Pard: Permutation-Invariant Autoregressive Diffusion for Graph Generation

Graph generation has been dominated by autoregressive models due to their simplicity and effectiveness, despite their sensitivity to ordering. Yet diffusion models have garnered increasing attention, as they offer comparable performance while being permutation-invariant. Current graph diffusion models generate graphs in a one-shot fashion, but they require extra features and thousands of denoising steps to achieve optimal performance. We introduce PARD, a Permutation-invariant Auto Regressive Diffusion model that integrates diffusion models with autoregressive methods. PARD harnesses the effectiveness and efficiency of the autoregressive model while maintaining permutation invariance without ordering sensitivity. Specifically, we show that contrary to sets, elements in a graph are not entirely unordered and there is a unique partial order for nodes and edges. With this partial order, PARD generates a graph in a block-by-block, autoregressive fashion, where each block's probability is conditionally modeled by a shared diffusion model with an equivariant network. To ensure efficiency while being expressive, we further propose a higher-order graph transformer, which integrates transformer with PPGN. Like GPT, we extend the higher-order graph transformer to support parallel training of all blocks. Without any extra features, PARD achieves state-of-the-art performance on molecular and non-molecular datasets, and scales to large datasets like MOSES containing 1.9M molecules. Pard is open-sourced at https://github.com/LingxiaoShawn/Pard.

Paper

Similar papers

Peer review

Reviewer KWRX6/10 · confidence 3/52024-07-04

Summary

The paper introduces PARD, a graph generation model that combines autoregressive and diffusion models. Traditional autoregressive models are effective but sensitive to order, while diffusion models are permutation-invariant but need many denoising steps and extra features. PARD overcomes these issues by generating graphs block-by-block using a partial order of nodes and edges. It employs a shared diffusion model with an equivariant network and a higher-order graph transformer, supporting parallel training like GPT. PARD achieves state-of-the-art performance on various datasets, including large ones like MOSES, without extra features.

Strengths

1. This work presents a successful showcase of the combination of autoregressive modeling with diffusion model on graph. 2. The proposed partial order ensures the permutation-invariance in the autoregressive generation process. 3. Impressive experimental results show the effectiveness and efficiency.

Weaknesses

1. It is unclear how the diffusion model is employed in PARD. Sec 3.1 and the second part of Eq. 6 are not quite relevant to each other. Can you elaborate on that? 2. Please provide proof or reference for some statements. e.g.: 2-FWL expressivity for the proposed higher-order transformer 3. Please provide the results of other baselines on QM9 if possible.

Questions

1. Seems that in Fig. 2 the prior of the diffusion process is not the same as the second part of Eq. 6. What is the choice of the graph distribution at timestep T? 2. The total number of diffusion steps is directly related to number of blocks. I anticipate the generic graphs will have more blocks than QM9. Can you show the total number of diffusion steps for other datasets? 3. Some of the discussions are redundant can be moved to appendix, like the comparison to DiGress and GRAN in Sec. 3.1 and Sec 3.2, the energy view in Sec. 3.4. The running time comparison can be moved to the experiment section.

Rating

6

Confidence

3

Soundness

3

Presentation

2

Contribution

4

Limitations

There is no discussion about the limitation in the manuscript.

Reviewer KWRX2024-08-11

Thank you for the rebuttal

Thank you for the response. I want to mention that one of the main contributions of this work is its improvement in the efficiency. Given the discussion, the inference time of the proposed method highly relies on the number of blocks and does not necessarily offer efficiency on large graphs in the current version. However, the idea it self is interesting and the results are promising. Therefore, I have increased my score to 6 to support this work.

Authorsrebuttal2024-08-11

Thank you for your further support. We want to mention that for larger graph, our Pard should still outperforms DiGress in both efficiency and performance. When consider larger graph, each block's number of diffusion steps can be further reduced as there can be dramatically less symmetry inside. In fact, we have found that DiGress struggle to perform good in the Grid dataset (the largest dataset we considered) given the rich symmetry inside. Our Pard breaks symmetry easily with the AR mechanism inside, such that later blocks will have less and less symmetry and lots of blocks does not need any diffusion steps (50% in QM9 dataset). In the final version of the paper, we will add the ablation study on Grid, to show that the effectiveness in both efficiency and performance comparing to single-block version DiGress. At the end, we appreciate the discussion you provided, and we are grateful for the feedback to improving our paper.

Reviewer 2orD6/10 · confidence 3/52024-07-06

Summary

This paper proposes a graph generation method that combines AutoRegressive (AR) models and diffusion models. By utilizing a unique partial order, it addresses the issue of non-exchangeable probabilities in AR models and the efficiency problem in diffusion models.

Strengths

1. The proposed block-wise AR diffusion model in this paper offers a new idea for graph generation, particularly by introducing the use of weight-degree to differentiate blocks. 2. The limitations of equivariant networks demonstrated in this paper also hold value for further exploration and resolution within the community. 3. The overall structure and writing of the paper are relatively clear.

Weaknesses

1. There is a part in the paper that I believe needs to be clarified more clearly to ensure logical coherence. Why does diffusion based on equivariant network solve the flaw in equivariant modeling? I think besides the analogy of tempering iron (or higher/lower energy), more mathematical proofs are needed. 2. Ablation of PPGN is necessary to demonstrate its effectiveness. 3. Following the experimental settings of GDSS, NSPDK is also an important metric for QM9 and ZINC250K.

Questions

1. Is there a reasonable explanation for the significant improvement of FCD on ZINC250K compared to other baselines? Similarly, why is there such a large difference in performance between Scaf. and baseline methods on MOSES?

Rating

6

Confidence

3

Soundness

3

Presentation

3

Contribution

3

Limitations

Yes

Reviewer adow3/10 · confidence 4/52024-07-12

Summary

The work proposes a new graph generative model based on an autoregressive procedure. It proposes an approach to deciding a partial order of graph nodes according to their degrees in a node-removal procedure. Based on the partial order, the work devises a new graph generative model.

Strengths

The graph algorithm of deciding a partial order of graph nodes would be interesting if such an algorithm does not exist in the literature of graph theory.

Weaknesses

The work lacks justification. As the field has moved to generative methods with discrete-diffusion models, which are already permutation-invariant, it is less clear about the advantage of designing a complex autoregressive model to satisfy the permutation-invariant property. The advantage of the model is not obvious even considering only autoregressive models. Note that Chen et al. [9] have an approach of "optimizing" node orders for the generative model and show that the likelihood calculation is more accurate with their approach than a pre-determined order. How does the work justify its advantage over such an approach? The analysis in 3.3 does not seem to be reasonable. The **probability calculations** are indeed the same for nodes in the same orbit, but they may get different connections in the sampling procedure and then break the symmetry. The analysis in 3.3 is well known, and it is not a concern for generative models. In some diffusion-based generative models, the starting graph is a graph with no edges, then all nodes are in the same orbit, but it is not an issue at all because the edge sampling process will break the symmetry. Without clear justification, I don't know where performance improvements are from (maybe architecture improvement?). I feel that the work should have a thorough investigation of the model.

Questions

How do you justify the advantage of using an autoregressive model with partial order?

Rating

3

Confidence

4

Soundness

1

Presentation

3

Contribution

2

Limitations

The proposed model seems to have a long running time because it needs to run a diffusion model at the generation of each block.

Authorsrebuttal2024-08-09

Response to reviewer's question

Thank you for the timely response. For your additional two questions: 1. Yes, each block only takes 1/20 of DiGress iterations. Please see the first ablation study table, you will find the 'Diffusion steps per block' indicates the number of steps we used for each block. Total diffusion steps = num of blocks * diffusion steps per block. 2. Yes, all generated blocks are fixed, and are used to be conditioned on to generate the next block. The noise and randomness is only introduced in the target block. In Section 4.2, we leverage this property to enable parallel training of all blocks, similar to how next-token predictions in LLM training are parallelized. Please let us know for any further questions!

Reviewer adow2024-08-10

About the update to generated block

I feel a little strange that the generated block is not updated. Initial blocks should have a lot of symmetry, and late blocks break the symmetry by adding new structures. If the representation of initial blocks is not updated, they will provide less information than they should. Is that true?

Authorsrebuttal2024-08-10

Further response to reviewer

You are correct: the symmetry is not evenly distributed in all blocks. Actually, we have found that about 50% blocks have no symmetry inside: directly predict the next block gives 100% accuracy and no noise is needed at all. This means that the 1/4 total diffusion steps of the DiGress is not the optimal: AT LEAST you can achieve 1/8 fraction of total diffusion steps comparing with DiGress and still outperform it (as there are about 50% blocks does not need any diffusion steps). In fact, in the response to the last reviewer, we have mentioned the following: > One major limitation is that each block currently uses the same number of diffusion steps, which is not ideal and can result in unnecessary sampling steps. Empirical evidence shows that approximately 50% of blocks can be predicted directly without any sampling steps, as they do not encounter transformation problems (introduced in Sec. 3.3). It would be highly beneficial to develop a hardness measure (such as graph energy) for the symmetry problem and use this measure to determine the appropriate number of diffusion steps for each block. This approach could significantly reduce the total number of diffusion steps. However, since we haven't yet found a straightforward solution, we decided to assign the same number of diffusion steps to each block. If the reviewer has concerns about our results, we encourage you to run the provided source code, as our results are fully reproducible. If any issues arise, we are also able to provide checkpoints for further verification. --- We are more than willing to provide any additional information you require and kindly ask that you reconsider our work. We believe that our paper does not exhibit "technical flaws, weak evaluation, inadequate reproducibility, or incompletely addressed ethical considerations."

Authorsrebuttal2024-08-10

For the reviewer's another potential question

We realized that you may also have another question: the parallel version of our algorithm shares representations across blocks, hence the earlier generated blocks provided less information to the future block as their representation cannot be updated. Actually, we have fully described the answer to this question in our original paper's section 4.2: why we want to design a parallel version of our algorithm. Initially, our algorithm is not parallel at all: representations are not shared across steps, and each step uses its own graph representation to gain the best performance. Nevertheless, we realized that this approach has a huge suffer in training time: assume that you have K blocks in total, you get roughly K times more training time than the DiGress as you have K times more input graphs by viewing each conditional step's input graph as an individual graph. We solve the training time issue with our proposed **nontrivial, novel and critical** parallel training algorithm, such that all steps share the same blocks representation. Notice that this is an extremely important design: the advantage of causal transformer over RNN is the ability to parallel train all next-token predictions. And of course, you get less information from the previous tokens for the future token predictions: that's why Bert is preferred for document embedding instead of decoder-only GPT. Nevertheless, given the efficiency of GPT for capturing the whole distribution and parallel training, it is still the dominant approach of LLM, and the problem you mentioned does not block its effectiveness. We suggest the reviewer to take a look at the section 4.2 for the detailed designs and explanations.

Authorsrebuttal2024-08-12

As the discussion deadline is approaching, we kindly ask whether you still have additional questions. Given that we have answered all questions you have now, and demonstrated extensive ablations, we would like to hear you back for your thoughts.

Authorsrebuttal2024-08-14

Dear Reviewer **adow**, We hope this message finds you well. As the discussion deadline is rapidly approaching (in approximately 10 hours), we are reaching out to respectfully request your final feedback on our rebuttal. You provided the lowest score with soundness 1 (poor) and contribution 2 in the category of "technical flaws, weak evaluation, inadequate reproducibility, or incompletely addressed ethical considerations." We greatly appreciate the thorough review and the numerous questions you raised, as they have helped us improve our work. In response, **we have diligently addressed all of your questions in detail in many rounds, providing extensive ablation studies to support our claims and clarify any potential misunderstandings**. We believe this additional information directly addresses the concerns that led to the low score. Given the significance of your evaluation and the substantial effort we've put into addressing your queries, we kindly request that you review our responses and provide your updated assessment. Your feedback is crucial for a fair evaluation of our work and will greatly **assist the area chair** in making an informed decision. We understand that time constraints can be challenging, but we would be incredibly grateful if you could take a moment to review our rebuttal and adjust your feedback accordingly. Your expertise and insights are invaluable to this process, and we look forward to your response.Thank you for your time and consideration. We appreciate your dedication to maintaining the high standards of our field.

Reviewer SjHr7/10 · confidence 3/52024-07-16

Summary

This paper proposes to integrate autoregression models with diffusion models seamlessly to harnesses the effectiveness and efficiency of the autoregressive model while maintaining permutation invariance without order sensitivity. It also proposes architectural improvement to make the model and algorithm efficient and scalable. The presentation is smooth and the experimental results on both molecular and general graph generation demonstrate its effectiveness.

Strengths

It proposes a novel graph decomposition method considering not individual node and its degree but subsets of nodes with structual similarity. In this way, it removes node order sensitivity in the graph but only needs to maintain the order of the blocks. Within each block, the diffusion model focuses on a much smaller graph and thus has the efficiency to generate a denoised graph.

Weaknesses

It would be better if the authors can provide some insights about the hyperparameter the maximum of hops $K_h$.

Questions

It would be better if the authors can provide some insights about the hyperparameter the maximum of hops $K_h$.

Rating

7

Confidence

3

Soundness

3

Presentation

4

Contribution

3

Limitations

The authors have adequately mentioned several limitations of their work which sound quite reasonable.

Reviewer adow2024-08-09

Thank you for your response

Can you further elaborate on how the proposed model uses fewer steps than DiGress? If my understanding is correct, the generation of each block would require multiple denoising iterations. Suppose there are 5 blocks, and the total number of iterations is 1/4 of DiGress, then on average each block takes 1/20 of DiGress iterations. Is this correct? If the generated blocks are cached, does it mean that their representations are not updated by later generated structures?

Authorsrebuttal2024-08-12

As the discussion deadline is approaching, we kindly ask whether you still have additional questions. Given that we have answered all questions you have now, and demonstrated extensive ablations, we would like to hear you back for your thoughts.

Reviewer 2orD2024-08-13

thank you for your rebuttal

After reviewing the additional experimental results, I maintain my positive score.

Authorsrebuttal2024-08-12

As the discussion deadline is approaching, we kindly ask whether you still have additional questions. Thanks again for supporting us.

Program Chairsdecision2024-09-25

Decision

Accept (poster)

© 2026 NYSGPT2525 LLC