Graph neural networks (GNNs) have been successful in learning representations from graphs. Many popular GNNs follow the pattern of: they aggregate the neighbors' attributes and then transform the results of aggregation with a learnable function. Analyses of these GNNs explain which pairs of non-identical graphs have different representations. However, we still lack an understanding of how similar these representations will be. We adopt kernel distance and propose as an alternative to aggregate-transform to reflect the continuous similarity between the node neighborhoods in the neighborhood aggregation. The idea leads to a simple and efficient graph similarity, which we name Weisfeiler-Leman similarity (WLS). In contrast to existing graph kernels, WLS is easy to implement with common deep learning frameworks. In graph classification experiments, transform-sum-cat significantly outperforms other neighborhood aggregation methods from popular GNN models. We also develop a simple and fast GNN model based on transform-sum-cat, which obtains, in comparison with widely used GNN models, (1) a higher accuracy in node classification, (2) a lower absolute error in graph regression, and (3) greater stability in adversarial training of graph generation.

--Accurate graph similarity is critical for knowledge transfer in VLSI design, enabling the reuse of prior solutions to reduce engineering effort and turnaround time. We propose Pieceformer, a scalable, self-supervised similarity assessment framework, equipped with a hybrid message-passing and graph transformer encoder . T o address transformer scalability, we incorporate a linear transformer backbone and introduce a partitioned training pipeline for efficient memory and parallelism management. Evaluations on synthetic and real-world CircuitNet datasets show that Pieceformer reduces mean absolute error (MAE) by 24.9% over the baseline and is the only method to correctly cluster all real-world design groups. We further demonstrate the practical usage of our model through a case study on a partitioning task, achieving up to 89% runtime reduction. The increasing complexity of VLSI systems--driven by advanced packaging technologies, shrinking technology nodes, and rapid product cycles--has placed enormous pressure on modern semiconductor design workflows. Meanwhile, tasks such as synthesis, placement, routing, and verification remain highly iterative, computationally expensive, and dependent on deep domain expertise. As a result, there is a growing need for automated methods that can effectively reuse knowledge from existing, optimized designs to accelerate new design efforts.

--Graph similarity learning, crucial for tasks such as graph classification and similarity search, focuses on measuring the similarity between two graph-structured entities. The core challenge in this field is effectively managing the interactions between graphs. Traditional methods often entail separate, redundant computations for each graph pair, leading to unnecessary complexity. This paper revolutionizes the approach by introducing a parallel graph interaction method called graph fusion. By merging the node sequences of graph pairs into a single large graph, our method leverages a global attention mechanism to facilitate interaction computations and to harvest cross-graph insights. We further assess the similarity between graph pairs at two distinct levels--graph-level and node-level--introducing two innovative, yet straightforward, similarity computation algorithms. Extensive testing across five public datasets shows that our model not only outperforms leading baseline models in graph-to-graph classification and regression tasks but also sets a new benchmark for performance and efficiency. I NTRODUCTION Applications based on graph data structures, such as social network analysis [1], bioinformatics [2], and recommendation systems [3], play a crucial role in both academia and industry. Among them, graph similarity learning is one of the most significant challenges in graph-related machine learning tasks.

Drug development is a critical but notoriously resource- and time-consuming process. In this manuscript, we develop a novel generative artificial intelligence (genAI) method DiffSMol to facilitate drug development. DiffSmol generates 3D binding molecules based on the shapes of known ligands. DiffSMol encapsulates geometric details of ligand shapes within pre-trained, expressive shape embeddings and then generates new binding molecules through a diffusion model. DiffSMol further modifies the generated 3D structures iteratively via shape guidance to better resemble the ligand shapes. It also tailors the generated molecules toward optimal binding affinities under the guidance of protein pockets. Here, we show that DiffSMol outperforms the state-of-the-art methods on benchmark datasets. When generating binding molecules resembling ligand shapes, DiffSMol with shape guidance achieves a success rate 61.4%, substantially outperforming the best baseline (11.2%), meanwhile producing molecules with novel molecular graph structures. DiffSMol with pocket guidance also outperforms the best baseline in binding affinities by 13.2%, and even by 17.7% when combined with shape guidance. Case studies for two critical drug targets demonstrate very favorable physicochemical and pharmacokinetic properties of the generated molecules, thus, the potential of DiffSMol in developing promising drug candidates.

Summary and Contributions: The paper proposes a novel graph neural network architecture which is motivated both by the Weisfeiler-Lehman isomorphism test and kernel theory. In more detail, the paper states that the natural representation of a neighborhood of a node is not a simple sum but a sum of features in the kernel space, because this yields a meaningful kernel/distance between sets. Accordingly, the paper suggests that the lth-layer representation of a node should not be the transformed sum of previous layer representations in the neighborhood, but rather the sum of transformed previous-layer representations. This scheme is evaluated in node classification, graph classification, graph regression, and graph generation tasks, yielding performance gains in all cases, with particularly impressive gains in graph kernel classification.

The reviewers liked the motivation and presentation of this new WL kernel-inspired GNN architecture, despite the actual architectural change to existing GNNs is relatively incremental. I hope the authors can revise their paper to address the reviewers' comments in the camera ready version, and give proper credit to prior work.

Graph similarity computation (GSC) aims to quantify the similarity score between two graphs. Although recent GSC methods based on graph neural networks (GNNs) take advantage of intra-graph structures in message passing, few of them fully utilize the structures presented by edges to boost the representation of their connected nodes. Moreover, previous cross-graph node embedding matching lacks the perception of the overall structure of the graph pair, due to the fact that the node representations from GNNs are confined to the intra-graph structure, causing the unreasonable similarity score. Intuitively, the cross-graph structure represented in the assignment graph is helpful to rectify the inappropriate matching. Therefore, we propose a structure-enhanced graph matching network (SEGMN). Equipped with a dual embedding learning module and a structure perception matching module, SEGMN achieves structure enhancement in both embedding learning and cross-graph matching. The dual embedding learning module incorporates adjacent edge representation into each node to achieve a structure-enhanced representation. The structure perception matching module achieves cross-graph structure enhancement through assignment graph convolution. The similarity score of each cross-graph node pair can be rectified by aggregating messages from structurally relevant node pairs. Experimental results on benchmark datasets demonstrate that SEGMN outperforms the state-of-the-art GSC methods in the GED regression task, and the structure perception matching module is plug-and-play, which can further improve the performance of the baselines by up to 25%.

Graph neural networks (GNNs) have been successful in learning representations from graphs. Many popular GNNs follow the pattern of aggregate-transform: they aggregate the neighbors' attributes and then transform the results of aggregation with a learnable function. Analyses of these GNNs explain which pairs of non-identical graphs have different representations. However, we still lack an understanding of how similar these representations will be. We adopt kernel distance and propose transform-sum-cat as an alternative to aggregate-transform to reflect the continuous similarity between the node neighborhoods in the neighborhood aggregation.

Modeling complex networks allows us to analyze the characteristics and discover the basic mechanisms governing phenomena such as disease outbreaks, information diffusion, transportation efficiency, social influence, and even human brain function. Consequently, various network generative models (called temporal network models) have been presented to model how the network topologies evolve dynamically over time. Temporal network models face the challenge of results evaluation because common evaluation methods are appropriate only for static networks. This paper proposes an automatic approach based on deep learning to handle this issue. In addition to an evaluation method, the proposed method can also be used for anomaly detection in evolving networks. The proposed method has been evaluated on five different datasets, and the evaluations show that it outperforms the alternative methods based on the error rate measure in different datasets.

Fault localization is challenging in online micro-service due to the wide variety of monitoring data volume, types, events and complex interdependencies in service and components. Faults events in services are propagative and can trigger a cascade of alerts in a short period of time. In the industry, fault localization is typically conducted manually by experienced personnel. This reliance on experience is unreliable and lacks automation. Different modules present information barriers during manual localization, making it difficult to quickly align during urgent faults. This inefficiency lags stability assurance to minimize fault detection and repair time. Though actionable methods aimed to automatic the process, the accuracy and efficiency are less than satisfactory. The precision of fault localization results is of paramount importance as it underpins engineers trust in the diagnostic conclusions, which are derived from multiple perspectives and offer comprehensive insights. Therefore, a more reliable method is required to automatically identify the associative relationships among fault events and propagation path. To achieve this, KGroot uses event knowledge and the correlation between events to perform root cause reasoning by integrating knowledge graphs and GCNs for RCA. FEKG is built based on historical data, an online graph is constructed in real-time when a failure event occurs, and the similarity between each knowledge graph and online graph is compared using GCNs to pinpoint the fault type through a ranking strategy. Comprehensive experiments demonstrate KGroot can locate the root cause with accuracy of 93.5% top 3 potential causes in second-level. This performance matches the level of real-time fault diagnosis in the industrial environment and significantly surpasses state-of-the-art baselines in RCA in terms of effectiveness and efficiency.