M OTIF -D RIVEN C ONTRASTIVE L EARNING OF G RAPH R EPRESENTATIONS
Anonymous authors
Paper under double-blind review
A BSTRACT
Graph motifs are signiﬁcant subgraph patterns occurring frequently in graphs, and they play important roles in representing the whole graph characteristics.
For example, in chemical domain, functional groups are motifs that can determine molecule properties.
Mining and utilizing motifs, however, is a non-trivial task for large graph datasets.
Traditional motif discovery approaches rely on exact counting or statistical estimation, which are hard to scale for large datasets with continuous and high-dimension features.
In light of the signiﬁcance and challenges of motif mining, we propose MICRO-Graph : a framework for MotIf-driven
Contrastive leaRning Of Graph representations to: 1) pre-train Graph Neural Networks (GNNs) in a self-supervised manner to automatically extract motifs from large graph datasets; 2) leverage learned motifs to guide the contrastive learning of graph representations, which further beneﬁt various downstream tasks.
Specifically, given a graph dataset, a motif learner cluster similar and signiﬁcant subgraphs into corresponding motif slots.
Based on the learned motifs, a motif-guided subgraph segmenter is trained to generate more informative subgraphs, which are used to conduct graph-to-subgraph contrastive learning of GNNs.
By pretraining on ogbg-molhiv molecule dataset with our proposed MICRO-Graph , the pre-trained GNN model can enhance various chemical property prediction downstream tasks with scarce label by 2.0 % , which is signiﬁcantly higher than other state-of-the-art self-supervised learning baselines.
I NTRODUCTION
Graph-structured data, such as molecules and social networks, is ubiquitous in many scientiﬁc research areas and real-world applications.
To represent graph characteristics, graph motifs were proposed in Milo et al.
(2002) as signiﬁcant subgraph patterns occurring frequently in graphs and uncovering graph structural principles.
For example, functional groups are important motifs that can determine molecule properties.
Like the hydroxide (– OH ) usually implies higher water solubility, and for proteins, Zif268 can mediate protein-protein interactions in sequence-speciﬁc DNA-binding proteins.
(Pabo et al., 2001).
Graph motifs has been studied for years.
Meaningful motifs can beneﬁt many important applications like quantum chemistry and drug discovery (Ramsundar et al., 2019).
However, extracting motifs from large graph datasets remains a challenging question.
Traditional motif discovery approaches (Milo et al., 2002; Kashtan et al., 2004; Chen et al., 2006; Wernicke, 2006) rely on discrete counting or statistical estimation, which are hard to generalize to large-scale graph datasets with continuous and high-dimension features, as often the case in real-world applications.
Recently, Graph Neural Networks (GNNs) have shown great expressive power for learning graph representations without explicit feature engineering (Kipf & Welling, 2016; Hamilton et al., 2017;
Veliˇckovi´c et al., 2017; Xu et al., 2018).
In addition, GNNs can be trained in a self-supervised manner without human annotations to capture important graph structural and semantic properties (Veliˇckovi´c et al., 2018;
Hu et al., 2020c; Qiu et al., 2020; Bai et al., 2019; Navarin et al., 2018;
Wang et al., 2020; Sun et al., 2019; Hu et al., 2020b).
This motivates us to rethink about motifs as more general representations than exact structure matches and ask the following research questions:
• Can we use GNNs to automatically extract graph motifs from large graph datasets?
• Can we leverage the learned graph motif to beneﬁt self-supervised GNN learning?
In this paper, we propose MICRO-Graph : a framework for MotIf-driven Contrastive leaRning Of
Graph representations.
The key idea of this framework is to learn graph motifs as prototypical cluster centers of subgraph embeddings encoded by GNNs.
In this way, the discrete counting problem is transfered to a fully-differentiable framework that can generalize to large-scale graph datasets with continuous and high-dimensional features.
In addition, the learned motifs can help generate more informative subgraphs for graph-to-subgraph contrastive learning.
The motif learning and contrastive learning are mutually reinforced to pre-train a more generalizable GNN encoder.
For motif learning, given a graph dataset, a motif-guided subgraph segmenter generates subgraphs from each graph, and a GNN encoder turns these subgraphs into vector representations.
We then learn graph motifs through clustering, where we keep the K prototypical cluster centers as representations of motifs.
Similar and signiﬁcant subgraphs are assigned to the same motif and become closer to their corresponding motif representation.
We train our model in an Expectation-Maximization (EM) fashion to update both the motif assignment of each subgraph and the motif representations.
For leveraging learned motifs, we propose a graph-to-subgraph contrastive learning framework for
GNN pre-training.
One of the key components for contrastive learning is to generate semantically meaningful views of each instance.
For example, a continuous span within a sentence (Joshi et al., 2020) or a random crop of an image (Chen et al., 2020).
For graph data, previous approaches leverage node-level views, which is not sufﬁcient to capture high-level graph structural information
Sun et al.
As motifs can represent the key graph properties by its nature, we propose to leverage the learned motifs to generate more informative subgraph views.
For example, alpha helix and beta sheet can come together as a simple ββα fold to form a zinc ﬁnger protein with unique properties.
By learning such subgraph co-occurrence via contrastive learning, the pre-trained GNN can capture higher-level information of the graph that node-level contrastive can’t capture.
The pre-trained GNN using MICRO-Graph on the ogbg-molhiv molecule dataset can successfully learn meaningful motifs, including Benzene rings, nitro, acetate, and etc.
Meanwhile, ﬁne-tune this GNN on seven chemical property prediction benchmarks yielding 2.0% average improvement over non-pretrained GNNs and outperforming other self-supervised pre-training baselines.
Also, extensive ablation studies show the signiﬁcance of the learned motifs for the contrastive learning.
R ELATED W ORK
The goal of self-supervised learning is to train a model to capture signiﬁcant characteristics of data without human annotations.
This paper studies whether we can use such approach to automatically extract graph motifs, i.e. the signiﬁcant subgraph patterns, and leverage the learned motifs to beneﬁt self-supervised learning.
In the following, we ﬁrst review graph motifs especially challenges for motif mining, and then discuss approaches for pre-training GNNs in a self-supervised manner.
Graph motifs are building blocks of complex graphs.
They reveal the interconnections of graphs and represent graph characteristics.
Mining motifs can beneﬁt many tasks from exploratory analysis to transfer learning (Henderson et al., 2012).
For many years, various motif mining algorithms have been proposed.
There are generally two categories, either exact counting as in Milo et al.
Kashtan et al.
(2004); Schreiber & Schw¨obbermeyer (2005); Chen et al.
(2006), or sampling and statistical estimation as in Wernicke (2006).
However, both approaches cannot scale to large graph datasets with high-dimension and continuous features, which is common in real-world applications.
In this paper, we proposes to turn the discrete motif mining problem into a GNN-based differentiable cluster learning problem that can generalize to large-scale datasets.
Another GNN-based work related to graph motifs is the GNNExplainer, which focuses on post-process model interpretation(Ying et al., 2019).
It can identify substructures that are important for graph property prediciton, e.g. motifs.
The difference between GNNExplainer and MICRO-Graph is that the former identify motifs at a single graph level, and the later learns motifs across the whole dataset.
Contrastive learning is one of the state-of-the-art self-supervised representation learning algorithms.
It achieves great results for visual representation learning (Chen et al., 2020;
He et al., 2019).
Contrastive learning forces views generated from the same instance (e.g. different crops of the same image) to become closer, while views from different instances apart.
One key component in contrastive learning is to generate informative and diverse views from each data instance.
In computer vision, researchers use various techniques, including cropping, color distortion, and Gaussian blurs to generate views.
However, when it comes to graphs, constructing informative view of graph is a challenging task.
In our framework, we utilize the learned motifs, which are signiﬁcant subgraph patterns, to guide view (subgraph) generation, and conduct graph-to-subgraph contrastive learning.
Self-supervised learning for GNNs also draws many attention recently.
For graphs, representations can be at different levels, e.g. node level and (sub)graph level.
Veliˇckovi´c et al.
; Hu et al.
(2020c)
; Qiu et al.
(2020) mainly focus on node-level representation learning in a single large graph, as opposed to the focus of this paper, which is representation learning of whole graphs.
Hu et al.
(2020b) provides a systematic analysis of pre-training strategies on graphs for both node-level and graph-level.
However, only the node-level learning is self-supervised, and annotated labels are utilized for supervised learning at the graph level.
For graph level self-supervised representation learning, Sun et al.
(2019) proposed a contrastive framework, InfoGraph, to maximize the mutual information between graph representations and node representations.
In Rong et al.
(2020), the
GROVER model and a motif based self-supervised learning task was proposed, where the discrete motifs are ﬁrst extracted using a professional software, and then these motifs are used as prediction labels for pre-training the model.
The difference between motifs in GROVER and in MICRO-Graph is that GROVER uses discrete structures, but MICRO-Graph uses continuous vector embeddings
To alleviate these issues, we propose graph-to-subgraph view self-supervised contrastive learning, and the subgraph generation is guided by the learned motifs.
M ETHODOLOGY
The goal of this paper is to train a GNN encoder that can automatically extract graph motifs, i.e. signiﬁcant subgraph patterns.
Motif discovery on discrete graph structures is a combinatorial problem, and it is hard to generalize to large datasets with continuous features.
We thus propose to formalize this problem as a differentiable clustering learning problem and solve it via self-supervised GNN learning.
In this section, we formalize the problem and introduce the overall framework of MICROGraph in Section 3.1, and then describe each module in details in the following sections.
3. T HE OVERALL F RAMEWORK OF MICRO-Graph
Given a dataset with M graphs G = {G 1 , ..., G M } , the differentiable clustering learning problem is meant to learn two things.
One is a GNN-based graph encoder E ( · ) that maps input (sub)graphs an embedding vector.
The other is a K-slot embedding table { m 1 , ..., m K } , where each slot is a motif vector m corresponding to a cluster center of embeddings of frequently occurred subgraphs.
To tackle this problem, we introduce the MICRO-Graph framework which consists three modules: 1) a Motif-guided Segmenter to extract important subgraphs; 2) a Motif-Learner to cluster sampled subgraphs and identify motifs; 3) a constrastive learning module for graph-to-subgraph contrastive learning.
The overall framework is shown in Figure1.
We describe details of each module in the following sections.
The Motif Learner is introduced ﬁrst in Section 3.2, and then the Motif-guided
Segmenter and the constrastive learning module in Section 3.3 and 3.4 respectively.
3. M OTIF LEARNER VIA EM CLUSTERING
The Motif Learner learns motifs by applying an Expectation-Maximization (EM) style clustering algorithm on sampled subgraphs.
To start clustering, the Motif-guided Segmenter ﬁrst extracts N subgraphs { g j } Nj =1 from the input whole graphs.
For each subgraph g j , we generate its embedding e j = E ( g j ) and calculate the cosine similarity between e j and each of the K motif vectors { m 1 , ..., m K } .
We denote the similarity between e j and the kth motif vector as
S k,j = φ ( m k ) T φ ( e j ) 1 .
In vector notation, the K-dimensional vector of similarities between g j and all K motif vectors is denoted as s j , and the K-by-N-dimensional motif-to-subgraph similarity matrix is denoted as S , where the j -th column of S is s j and the entry (k, j) of S is S k,j .
E-Step.
The goal of the E-step is to come up with motif-based cluster assignments for subgraph embeddings { e j } Nj =1 .
The assignments can be represented by a K-by-N-dimensional matrix Q =
[ q 1 , ..., q N ] , where the j -th column q j contains the probabilities of assigning the j -th subgraph to each of the K motifs.
Each q j can be a one-hot vector for hard clustering or a probability vector with all the entries sum up to one for soft-clustering.
This vanilla version clustering problem boils down to maximizing the objective Tr ( Q T S ) , which corresponds to an assignment Q that maximizes similarities between embeddings and its assigned motif.
This objective works ﬁne for a traditional
EM clustering algorithm when embeddings are ﬁxed.
However, since representations will change when doing representation learning, this vanilla objective in the E-step can lead to a degenerate solution, i.e. all representations collapse to a single cluster center.
To avoid this issue, we follow
YM.
et al.
(2020) to introduce an entropy term and an equal-size constraint on Q for clusters to have similar sizes.
Our ﬁnal objective is:
[Equation]
where H ( Q ) = − (cid:80) i,j Q i,j log Q
i,j is the entropy function, and the constraint set Q requires the marginal projection of Q onto its columns and rows to be uniform.
[Equation]
where 1 N and 1 K are all one vectors.
This constraint optimization problem turns out to be an optimal transportation problem with a closed-form solution as (3) and can be solved efﬁciently using a fast Sinkhorn-Knopp algorithm.
[Equation]
Here u and v are normalization vectors.
The derivations can be found in Cuturi (2013).
M-Step.
The goal of the M-step is to maximize the log-likelihood of our data given the cluster assignment matrix Q estimated in the E-step.
We update parameters in the GNN encoder and the motif embedding table through the M-step.
This step is equivalent to a supervised K-class classiﬁcation problem with labels Q and prediction scores S .
Thus, we ﬁrst apply a columnwise softmax normalization with temperature τ g to S to convert all entries of S to probabilities, i.e.
˜ S k,j = softmax k (cid:0) S k,j /τ g (cid:1) .
Then we use the negative likelihood as the loss function.
[Equation]
3. M OTIF - GUIDED S UBGRAPH S EGMENTER
Sampling informative subgraphs is crucial for both the Motif-Learner and the contrastive learning module .
Traditional heuristic approaches such as random walk and k-hop neighbour sampling cannot guarantee to generate semantically reasonable and informative subgraphs.
For example, heuristically sampled molecule subgraphs are likely to be a chain of carbons, which doesn’t contain much information about the original molecule, or it can be a fragment of a meaningful chemical structure, which loses the original chemical property.
Since motifs are by nature informative subgraph patterns, we propose to leverage the learned graph motifs to design the Motif-guided segmenter , which will learn to segment a given graph into several subgraphs that are close to some discovered motifs.
Subgraph Sampling via Segmentation.
To generate subgraphs from a graph G i via segmentation, we ﬁrst generate a node afﬁnity matrix A ( i ) , and then do segmentation based on A ( i ) .
Speciﬁcally, given the graph G i with n nodes, we use the GNN encoder E ( · ) to generate the D-dimensional node embeddings { n 1 , ..., n n } of all n nodes in G i .
After that, we compute the n-by-n-dimensional
node
afﬁnity
matrix A ( i ) by ﬁrst computing pairwise cosine similarities between node embeddings, and then applying row-wise softmax normalization with temperature τ n to the cosine similarity matrix.
This normalization step is important because it transforms all the afﬁnity scores to be in the range (0,1) and make the afﬁnity scores of node pairs with high cosine similarities further stand out.
The formula for computing the afﬁnity score between node s and node t in graph G i , i.e. the entry ( s , t ) of A ( i ) is the following.
[Equation]
Afterwards, we treat this afﬁnity matrix
A ( i ) as a complete graph with n nodes and afﬁnity scores as edge weights.
Applying spectral clustering on this complete graph segments nodes into different groups.
Within these groups, the connected components that have more than three nodes are collected as our sampled subgraphs.
Multiple subgraphs may be sampled from the whole graph
G i .
For a particular subgraph g j , its embedding e j will be generated by indexing and aggregating the node embeddings generated when computing the afﬁnity matrix.
For example, if I is the indices of the nodes forming the subgraph g j selected by the Motif-guided segmenter , then e j = Aggregate ( { n 1 , ..., n n } [ I ]) .
The aggregate operation can be any order-invariant operation over a set of vectors, e.g. mean, sum, or elementwise max.
In our experiment, we follow the startof-the-art result from previous works and use the mean.
Collecting subgraphs from all M whole graphs result in the total set of subgraphs { g j } Nj =1 mentioned above.
Motif-guided Training.
To train the segmenter to produce subgraphs close to motifs, the motifto-subgraph similarity matrix S is used as the guidance.
For a subgraph g j sampled from a whole graph G i whose node afﬁnity matrix is A ( i ) .
If the similarity between g j and any motif is higher than a threshold, we make the afﬁnity values among all the nodes within g j to increase, and the afﬁnity value between these nodes and other nodes not in g j to decrease.
The loss function is as below.
[Equation] [Equation]
Here η k is the threshold used to decide whether a subgraph is similar enough to the learned moﬁt k, and it is dynamically computed.
In each iteration, we set η k to select the top 10% most similar subgraphs to motif k.
The intuition is that if the subgraph g j is considered similar to a motif, then we update the embeddings of its nodes to become similar.
By optimizing this loss, during the next sampling round, nodes produced motif-like subgraphs are more likely to be segmented together, which leads to more subgraph samples align with the motifs.
3. C ONTRASTIVE L EARNING BETWEEN GRAPHS AND SUBGRAPHS
An expressive GNN encoder E ( · ) is essential for capturing graph properties and accurately identifying motifs.
We thus introduce a constrastive learning module to help the GNN learning.
This module and the Motif Learner will mutually enhance each other to train a better GNN.
Contrastive learning is one of the state-of-the-art self-supervised learning methods.
One key component in contrastive learning is to generate informative and diverse views of data instances.
Previous contrastive methods on graphs utilized either nodes or whole graphs as views, which do not very well capture the micro-structure of graphs.
To alleviate this issue in our constrastive learning module, we use the subgraph generated by our Motif-guided segmenter as one view of the graph, and the whole graph as another view.
Similarly to how we generate the subgraph embeddings, the whole graph embedding h i of a graph G i is generated by aggregating node embeddings output by the GNN encoder E ( · ) , h i =
Aggregate ( { n 1 , ..., n n } ) .
Then we construct the M-by-N dimensional graph-to-subgraph similarity matrix W , which is cosine similarity between each graph-subgraph pair followed by a row-wise softmax normalization with temperature τ g .
[Equation]
For the whole graph G i , subgraphs sampled from it are considered as positive pairs to it, and subgraphs sampled from other graphs are considered as negative pairs to it.
Then the contrastive objective function is the following:
[Equation]
Our method uses a higher-level subgraph as one view and the whole graph as another; thus the GNN can capture more global contextual information.
We show the view-generation difference between our framework and other existing methods in
Figure 2.
Existing contrastive learning methods rely on node-node views or node-graph views.
Researchers in computer vision domain have found that conducting contrastive learning on more ﬂexible views, e.g. arbitrary-sized image crops, leads to better representations, especially much better than lower pixel-level views (Chen et al., 2020).
In our framework, the contrastive learning on graph-subgraph views is similar to this intuition from computer vision.
It can capture higher-level information the node views cannot capture, and thus produce more meaningful representations.
Note that the subgraphs we utilize is generated by our Motif-guided Segmenter .
In section 4, we systematically study the inﬂuence of subgraph sampling methods.
Experiment results show that simple heuristic sampling methods lead to bad generalization performance.
This shows the signiﬁcance of leveraging the learned graph motifs to generate more informative views of graph-structured data.
3. J OINT TRAINING
The overall objective of MICRO-Graph is a weighted sum of all three loss terms described above.
[Equation]
With the proper constraints introduced to the E-step of the Motif-Learner (equation (1) and (2)), the whole framework can be trained end-to-end without worrying about degenerate solutions.
MICRO-Graph can simultaneously train an expressive GNN encoder and learn motifs of the given graph dataset.
Moreover, the motif learning and contrastive learning are mutually reinforced: a better GNN produces more accurate subgraph embeddings and thus help motif mining, while better motifs can help generate more informative graph-to-subgraph views and beneﬁt contrastive learning.
We show the the pseudocode of our approach in Algorithm 1.
First, initialize the motif vectors and
GNN encoder (line 2 - 3).
For each batch of graphs G , our segmenter will calculate the node-node afﬁnity matrices A and extract subgraphs based on the afﬁnity scores (line 5 - 6).
After that, we apply GNN message passing on whole graphs to get the node embeddings and aggregate them for both graph and subgraph embeddings (line 7 - 9).
The next step is to compute the motif-to-subgraph similarity matrix S .
Using S we compute both the threshold η and cluster assignment matrix Q (line 11 - 13).
With all these values, the three loss terms and the ﬁnal joint loss introduced above can be computed (line 15 - 20).
[Table]
E XPERIMENTS
We evaluate the effectiveness of MICRO-Graph from two perspective: 1) Whether the selfsupervised framework can learn better GNNs that generalize well on graph classiﬁcation tasks; 2) whether the learned motifs are reasonable and can truly beneﬁt contrastive learning.
We mainly focus on chemical property prediction tasks.
Speciﬁcally, we pre-train GNNs using
MICRO-Graph on the ogbg-molhiv dataset from Open Graph Benchmark (OGB) (Hu et al., 2020a).
This dataset contains 40K molecules.
We test our pre-trained model on smaller molecule graph classiﬁcation datasets.
For more details of the datasets, please see Appendix E.
4. E VALUATION P ROTOCOLS
We evaluate the effectiveness of pre-training using the following two evaluation protocols.
Transfer Learning Setting : we ﬁne-tune the pre-trained GNN model with a small portion of labels on downstream tasks.
We adopt the same train-test and model selection procedure as in Yanardag & Vishwanathan (2015); Zhang et al.
Xu et al.
(2018), where we perform 10-fold crossvalidation and select the epoch with the best cross-validation performance averaged over thefolds.
The evaluation metric is ROC-AUC score.
Feature Extraction Setting : the setting is almost the same as transfer learning.
Except that we ﬁx the pre-trained GNN, use it as feature extractor to get graph representations of all the data in downstream tasks, and then train a linear classiﬁers on top.
4. B ASELINES AND M ODEL C ONFIGURATION
We consider ﬁve baselines, including non-pretrain (direct supervised learning) and four state-of-theart GNN self-supervised learning (SSL) methods.
InfoGraph (Sun et al., 2019) maximizes the mutual information between the representations of the whole graphs and the representations of its substructures at different granularity.
Context prediction (Hu et al., 2020b) predicts surrounding graph structures of each node, so nodes appearing in similar structural contexts will be mapped to nearby representations.
GPT-GNN (Hu et al., 2020c) predicts masked edges and masked node attributes.
The edge prediction makes node representations to be close when there are edges between them.
The attribute prediction captures how node attributes are distributed over all graphs.
GROVER (Rong et al., 2020)
ﬁrst uses professional software, e.g. RDKit(Landrum et al., 2006), to extract functional groups (motifs) from a whole dataset.
Using these motifs as a label set, each molecule is assigned a label representing which motif shows up in it and which doesn’t.
The model is then pre-trained by predicting this motif label as a multi-class classiﬁcaiton problem.
The state-of-the-art GNN model, Deeper Graph Convolutional Networks (DeeperGCNs) proposed in Li et al.
(2020), is used as the base GNN encoder for MICRO-Graph and all baselines.
We use the same hyperparameters for all experiments.
Details about hyperparameters and model conﬁgurations are in Appendix F.
4. E VALUATION R ESULT
The evaluation results under transfer learning setting and feature extraction setting is illustrated in Table 1 and Table 2.
For both setting, the proposed MICRO-Graph outperforms all baselines on average performance and achieves the highest results on most datasets.
For transfer learning setting, we gain about 2.0 % performance enhancement against non-pretrain baseline.
This shows the effectiveness of our self-supervised learning framework for pre-training GNNs.
[Table] [Table]
4. A BLATION S TUDY
We conduct a series of ablation studies to systematically analyze how the motif learning can beneﬁt the contrastive learning.
4.4. W HETHER M OTIF IS HELPFUL FOR SUBGRAPH SAMPLING ?
As previously discussed
[Table]
the main difference of our contrastive framework with existing works is that we leverage the graph-to-subgraph views for contrastive learning.
We ﬁrst study whether our proposed motif-guided subgraph segmenter can indeed help contrastive learning.
We implement two more widely adopted heuristic subgraph sampling baselines: random walk (RW) and K-hop neighbours (K-hop).
We replace our Motif-guided Segmenter (MS) component with these two heuristic sampling algorithm for the transfer learning experiments.
All the other settings stay the same.
[Table] [Table]
As shown in Table
[Table]
replacing MS with heuristic subgraph samplers will signiﬁcantly inﬂuence the performance.
With random walk or k-hop sampling, graph-to-subgraph contrastive learning can only bring in 0.2-0.4 % average performance enhancement against non-pretrain, which are far less than MS.
This shows that the key for the overall performance enhancement of MICRO-Graph is not only the graph-to-subgraph views, but also the informative motif-guided subgraphs.
For the details of each sampling strategy and the corresponding subgraphs examples, please refer to Appendix D.
4.4. W HETHER M OTIF NUMBER WILL INFLUENCE CONTRASTIVE L EARNING ?
Number of motif slots, K , is an important hyperparameter in our motif learning framework.
We thus conduct ablation study with three different K values, 5, 20, and 100.
As illustrated in Table 4, with different K values, MICRO-Graph can consistently enhance the transfer performance by a large margin.
Among the three numbers used, the middle one (20) gives the best result on average.
4. V ISUALIZATION OF THE LEARNED M OTIFS
We further show learned motifs by collecting the closest subgraphs to them.
As illustrated in Figure 3, MICRO-Graph automatically learns motifs that are similar to meaningful functional groups in molecule domain, such as Benzene rings and acetate.
This shows that MICRO-Graph can learn reasonable and meaningful motifs.
A complete list of the learned motifs is shown in Appendix C.
C ONCLUSION
In this paper, we propose MICRO-Graph to pre-train a GNN in a self-supervised manner to automatically extract graph motifs from large-scale graph datasets.
In addition, the learned motifs can guide the generation of more informative subgraphs, and help to conduct graph-to-subgraph contrastive learning.
The motif learning and contrastive learning are mutually reinforced, and eventually help pre-train a generalizable GNN encoder.
By pre-training on ogbg-molhiv molecule dataset with
MICRO-Graph , we can learn meaningful motifs that align with existing molecular functional groups.
Meanwhile, ﬁne-tune the pre-trained GNN on seven chemical property prediction benchmarks yielding 2.0% average improvement over non-pretrained GNNs and outperforming other self-supervised pre-training baselines.
A P SEUDOCODE OF THE MAIN ALGORITHM
[Table]
temperature
[Table] [Table]
[Table] [Table]
[Table]
contains all
[Table] [Table]
.motifs
[Table]
for pretraining 67 for
[Table]
in loader:
[Table] [Table]
[Table] [Table]
[Table] [Table]
no
[Table]
grad
[Table] [Table]
[Table]
) > 0 # 1 x N # compute the sampler lossloss_s = sum_A[S_mask]
# normalize S
S_tilde =
torch.softmax(S / tau_g, dim=0)
# K x N # compute motif learning lossloss_m = - (Q * S_tilde.log()).sum(dim=0).mean()
[Table]
similarities between each
[Table] [Table]
[Table] [Table]
[Table] [Table]
[Table] [Table]
60 def
[Table]
):with torch.no
[Table] [Table]
[Table] [Table]
[Table] [Table]
to get
[Table]
n
[Table] [Table]
i
[Table]
# compute the
[Table]
affinity
[Table]
A
[Table]
A_
[Table]
torch.softmax(pairwise_cosine_sim(n, n) / tau_n, dim=1)
# apply
[Table]
# to
[Table] [Table]
[Table]
is
[Table]
list
I_
[Table] [Table]
[Table] [Table]
I
[Table]
[Figure]
[Table]
[Figure]
B N OTATION SUMMARY
Below, we summary the important notations and symbols used paper in the order they appeared.
Graph
[Table]
Node afﬁnity matrix, n-by-n dimensional for a whole graph with n nodes
[Table]
Node afﬁnity between node s and node t in a graph
I
Indices of nodes forming a subgraph selected by the Motif-guided Segmenter
Motifs
[Table]
vectors
[Table]
Similarities between all K motifs and all N subgraphs, K-by-N dimensional
[Table]
Similarities between all K motifs and the subgraph j, K-by-1 dimensional
[Table]
Similarity between the motif k and the subgraph j, scalar ˜
[Table]
j
Normalized similarity between the motif k and the subgraph j
Q
Motif-based cluster assignment matrix, K-by-N dimensional q
[Table]
Motif-based cluster assignment of subgraph j, 1-by-N dimensional
[Table]
Threshold for deciding whether a subgraph is similar enough to motif k
Contrastive
W
Normalized similarities between M graphs and N subgraphs, M-by-N dimensional
[Table]
i
[Table]
Normalized similarities between graph i and subgraph j
Others
[Table]
Temperature for the
softmax
normalization of node-node similarity τ g Temperature for the softmax of motif-subgraph and graph-subgraph similarity E
[Table]
GNN encoder used to generate node embeddings and (sub)graph embeddings
D
Dimension of node embeddings, (sub)graph embeddings, and motif vectors
C T OP K CLOSESET SUBGRAPHS TO LEARNED MOTIFS
Examples of the ﬁrst 10 learned motifs of the ogbg-molhiv dataset is shown in Figure 4 and 5.
D S AMPLING S TRATEGIES AND S AMPLED S UBGRAPHS
Here we describe the details of our heuristic sampling strategies.
For random walk, we use a random walk length uniform in [10, 40].
Starting from a randomly selected seed node, we randomly select its neighborhood as next hop, until reaching the walk length threshold.
For K -hop neighbors, we pick hop number k
to be 1 or 2 with equal probability.
Starting randomly selected seed node, we collect all the neighbors within k hop as the sampled subgraph.
We also shows some subgraph examples generated by these two heuristic strategies and our proposed motif-guided subgraph segmenter in Figure 6.
From the sampled subgraphs, we can see that random walk is more likely to generate chains, while k-hop sampling is more likely to generate half part of a Benzene ring.
Neither of these two heuristic approaches can successfully generate a complete and clean functional group, and the generated subgraphs are not that meaningful.
On the contrary, our motif-guided sampler can succssfully generate a complete benzene ring and two other molecule substructures.
This intuitively explains why the graph-to-subgraph contrastive learning can only work with our proposed subgraph segmenter.
E C HEMICAL P ROPERTY P REDICTION B ENCHMARKS
In our experiments, we evaluated model performance on seven Open Graph Benchmark (OGB) molecule property prediction datasets.
We provide a synopsis of each downstream task dataset from
Hu et al.
(2020b) below:
• bace: Qualitative binding results for a set of inhibitors of human β -secretase 1. • bbbp: Blood-brain barrier penetration (membrane permeability).
• clintox: Qualitative data classifying drugs approved by the FDA and those that have failed clinical trials for toxicity reasons.
• hiv:
Experimentally measured abilities to inhibit HIV replication.
[Table]
• sider: Database of marketed drugs and adverse drug reactions (ADR), grouped into
organ
• tox21: Toxicity data on 12 biological targets, including nuclear receptors and stress response pathways.
• toxcast: Toxicology measurements based on over 600 in vitro high-throughput screenings.
Table 5 summarizes important statistics of the OGB molecule datasets related to the number of graphs, the size of graphs, and number of properties that require prediction for each molecule.
For these datasets, there are 9-dimensional node features including atomic number, chirality, and etc.
There are also 3-dimensional edge features including bond type, bond stereochemistry, and an additional bond feature indicating whether the bond is conjugated.
For further information on the
OGB datasets, please refer to Hu et al.
(2020b) and Hu et al.
(2020a).
F H YPERPARAMETERS AND M ODEL C ONFIGURATION
We show the hyper-parameters we used for running our experiments.
We use the same hyperparameters, 5 hidden layers and 300 hidden dimension, recommended in Li et al.
(2020) for all DeeperGCN models.
We pre-train our model using Adam optimizer for 100 epochs, with batch size (number of graphs per batch) 512.
For ﬁne-tuning, we train the model for 100 epochs with batch size 32.
We select model with highest validation result and report its test result.
Corresponding experiment results are shown in Section 4.3.
The parameters for running context prediction baseline is shown in Table 6.
We show additional experiments of ContextPred with different parameters in Table
[Table]
Context represent mode cbow
[Table]
[Table]
G M OTIF C LUSTER S IZE D ISTRIBUTION
In Figure
[Table]
we show the distribution of cluster sizes of all the learned motifs.
Although with the equal-size constraint, the distribution is not completely uniform.
H V ISUALIZING S IMILARITIES
In this section, we visualize the similarity scores between the learned graph and subgraph representations.
In particular, we consider a whole graph G 1 within a batch of graphs {G 1 , ..., G B } , and three different subgraphs g 1 , g 2 , and g 3 sampled from G 1 .
In Figure 8, we visualize the distribution of pairwise cosine similarity between all graph-motifassignment vectors a i .
Here each a i is associated with a graph G i with N i subgraphs g i , ..., g N i .
It is a K-dimensional vector representing which motif the graph G i contains.
We compute a i by aggregating the corresponding normalized motif-subgraph similarities ˜ S as the following.
[Equation]
This distribution in Figure 8 is over the pairwise cosine similarities of all a i ’s in the batch.
In this case, only 8.7% of these pairwise cosine similarities are higher than 0.5, and only 1.7% higher than 0.9, which shows the graph dataset is well distributed and contains diverse whole graphs.
It is relatively uncommon for whole graphs to share many subgraphs.
In Figure 9, we visualize the distribution of similarity scores between G 1 and all the subgraphs sampled from the whole batch of graphs {G 1 , ..., G B } .
We see that the distribution is centered around 0, with maximum roughly equal to 0.6.
In Figure 10, we visualize similarity scores between G 1 and g 1 , g 2 , and g 3 , and we zoom in to each dimension.
The similarity score we use is cosine similarity.
In this case, the cosine similarity scores are 0.6026, 0.6020, and 0.4786 respectively, which are signiﬁcantly higher than subgraphs sampled from other whole graphs as shown in Figure 9.
To ﬁgure out how we got these high scores, we can zoom into each dimension.
In other words, we check the elementwise product of the 300-dimensional graph and subgraph representation vectors, without summing these 300 number together.
We ﬁnd that the three distribution corresponding to these subgraphs look very different, which indicates these three subgraph representations activate different dimensions of the multi-view whole graph representation.
In other words, they are only similar to the projection of the whole graph representation on different basis.
In Figure 11, we further show that pairwise similarity scores between these three subgraphs g 1 , g 2 , and g 3 , which are not very high.
This veriﬁes our claim in Figure 10.
In Figure 12, we show the pairwise similarity scores between the ﬁrst 30 subgraphs sampled from {G 1 , ..., G B } .
We see that even though these subgraphs are listed in order, i.e. g 1 , ..., g 3 are from
G 1 , g 4 , g 5 are from G 2 , g 6 , ...
g 8 are from G 3 , and etc, similarity scores are roughly uniform.
In other words, this heat matrix is not strictly block diagonal, indicating subgraphs from the same whole graph do not necessarily have high similarities among them.
I L INEAR E VALUATION IN A CCURACY
We show the linear evaluation result in accuracy of our model and the baselines in Table ?? .
Note that the results of tables in Section 4 are in AUC-ROC rather than accuracy.
[Table]
Use pretrainedmodels to extract
J A S YNTHETIC DATASET TO STUDY MOTIF LEARNING
In addition to studying the pre-training in chemical domain, we also construct a synthetic dataset to that align with our assumptions to verify the effectiveness of the propose method.
We assume there exist K graph motifs
[Table]
and each whole graph can be representated by certain combinations of these motifs.
Following this rule, we ﬁrst select some graph structures as motifs, and randomly sample some combinations, and generate graphs (as is illustrated in Figure 13) by combining the motifs, with some randomly added or deleted nodes and edges.
Each graph will also be assigned a corresponding one-hot vector label, whose dimension is the total number of combinations we generated for the dataset.
Eight subgraph templates and examples of generated whole graphs are shown below.
As is illustrated in Figure 14, our MICRO-Graph can successfully learn the underlying graph motifs and templates without any annotations.
The advantage of constructing such synthetic dataset is that we can know the underlying groundtruth of graph motifs and combination rules.
We believe on top of this toy dataset, more complex