Learning on Large Graphs using Intersecting Communities

Message Passing Neural Networks (MPNNs) are a staple of graph machine learning. MPNNs iteratively update each node's representation in an input graph by aggregating messages from the node's neighbors, which necessitates a memory complexity of the order of the number of graph edges. This complexity might quickly become prohibitive for large graphs provided they are not very sparse. In this paper, we propose a novel approach to alleviate this problem by approximating the input graph as an intersecting community graph (ICG) -- a combination of intersecting cliques. The key insight is that the number of communities required to approximate a graph does not depend on the graph size. We develop a new constructive version of the Weak Graph Regularity Lemma to efficiently construct an approximating ICG for any input graph. We then devise an efficient graph learning algorithm operating directly on ICG in linear memory and time with respect to the number of nodes (rather than edges). This offers a new and fundamentally different pipeline for learning on very large non-sparse graphs, whose applicability is demonstrated empirically on node classification tasks and spatio-temporal data processing.

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Peer review

Reviewer XnC35/10 · confidence 4/52024-07-09

Summary

This paper introduces a novel approach for graph machine learning on large graphs using a concept called Intersecting Community Graphs (ICG). Traditional MPNNs face memory and computational challenges when dealing with large graphs due to their reliance on graph edges. The proposed method approximates the input graph as a combination of ICG, which requires fewer communities than the size of the graph. The ICG approach leverages a new constructive version of the Weak Graph Regularity Lemma to construct these approximations efficiently. The resultant learning algorithm operates with memory and time complexity linear to the number of nodes, rather than edges, making it suitable for very large, non-sparse graphs. Empirical evaluations demonstrate the method's applicability to tasks like node classification and spatio-temporal data processing.

Strengths

1. In theory, the approach scales linearly with the number of nodes, addressing the memory complexity issues that plague traditional MPNNs when applied to large graphs. 2. The paper introduces a constructive version of the Weak Graph Regularity Lemma, which could be of independent interest in graph theory and its applications. 3. The method has been empirically validated on real-world tasks, showing competitive performance against existing models in node classification and spatio-temporal graph tasks.

Weaknesses

1. The proposed method's speed advantage over MPNNs hinges on the assumption that the chosen number of communities K should be less than the node degree (line 170). However, real-world experiments sometimes require a K value larger than the node degree. For example, in the twitch-gamers dataset, K is set to 500 while the average node degree is 40.32. This discrepancy raises concerns about the practical speed benefits of the proposed method on real-world benchmarks. 2. The computation of the ICG requires an offline pre-computation step that, while only performed once, involves a time complexity linear to the number of edges. 3. In the Runtime Analysis section, the authors should also include a time comparison for the model's convergence, in addition to the per-epoch runtime. 4. To demonstrate the efficacy of the proposed initialization method, the paper should include a comparison with existing initialization methods, such as random initialization.

Questions

Has the author evaluated the relationship between the model's performance and the cut-metric between the approximated graph and the original graph? While I agree that in certain situations, such as social networks, ICG can approximate the original graph well, it is important to question whether this assumption holds in other contexts, such as molecular graphs.

Rating

5

Confidence

4

Soundness

3

Presentation

3

Contribution

2

Limitations

N/A.

Reviewer hec56/10 · confidence 4/52024-07-10

Summary

The paper proposes a novel method to improve the GNN efficiency for large and dense graphs by approximating them as Intersecting Community Graphs (ICGs). This approach significantly reduces time and memory complexity depending on the number of nodes rather than edges. The authors theoretically show the approximation of ICGs using the weak graph regularity lemma. Experiments demonstrate ICG’s efficiency in node classification and spatio-temporal data tasks.

Strengths

The authors propose an efficient method to train large (and dense) graphs. The method is theoretically well-motivated and concretely proved with detailed explanations. The theory is interesting, and the techniques used can be applied to future work in various ways. In addition, there are diverse types of benchmarks and evaluations (runtime analysis, node classification, spatio-temporal graphs), and the paper presents their results clearly.

Weaknesses

- From my perspective, ICG+GNN is similar to summarizing the graph into smaller units (e.g., coarsened nodes, communities, or subgraphs) and then performing message-passing between them. It is essential to acknowledge the line of research on GNNs with graph coarsening, summarization, and condensation. These methods have addressed the challenges in graph learning, especially for efficiency and scalability. The examples of recent papers are stated below, and some of the work should be compared with empirical experiments. - Hierarchical Inter-Message Passing for Learning on Molecular Graphs (ICML workshop 2020) - Scaling Up Graph Neural Networks Via Graph Coarsening (KDD 2021) - GRAPH CONDENSATION FOR GRAPH NEURAL NETWORKS (ICLR 2022) - A Provable Framework of Learning Graph Embeddings via Summarization (AAAI 2023) - Gapformer: Graph transformer with graph pooling for node classification (IJCAI 2023) - Structure-free Graph Condensation: From Large-scale Graphs to Condensed Graph-free Data (NeurIPS 2023) - Fast Graph Condensation with Structure-based Neural Tangent Kernel (WWW 2024) - Translating Subgraphs to Nodes Makes Simple GNNs Strong and Efficient for Subgraph Representation Learning (ICML 2024) - The time and memory required for real runtime to fit ICGs are not demonstrated. It makes sense that we only need to create the ICG once, but how much time and GPU memory does it take to create it? - Evaluation across datasets should be encouraged. Although various evaluations have been performed, a set of datasets was picked for each evaluation. A natural question arises as to whether this method robustly works across datasets. - Scalability should be validated by experiments on larger datasets and be compared with other efficient GNNs. The authors stated that constraints (single, large, undirected) restrict the number of datasets the authors can experiment on. But as far as I know, there are many more single, large, undirected graph datasets. Is the largest dataset used in the experiment large enough compared to existing efficient GNN research? Plus, is this method superior to existing scalable GNNs (e.g., sampling, coarsening) in practice (i.e., total training time)?

Questions

- p249: Why does the operation on Community feature vector F is O(K^2D^2) rather than O(KD^2)? F is a matrix, the shape of which is K x D, then MLP on this matrix will be computed in O(KD^2) like p252. - p253: Why is Q^{†}Q an identity matrix? Are the rows of Q linearly independent? I could not find the constraint or assumption on this. - Notations: How about using more distinguishable notations for node features S and signals \italic{S}? This might not be clear to readers.

Rating

6

Confidence

4

Soundness

2

Presentation

3

Contribution

3

Limitations

The authors adequately addressed the limitations.

Authorsrebuttal2024-08-11

We thank the reviewer for their comments and for acknowledging our work’s theoretical novelty and its future work potential. Since the author-reviewer discussion period is closing soon, we would highly appreciate feedback on our response. We are keen to take advantage of the author-reviewer discussion period to clarify any additional concerns.

Reviewer 2roR5/10 · confidence 3/52024-07-12

Summary

This paper proposes the Intersecting Communities Graph (ICG), which enables efficient learning on very large non-sparse graphs by representing the graph as a linear combination of intersecting communities such as cliques. Unlike Message Passing Neural Networks (MPNNs), the proposed method operates with memory complexity proportional to the number of nodes, even for extremely large graphs. Although constructing the ICG takes linear time, this is an offline preprocessing step that is performed only once, and subsequent learning tasks are conducted very efficiently. The effectiveness of the proposed method is empirically demonstrated using both synthetic and real-world data.

Strengths

- This paper is clearly and systematically written, effectively utilizing figures and equations to concisely present the entire logical development of the paper. - The methodology introduced with the Intersecting Communities Graph (ICG) offers a novel approach that is different from traditional graph machine learning methods. It provides a new pipeline that enables learning on large and dense graphs. - By leveraging the Weak Graph Regularity Lemma, the paper provides a theoretically rigorous and efficient method for constructing ICG. - The validity of the experimental results demonstrates the effectiveness of the proposed method.

Weaknesses

- The proposed method has been shown to dramatically accelerate the learning of dense large-scale graphs. However, it is necessary to have a straightforward way to determine how dense a graph needs to be for the proposed method to be effective, or under what conditions of sparsity it remains effective. It seems that the conditions mentioned in lines 169-172, such as $K > N^4/E^2$, $K < d$, $E > N^{5/3}$, and $d > N^{2/3}$, might serve this purpose. However, these conditions are derived based on the Weak Regularity Lemma, and it is not clearly stated whether they can be used as practical criteria for the above judgments. Furthermore, in the experimental section, these indicators for each dataset do not appear to be clearly presented, making it difficult for readers to understand the existence of such effective criteria. By clearly demonstrating such criteria, the applicability of the proposed method could potentially be broadened. - There are a few minor mistakes. For example, could (14) on line 110 be a mistake for (4)?

Questions

- Is there a straightforward way to determine how dense a graph needs to be for the proposed method to be effective, or under what conditions of sparsity it remains effective? Are these the conditions mentioned in lines 169-172? To what extent are these criteria met in each dataset in the experimental section?

Rating

5

Confidence

3

Soundness

3

Presentation

3

Contribution

4

Limitations

If there is no simple way to determine the applicability of the proposed method, it may limit the range of its practical application.

Reviewer Z1J66/10 · confidence 3/52024-07-14

Summary

The main idea of this paper is to break a graph into communities and approximate the graph with a limited number of these communities. The main idea of the work is rooted in the cut metric, which is defined for signals on the graphs and includes both graph structure and node features. They approximate the cut metric with a Frobenius norm version of the problem and prove a constructive version of the Weak Regularity lemma. Their reformulation allows the problem to be solved with a gradient descent algorithm. They also provide a version of subgraph gradient descent for larger graphs. They also theoretically analyze the approximation power of their subgraph gradient descent for finding the gradient on the whole graph. They introduce two models to be used after finding the communities and signals for these communities. The first model uses a Transformer architecture on the community signals, but the second one learns the community signals along the layers of their network. They provide time analysis on their work using random Erdős-Rényi graphs and show that their method is much more efficient than Graph Convolutional Network (GCN) in a forward pass of their model (used after finding the communities). They also get competitive results on node classification tasks for a few datasets and apply their work for a spatio-temporal task for traffic forecasting.

Strengths

1. The paper has deep roots in the theory and does not neglect to provide theoretical analysis for any decision made in their process. 2. I am not an expert in the domain of signal processing for graphs, and I do not know to what extent the proofs in this paper are novel. However, they seem to present interesting results, and introducing them to the modern graph learning community is valuable in itself. 3. Their initial algorithm for finding the communities does not appear to be any simpler than learning on the graph by a Message Passing Neural Network (MPNN). However, it has the advantage of not requiring any hyperparameter tuning and only needing to be done once. 4. They have done a good job of finding spatiotemporal tasks where the graph structure is fixed, but the signals are changing. The initial community finding process load can be better justified in this setup.

Weaknesses

1. Their analysis on the time complexity and efficiency of their method seems to be incorrect. Namely, in line 257, they mention that the message passing networks need $O(ED^2)$ operations. This is not correct. Message passing networks usually have a node-level processing which is $O(ND^2)$ and then a message aggregation process which is $O(ED)$, as there is no matrix multiplication along the edges and it is just adding the vectors of size D. Thus, the total complexity is $O(ND^2 + ED)$. This is a significant problem as they mention their method is efficient if $K = O(Dd)$, where $D$ is the size of the features and $d$ is the average degree of the graph. By correct complexity of the message passing networks, we can see that their method only works comparably efficiently if $K = O(d)$, which is very small for most of the graphs. While Figure 2 suggests that their method is much faster than the GCN, the reason is that the graphs they sample are very dense, with $d = O(N)$ and $E = O(N^2)$. This is evident from Figure 6 in their appendix, where they use a more sparse graph with $d = 50$. We can see that when $K=100$, the time required by their method is similar to that of the GCN. 2. The paper gets unnecessarily complex and hard to understand, especially with the notations, which are excessive and sometimes inconsistent. For example, starting from Definition 2.1. the definition of the matrix norm is just used for the adjacency matrix A and feature matrix S in this paper, defining new matrices B and Z here just makes it confusing. At any point, if you require to define a formula that is general on all matrices, like when you describe the Frobenius norm, you can use names like X which does not feel to be a special matrix that might next definitions depend on it. Starting in Section 3.1, the use of C and P for finding the ICG on (A, S) using b vectors, and continuing with F at another point, makes it very confusing. One reason for this can be that B seems to be defined earlier in Definition 2.1, but it is not really connected to the b vectors used here. Definition 3.1 defines $\mathcal{Q}$ as a set of functions. However, starting with Definition 3.2, it uses the term "soft affiliation model" for $\mathcal{Q}$. I am not sure what is meant by "model" here and whether we are still referring to the same $\mathcal{Q}$. This is particularly confusing because, as I understand it, each member of $\mathcal{Q}$ is a function from $[N]$ to $\mathbb{R}$. Therefore, $\mathcal{Q}$ is a subset of $\mathbb{R}^N$, and the space defined for $[\mathcal{Q}]$ in Definition 3.2 is not clear to me. 3. While the main point is the efficiency of the method, the results for node classification are very limited, both in the number of datasets and the size of the datasets, and do not quite reflect the effectiveness of the method. 4. Their theory (Theorem 3.1) only works for very large K values for reasonably sparse graphs that can be seen in most datasets.

Questions

1. Is there any time measured for fitting an ICG for a graph with the gradient descent? It seems to be at least as complex as learning the main task. However, I admit that it has the advantage of requiring no hyperparameter tuning and can be done once, with the condition that it can be done on large graphs with a reasonable calculation budget. 2. What is the relation of your work to graph coarsening methods? Methods such as DiffPool [1] seem to be learning a similar thing as a layer in the neural network, and thus their pooling is task-dependent. What are the advantages of your method over these techniques? [1] Ying, Zhitao, et al. "Hierarchical graph representation learning with differentiable pooling." Advances in neural information processing systems 31 (2018).

Rating

6

Confidence

3

Soundness

3

Presentation

3

Contribution

3

Limitations

The method seems to be more efficient for very dense graphs, which is discussed to some extent in the paper. However, there also seem to be some mistakes in their argument (discussed in the Weaknesses section).

Reviewer XnC32024-08-10

I thank the authors for their rebuttal, which partially addresses my concerns. In general, the paper contributes insights to the field, but there are still areas for improvement, such as further validation to ensure the robustness and scalability of the model. As a result, I will maintain my current score.

Authorsrebuttal2024-08-11

> In general, the paper contributes insights to the field We thank the reviewer for acknowledging the contribution of this work to the field. > there are still areas for improvement, such as further validation to ensure the robustness and scalability of the model. To further validate and ensure the robustness and scalability of our model, we conducted additional experiments which were not previously mentioned in our rebuttal to your review, testing ICG-NNs and their subgraph variation: * **Comparison to graph coarsening methods** - We provide an empirical comparison in **Table 1** of **rebuttal.pdf** between our method and a variety of graph coarsening/summarization methods on the **reddit** and **flickr** datasets. ICG-NNs achieve state-of-the-art performance, further solidifying its effectiveness. * **Subgraph ICG-NN and ICG-NN on the large graph flickr** - To highlight the usage of subgraph sgd ICG-NN on large graphs, we conducted additional experiments using the **flickr** dataset, which is significantly larger than the datasets used in our initial submission. The results indicate that ICG-NNs with subgraph ICGm, using a 1% sampling rate, outperform competing methods that operate on the full graph. > I thank the authors for their rebuttal, which partially addresses my concerns. We would like to use this opportunity to clarify remaining concerns. Could you give us specific issues you are concerned with, so we have the opportunity to address them? In light of this we would greatly appreciate a reconsideration of the current score.

Reviewer Z1J62024-08-11

I thank the authors for their rebuttal and new experiments. > While standard benchmarks of large graphs are quite sparse, we believe that this is a result of the research community focusing on sparse graphs when developing methods for large graphs. However, in industrial applications, one often has to work with large and not very sparse graphs ... Thanks this has been an insightful response. I also think that the focus of most of the methods on large graphs has been on the sparse graphs and there is not enough work on denser graphs. I would also suggest adding this argument to your work and encouraging the community to work more on the denser, real-world graphs. **New experiments**: Thank you for running new experiments; the results are more convincing now. Just for the Reddit dataset, the average degree mentioned does not seem correct. It should be near 500 if you are using the original one, or near 100 if you are using the GraphSAINT version (according to the PyTorch Geometric library website). Also, ogbn-proteins can be a good candidate as it has a high average degree of near 600. **New Theory**: Thank you for updating; this is a more reasonable bound now. In general, I would like to encourage the authors to keep revising their paper as some parts are hard to follow in the current version and to update their manuscript with their rebuttal experiments and potentially more new datasets. Most of my concerns have been addressed, so I want to raise my score to 6.

Authorsrebuttal2024-08-11

> Most of my concerns have been addressed, so I want to raise my score to 6. We warmly thank the reviewer for acknowledging our rebuttal and raising their score. > I would like to encourage the authors to keep revising their paper as some parts are hard to follow in the current version and to update their manuscript with their rebuttal experiments and potentially more new datasets. We will make sure to include all of the points that were mentioned during the rebuttal in the final version of our paper. > It should be near 500 if you are using the original one, or near 100 if you are using the GraphSAINT version (according to the PyTorch Geometric library website). Thank you for pointing this out. You are correct, reddit's average degree is 491.99.

Reviewer 2roR2024-08-12

Thank you for your thorough response. My concerns appear to be largely resolved by the more precise mathematical descriptions you provided. Additionally, the supplementary experiments with real data have demonstrated the validity of your approach. Therefore, I will keep my rating unchanged. Thank you again.

Authorsrebuttal2024-08-12

> Thank you for your thorough response. Additionally, the supplementary experiments with real data have demonstrated the validity of your approach. We thank the reviewer for acknowledging our rebuttal and participating in the discussion period. > My concerns appear to be largely resolved by the more precise mathematical descriptions you provided. We are glad to have resolved the reviewer's concerns. If the reviewer now sees the paper as worthy of publication, we hope they can increase their score above the threshold of acceptance to reflect that. We would like to use this opportunity to clarify remaining concerns that might prevent the a higher score. Regardless, we would like to warmly thank the reviewer again.

Reviewer hec52024-08-12

I acknowledged the author's response. Thank you for the detailed explanations and they resolved my concerns. I will raise my score. Please include our discussions on your camera-ready paper. Looking forward to seeing the revised paper!

Authorsrebuttal2024-08-12

> I acknowledged the author's response. Thank you for the detailed explanations and they resolved my concerns. I will raise my score. We warmly thank the reviewer for acknowledging our rebuttal and raising their score. > Please include our discussions on your camera-ready paper. Looking forward to seeing the revised paper! We will make sure to include all of the valuable points that the reviewers mentioned during the rebuttal in the final version of our paper. We would like to thank the reviewer again.

Program Chairsdecision2024-09-25

Decision

Accept (poster)

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