.early_stop_check(val_ap):
        break
    ...
...

Evaluator

Link Prediction Evaluation Metrics are Area Under the Receiver Operating Characteristic Curve (ROC AUC) and average precision (AP)

Node Classification Evaluation Metric is Area Under the Receiver Operating Characteristic Curve (ROC AUC)

Class:

Evaluator(task_name: str = "LP")

Parameters:

• task_name : str - the name of the task, choice in ["LP", "NC"].

Returns:

• benchtemp.Evaluator

Example:

import benchtemp as bt

# For example, Link prediction task. Evaluation Metrics: AUC, AP.
evaluator = bt.Evaluator("LP")

...
# test data
pred_score = model(test_data)
test_auc, test_ap = evaluator.eval(pred_score, true_label)
...

import benchtemp as bt

# For example, Node Classification task. Evaluation Metrics: AUC.
evaluator = bt.Evaluator("NC")

...
# test data
pred_score = model(test_data)
test_auc = evaluator.eval(pred_score, true_label)
...

Call for Contributions

BenchTemp project is looking for contributors with expertise and enthusiasm! If you have a desire to contribute to BenchTemp, please contact BenchTemp team.

\item We release \sys, a general benchmark library for evaluating temporal graph models;

\item We provides unified benckmark temporal graph datasets processed by \sys;

\item We benchmark existing temporal graph models based on \sys for robust developments and analysis the performance of models in detail;

\item We relsed the leaderboards for temporal graph models.