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Higher-order Spectral Clustering for Heterogeneous Graphs

by   Aldo G. Carranza, et al.

Higher-order connectivity patterns such as small induced sub-graphs called graphlets (network motifs) are vital to understand the important components (modules/functional units) governing the configuration and behavior of complex networks. Existing work in higher-order clustering has focused on simple homogeneous graphs with a single node/edge type. However, heterogeneous graphs consisting of nodes and edges of different types are seemingly ubiquitous in the real-world. In this work, we introduce the notion of typed-graphlet that explicitly captures the rich (typed) connectivity patterns in heterogeneous networks. Using typed-graphlets as a basis, we develop a general principled framework for higher-order clustering in heterogeneous networks. The framework provides mathematical guarantees on the optimality of the higher-order clustering obtained. The experiments demonstrate the effectiveness of the framework quantitatively for three important applications including (i) clustering, (ii) link prediction, and (iii) graph compression. In particular, the approach achieves a mean improvement of 43x over all methods and graphs for clustering while achieving a 18.7 and graph compression, respectively.


Higher-order clustering in networks

A fundamental property of complex networks is the tendency for edges to ...

Tools for higher-order network analysis

Networks are a fundamental model of complex systems throughout the scien...

Heterogeneous Network Motifs

Many real-world applications give rise to large heterogeneous networks w...

Multi-MotifGAN (MMGAN): Motif-targeted Graph Generation and Prediction

Generative graph models create instances of graphs that mimic the proper...

CHIEF: Clustering with Higher-order Motifs in Big Networks

Clustering a group of vertices in networks facilitates applications acro...

KNH: Multi-View Modeling with K-Nearest Hyperplanes Graph for Misinformation Detection

Graphs are one of the most efficacious structures for representing datap...

Heterogeneous Graphlets

In this paper, we introduce a generalization of graphlets to heterogeneo...

1. Introduction

Clustering in graphs has been one of the most fundamental tools for analyzing and understanding the components of complex networks. It has been used extensively in many important applications to distributed systems (Hendrickson and Leland, 1995; Simon, 1991; Van Driessche and Roose, 1995), compression (Rossi et al., 2015; Buehrer and Chellapilla, 2008), image segmentation (Shi and Malik, 2000; Felzenszwalb and Huttenlocher, 2004), document and word clustering (Dhillon, 2001), among others. Most clustering methods focus on simple flat/homogeneous graphs where nodes and edges represent a single entity and relationship type, respectively. However, heterogeneous graphs consisting of nodes and edges of different types are seemingly ubiquitous in the real-world. In fact, most real-world systems give rise to rich heterogeneous networks that consist of multiple types of diversely interdependent entities (Shi et al., 2017; Sun and Han, 2013)

. This heterogeneity of real systems is often due to the fact that, in applications, data usually contains semantic information. For example in research publication networks, nodes can represent authors, papers, or venues and edges can represent coauthorships, references, or journal/conference appearances. Such heterogeneous graph data can be represented by an arbitrary number of matrices and tensors that are coupled with respect to one or more types as shown in Figure 


Clusters in heterogeneous graphs that contain multiple types of nodes give rise to communities that are significantly more complex. Joint analysis of multiple graphs may capture fine-grained clusters that would not be captured by clustering each graph individually as shown in (Banerjee et al., 2007; Rossi and Zhou, 2015). For instance, simultaneously clustering different types of entities/nodes in the heterogeneous graph based on multiple relations where each relation is represented as a matrix or a tensor (Figure 1). It is due to this complexity and the importance of explicitly modeling how those entity types mix to form complex communities that make the problem of heterogeneous graph clustering a lot more challenging. Moreover, the complexity, representation, and modeling of the heterogeneous graph data itself also makes this problem challenging (See Figure 1). Extensions of clustering methods for homogeneous graphs to heterogeneous graphs are often nontrivial. Many methods require complex schemas and are very specialized, allowing for two graphs with particular structure. Furthermore, most clustering methods only consider first order structures in graphs, i.e., edge connectivity information. However, higher-order structures play a non-negligible role in the organization of a network.

Higher-order connectivity patterns such as small induced subgraphs called graphlets (network motifs) are known to be the fundamental building blocks of simple homogeneous networks (Milo et al., 2002) and are essential for modeling and understanding the fundamental components of these networks (Ahmed et al., 2015; Ahmed et al., 2016; Benson et al., 2016). However, such (untyped) graphlets are unable to capture the rich (typed) connectivity patterns in more complex networks such as those that are heterogeneous, labeled, signed, or attributed. In heterogeneous graphs (Figure 1), nodes and edges can be of different types and explicitly modeling such types is crucial. In this work, we introduce the notion of a typed-graphlet and use it to uncover the higher-order organization of rich heterogeneous networks. The notion of a typed-graphlet captures both the connectivity pattern of interest and the types. We argue that typed-graphlets are the fundamental building blocks of heterogeneous networks. Note homogeneous, labeled, signed, and attributed graphs are all special cases of heterogeneous graphs as shown in Section 2.

In this paper, we propose a general framework for higher-order clustering in heterogeneous graphs. The framework explicitly incorporates heterogeneous higher-order information by counting typed graphlets that explicitly capture node and edge types. Typed graphlets generalize the notion of graphlets to rich heterogeneous networks as they explicitly capture the higher-order typed connectivity patterns in such networks. Using these as a basis, we propose the notion of typed-graphlet conductance that generalizes the traditional conductance to higher-order structures in heterogeneous graphs. The proposed approach reveals the higher-order organization and composition of rich heterogeneous complex networks. Given a graph and a typed-graphlet of interest , the framework forms the weighted typed-graphlet adjacency matrix by counting the frequency that two nodes co-occur in an instance of the typed-graphlet. Next, the typed-graphlet Laplacian matrix is formed from

and the eigenvector corresponding to the second smallest eigenvalue is computed. The components of the eigenvector provide an ordering

of the nodes that produce nested sets of increasing size . We demonstrate theoretically that with the minimum typed-graphlet conductance is a near-optimal higher-order cluster.

The framework provides mathematical guarantees on the optimality of the higher-order clustering obtained. The theoretical results extend to typed graphlets of arbitrary size and avoids restrictive special cases required in prior work. Specifically, we prove a Cheeger-like inequality for typed-graphlet conductance. This gives bounds where is the minimum typed-graphlet conductance, is the value given by Algorithm 1, and is a constant—at least as small as which depends on the number of edges in the chosen typed graphlet. Notably, the bounds of the method depend directly on the number of edges of the arbitrarily chosen typed graphlet (as opposed to the number of nodes) and inversely on the quality of connectivity of occurrences of the typed graphlet in a heterogeneous graph. This is notable as the formulation for homogeneous graphs and untyped graphlets proposed in (Benson et al., 2016) is in terms of nodes and requires different theory for untyped-graphlets with a different amount of nodes (e.g., untyped graphlets with 3 nodes vs. 4 nodes and so on). In this work, we argue that it is not the number of nodes in a graphlet that are important, but the number of edges. This leads to a more powerful, simpler, and general framework that can serve as a basis for analyzing higher-order spectral methods. Furthermore, even in the case of untyped graphlets and homogeneous graphs, the formulation in this work leads to tighter bounds for certain untyped graphlets. Consider a 4-node star and 3-node clique (triangle), both have 3 edges, and therefore would have the same bounds in our framework even though the number of nodes differ. However, in (Benson et al., 2016), the bounds for the 4-node star would be different (and larger) than the 3-node clique. This makes the proposed formulation and corresponding bounds more general and in the above case provides tighter bounds compared to (Benson et al., 2016).

The experiments demonstrate the effectiveness of the approach quantitatively for three important tasks. First, we demonstrate the approach for revealing high quality clusters across a wide variety of graphs from different domains. In all cases, it outperforms a number of state-of-the-art methods with an overall improvement of x over all graphs and methods. Second, we investigate the approach for link prediction. In this task, we derive higher-order typed-graphlet node embeddings (as opposed to clustering) and use these embeddings to learn a predictive model. Compared to state-of-the-art methods, the approach achieves an overall improvement in and AUC of 18.7% and 14.4%, respectively. Finally, we also demonstrate the effectiveness of the approach quantitatively for graph compression where it is shown to achieve a mean improvement of across all graphs and methods. Notably, these application tasks all leverage different aspects of the proposed framework. For instance, link prediction uses the higher-order node embeddings given by our approach whereas graph compression leverages the proposed typed-graphlet spectral ordering (Definition 11).

The paper is organized as follows. Section 2 describes the general framework for higher-order spectral clustering whereas Section 3 proves a number of important results including mathematical guarantees on the optimality of the higher-order clustering. Next, Section 4 demonstrate the effectiveness of the approach quantitatively for a variety of important applications including clustering, link prediction, and graph compression. Section 5 discusses and summarizes related work. Finally, Section 6 concludes.

Figure 1. Heterogeneous graph represented as a third-order tensor and two matrices that all share at least one type. The third-order tensor can be coupled with the item by tag matrix and the social network (user by user) matrix .

2. Framework

In this work, we propose a general framework for higher-order clustering in heterogeneous graphs. Table 1 lists all our notation.

2.1. Heterogeneous Graph Model

We represent a heterogeneous complex system using the following heterogeneous graph model.

Definition 1 (Heterogeneous Graph).

A heterogeneous graph is an ordered tuple comprised of

  1. a graph where is the node set and is the edge set,

  2. a mapping referred to as the node-type mapping where is a set of node types,

  3. a mapping referred to as the edge-type mapping where is a set of edge types.

We denote the node set of a heterogeneous graph as and its edge set as .

A homogeneous graph can be seen as a special case of a heterogeneous graph where . Note that a heterogeneous graph may be unweighted or weighted and it may be undirected or directed, depending on the underlying graph structure. Moreover, it may also be signed or labeled where corresponds to a label assigned to node (or edge ).

In general, a heterogeneous network can be represented by an arbitrary number of matrices and tensors that are coupled, i.e., the tensors and matrices share at least one type with each other (Acar et al., 2011; Rossi and Zhou, 2016). See Figure 1 for an example of a heterogeneous network represented as a coupled matrix-tensor.

2.2. Graphlets

Graphlets are small connected induced subgraphs (Pržulj et al., 2004; Ahmed et al., 2015). The simplest nontrivial graphlet is the 1st-order structure of a node pair connected by an edge. Higher-order graphlets correspond to graphlets with greater number of nodes and edges. Most graph clustering algorithms only take into account edge connectivity, 1st-order graphlet structure, when determining clusters. Moreover, these methods are only applicable for homogeneous graphs. For example, spectral clustering on the normalized Laplacian of the adjacency matrix of a graph partitions it in a way that attempts to minimize the amount of edges, 1st-order structures, cut (Kannan et al., 2004).

In this section, we introduce a more general notion of graphlet called typed-graphlet that naturally extends to both homogeneous and heterogeneous networks. In this paper, we will use to represent a graph and or to represent graphlets.

2.2.1. Untyped graphlets

We begin by defining graphlets for homogeneous graphs with a single type.

Definition 2 (Untyped Graphlet).

An untyped graphlet of a homogeneous graph is a connected, induced subgraph of .

Given an untyped graphlet in some homogeneous graph, it may be the case that we can find other topologically identical “appearances” of this structure in that graph. We call these appearances untyped-graphlet instances.

Definition 3 (Untyped-Graphlet Instance).

An instance of an untyped graphlet in homogeneous graph is an untyped graphlet in that is isomorphic to .

As we shall soon see, it will be important to refer to the set of all instances of a given graphlet in a graph. Forming this set is equivalent to determining the subgraphs of a graph isomorphic to the given graphlet. Nevertheless, we usually only consider graphlets with up to four or five nodes, and have fast methods for discovering instances of such graphlets (Ahmed et al., 2015; Ahmed et al., 2016; Ahmed et al., 2016a, b; Rossi et al., 2017).

2.2.2. Typed graphlets

In heterogeneous graphs, nodes and edges can be of different types and so explicitly (and jointly) modeling such types is essential (Figure 1). To generalize higher-order clustering to handle such networks, we introduce the notion of a typed-graphlet that explicitly captures both the connectivity pattern of interest and the types. Notice that typed-graphlets are a generalization of untyped-graphlets and thus are a more powerful representation.

Definition 4 (Typed Graphlet).

A typed graphlet of a heterogeneous graph is a connected induced heterogeneous subgraph of in the following sense:

  1. is an untyped graphlet of ,

  2. , that is, is the restriction of to

  3. , that is, is the restriction of to .

We can consider the topologically identical “appearances” of a typed graphlet in a graph that preserve the type structure.

Definition 5 (Typed-Graphlet Instance).

An instance of a typed graphlet of heterogeneous graph is a typed graphlet of such that:

  1. is isomorphic to ,

  2. and , that is, the sets of node and edge types are correspondingly equal.

The set of unique typed-graphlet instances of in is denoted as .

Note that we are not interested in preserving the type structure via the isomorphism, only its existence, that is, we are not imposing the condition that the node and edge types coincide via the graph isomorphism. This condition is too restrictive.

2.2.3. Motifs

Before we proceed, we briefly address some discrepancies between our definition of graphlets and that of papers such as (Benson et al., 2016; Arenas et al., 2005). Although it might be a simple matter of semantics, the differences should be noted and clarified to avoid confusion. Some papers refer to what we refer to graphlets as motifs. Yet, motifs usually refer to recurrent and statistically significant induced subgraphs  (Pržulj et al., 2004; Milo et al., 2002).

To find the motifs of a graph, one must compare the frequency of appearances of a graphlet in the graph to the expected frequency of appearances in an ensemble of random graphs in a null model associated to the underlying graph. Current techniques for computing the expected frequency in a null model requires us to generate a graph that follows the null distribution and then compute the graphlet frequencies in this sample graph (Milo et al., 2002; Albert and Barabási, 2002). These tasks are computationally expensive for large networks as we have to sample many graphs from the null distribution. On the other hand, any graphlet can be arbitrarily specified in a graph and does not depend on being able to determine whether it is is statistically significant. In any case, a motif is a special type of graphlet, so we prefer to work with this more general object.

node set of
edge set of
graphlet of
set of unique instances of in
typed-graphlet adjacency matrix of based on
typed-graphlet normalized Laplacian of based on
weighted heterogeneous graph induced by
subset of
cut of where
degree of node
typed-graphlet degree of node based on
volume of under
typed-graphlet volume of based on under
cut size of under
typed-graphlet cut size of based on under
conductance of under
typed-graphlet conductance of based on under
conductance of
typed-graphlet conductance of based on
Table 1. Summary of notation. Matrices are bold, upright roman letters.

2.3. Typed-Graphlet Conductance

In this section, we introduce the measure that will score the quality of a heterogeneous graph clustering built from typed graphlets. It is extended from the notion of conductance defined as:

where is a cut of a graph, is the number of edges crossing cut and is the total degrees of the vertices in cluster (Fortunato, 2010; Kannan et al., 2004). Note that its minimization achieves the sparsest balanced cut in terms of the total degree of a cluster.

The following definitions apply for a fixed heterogeneous graph and typed graphlet. Assume we have a heterogeneous graph and a typed graphlet of .

Note 0 ().

We denote the set of unique instances of in as .

Definition 6 (Typed-Graphlet Degree).

The typed-graphlet degree based on of a node is the total number of incident edges to over all unique instances of . We denote and compute this as

Definition 7 (Typed-Graphlet Volume).

The typed-graphlet volume based on of a subset of nodes is the total number of incident edges to any node in over all instances of . In other words, it is the sum of the typed-graphlet degrees based on over all nodes in . We denote and compute this as

Recall that a cut in a graph is a partition of the underlying node set into two proper, nonempty subsets and where

. We denote such a cut as an ordered pair

. For any given cut in a graph, we can define a notion of cut size.

Definition 8 (Typed-Graphlet Cut Size).

The typed-graphlet cut size based on of a cut in is the number of unique instances of crossing the cut. We denote and compute this as

Note that a graphlet can cross a cut with any of its edges. Therefore, it has more ways in which it can add to the cut size than just an edge.

Having extended notions of volume and cut size for higher-order typed substructures, we can naturally introduce a corresponding notion of conductance.

Definition 9 (Typed-Graphlet Conductance).

The typed-graphlet conductance based on of a cut in is

and the typed-graphlet conductance based on of is defined to be the minimum typed-graphlet conductance based on over all possible cuts in :


The cut which achieves the minimal typed-graphlet conductance corresponds to the cut that minimizes the amount of times instances of are cut and still achieves a balanced partition in terms of instances of in the clusters.

2.4. Typed-Graphlet Laplacian

In this section, we introduce a notion of a higher-order Laplacian of a graph. Assume we have a heterogeneous graph and a typed graphlet of .

2.4.1. Typed-graphlet adjacency matrix

Suppose we have the set . Then, we can form a matrix that has the same dimensions as the adjacency matrix of and has its entries defined by the count of unique instances of containing edges in .

Definition 10 (Typed-Graphlet Adjacency Matrix).

Suppose that . The typed-graphlet adjacency matrix of based on is a weighted matrix defined by

for . That is, the -entry of   is equal to the number of unique instances of that contain nodes as an edge.

Having defined , a weighted adjacency matrix on the set of nodes , we can induce a weighted graph. We refer to this graph as the graph induced by and denote it as .

Note 0 ().

From the definition of , we can easily show that for any .

2.4.2. Typed-graphlet Laplacian

We can construct the weighted normalized Laplacian of :

where is defined by

for . We also refer to this Laplacian as the typed-graphlet normalized Laplacian based on of . The normalized typed-graphlet Laplacian is the fundamental structure for the method we present in Section 2.5.

2.5. Typed-Graphlet Spectral Clustering

In this section, we present an algorithm for approximating the optimal solution to the minimum typed-graphlet conductance optimization problem:


Minimizing the typed-graphlet conductance encapsulates what we want: the solution achieves a bipartition of that minimizes the number of instances of that are cut and is balanced in terms of the total graphlet degree contribution of all instances of on each partition.

The issue is that minimizing typed-graphlet conductance is -hard. To see this, consider the case where your graphlet is the 1st-order graphlet, that is, a pair of nodes connected by an edge. Minimizing the standard notion of conductance, which is known to be NP-hard  (Cook, 1971), reduces to minimizing this special case of 1st-order untyped-graphlet conductance minimization. Therefore, obtaining the best graphlet-preserving clustering for large graphs is an intractible problem. We can only hope to achieve a near-optimal approximation.

2.5.1. Algorithm

We present a typed-graphlet spectral clustering algorithm for finding a provably near-optimal bipartition in Algorithm 1. We build a sweeping cluster in a greedy manner according to the typed-graphlet spectral ordering defined as follows.

Definition 11 (Typed-Graphlet Spectral Ordering).

Let denote the eigenvector corresponding to the nd smallest eigenvalue of the normalized typed-graphlet Laplacian . The typed-graphlet spectral ordering is the permutation

of coordinate indices such that

that is, is the permutation of coordinate indices of that sorts the corresponding coordinate values from smallest to largest.

Input: Heterogeneous graph , typed graphlet
Output: Near-optimal cluster
for  do
       if  then
             if  then
             end if
       end if
end for
Algorithm 1 Typed-Graphlet Spectral Clustering

2.5.2. Extensions

Algorithm 1 generalizes the spectral clustering method for standard conductance minimization (Shi and Malik, 2000) and untyped-graphlet conductance minimization. We demonstrated the reduction of standard conductance minimization above. Untyped-graphlet conductance minimization is also generalized since homogeneous graphs can be seen as heterogeneous graphs with a single node and edge type. It is straightforward to adapt the framework to other arbitrary (sparse) cut functions such as ratio cuts (Gaertler, 2005), normalized cuts (Shi and Malik, 2000), bisectors (Gaertler, 2005), normalized association cuts (Shi and Malik, 2000), among others (Schaeffer, 2007; Fortunato, 2010; Shi and Malik, 2000).

Multiple clusters can be found through simple recursive bipartitioning (Kannan et al., 2004). We could also embed the lower eigenvectors of the normalized typed-graphlet Laplacian into a lower dimensional Euclidean space and perform -means, or any other Euclidean clustering algorithm, then associate to each node its corresponding cluster in this space (Ng et al., 2002; Kannan et al., 2004). It is also straightforward to use multiple typed-graphlets for clustering or embeddings as opposed to using only a single typed-graphlet independently. For instance, the higher-order typed-graphlet adjacency matrices can be combined in some fashion (e.g., summation) and may even be assigned weights based on the importance of the typed-graphlet. Moreover, the typed-graphlet conductance can be adapted in a straightforward fashion to handle multiple typed-graphlets.

2.5.3. Discussion

Benson et al. (Benson et al., 2016) refers to their higher-order balanced cut measure as motif conductance and it differs from our proposed notion of typed-graphlet conductance. However, the definition used matches more with a generalization known as the edge expansion. The edge expansion of a cut is defined as


The balancing is in terms of the number of vertices in a cluster. Motif conductance was defined with a balancing in terms of the number of vertices in any graphlet instance. To be precise, for any set of vertices , let the cluster size of in based on be


Note that this does not take into account the degree contributions of each graphlet, only its node count contributions to a cluster . In terms of our notation, untyped “motif conductance” of a cut is defined in that work as

Since this does not take into account node degree information, this is more of a generalization of edge expansion (Hoory et al., 2006; Alon, 1997), “graphlet expansion”, if you will, rather than conductance. The difference is worth noting because it has been shown that conductance minimization gives better partitions than expansion minimization (Kannan et al., 2004). By only counting nodes, we give equal importance to all the vertices in a graphlet. Arguably, it is more reasonable to give greater importance to the vertices that not only participate in many graphlets but also have many neighbors within a graphlet and give lesser importance to vertices that have more neighbors that do not participate in a graphlet or do not have many neighbors within a graphlet. Our definition of typed-graphlet volume captures this idea to give an appropriate general notion of conductance.

2.6. Typed-Graphlet Node Embeddings

Algorithm 2 summarizes the method for deriving higher-order typed motif-based node embeddings (as opposed to clusters/partitions of nodes, or an ordering for compression/analysis, see Section 4.3). In particular, given a typed-graphlet adjacency matrix, Algorithm 2 outputs a matrix of node embeddings. For graphs with many connected components, Algorithm 2 is called for each connected component of and the resulting embeddings are stored in the appropriate locations in the overall embedding matrix .

Multiple typed-graphlets can also be used to derive node embeddings. One approach that follows from (Rossi et al., 2018a) is to derive low-dimensional node embeddings for each typed-graphlet of interest using Algorithm 2. After obtaining all the node embeddings for each typed-graphlet, we can simply concatenate them all into one single matrix . Given , we can simply compute another low-dimensional embedding to obtain the final node embeddings that capture the important latent features from the node embeddings from different typed-graphlets.

Input: Heterogeneous graph , typed graphlet , embedding dimension
Output: Higher-order embedding matrix for
eigenvectors of smallest eigenvalues of return
Algorithm 2 Typed-Graphlet Spectral Embedding

3. Theoretical Analysis

In this section, we show the near-optimality of Algorithm 1. The idea is to translate what we know about ordinary conductance for weighted homogeneous graphs, for which there has been substantial theory developed (Chung, 1997; Chung and Oden, 2000; Chung, 1996), to this new measure we introduce of typed-graphlet conductance by relating these two quantities. Through this association, we can derive Cheeger-like results for and for the approximation given by the typed-graphlet spectral clustering algorithm (Algorithm 1). As in the previous section, assume we have a heterogeneous graph and a typed graphlet . Also, assume we have the weighted graph induced from the typed-graphlet adjacency matrix .

We prove two lemmas from which our main theorem will immediately hold. Lemma 1 shows that the typed-graphlet volume and ordinary volume measures match: total typed-graphlet degree contributions of typed-graphlet instances matches with total counts of typed-graphlet instances on edges for any given subset of nodes. In contrast, Lemma 2 shows that equality does not hold for the notions of cut size. The reason lies in the fact that for any typed-graphlet instance, typed-graphlet cut size on only counts the number of typed-graphlet instances cut whereas ordinary cut size on counts the number of times typed-graphlet instances are cut. Therefore, these two measure at least match and at most differ by a factor equal to the size of the , which is a fixed value that is small for the typed graphlets we are interested in, of size 3 or 4. Thus, we are able to reasonably bound the discrepancy between the notions of cut sizes.

Using these two lemmas, we immediately get our main result in Theorem 3 which shows the relationship between and in the form of tightly bound inequality that is dependent only on the number of edges in . From this theorem, we arrive at two important corollaries. In Corollary 4, we prove Cheeger-like bounds for typed-graphlet conductance. In Corollary 5, we show that the output of Algorithm 1 gives a near-optimal solution up to a square root factor and it goes further to show bounds in terms of the optimal value to show the constant of the approximation algorithm which depends on the second smallest eigenvalue of the typed-graphlet adjacency matrix and the number of edges in . This last result does not give a purely constant-factor approximation to the graph conductance because of their dependence on and , yet it still gives a very efficient, and non-trivial, approximation for fixed and . Moreover, the second part of Corollary 5 provides intuition as to what makes a specific typed-graphlet a suitable choice for higher-order clustering. Typed-graphlets that have a good balance of small edge set size and strong connectivity in the heterogeneous graph—in the sense that the second eigenvalue of the normalized typed-graphlet Laplacian is large—will have a tighter upper bound to their approximation for minimum typed-graphlet conductance. Therefore, this last result in Corollary 5 provides a way to quickly and quantitatively measure how good a typed graphlet is for determining higher-order organization before even executing the clustering algorithm.

Note 0 ().

In the case of the simple 1st-order untyped graphlet, i.e., a node pair with an interconnecting edge, we recover the results for traditional spectral clustering since in this case. Furthermore, if is a homogeneous graph, i.e., , we get the special case of untyped graphlet-based spectral clustering. Therefore, our framework generalizes the methods of traditional spectral clustering and untyped-graphlet spectral clustering for homogeneous graphs.

In the following analysis, we let represent the Boolean predicate function and let be the edge weight of edge in .

Lemma 0 ().

Let be a subset of nodes in . Then,


Lemma 0 ().

Let be a cut in . Then,


For subsequent simplification, we define to be the set of edges in that cross cut :




Note that for an instance such that , there exists at least one edge in cut by and at most all edges in are cut by . Clearly, if , then no edge is cut by . This shows that for such an instance we have


Therefore, Equation 18 satisfies the following inequalities:


Referring to Definition 8 for typed-graphlet cut size and noting that since is a connected graph,


we find that


Plugging this into Inequalities 20-21, we get


or, equivalently,


Theorem 3 ().

Let be any cut in . From Lemma 2, we have that


Lemma 1 shows that . Therefore, if we divide these inequalities above by , we get that


by the definitions of conductance and typed-graphlet conductance. Since this result holds for any subset , it implies that


Corollary 0 ().

Let be the second smallest eigenvalue of . Then,


Cheeger’s inequality for weighted undirected graphs (see proof in  (Chung, 1997)) gives


Using these bounds for and applying them to Theorem 3, we find that


Corollary 0 ().

Let be the cluster output of Algorithm 1 and let be its corresponding typed-graphlet conductance on based on . Then,

Moreover, if we let be the second smallest eigenvalue of , then


showing that, for a fixed and , Algorithm 1 is a -approximation algorithm to the typed-graphlet conductance minimization problem.


Clearly since is the minimal typed-graphlet conductance. To prove the upper bound, let be the cut that achieves the minimal conductance on , that is, . Then,


Inequality 31 follows from the fact that achieves the minimal typed-graphlet conductance. Inequality 32 follows from Inequality 27 in Theorem 3. Inequality 33 follows from Cheeger’s inequality for weighted graphs (see (Chung, 1996) for a proof). Inequality 34 follows from the lower bound in Corollary 4.

We can go a bit further to express the bounds entirely in terms of by noting that


where Inequality 37 follows from the fact that by the lower bound of Corollary 4.

4. Experiments

This section empirically investigates the effectiveness of the proposed approach quantitatively for typed-graphlet spectral clustering (Section 4.1), link prediction using the higher-order node embeddings from our approach (Section 4.2) and the typed-graphlet spectral ordering for graph compression (Section 4.3). Unless otherwise mentioned, we use all 3 and 4-node graphlets.

yahoo-msg 100.1k 739.8k 2 3 2 3 4 3 3 3 2
dbpedia 495.9k 921.7k 4 8 0 6 10 5 0 0 0
digg 283.2k 4.6M 2 4 3 4 5 4 4 4 2
movielens 28.1k 170.4k 3 7 1 6 9 6 3 3 0
citeulike 907.8k 1.4M 3 5 0 3 6 3 0 0 0
fb-CMU 6.6k 250k 3 10 10 15 15 15 15 15 15
reality 6.8k 7.7k 2 4 3 4 5 4 4 4 2
gene 1.1k 1.7k 2 4 4 5 5 5 5 5 5
citeseer 3.3k 4.5k 6 56 40 124 119 66 98 56 19
cora 2.7k 5.3k 7 82 49 202 190 76 157 73 19
webkb 262 459 5 31 21 59 59 23 51 32 8
pol-retweet 18.5k 48.1k 2 4 4 5 5 5 5 5 4
web-spam 9.1k 465k 3 10 10 15 15 15 15 15 15
fb-relationship 7.3k 44.9k 6 50 47 112 109 85 106 89 77
Enzymes-g123 90 127 2 4 3 5 5 5 4 3 0
Enzymes-g279 60 107 2 4 4 5 5 5 5 5 0
Enzymes-g293 96 109 2 4 1 5 5 1 2 1 0
Enzymes-g296 125 141 2 4 1 4 5 2 1 1 0
NCI109-g4008 90 105 2 3 0 3 3 0 0 0 0
NCI109-g1709 102 106 3 5 0 5 5 1 0 0 0
NCI109-g3713 111 119 3 4 0 6 4 0 0 0 0
NCI1-g3700 111 119 3 4 0 6 4 0 0 0 0
Table 2. Network properties and statistics. Note = # of node types. Comparing the number of unique typed motifs that occur for each induced subgraph (e.g., there are 3 different typed 3-path graphlets that appear in yahoo).








yahoo-msg 0.5697 0.6624 0.2339 0.3288 0.0716 0.2000 0.0588
dbpedia 0.7414 0.5586 0.4502 0.8252 0.9714 0.9404 0.0249
digg 0.4122 0.4443 0.7555 0.3232 0.0006 0.0004 0.0004
movielens 0.9048 0.9659 0.7681 0.8620 0.9999 0.6009 0.5000
citeulike 0.9898 0.9963 0.9620 0.8634 0.9982 0.9969 0.7159
fb-CMU 0.6738 0.9546 0.9905 0.8761 0.5724 0.8571 0.5000
reality 0.7619 0.3135 0.2322 0.1594 0.6027 0.0164 0.0080
gene 0.8108 0.9298 0.9151 0.8342 0.4201 0.1667 0.1429
citeseer 0.5000 0.6667 0.6800 0.6220 0.0526 0.0526 0.0333
cora 0.0800 0.9057 0.8611 0.8178 0.0870 0.0870 0.0500
webkb 0.2222 0.9286 0.6154 0.8646 0.6667 0.3333 0.2222
pol-retweet 0.5686 0.6492 0.0291 0.0918 0.6676 0.0421 0.0220
web-spam 0.8551 0.9331 0.9844 0.7382 0.9918 0.5312 0.5015
fb-relationship 0.6249 0.9948 0.5390 0.8392 0.9999 0.5866 0.4972
Enzymes-123 0.8667 0.8889 0.5696 0.6364 0.6768 0.5204 0.3902
Enzymes-279 0.9999 0.4444 0.5179 0.4444 0.2929 0.3298 0.2747
Enzymes-293 1.0000 0.4857 0.9444 0.3793 0.7677 0.5000 0.3023
Enzymes-296 1.0000 0.7073 0.9286 0.7344 0.6406 0.5000 0.3212
NCI109-4008 0.7619 0.4324 0.8462 0.8235 0.3500 0.4556 0.3204
NCI109-1709 0.4000 0.3171 0.1429 0.4615 0.3922 0.3654 0.1333
NCI109-3713 0.4074 0.3793 0.7500 0.4583 0.6667 1.0000 0.2000
NCI1-3700 0.4074 0.3793 0.7500 0.4583 0.3333 0.6667 0.2500
Avg. Rank 4.59 4.77 4.64 4.32 4.27 3.27 1
Table 3. Quantitative evaluation of the methods (external conductance (Almeida et al., 2011)). Note TGS is the approach proposed in this work. The best result for each graph is bold.

4.1. Clustering

We quantitatively evaluate the proposed approach by comparing it against a wide range of state-of-the-art community detection methods on multiple heterogeneous graphs from a variety of application domains with fundamentally different structural properties (Rossi and Ahmed, 2015a).

  1. Densest Subgraph (DS-H) (Khuller and Saha, 2009): This baseline finds an approximation of the densest subgraph in using degeneracy ordering (Erdős and Hajnal, 1966; Rossi and Ahmed, 2014). Given a graph with nodes, let be the subgraph induced by nodes. At the start, and thus . At each step, node with smallest degree is selected from and removed to obtain . Afterwards, we update the corresponding degrees of and density . This is repeated to obtain . From , we select the subgraph with maximum density .

  2. KCore Communities (KCore-H) (Rossi et al., 2015; Shin et al., 2016): Many have observed the maximum k-core subgraph of a real-world network to be a highly dense subgraph that often contains the maximum clique (Rossi et al., 2015). The KCore baseline simply uses the maximum k-core subgraph as and .

  3. Label Propagation (LP-H) (Raghavan et al., 2007): Label propagation takes a labeling of the graph (in this case, induced by the heterogeneous graph), then for each node in some random ordering of the nodes, the node label is updated according to the label with maximal frequency among its neighbors. This iterative process converges when each node has the same label as the maximum neighboring label, or the number of iterations can be fixed. The final labeling induces a partitioning of the graph and the partition with maximum modularity is selected.

  4. Louvain (Louv-H) (Blondel et al., 2008): Louvain performs a greedy optimization of modularity by forming small, locally optimal communities then grouping each community into one node. It iterates over this two-phase process until modularity cannot be maximized locally. The community with maximum modularity is selected.

  5. Spectral Clustering (Spec-H) (Chung, 1997): This baseline executes spectral clustering on the normalized Laplacian of the adjacency matrix to greedily build the sweeping cluster that minimizes conductance.

  6. Untyped-Graphlet Spec. Clustering (GSpec-H) (Benson et al., 2016): This baseline computes the untyped-graphlet adjacency matrix and executes spectral clustering on the normalized Laplacian of this matrix to greedily build the sweeping cluster that minimizes the untyped-graphlet conductance.

Note that we append the original method name with to indicate that it was adapted to support community detection in arbitrary heterogeneous graphs (Figure 1) since the original methods were not designed for such graph data.

DS KC LP Louv Spec GSpec Gain
yahoo-msg 9.69x 11.27x 3.98x 5.59x 1.22x 3.40x 5.86x
dbpedia 29.78x 22.43x 18.08x 33.14x 39.01x 37.77x 30.03x
digg 1030x 1110x 1888x 808x 1.50x 1.00x 806.75x
movielens 1.81x 1.93x 1.54x 1.72x 2.00x 1.20x 1.70x
citeulike 1.38x 1.39x 1.34x 1.21x 1.39x 1.39x 1.35x
fb-CMU 1.35x 1.91x 1.98x 1.75x 1.14x 1.71x 1.64x
reality 95.24x 39.19x 29.02x 19.92x 75.34x 2.05x 43.46x
gene 5.67x 6.51x 6.40x 5.84x 2.94x 1.17x 4.75x
citeseer 15.02x 20.02x 20.42x 18.68x 1.58x 1.58x 12.88x
cora 10.00x 13.33x 17.22x 16.36x 1.74x 1.74x 10.07x
webkb 1.00x 4.18x 2.77x 3.89x 3.00x 1.50x 2.72x
pol-retweet 25.85x 29.51x 1.32x 4.17x 30.35x 1.91x 15.52x
webkb-spam 1.71x 1.86x 1.96x 1.47x 1.98x 1.06x 1.67x
fb-relationship 1.26x 2.00x 1.08x 1.69x 2.01x 1.18x 1.54x
Enzymes-g123 2.22x 2.28x 1.46x 1.63x 1.73x 1.33x 1.78x
Enzymes-g279 3.64x 1.62x 1.89x 1.62x 1.07x 1.20x 1.84x
Enzymes-g293 3.31x 1.61x 3.12x 1.25x 2.54x 1.65x 2.25x
Enzymes-g296 3.11x 2.20x 2.89x 2.29x 1.99x 1.56x 2.34x
NCI109-g4008 2.38x 1.35x 2.64x 2.57x 1.09x 1.42x 1.91x
NCI109-g1709 3.00x 2.38x 1.07x 3.46x 2.94x 2.74x 2.60x
NCI109-g3713 2.04x 1.90x 3.75x 2.29x 3.33x 5.00x 3.05x
NCI1-g3700 1.63x 1.52x 3.00x 1.83x 1.33x 2.67x 2.00x
Mean Gain 56.89x 58.23x 91.62x 42.74x 8.24x 3.47x (43.53x)
Table 4. Gain/loss achieved by TGS over the other methods. Overall, TGS achieves a mean improvement of 43.53x over all graph data and baseline methods. Note the last column reports the mean improvement achieved by TGS over all methods for each graph whereas the last row reports the mean improvement achieved by TGS over all graphs for each method.
Figure 2. Typed graphlet conductance as a function of S from the sweep in Algorithm 1 for a variety of typed 4-path graphlets and typed 4-tailed-triangle graphlets. For this experiment, we consider the largest connected component for the graph derived from each typed graphlet.

We evaluate the quality of communities using their external conductance score (Gleich and Seshadhri, 2012; Almeida et al., 2011). This measure has been identified as one of the most important cut-based measures in a seminal survey by Schaeffer (Schaeffer, 2007) and extensively studied in many disciplines and applications (Shi and Malik, 2000; Voevodski et al., 2009; Chung, 1997; Gleich and Seshadhri, 2012; Almeida et al., 2011; Kannan et al., 2004; Schaeffer, 2007). Results are reported in Table 3. As an aside, all methods take as input the same heterogeneous graph . Overall, the results in Table 3 indicate that the proposed approach is able to reveal better high quality clusters across a wide range of heterogeneous graphs. The heterogeneous network statistics and properties including the number of unique typed motifs for each induced subgraph pattern is shown in Table 2.

We also provide the improvement (gain) achieved by TGS clustering over the other methods in Table 4. Note improvement is simply where is the external conductance of the solution given by algorithm and denotes the TGS algorithm. Values less than 1 indicate that TGS performed worse than the other method whereas values indicate the improvement factor achieved by TGS. Overall, TGS achieves a mean improvement of x over all graph data and baseline methods (Table 4). Note the last column of Table 4 reports the mean improvement achieved by TGS over all methods for each graph whereas the last row reports the mean improvement achieved by TGS over all graphs for each method. Figure 2 shows how typed graphlet conductance (Eq. 1) changes as a function of community size for three different typed-graphlets.

4.2. Link Prediction in Heterogeneous Graphs

This section quantitatively demonstrates the effectiveness of TGS for link prediction.

4.2.1. Higher-order Typed-Graphlet Embeddings

In Section 4.1 we used the approach for higher-order clustering and quantitatively evaluated the quality of them. In this section, we use the approach proposed in Section 2 to derive higher-order typed-graphlet node embeddings and quantitatively evaluate them for link prediction. Algorithm 2 summarizes the method for deriving higher-order typed motif-based node embeddings (as opposed to clusters/partitions of nodes, or an ordering for compression/analysis, see Section 4.3). In particular, given a typed-graphlet adjacency matrix, Algorithm 2 outputs a matrix of node embeddings. For graphs with many connected components, Algorithm 2 is called for each connected component of and the resulting embeddings are stored in the appropriate locations in the overall embedding matrix .

Graph Heterogeneous Edge Types
movielens 3 user-by-movie, user-by-tag
dbpedia 4 person-by-work (produced work),
work-by-genre (work-associated-with-genre)
yahoo-msg 2 user-by-user (communicated with),
user-by-location (communication location)
Table 5. Link prediction edge types and semantics. We bold the edge type that is predicted by the models.

4.2.2. Experimental Setup

We evaluate the higher-order typed-graphlet node embedding approach (Algorithm 2) against the following methods: DeepWalk (DW) (Perozzi et al., 2014), LINE (Tang et al., 2015), GraRep (Cao et al., 2015), spectral embedding (untyped edge motif) (Ng et al., 2002), and spectral embedding using untyped-graphlets. All methods output (=128)-dimensional node embeddings where . For DeepWalk (DW) (Perozzi et al., 2014), we perform 10 random walks per node of length 80 as mentioned in (Grover and Leskovec, 2016). For LINE (Tang et al., 2015), we use 2nd-order proximity and perform 60 million samples. For GraRep (GR) (Cao et al., 2015), we use

. In contrast, the spectral embedding methods do not have any hyperparameters besides

which is fixed for all methods. As an aside, all methods used for comparison were modified to support heterogeneous graphs (similar to how the other baseline methods from Section 4.1 were modified). In particular, we adapted the methods to allow multiple graphs as input consisting of homogeneous or bipartite graphs that all share at least one node type (See Table 5 and Figure 1) and from these graphs we construct a single large graph by simply ignoring the node and edge types and relabeling the nodes to avoid conflicts.

4.2.3. Comparison

Given a partially observed graph with a fraction of missing/unobserved edges, the link prediction task is to predict these missing edges. We generate a labeled dataset of edges. Positive examples are obtained by removing of edges uniformly at random, whereas negative examples are generated by randomly sampling an equal number of node pairs

. For each method, we learn embeddings using the remaining graph. Using the embeddings from each method, we then learn a logistic regression (LR) model to predict whether a given edge in the test set exists in

or not. Experiments are repeated for 10 random seed initializations and the average performance is reported. All methods are evaluated against four different evaluation metrics including

, Precision, Recall, and AUC.

movielens 0.8544 0.8638 0.8550 0.8774 0.8728 0.9409
Prec. 0.9136 0.8785 0.9235 0.9409 0.9454 0.9747
Recall 0.7844 0.8444 0.7760 0.8066 0.7930 0.9055
AUC 0.9406 0.9313 0.9310 0.9515 0.9564 0.9900
dbpedia 0.8414 0.7242 0.7136 0.8366 0.8768 0.9640
Prec. 0.8215 0.7754 0.7060 0.7703 0.8209 0.9555
Recall 0.8726 0.6375 0.7323 0.9669 0.9665 0.9733
AUC 0.8852 0.8122 0.7375 0.9222 0.9414 0.9894
yahoo 0.6927 0.6269 0.6949 0.9140 0.8410 0.9303
Prec. 0.7391 0.6360 0.7263 0.9346 0.8226 0.9432
Recall 0.5956 0.5933 0.6300 0.8904 0.8699 0.9158
AUC 0.7715 0.6745 0.7551 0.9709 0.9272 0.9827
Note DW=DeepWalk and GR=GraRep.
Table 6. Link prediction results.

For link prediction (Liben-Nowell and Kleinberg, 2003; Ahmed et al., 2018), entity resolution/network alignment, recommendation and other machine learning tasks that require edge embeddings (features) (Rossi et al., 2018a)

, we derive edge embedding vectors by combining the learned node embedding vectors of the corresponding nodes using an edge embedding function

. More formally, given -dimensional embedding vectors and for node and , we derive a -dimensional edge embedding vector where is defined as one of the following edge embedding functions:

Note is the element-wise (Hadamard) product, is the Hadamard power, and is the element-wise max.

(a) Spectral clustering (untyped edge)
(b) Untyped 3-path
(c) Typed 4-cycle
Figure 3. Typed graphlet-based spectral ordering achieves significant compression by partitioning users, tags, and movies (from the movielens data) into homogeneous groups that are either nearly fully-connected (near-clique) or fully-disconnected. Strikingly, TGS partitions the rows/columns according to types without explicitly leveraging types (i.e., types are not used when deriving the typed-graphlet spectral ordering). For instance, the first 5k rows/columns correspond to tags, whereas the following 4k rows/columns are users, and so on. This is in contrast to the other methods where the rows/columns of different types are mixed with one another in a seemingly random fashion. Moreover, these approaches fail to partition the graph into homogeneous groups that are dense or completely empty. The typed 4-cycle graphlet used above consists of 2 nodes representing movies and the other two representing tags assigned to the movies. Other typed-graphlets gave other interesting results with comparable compression.

Table 5 summarizes the heterogeneous network data used for link prediction. In particular, the types used in each of the heterogeneous networks are shown in Table 5 as well as the specific types involved in the edges that are predicted (e.g., the edge type being predicted). The results are provided in Table 6. Results are shown for the best edge embedding function. In Table 6, TGS is shown to outperform all other methods across all four evaluation metrics. In all cases, the higher-order typed-graphlet spectral embedding outperforms the other methods (Table 6) with an overall mean gain (improvement) in of 18.7% (and up to 48.4% improvement) across all graph data. In terms of AUC, TGS achieves a mean gain of 14.4% (and up to 45.7% improvement) over all methods. We posit that an approach similar to the one proposed in (Rossi et al., 2018a) could be used with the typed-graphlet node embeddings to achieve even better predictive performance. This approach would allow us to leverage multiple typed-graphlet Laplacian matrices for learning more appropriate higher-order node embeddings.

4.3. Graph Compression

In Section 4.1 we used the approach for higher-order clustering whereas Section 4.2 demonstrated the effectiveness of the approach for link prediction. However, the framework can be leveraged for many other important applications including graph compression (Boldi and Vigna, 2004; Boldi et al., 2011; Chierichetti et al., 2009; Rossi and Zhou, 2018; Liakos et al., 2014). In this section, we explore the proposed approach for graph compression. Compression has two key benefits. First, it reduces the amount of IO traffic (Rossi and Zhou