Expert Systems With Applications 241 (2024) 122685

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Expert Systems With Applications

journal homepage: www.elsevier.com/locate/eswa

Dynamic link prediction by learning the representation of node-pair via

graph neural networks
Hu Dong a , Longjie Li a,b ,∗, Dongwen Tian a , Yiyang Sun a , Yuncong Zhao a
a
School of Information Science and Engineering, Lanzhou University, Lanzhou 730000, China
b
Key Laboratory of Media Convergence Technology and Communication, Gansu Province, Lanzhou 730000, China

ARTICLE INFO ABSTRACT

Keywords: Many real-world networks are dynamic, whose structure keeps changing over time. Link prediction, which
Link prediction can foretell the emergence of future links, is one crucial task in dynamic network analysis. Compared to link
Dynamic networks prediction in static networks, it is more challenging and complicated in dynamic ones due to the dynamic
Graph neural networks
nature. On the other hand, effective use of the information carried out by dynamic networks can enhance
Representations learning
prediction accuracy. In this study, we presents a new end-to-end solution for dynamic link prediction, in
which the representations of node-pairs can be effectively learned via an improved graph neural network and
a nonlinear function by leveraging the structural information of individual snapshots, historical features from
network evolution, and global knowledge of the collapsed network. The proposed method can effectively cope
with the challenge of dynamic link prediction. Extensive tests are implemented on several dynamic networks
to assess the prediction performance of our proposed method. The results on these networks demonstrate that
our proposed method achieves superior effectiveness compared to the baselines in most cases.

1. Introduction
Many complicated systems in the real world can be naturally repre-
sented by complex networks (Boccaletti et al., 2006), in which entities
and relationship between them are modeled as nodes and links, re-
spectively. Link prediction (Liben-Nowell & Kleinberg, 2007; Martínez
et al., 2017), which aims to uncover missing links and foretell new
connections in a network, is a crucial task of complex network analysis.
In a host of applications, such as friendships recommendation in online
social networks (Adamic & Adar, 2003; Li et al., 2020), product rec-
ommendation in e-commerce websites (Xie et al., 2015), and protein
interaction prediction in biological networks (Hamilton et al., 2017),
link prediction plays a critical role. To date, researchers have developed
numerous methods to handle the link prediction problem by computing
the similarities of nodes or training prediction models (Daud et al.,
2020; Zhou, 2021). However, the majority of these techniques are
developed for static networks, which do not take the evolution of
networks into account.
Actually, most of the real-world networks keep evolving with time.
For instance, the connections between individuals in a social network
are usually dynamically varying in accordance with the behaviors of
their social partners (Ibrahim & Chen, 2015). These kinds of networks
are called dynamic networks, which can provide more accurate descrip-
tions for complex systems (Holme & Saramäki, 2012; Yang et al., 2020).
Compared to link prediction in static networks, link prediction in a
dynamic network (i.e., dynamic link prediction) is a challenging and
complex process because not only the current structure of the network
but also its historical evolution affect the formation of links (Divakaran
& Mohan, 2020; Selvarajah et al., 2020).
To address the problem of dynamic link prediction, one simple effort
is to collapse a dynamic network into a collapsed network (Lei et al.,
2019; Yang et al., 2020) and then to predict links on the collapsed net-
work (Liben-Nowell & Kleinberg, 2007; Sharan & Neville, 2008). How-
ever, such approaches ignore the evolution information of consecutive
snapshots, which leads to undesirable prediction performance. To over-
come this weakness, (Wu et al., 2020) introduced a similarity-based
approach that uses node ranking to determine the similarity of two
nodes and predicts their future similarity using the historical similarity
series. Chiu and Zhan (2018) proposed a deep learning-based method,
in which features of node-pair are denoted using weak estimators
and conventional similarity indexes. In recent years, node embedding
approaches like DeepWalk (Perozzi et al., 2014) and node2vec (Grover
& Leskovec, 2016), have been designed to project the representation
of a node into a low-dimensional vector space. Subsequently, some

∗ Corresponding author at: School of Information Science and Engineering, Lanzhou University, Lanzhou 730000, China.
E-mail addresses: dongh20@lzu.edu.cn (H. Dong), ljli@lzu.edu.cn (L. Li), tiandw21@lzu.edu.cn (D. Tian), sunyy20@lzu.edu.cn (Y. Sun),
zhaoyc20@lzu.edu.cn (Y. Zhao).

https://doi.org/10.1016/j.eswa.2023.122685
Received 19 June 2023; Received in revised form 12 October 2023; Accepted 19 November 2023
Available online 23 November 2023
0957-4174/© 2023 Elsevier Ltd. All rights reserved.
H. Dong et al.
researchers (De Winter et al., 2018; Tripathi et al., 2022) proposed
to predict links in dynamic networks by learning node embeddings in
historical snapshots. However, in these methods, the representations
of nodes are not learned from the downstream task. As a result,
their performance may not be satisfactory. Due to their ability to
extract effective node representations according to downstream tasks,
graph neural networks (GNNs) (Zhou et al., 2020) have been adopted
to handle link prediction (Yang et al., 2020; Zhang & Chen, 2018).
Moreover, the long short-term memory network (LSTM) (Hochreiter
& Schmidhuber, 1997) has been used to learn the temporal features
from historical snapshots of a dynamic network (Chen et al., 2021;
Selvarajah et al., 2020).
To address the problem of dynamic link prediction, this work de-
signs a new method, named DLP-LRN (Dynamic Link Prediction by
Learning the Representation of Node-pair). The DLP-LRN method first
learns multiple representations of a node-pair from different snapshots
via an improved GNN, and then aggregates these representations using
a nonlinear function. Moreover, DLP-LRN also learns the representation
of the node-pair from the collapsed network to replenish some global
information. Then, the final representation of the node-pair is obtained
by fusing the above two parts, and sent to a Multi-Layer Perception
(MLP) to determine if the node-pair will have a link. In summary, we
have the following main contributions:
(1) We propose a new dynamic link prediction method, in which
the representation of a node-pair is learned from both multiple
snapshots and the collapsed network.
(2) We design an improved GNN to learn the representation of a
node-pair from each snapshot and adopts a nonlinear function
to aggregate the representations of the node-pair from multiple
snapshots.
(3) We validate the effectiveness of the proposed method via exten-
sive experiments on six dynamic networks.
The rest of this paper is structured as follows. Section 2 briefly
introduce the related work. Section 3 defines the problem of dynamic
link prediction. The detailed description of the proposed method is
shown in Section 4. Comparison with baseline and ablation study
are discussed in Section 5. At last, Section 6 concludes the proposed
method.
2. Related work
We briefly sum up the research on deep learning-based dynamic
link prediction in this section. (Chiu & Zhan, 2018) proposed a deep
learning-based method to perform dynamic link prediction, which gen-
erated the feature vectors of node-pairs using static similarity metrics
and weak estimators, and trained a prediction model via a deep neu-
ral network. However, the features of node-pairs in the approach
are handcrafted, thereby limiting its generalization ability. In this
regard, Tripathi et al. (2022) developed an embedding-based dynamic
link prediction method, where they learned node embeddings using bi-
ased random walk and skip-gram model, and derived edge embeddings
via a max aggregator. Likewise, (De Winter et al., 2018) learned node
embeddings using node2vec (Grover & Leskovec, 2016) and computed
the Hadamard product of node embeddings to get the embeddings of
node-pairs. Then, embeddings of a node-pair from multiple snapshots
were integrated with simple concatenation. At last, a classifier was
trained to complete the dynamic link prediction task. Hao et al. (2020)
presented a link prediction model that combined node vector evolution
and local neighborhood representation. In their model, node vectors
are learned by some node embedding algorithm, and edge representa-
tions are obtained according to node vectors and local neighborhood
information.
However, the above algorithms are not end-to-end ones, i.e., the
learning of embeddings is independent of link prediction. Owing to
2
Expert Systems With Applications 241 (2024) 122685
their ability to capture critical characteristics of networks for down-
stream tasks, GNNs have been applied in link prediction. Chen et al.
(2021) designed an end-to-end dynamic link prediction paradigm using
the Graph Convolution Network (GCN) (Kipf & Welling, 2017) em-
bedded LSTM (Hochreiter & Schmidhuber, 1997), named GC-LSTM.
In this model, GCN is embedded in LSTM cell to better learn spatio-
temporal features. In order to conduct link prediction in weighted
dynamic networks, Lei et al. (2019) presented the model of GCN-GAN,
which utilized GCN, LSTM, and the generative adversarial network
(GAN) (Goodfellow et al., 2014) to exploit multiple kinds of infor-
mation extracted from weighted dynamic networks. Li et al. (2022)
proposed the TSAM model to deal with dynamic link prediction in
directed networks, where graph attentional layers and graph convolu-
tional layers were used to capture neighborhood structural features and
motif features, respectively. Moreover, temporal features were learned
via a graph recurrent unit layer with self-attention. Jiao et al. (2021)
developed a temporal network embedding approach for link prediction,
where the essential features of temporal networks were learned by a
variational autoencoder.
Research gap: Although the above studies have handled the dy-
namic link prediction problem using different techniques and designs,
there are still some shortcomings in them. The features of node-pairs
used in Chiu and Zhan (2018) are handcrafted, which may fail to
express some complex nonlinear patterns that actually determine the
link formations (Zhang & Chen, 2018). Hao et al. (2020), Tripathi
et al. (2022) and De Winter et al. (2018), represented node-pairs based
on node embeddings that were learned according to the topological
structures of a network. However, the embeddings of nodes are learned
independently of the downstream task. As a result, the key character-
istics that determine link formation may not be captured. The methods
in Chen et al. (2021), Jiao et al. (2021), Lei et al. (2019) and Li
et al. (2022) are end-to-end ones, which learn node embeddings using
GNNs. Essentially, link prediction is a binary classification problem
that predicts the label of a node-pair. Therefore, it is better to directly
learn the features of node-pairs rather than the embeddings of nodes.
In addition, all of these methods forecast links using the information
obtained from the snapshots. None of them further consider to learn
some global information from the collapsed network.
3. Problem definition
A dynamic network is described by a series of network snapshots
 = {𝐺1 , 𝐺2 , … , 𝐺𝑇 }, in which 𝐺𝑡 = (𝑉 , 𝐸𝑡 ) is a snapshot of the dynamic
network at time 𝑡. For simplicity, we assume that the nodes remain
unchanged across all snapshots. In this work, 𝑉 specifies all nodes in
 and 𝐸𝑡 denotes the set of links (edges) appeared in the snapshot
𝐺𝑡 . We can use the adjacency matrix 𝐀𝑡 = [𝑎𝑡;𝑖,𝑗 ]𝑁×𝑁 to depict the
topological structure of 𝐺𝑡 , here 𝑁 = |𝑉 | is the number of nodes in
the dynamic network. If nodes 𝑣𝑖 and 𝑣𝑗 are linked in 𝐺𝑡 , 𝑎𝑡;𝑖,𝑗 = 1;
otherwise 𝑎𝑡;𝑖,𝑗 = 0.
In a static network, the purpose of link prediction is to uncover
the links that are actually existent but unknown based on the observed
network structures. However, link prediction in a dynamic network pre-
dicts the future structure of the network according to the information
obtained from previous snapshots. Given 𝑙 + 1 consecutive snapshots,
denoted as {𝐺𝑇 −𝑙 , 𝐺𝑇 −𝑙+1 , … , 𝐺𝑇 }, the task of dynamic link prediction
is to forecast the network structure at time 𝑇 + 1, i.e., 𝐺𝑇 +1 , according
to the information of previous 𝑙+1 snapshots. Mathematically, dynamic
link prediction can be described as
𝐺𝑇 +1 = 𝑓 (𝐺𝑇 −𝑙 , 𝐺𝑇 −𝑙+1 , … , 𝐺𝑇 ), (1)
where 𝑓 (⋅) is a function that converts the input snapshots to graph 𝐺𝑇 +1 .
H. Dong et al.
Fig. 1. The overall framework of the DLP-LRN method.
Fig. 2. Subgraph extraction and feature vector initialization.
4. The proposed method
4.1. Model overview
The motivation of this study is to design an end-to-end link predic-
tion method for dynamic networks, in which we are able to learn the
features of node-pairs directly, rather than learning the embeddings of
nodes individually. Specially, in order to learn more accurate represen-
tations of node-pairs, this method should leverage not only the informa-
tion from consecutive snapshots but also the overall information from
the collapsed network.
To this end, we propose a new method, namely DLP-LRN, to address
the problem of dynamic link prediction. Fig. 1 presents the framework
of DLP-LRN, which is made up of the following three components:
(1) Feature learning from snapshots (Part A in Fig. 1). Given a target
node-pair, 𝑙 + 1 subgraphs around this node-pair are extracted
from different snapshots of the dynamic network. Then, the
feature representation of the node-pair with respect to each
subgraph is learned via a GNN. Subsequently, all feature rep-
resentations of the node-pair are aggregated with a nonlinear
function.
(2) Feature learning from collapsed network (Part B in Fig. 1). In this
component, we first combine the 𝑙 + 1 snapshot networks into a
collapsed network. Next, a subgraph around the target node-pair
is extracted, and then the feature representation of the node-pair
with respect to the subgraph is learned.
(3) Feature fusion and link prediction (Part C in Fig. 1). Both kinds
of feature representation of the target node-pair are combined in
this component. Then, we feed the combined feature vector into
an MLP to predict whether the link of the node-pair exists.
3
Expert Systems With Applications 241 (2024) 122685
4.2. Feature learning from snapshots
4.2.1. Subgraph extraction and feature vector initialization
To gauge whether a link exists among two nodes, the topological
structure surrounding them plays a key role. As a consequence, some
studies, such as SEAL (learning from Subgraphs, Embeddings and At-
tributes for Link prediction) (Zhang & Chen, 2018), SHFF (Subgraph
Hierarchy Feature Fusion) (Liu et al., 2020), and DLP-LES (Dynamic
network Link Prediction by Learning Effective Subgraphs) (Selvarajah
et al., 2020), extract subgraphs for target node-pairs, and then learn
their features from the subgraphs. Inspired by the same idea, in this
work, we also extract subgraphs for node-pairs to learn their feature
representations. Given a target node-pair (𝑣𝑖 , 𝑣𝑗 ) and a snapshot 𝐺𝑡
in the network , this component first extracts an ℎ-hop enclosing
ℎ . Fig. 2 shows the
subgraph around (𝑣𝑖 , 𝑣𝑗 ) from 𝐺𝑡 , marked as 𝐺𝑡;𝑖,𝑗
process of this step. In this study, we employ the method used in
SEAL (Zhang & Chen, 2018) to extract the enclosing subgraph. The
ℎ-hop neighborhood of (𝑣𝑖 , 𝑣𝑗 ) is defined as
𝛤𝑡ℎ (𝑣𝑖 , 𝑣𝑗 ) = {𝑣𝑘 |𝑣𝑘 ∈ 𝐺𝑡 , min(𝑑(𝑣𝑘 , 𝑣𝑖 ), 𝑑(𝑣𝑘 , 𝑣𝑗 )) ≤ ℎ}, (2)
ℎ
where 𝑑(𝑣𝑘 , 𝑣𝑖 ) is the distance between 𝑣𝑘 and 𝑣𝑖 . 𝐺𝑡;𝑖,𝑗 is the subgraph
induced by 𝛤𝑡ℎ (𝑣𝑖 , 𝑣𝑗 ) ∪ {𝑣𝑖 , 𝑣𝑗 }.
ℎ ,
Next, we generate the feature vectors for all nodes in subgraph 𝐺𝑡;𝑖,𝑗
which are regarded as their initial features. The feature vector of a
ℎ is composed of two parts. The first part is the information
node in 𝐺𝑡;𝑖,𝑗
associated with the node. If there is no initial information associated
with nodes in the network, we can employ some embedding method,
such as LINE (Large-scale Information Network Embedding) (Tang
et al., 2015) and node2vec (Grover & Leskovec, 2016), to extract a
representation for each node. The second part is the structural label of
the node denoted by a one-hot vector. The purpose of node labeling is
to distinguish the positions of nodes in an enclosing subgraph. Here, we
use the DRNL (Double Radius Node Labeling) method (Zhang & Chen,
2018) to obtain node labels in the subgraph.
H. Dong et al. Expert Systems With Applications 241 (2024) 122685

Fig. 3. Feature learning from subgraph.

4.2.2. Feature learning from subgraph 4.2.3. Feature aggregation from snapshots
ℎ
After obtaining the enclosing subgraph 𝐺𝑡;𝑖,𝑗 and the initial feature Since we have 𝑙 + 1 snapshots, we can get 𝑙 + 1 representations of
vectors of nodes in the subgraph, the representation of node-pair (𝑣𝑖 , 𝑣𝑗 ) 𝑇 −𝑙 , 𝐙𝑇 −𝑙+1 , … , 𝐙𝑇 . In
node-pair (𝑣𝑖 , 𝑣𝑗 ) from the last step, which are 𝐙𝑖𝑗 𝑖𝑗 𝑖𝑗
with respect to snapshot 𝐺𝑡 is learned in this step. The process is de- this step, we introduce an exponential function to aggregate the 𝑙 + 1
ℎ centers on (𝑣 , 𝑣 ), we
picted in Fig. 3. Since the enclosing subgraph 𝐺𝑡;𝑖,𝑗 𝑖 𝑗 representations which is defined as
believe that not only the representation of (𝑣𝑖 , 𝑣𝑗 ) is critical to the link
∑
𝑇
prediction task, but also the representations of other nodes are benefit 𝐙(𝑠) (1 − 𝛽)𝑇 −𝑡 ∗ 𝐙𝑡𝑖𝑗 , (5)
𝑖𝑗 =
to the task. To this end, we improve the Deep Graph Convolutional 𝑡=𝑇 −𝑙
Neural Network (DGCNN) (Zhang et al., 2018) to achieve our goal.
DGCNN is a GNN architecture for graph classification, and thence it where 𝛽 is a learnable weight within the range [0, 1], 𝐙(𝑠) 𝑖𝑗 denotes the
outputs the embedding of the subgraph. In addition to the embedding representation of node-pair (𝑣𝑖 , 𝑣𝑗 ) learned from the 𝑙 + 1 snapshots.
of the subgraph, in our method, we also use the embeddings of both 𝑣𝑖
and 𝑣𝑗 . To be specific, the process of this step is described below. 4.3. Feature learning from collapsed network
(1) At first, we use multiple graph convolution layers to learn the
embeddings of nodes in subgraph 𝐺𝑡;𝑖,𝑗 ℎ . Given an enclosing subgraph, In the proposed DLP-LRN model, we learn the representations of
denoted by adjacency matrix 𝐀, the form of the graph convolution layer node-pairs from not only individual snapshots but also the general
in DGCNN is structure of the network. Therefore, we summarize the multiple snap-
shots as a collapsed network (Lei et al., 2019; Yang et al., 2020), and
̃ −1 𝐀𝐗𝐖)
𝐙 = 𝑓 (𝐃 ̃ (3) learn the representation of a node-pair from the collapsed network.
where 𝐀 ̃ is the adjacency matrix of the enclosing subgraph with self- We are given a dynamic network with 𝑙 + 1 snapshots,
connection, 𝐀 ̃ = 𝐀 + 𝐈 (𝐈 is an identify matrix). 𝐃 ̃ is the diagonal  = {𝐺𝑇 −𝑙 , 𝐺𝑇 −𝑙+1 , … , 𝐺𝑇 }, in which 𝐺𝑡 = (𝑉 , 𝐸𝑡 ), 𝑡 ∈ [𝑇 − 𝑙, 𝑇 ].
matrix with 𝐃 ̃ 𝑖𝑖 = ∑ 𝐀 ̃ The collapsed network of  is denoted as 𝐺(𝑐) (𝑉 , 𝐸(𝑐) ), where 𝐸(𝑐) =
𝑗 𝑖𝑗 , 𝐖 is a trainable parameter matrix, and 𝑓
is a nonlinear activation function. 𝐗 is the feature matrix, each row ∪𝑇𝑡=𝑇 −𝑙 𝐸𝑡 .
of which is the feature vector of a node in the subgraph. 𝐙 is the Given the collapsed network 𝐺(𝑐) and the target node-pair (𝑣𝑖 , 𝑣𝑗 ), we
embedding matrix of nodes learned by this graph convolution layer. learn the representation of (𝑣𝑖 , 𝑣𝑗 ) from 𝐺(𝑐) using the same approach
(2) Next, we take out the embeddings of nodes 𝑣𝑖 and 𝑣𝑗 with respect as in the last component. Specifically, we extract an ℎ-hop enclosing
ℎ , denoted as 𝐙𝑡 and 𝐙𝑡 , respectively. Then, we use Hadamard ℎ
subgraph around (𝑣𝑖 , 𝑣𝑗 ) from 𝐺(𝑐) , denoted as 𝐺(𝑐);𝑖,𝑗 , and then initialize
to 𝐺𝑡;𝑖,𝑗 𝑖 𝑗
product between 𝐙𝑡𝑖 and 𝐙𝑡𝑗 , i.e., 𝐙𝑡𝑖 ⊙ 𝐙𝑡𝑗 , to capture the structural inter- ℎ
the representation of each node in 𝐺(𝑐);𝑖,𝑗 . Subsequently, the represen-
action features of (𝑣𝑖 , 𝑣𝑗 ). Hadamard product is a matrix multiplication ℎ
tation of (𝑣𝑖 , 𝑣𝑗 ) with respect to 𝐺(𝑐);𝑖,𝑗 are learned via our improved
that takes in two matrices of the same dimensions and returns a matrix DGCNN. Suppose 𝐙(𝑐) (𝑐)
𝑖 and 𝐙𝑗 are the embeddings of nodes 𝑣𝑖 and 𝑣𝑗 ,
of the multiplied corresponding elements. Particularly, the Hadamard
and 𝐙(𝑐) ℎ
is the embedding of 𝐺(𝑐);𝑖,𝑗 according to the improved DGCNN,
product of two embeddings is the element-wise multiplication of the 𝐺
ℎ
two embeddings. the representation of (𝑣𝑖 , 𝑣𝑗 ) with respect to 𝐺(𝑐);𝑖,𝑗 is computed as
(3) As mentioned above, besides the features of (𝑣𝑖 , 𝑣𝑗 ), the embed-
𝐙(𝑐) (𝑐) (𝑐) (𝑐)
𝑖𝑗 = (𝐙𝑖 ⊙ 𝐙𝑗 ) ∥ 𝐙𝐺 . (6)
ding of the subgraph is also considered when learning the representa-
tion of (𝑣𝑖 , 𝑣𝑗 ). In this regard, we employ the SortPooling layer (Zhang
4.4. Feature fusion and link prediction
et al., 2018) to obtain the subgraph’s embedding. Afterward, we use
two 1-D convolution layers to reduce the dimension and enhance the
expressiveness of the subgraph’s embedding. For the sake of conve- After obtaining the representations 𝐙(𝑠) (𝑐)
𝑖𝑗 , 𝐙𝑖𝑗 of node-pair (𝑣𝑖 , 𝑣𝑗 ),
nience, we adopt the notation of 𝐙𝑡𝐺 to indicate the output of the 1-D DLP-LRN gets the final representation of (𝑣𝑖 , 𝑣𝑗 ) using the following
convolution layers. concatenation operation:
(4) Finally, we achieve the representation of (𝑣𝑖 , 𝑣𝑗 ) with respect to 𝐙𝑖𝑗 = 𝐙(𝑠) (𝑐)
(7)
ℎ 𝑖𝑗 ∥ 𝐙𝑖𝑗 .
𝐺𝑡;𝑖,𝑗 as
Then, DLP-LRN employs an MLP to compute the class of (𝑣𝑖 , 𝑣𝑗 ). The
𝐙𝑡𝑖𝑗 = (𝐙𝑡𝑖 ⊙ 𝐙𝑡𝑗 ) ∥ 𝐙𝑡𝐺 , (4) MLP used in our method includes three layers, which takes 𝐙𝑖𝑗 as the
where ∥ represents concatenation. According to Eq. (4), 𝐙𝑡𝑖𝑗 is composed input and outputs 0 or 1 as the class of (𝑣𝑖 , 𝑣𝑗 ). Here, 1 means a link
of two parts (as shown in Fig. 3). The first part is the Hadamard product exists between 𝑣𝑖 and 𝑣𝑗 , whereas 0 indicates no link between 𝑣𝑖 and 𝑣𝑗 .
of 𝐙𝑡𝑖 and 𝐙𝑡𝑗 , which highlights the importance of the target node-pair. In our model, we choose the binary cross-entropy function to compute
The second one is the embedding of the subgraph 𝐺𝑡;𝑖,𝑗 ℎ (i.e., 𝐙𝑡 ), which the loss:
1 ∑ [ ]
𝐺
further supplements some structural information of the subgraph to = − 𝑦𝑖𝑗 ln(𝑦̂𝑖𝑗 ) + (1 − 𝑦𝑖𝑗 ) ln(1 − 𝑦̂𝑖𝑗 ) , (8)
the target node-pair. To generate 𝐙𝑡𝑖𝑗 , we combine both parts using 
the concatenation operator, with the purpose of incorporating but not where 𝑦𝑖𝑗 is the label of (𝑣𝑖 , 𝑣𝑗 ), 𝑦̂𝑖𝑗 is the predicted result of (𝑣𝑖 , 𝑣𝑗 ), and
mixing them together.  is the number of samples of node-pairs.

4
H. Dong et al. Expert Systems With Applications 241 (2024) 122685

Table 1 Table 2
Topological information of the six networks. #Nodes and #Edges denote the union of AUC results of DLP-LRN and baselines. For each benchmark, the optimal value is
nodes and edges of all snapshots. presented in bold and the suboptimal value is underlined.
Enron Rado Forum Mess Call Digg Data Enron Rado Forum Mess Call Digg Mean
#Nodes 150 167 899 1899 6416 30 398 JC 0.8996 0.8579 0.6420 0.7055 0.5162 0.5284 0.6916
#Edges 1588 3251 7046 15 737 7250 86 312 AA 0.9035 0.9148 0.6190 0.7315 0.5165 0.5284 0.7023
Density 0.1421 0.2345 0.0175 0.0087 0.0004 0.0002 Node2vec 0.8105 0.8335 0.8264 0.8137 0.9025 0.5326 0.7865
Average degree 21.17 38.93 15.58 16.57 2.26 5.68 SEAL 0.8769 0.8896 0.8683 0.9065 0.9869 0.8489 0.8966
#Snapshots 8 9 6 6 7 5 LinkVec 0.8849 0.8573 0.8794 0.9376 0.9156 0.7152 0.8650
Winter’s 0.9142 0.9206 0.9568 0.9183 0.9739 0.8061 0.9150
GC-LSTM 0.9131 0.9278 0.9281 0.9475 0.9875 0.8322 0.9227
Hao’s 0.9213 0.9293 0.9465 0.9325 0.9844 0.8364 0.9250
5. Experiments DLP-LRN 0.9364 0.9338 0.9506 0.9757 0.9987 0.8701 0.9442

Table 3
In order to demonstrate the effectiveness of our DLP-LRN method,
AP results of DLP-LRN and baselines. For each benchmark, the optimal value is
multiple experiments are carried out on a collection of dynamic net- presented in bold and the suboptimal value is underlined.
works in this section. We adopt both AUC (area under the receiver oper- Data Enron Rado Forum Mess Call Digg Mean
ating characteristic curve) (Provost & Fawcett, 1997) and AP (average JC 0.8936 0.8315 0.5773 0.6332 0.5050 0.5244 0.6608
precision) (Aslam et al., 2005) as the evaluation metrics. AA 0.8997 0.9076 0.6584 0.7277 0.5204 0.5281 0.7070
Node2vec 0.8053 0.8255 0.7949 0.9009 0.8912 0.5431 0.7935
For our DLP-LRN method, the hop ℎ of enclosing subgraphs is set to SEAL 0.8742 0.8857 0.8803 0.8909 0.9747 0.8482 0.8923
1 because, when ℎ ≤ 2, it has no significant performance improvement LinkVec 0.8730 0.8446 0.8671 0.9155 0.9136 0.7028 0.8528
but is more time consuming. The learning rate is 0.0001 and patience Winter’s 0.9117 0.9088 0.9555 0.9110 0.9703 0.8007 0.9097
GC-LSTM 0.9075 0.9205 0.9269 0.9457 0.9851 0.8437 0.9215
is 10 in the early stopping strategy. The dimensions for the three graph
Hao’s 0.9285 0.9218 0.9428 0.9376 0.9812 0.8428 0.9258
convolution layers in the improved DGCNN are (128 + 𝑚𝑎𝑥_𝑙𝑎𝑏𝑒𝑙, 32), DLP-LRN 0.9412 0.9346 0.9532 0.9750 0.9987 0.8728 0.9459
(32, 32), and (32, 1), where 𝑚𝑎𝑥_𝑙𝑎𝑏𝑒𝑙 is the longest vector dimension
formed by node labels in historical snapshots. The detail settings of
DLP-LRN can be find in our codes.1
5.2. Comparison with baselines

The baselines methods are Jaccard Coefficient (JC) (Liben-Nowell

5.1. Benchmark networks
In our experiments, six dynamic networks are utilized. Table 1
outlines their basic statistics and the following provides their succinct
overview.
Enron: This network is generated according to the email commu-
nication among employees of the company of Enron (Rossi & Ahmed,
2015).
Rado: This is another email network among staffs of a mid-sized
manufacturing company (Rossi & Ahmed, 2015).
Forum: This network was compiled in 2004 from a student social
networking forum at the University of California, Irvine (Opsahl, 2013).
The network recorded student activities in the forum between May and
October 2004.
Mess: This network records the message sending of students from
the University of California, Irvine in an online community from in
April to October 2004 (Opsahl & Panzarasa, 2009).
Call: This network is composed of mobile phone calls between a
group of students at MIT from September 2004 to January 2005 (Eagle
& (Sandy) Pentland, 2006). The network was gathered by the Reality
Mining experiment performed in 2004.
Digg: This network is complied from the social website Digg (De
Choudhury et al., 2009). In the network, users are modeled as nodes
and the replays between users are denoted as edges. The dataset covers
a period from October 29 to November 13 2008.
In our experiments, the edges in the last snapshot are partitioned
into a training set, a validation set, and a testing set. The percentages of
edges contained in the three sets are 70%, 10%, and 20%, respectively.
We also sample the same numbers of unconnected node-pairs (negative
samples) for the three sets to keep the balance of class.
1
https://github.com/ljlilzu/DLP-LRN
& Kleinberg, 2007), Adamic–Adar (AA) index (Adamic & Adar, 2003),
node2vec (Grover & Leskovec, 2016), SEAL (Zhang & Chen, 2018),
LinkVec (Tripathi et al., 2022), Winter’s method (De Winter et al.,
2018), GC-LSTM (Chen et al., 2021), and Hao’s method (Hao et al.,
2020). Among these methods, JC and AA are two similarity ones
that compute the similarities of node-pairs based on local structures.
Node2vec is a node embedding method. We use Hadamard product
between the embeddings of two nodes to obtain the representation of
the node-pair, then we adopt logistic regression to gauge the linked
probability of the node-pair. SEAL is an end-to-end link prediction
method based on GNN. Since these four methods are designed for
static networks, we apply them on the collapsed network. LinkVec,
Winter’s method, GC-LSTM, and Hao’s Method are dynamic link predic-
tion methods. LinkVec (Tripathi et al., 2022) uses Skip-gram and max
aggregator to learn edge embeddings for link prediction. In Winter’s
method (De Winter et al., 2018), the embedding of a node-pair in
a snapshot is obtained based on node2vec; embeddings of the node-
pair in different snapshots are aggregated with simple concatenation.
GC-LSTM (Chen et al., 2021) is an end-to-end approach with GCN
embedded LSTM. Hao et al. (2020) use a gated recurrent unit network
to learn node representation, and train a binary classifier to forecast
links.
The experimental results subject to AUC and AP are reported in Ta-
bles 2 and 3, respectively. For the AUC results in Table 2, the proposed
DLP-LRN method outperforms all baselines on all networks except
Forum, and achieves the suboptimal score on Forum. While JC and AA
perform the worst on most networks because they only consider the
local structural information. Furthermore, Winter’s method, GC-LSTM,
and Hao’s method all have higher AUC scores in most cases than other
baselines. The reason is the three methods have the ability to capture
the dynamic characteristics of networks, whereas other baselines are
inadequate for dynamic link prediction because they are designed for
static networks. Moreover, subject to the average AUC score shown
in the last column of Table 2, our proposed method outnumbers all
baselines. Besides, the similar phenomenon can be observed from the
AP results presented in Table 3. As a consequence, the proposed DLP-
LRN method achieved the best prediction performance compared to
these baselines.

5
H. Dong et al. Expert Systems With Applications 241 (2024) 122685

Fig. 4. Performance of DLP-LRN with different ways for aggregating historical information.

Table 4 than the earlier ones. On the other hand, it is easy to know that
Performance of DLP-LRN with different ways for representation learning of node-pair.
the aggregation operation based on the exponential function is much
𝐇𝑖𝑗 means the Hadamard product of nodes, 𝐙𝐺 indicates the embedding of subgraph,
and 𝐇𝑖𝑗 ∥ 𝐙𝐺 is the way proposed in this work, i.e., the concatenation of Hadamard faster than that based on LSTM. Therefore, the exponential function is
product of nodes and the embedding of subgraph. appropriate for our method.
Metric Way Enron Rado Forum Mess Call Digg
𝐇𝑖𝑗 0.9257 0.9231 0.9463 0.9769 0.9955 0.8436
AUC 𝐙𝐺 0.9234 0.9229 0.9317 0.9400 0.9932 0.8573 5.3.3. Influence of the collapsed network
𝐇𝑖𝑗 ∥ 𝐙𝐺 0.9364 0.9338 0.9506 0.9757 0.9987 0.8701
In our DLP-LRN method, we introduce the collapsed network for a
𝐇𝑖𝑗 0.9320 0.9242 0.9429 0.9725 0.9952 0.8501
dynamic network to describe its summarized structure. In the previous
AP 𝐙𝐺 0.9299 0.9240 0.9238 0.9472 0.9904 0.8591
𝐇𝑖𝑗 ∥ 𝐙𝐺 0.9412 0.9346 0.9532 0.9750 0.9987 0.8728 works, the researchers mainly focused on how to preferably capture
the structural and evolutionary characteristics of a network from its
consecutive snapshots, but ignored the global information of the net-
work hidden in its collapsed network. In our opinion, the collapsed
5.3. Ablation study
network can complement some information from global perspective
to the representations of nodes/node-pairs, and thus boost the per-
5.3.1. Influence of the way for representation learning
The DLP-LRN method learns the representation of a node-pair formance of the downstream task. Accordingly, the DLP-LRN method
based on its enclosing subgraph via an improved DGCNN. Because generates the final representation of a node-pair by combining the
DGCNN (Zhang et al., 2018) is designed for graph classification, we outcomes learned from both the consecutive snapshots and the col-
improved its architecture as in Fig. 3 to learn the representation of a lapsed network. To investigate the influence of the collapsed network
node-pair. In our method, the representation of a node-pair, say (𝑣𝑖 , 𝑣𝑗 ), on the prediction accuracy of DLP-LRN, we compare the results of DLP-
is obtained by concatenating the Hadamard product of the embeddings LRN with and without incorporating the information of the collapsed
of 𝑣𝑖 and 𝑣𝑗 , which emphasizes the importance of the node-pair, and the network. From the results, reported in Fig. 5, one can see that, when
embedding of the subgraph, which combines the information of neigh- using the collapsed network, DLP-LRN can attain superior performance,
bors. Here, we conduct an ablation experiment to confirm the efficacy especially on the networks of Forum and Mess. Besides, although DLP-
of the way, designed in this study, for learning the representation of LRN has been able to achieve very high performance on the network
a node-pair. Table 4 reports the results, in which three different ways of Call when the collapsed network is not used, its performance can be
are compared: Hadamard product of nodes, embedding of subgraph, further improved when using the collapsed network. As a consequence,
and concatenation of both (i.e., the proposed way). The results present
the collapsed network has a positive effect on the performance of the
that DLP-LRN attains the best performance, in most cases, under the
proposed DLP-LRN method.
proposed way, which proves the efficacy of the proposed representation
learning way for link prediction. The main reason is that the proposed
way not only pays close attention to the embeddings of target nodes
5.4. Discussion
but also leverages structural features of the subgraph around them.

5.3.2. Influence of the way for aggregating historical information
To aggregate the representations of a node-pair learned from differ-
ent snapshots, we introduce an exponential function in this study (see
Eq. (5)), which is effective and efficient. This function combines the
representations of a node-pair learned from different historical snap-
shots to generate a summarized representation of the node-pair. In the
literature, LSTM has always been employed to aggregate information
from historical snapshots (Chen et al., 2021; Selvarajah et al., 2020;
Yang et al., 2020). Here, we investigate the influence of LSTM and
our exponential function, marked as EF, to the prediction accuracy of
the proposed DLP-LRN method through an experiment. Fig. 4 presents
the experimental results. One can see from Fig. 4 that the accuracy of
DLP-LRN under EF is better than that under LSTM on all benchmark
networks except Mess, on which two versions of DLP-LRN achieve very
similar results. The reason why the proposed method performs better
under EF is that this function assigns more weight to the later snapshots
From the above experimental results, we conclude that our DLP-LRN
method has the following advantages. (1) DLP-LRN outperforms the
baseline methods on networks with diverse characteristics, indicating
that it works very well for dynamic link prediction. (2) By combining
two parts of information, DLP-LRN enhances the representations of
node-pairs, and consequently benefits the downstream link prediction
task. (3) By introducing the collapsed network, which can comple-
ment some global information to the representations of node-pairs, the
performance of DLP-LRN is further improved.
Besides, there are two main limitations in our DLP-LRN method.
(1) DLP-LRN assumes that the nodes do not change across different
snapshots. Actually, in a dynamic network, not only links but also nodes
keep changing over time. (2) When generating the collapsed network,
DLP-LRN does not take into account the appearance time of a link,
which may be important to predict new links.

6
H. Dong et al.
Fig. 5. Performance of DLP-LRN with (w) and without (w/o) the collapsed network.
6. Conclusion and future work
This work studied the problem of link prediction in dynamic net-
works, which is more challenging and complicated because dynamic
networks continue to evolve over time. In this work, we presented a
new link prediction paradigm, namely DLP-LRN, to deal with this prob-
lem. Our method can effectively cope with the challenge of dynamic
link prediction because it is able to learn the representations of node-
pairs from both historical and global perspectives via an improved GNN
and an exponential function for the downstream task. Experimental
results on six dynamic networks demonstrate the superior performance
of DLP-LRN compared to eight baselines. Moreover, ablation studies
show the effectiveness of the three critical operations in the proposed
method.
For the future work, we will extend DLP-LRN to deal with the
more challenging link prediction problem in dynamic networks with
unfixed node sets. Then, we will explore how to preserve and utilize
the appearance times of links in the collapsed network. Moreover, we
also consider to apply DLP-LRN to some practical application scenarios
of real network systems, such as social networks and traffic networks.
CRediT authorship contribution statement
Hu Dong: Methodology, Software, Writing – original draft. Longjie
Li: Conceptualization, Formal analysis, Writing – review & editing,
Funding acquisition. Dongwen Tian: Methodology, Software, Writing
– original draft. Yiyang Sun: Methodology, Validation, Resources.
Yuncong Zhao: Formal analysis, Writing – review & editing.
Declaration of competing interest
The authors declare that they have no known competing finan-
cial interests or personal relationships that could have appeared to
influence the work reported in this paper.
Data availability
Data will be made available on request.
Acknowledgments
This work was supported in part by the Science and Technology
Program of Gansu Province (Nos. 21JR7RA458 and 21ZD8RA008), and
the Supercomputing Center of Lanzhou University.
7
Expert Systems With Applications 241 (2024) 122685
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