NN-Former: Rethinking Graph Structure in Neural Architecture Representation

The growing use of deep learning necessitates efficient network design and deployment, making neural predictors vital for estimating attributes such as accuracy and latency. Recently, Graph Neural Networks (GNNs) and transformers have shown promising performance in representing neural architectures. However, each of both methods has its disadvantages. GNNs lack the capabilities to represent complicated features, while transformers face poor generalization when the depth of architecture grows. To mitigate the above issues, we rethink neural architecture topology and show that sibling nodes are pivotal while overlooked in previous research. We thus propose a novel predictor leveraging the strengths of GNNs and transformers to learn the enhanced topology. We introduce a novel token mixer that considers siblings, and a new channel mixer named bidirectional graph isomorphism feed-forward network. Our approach consistently achieves promising performance in both accuracy and latency prediction, providing valuable insights for learning Directed Acyclic Graph (DAG) topology. The code is available at https://github.com/XuRuihan/NNFormer.

Scalable Feature Learning on Huge Knowledge Graphs for Downstream Machine Learning

Many machine learning tasks can benefit from external knowledge. Large knowledge graphs store such knowledge, and embedding methods can be used to distill it into ready-to-use vector representations for downstream applications. For this purpose, current models have however two limitations: they are primarily optimized for link prediction, via local contrastive learning, and they struggle to scale to the largest graphs due to GPU memory limits. To address these, we introduce SEPAL: a Scalable Embedding Propagation ALgorithm for large knowledge graphs designed to produce high-quality embeddings for downstream tasks at scale. The key idea of SEPAL is to enforce global embedding alignment by optimizing embeddings only on a small core of entities, and then propagating them to the rest of the graph via message passing. We evaluate SEPAL on 7 large-scale knowledge graphs and 46 downstream machine learning tasks. Our results show that SEPAL significantly outperforms previous methods on downstream tasks. In addition, SEPAL scales up its base embedding model, enabling fitting huge knowledge graphs on commodity hardware.

AGTCNet: A Graph-Temporal Approach for Principled Motor Imagery EEG Classification

Brain-computer interface (BCI) technology utilizing electroencephalography (EEG) marks a transformative innovation, empowering motor-impaired individuals to engage with their environment on equal footing. Despite its promising potential, developing subject-invariant and session-invariant BCI systems remains a significant challenge due to the inherent complexity and variability of neural activity across individuals and over time, compounded by EEG hardware constraints. While prior studies have sought to develop robust BCI systems, existing approaches remain ineffective in capturing the intricate spatiotemporal dependencies within multichannel EEG signals. This study addresses this gap by introducing the attentive graph-temporal convolutional network (AGTCNet), a novel graph-temporal model for motor imagery EEG (MI-EEG) classification. Specifically, AGTCNet leverages the topographic configuration of EEG electrodes as an inductive bias and integrates graph convolutional attention network (GCAT) to jointly learn expressive spatiotemporal EEG representations. The proposed model significantly outperformed existing MI-EEG classifiers, achieving state-of-the-art performance while utilizing a compact architecture, underscoring its effectiveness and practicality for BCI deployment. With a 49.87% reduction in model size, 64.65% faster inference time, and shorter input EEG signal, AGTCNet achieved a moving average accuracy of 66.82% for subject-independent classification on the BCI Competition IV Dataset 2a, which further improved to 82.88% when fine-tuned for subject-specific classification. On the EEG Motor Movement/Imagery Dataset, AGTCNet achieved moving average accuracies of 64.14% and 85.22% for 4-class and 2-class subject-independent classifications, respectively, with further improvements to 72.13% and 90.54% for subject-specific classifications.

Discrepancy-Aware Graph Mask Auto-Encoder

Masked Graph Auto-Encoder, a powerful graph self-supervised training paradigm, has recently shown superior performance in graph representation learning. Existing works typically rely on node contextual information to recover the masked information. However, they fail to generalize well to heterophilic graphs where connected nodes may be not similar, because they focus only on capturing the neighborhood information and ignoring the discrepancy information between different nodes, resulting in indistinguishable node representations. In this paper, to address this issue, we propose a Discrepancy-Aware Graph Mask Auto-Encoder (DGMAE). It obtains more distinguishable node representations by reconstructing the discrepancy information of neighboring nodes during the masking process. We conduct extensive experiments on 17 widely-used benchmark datasets. The results show that our DGMAE can effectively preserve the discrepancies of nodes in low-dimensional space. Moreover, DGMAE significantly outperforms state-of-the-art graph self-supervised learning methods on three graph analytic including tasks node classification, node clustering, and graph classification, demonstrating its remarkable superiority. The code of DGMAE is available at https://github.com/zhengziyu77/DGMAE.

GeoRecon: Graph-Level Representation Learning for 3D Molecules via Reconstruction-Based Pretraining

The pretraining-and-finetuning paradigm has driven significant advances across domains, such as natural language processing and computer vision, with representative pretraining paradigms such as masked language modeling and next-token prediction. However, in molecular representation learning, the task design remains largely limited to node-level denoising, which is effective at modeling local atomic environments, yet maybe insufficient for capturing the global molecular structure required by graph-level property prediction tasks, such as energy estimation and molecular regression. In this work, we present GeoRecon, a novel graph-level pretraining framework that shifts the focus from individual atoms to the molecule as an integrated whole. GeoRecon introduces a graph-level reconstruction task: during pretraining, the model is trained to generate an informative graph representation capable of accurately guiding reconstruction of the molecular geometry. This encourages the model to learn coherent, global structural features rather than isolated atomic details. Without relying on additional supervision or external data, GeoRecon outperforms node-centric baselines on multiple molecular benchmarks (e.g., QM9, MD17), demonstrating the benefit of incorporating graph-level reconstruction for learning more holistic and geometry-aware molecular embeddings.

Uncertainty-Aware Graph Neural Networks: A Multi-Hop Evidence Fusion Approach

Graph neural networks (GNNs) excel in graph representation learning by integrating graph structure and node features. Existing GNNs, unfortunately, fail to account for the uncertainty of class probabilities that vary with the depth of the model, leading to unreliable and risky predictions in real-world scenarios. To bridge the gap, in this paper, we propose a novel Evidence Fusing Graph Neural Network (EFGNN for short) to achieve trustworthy prediction, enhance node classification accuracy, and make explicit the risk of wrong predictions. In particular, we integrate the evidence theory with multi-hop propagation-based GNN architecture to quantify the prediction uncertainty of each node with the consideration of multiple receptive fields. Moreover, a parameter-free cumulative belief fusion (CBF) mechanism is developed to leverage the changes in prediction uncertainty and fuse the evidence to improve the trustworthiness of the final prediction. To effectively optimize the EFGNN model, we carefully design a joint learning objective composed of evidence cross-entropy, dissonance coefficient, and false confident penalty. The experimental results on various datasets and theoretical analyses demonstrate the effectiveness of the proposed model in terms of accuracy and trustworthiness, as well as its robustness to potential attacks. The source code of EFGNN is available at https://github.com/Shiy-Li/EFGNN.

AST-Enhanced or AST-Overloaded? The Surprising Impact of Hybrid Graph Representations on Code Clone Detection

As one of the most detrimental code smells, code clones significantly increase software maintenance costs and heighten vulnerability risks, making their detection a critical challenge in software engineering. Abstract Syntax Trees (ASTs) dominate deep learning-based code clone detection due to their precise syntactic structure representation, but they inherently lack semantic depth. Recent studies address this by enriching AST-based representations with semantic graphs, such as Control Flow Graphs (CFGs) and Data Flow Graphs (DFGs). However, the effectiveness of various enriched AST-based representations and their compatibility with different graph-based machine learning techniques remains an open question, warranting further investigation to unlock their full potential in addressing the complexities of code clone detection. In this paper, we present a comprehensive empirical study to rigorously evaluate the effectiveness of AST-based hybrid graph representations in Graph Neural Network (GNN)-based code clone detection. We systematically compare various hybrid representations ((CFG, DFG, Flow-Augmented ASTs (FA-AST)) across multiple GNN architectures. Our experiments reveal that hybrid representations impact GNNs differently: while AST+CFG+DFG consistently enhances accuracy for convolution- and attention-based models (Graph Convolutional Networks (GCN), Graph Attention Networks (GAT)), FA-AST frequently introduces structural complexity that harms performance. Notably, GMN outperforms others even with standard AST representations, highlighting its superior cross-code similarity detection and reducing the need for enriched structures.

Optimizing Federated Learning using Remote Embeddings for Graph Neural Networks

Graph Neural Networks (GNNs) have experienced rapid advancements in recent years due to their ability to learn meaningful representations from graph data structures. Federated Learning (FL) has emerged as a viable machine learning approach for training a shared model on decentralized data, addressing privacy concerns while leveraging parallelism. Existing methods that address the unique requirements of federated GNN training using remote embeddings to enhance convergence accuracy are limited by their diminished performance due to large communication costs with a shared embedding server. In this paper, we present OpES, an optimized federated GNN training framework that uses remote neighbourhood pruning, and overlaps pushing of embeddings to the server with local training to reduce the network costs and training time. The modest drop in per-round accuracy due to pre-emptive push of embeddings is out-stripped by the reduction in per-round training time for large and dense graphs like Reddit and Products, converging up to $\approx2\times$ faster than the state-of-the-art technique using an embedding server and giving up to $20\%$ better accuracy than vanilla federated GNN learning.

Learning Augmented Graph $k$-Clustering

Clustering is a fundamental task in unsupervised learning. Previous research has focused on learning-augmented $k$-means in Euclidean metrics, limiting its applicability to complex data representations. In this paper, we generalize learning-augmented $k$-clustering to operate on general metrics, enabling its application to graph-structured and non-Euclidean domains. Our framework also relaxes restrictive cluster size constraints, providing greater flexibility for datasets with imbalanced or unknown cluster distributions. Furthermore, we extend the hardness of query complexity to general metrics: under the Exponential Time Hypothesis (ETH), we show that any polynomial-time algorithm must perform approximately $\Omega(k / \alpha)$ queries to achieve a $(1 + \alpha)$-approximation. These contributions strengthen both the theoretical foundations and practical applicability of learning-augmented clustering, bridging gaps between traditional methods and real-world challenges.

Semi-supervised Graph Anomaly Detection via Robust Homophily Learning

Semi-supervised graph anomaly detection (GAD) utilizes a small set of labeled normal nodes to identify abnormal nodes from a large set of unlabeled nodes in a graph. Current methods in this line posit that 1) normal nodes share a similar level of homophily and 2) the labeled normal nodes can well represent the homophily patterns in the normal class. However, this assumption often does not hold well since normal nodes in a graph can exhibit diverse homophily in real-world GAD datasets. In this paper, we propose RHO, namely Robust Homophily Learning, to adaptively learn such homophily patterns. RHO consists of two novel modules, adaptive frequency response filters (AdaFreq) and graph normality alignment (GNA). AdaFreq learns a set of adaptive spectral filters that capture different frequency components of the labeled normal nodes with varying homophily in the channel-wise and cross-channel views of node attributes. GNA is introduced to enforce consistency between the channel-wise and cross-channel homophily representations to robustify the normality learned by the filters in the two views. Experiments on eight real-world GAD datasets show that RHO can effectively learn varying, often under-represented, homophily in the small normal node set and substantially outperforms state-of-the-art competing methods. Code is available at https://github.com/mala-lab/RHO.