Graph Neural Networks (GNNs)excel at jointly modeling node features and topology, yet their black-box nature limits their adoption in real-world applications where interpretability is desired. Inspired by the success of interpretable Neural Additive Models (NAM)for tabular data, Graph Neural Additive Network (GNAN) extends the additive modeling approach to graph data to overcome limitations of GNNs. While being interpretable, GNANrepresentation learning overlooks the importance of local aggregation and more importantly suffers from parameter complexity. To mitigate the above challenges, we introduce Graph Neural Additive Model with Random Fourier Features (G-NAMRFF), a lightweight, self-interpretable graph additive architecture. G-NAMRFF represents each node embedding as the sum of feature-wise contributions where contributions are modeled via a Gaussian process (GP)with a graph-and feature-aware kernel. Specifically, we construct a kernel using Radial Basis Function (RBF) with graph structure induced by Laplacian and learnable Finite Impulse Response (FIR) filter. We approximate the kernel using Random Fourier Features (RFFs) which transforms the GPprior to a Bayesian formulation, which are subsequently learnt using a single layer neural network with size equal to number of RFF features. G-NAMRFF is light weight with 168 fewer parameters compared to GNAN. Despite its compact size, G-NAMRFFmatches or outperforms state-of-the-art GNNs and GNAN on node and graph classification tasks, delivering real-time interpretability without sacrificing accuracy 1.

Recent advances in graph machine learning have shifted to data-centric paradigms, driven by two emerging research fields: (1) Federated graph learning (FGL) facilitates multi-client collaboration but struggles with data and task heterogeneity, resulting in limited practicality; (2) Graph foundation model (GFM) enables desirable domain generalization but is typically confined to single-machine training, neglecting the potential of cross-silo data and computational resources. It is evident that these two paradigms are complementary, and their integration offers substantial advantages. Motivated by this, we present a pioneering study about the federated graph foundation model (FedGFM), a novel decentralized GFM training paradigm. Despite the promising vision of FedGFM, knowledge entanglement has emerged as a critical challenge, where multi-domain knowledge is encoded into indistinguishable representations, thereby limiting downstream adaptation. To this end, we propose FedGFM+, an effective FedGFM framework with two key modules to mitigate knowledge entanglement in a dual-pronged manner.

While deep learning has achieved remarkable success across many domains, it has historically underperformed on tabular learning tasks, which remain dominated by gradient boosting decision trees. However, recent advancements are paving the way for Tabular Foundation Models, which can leverage real-world knowledge and generalize across diverse datasets, particularly when the data contains free-text. Although incorporating language model capabilities into tabular tasks has been explored, most existing methods utilize static, target-agnostic textual representations, limiting their effectiveness. We introduce TabSTAR: a Tabular Foundation Model with Semantically Target-Aware Representations. TabSTAR is designed to enable transfer learning on tabular data with textual features, with an architecture free of dataset-specific parameters. It unfreezes a pretrained text encoder and takes as input target tokens, which provide the model with the context needed to learn task-specific embeddings. TabSTAR achieves state-of-the-art performance for both medium-and large-sized datasets across known benchmarks of classification tasks with text features, and its pretraining phase exhibits scaling laws in the number of datasets, offering a pathway for further performance improvements.1

Tabular datasets are inherently heterogeneous, presenting significant challenges for developing pre-trained foundation models. The recently introduced transformerbased Tabular Prior-data Fitted Network v2 (TabPFN v2) achieves unprecedented in-context learning performance across diverse downstream datasets, marking a pivotal advancement in tabular foundation models. In this paper, we take a closer look at TabPFN v2 to examine how it effectively handles heterogeneity and achieves high predictive accuracy, and to explore how its limitations in high-dimensional, many-category, and large-scale tasks can be mitigated. We find that TabPFN v2 can infer attribute relationships even when provided with randomized attribute token inputs, eliminating the need to explicitly learn dataset-specific attribute embeddings to address heterogeneity. We further show that TabPFN v2 can be transformed into a feature extractor, revealing its ability to construct a highly separable feature space for accurate predictions. Lastly, we demonstrate that TabPFN v2's limitations can be addressed through a test-time divide-and-conquer strategy, enabling scalable inference without requiring re-training. By uncovering the mechanisms behind TabPFN v2's success and introducing strategies to extend its applicability, this study offers key insights into the design of future tabular foundation models.

Network traffic classification is essential for network management and security. In recent years, deep learning (DL) algorithms have emerged as essential tools for classifying complex traffic. However, they rely heavily on high-quality labeled training data. In practice, traffic data is often noisy due to human error or inaccurate automated labeling, which could render classification unreliable and lead to severe consequences. Although some studies have alleviated the label noise issue in specific scenarios, they are difficult to generalize to general traffic classification tasks due to the inherent semantic complexity of traffic data.

Transformers have revolutionized nucleotide sequence analysis, yet capturing long-range dependencies remains challenging. Recent studies show that autoregressive transformers often exhibit Markovian behavior by relying on fixed-length context windows for next-token prediction. However, standard self-attention mechanisms are computationally inefficient for long sequences due to their quadratic complexity and do not explicitly enforce global transition consistency. We introduce CARMANIA (Context-Aware Regularization with Markovian Integration for Attention-Based Nucleotide Analysis), a self-supervised pretraining framework that augments next-token (NT) prediction with a transition-matrix (TM) loss. The TM loss aligns predicted token transitions with empirically derived ngram statistics from each input sequence, encouraging the model to capture higherorder dependencies beyond local context.

Graph Machine Learning is essential for understanding and analyzing relational data. However, privacy-sensitive applications demand the ability to efficiently remove sensitive information from trained graph neural networks (GNNs), avoiding the unnecessary time and space overhead caused by retraining models from scratch. To address this issue, Graph Unlearning (GU) has emerged as a critical solution to support dynamic graph updates while ensuring privacy compliance. Unlike machine unlearning in computer vision or other fields, GU faces unique difficulties due to the non-Euclidean nature of graph data and the recursive message-passing mechanism of GNNs. Additionally, the diversity of downstream tasks and the complexity of unlearning requests further amplify these challenges. Despite the proliferation of diverse GU strategies, the absence of a benchmark providing fair comparisons for GU, and the limited flexibility in combining downstream tasks and unlearning requests, have yielded inconsistencies in evaluations, hindering the development of this domain. To fill this gap, we present OpenGU, the first GU benchmark, where 16 SOTAGU algorithms and 37 multi-domain datasets are integrated, enabling various downstream tasks with 13 GNN backbones when responding to flexible unlearning requests. Through extensive experimentation, we have drawn 10crucial conclusions about existing GU methods, while also gaining valuable insights into their limitations, shedding light on potential avenues for future research.

Memory Mosaics [Zhang et al., 2025], networks of associative memories, have demonstrated appealing compositional and in-context learning capabilities on medium-scale networks (GPT-2 scale) and synthetic small datasets. This work shows that these favorable properties remain when we scale memory mosaics to large language model sizes (llama-8B scale) and real-world datasets. To this end, we scale memory mosaics to 10B size, we train them on one trillion tokens, we introduce a couple architectural modifications ("memory mosaics v2"), we assess their capabilities across three evaluation dimensions: training-knowledge storage, new-knowledge storage, and in-context learning. Throughout the evaluation, memory mosaics v2 match transformers on the learning of training knowledge (first dimension) and significantly outperforms transformers on carrying out new tasks at inference time (second and third dimensions). These improvements cannot be easily replicated by simply increasing the training data for transformers. A memory mosaics v2 trained on one trillion tokens still perform better on these tasks than a transformer trained on eight trillion tokens.

Explaining graph neural networks (GNNs) is a key approach to improve the trustworthiness of GNN in high-stakes applications, such as finance and healthcare. However, existing methods are vulnerable to perturbations, raising concerns about explanation reliability. Prior methods enhance explanation robustness using model retraining or explanation ensemble, with certain weaknesses. Retraining leads to models that are different from the original target model and misleading explanations, while ensemble can produce contradictory results due to different inputs or models. To improve explanation robustness without the above weaknesses, we take an unexplored route and exploit the two edge geometry properties curvature and resistance to enhance explanation robustness. We are the first to prove that these geometric notions can be used to bound explanation robustness. We design a general optimization algorithm to incorporate these geometric properties into a wide spectrum of base GNN explanation methods to enhance the robustness of base explanations. We empirically show that our method outperforms six base explanation methods in robustness across nine datasets spanning node classification, link prediction, and graph classification tasks, improving fidelity in 80% of the cases and achieving up to a 10% relative improvement in robust performance.

Multimodal molecular models often suffer from 3D conformer unreliability and modality collapse, limiting their robustness and generalization. We propose MuMo, a structured multimodal fusion framework that addresses these challenges in molecular representation through two key strategies. To reduce the instability of conformer-dependent fusion, we design a Structured Fusion Pipeline (SFP) that combines 2D topology and 3D geometry into a unified and stable structural prior. To mitigate modality collapse caused by naive fusion, we introduce a Progressive Injection (PI) mechanism that asymmetrically integrates this prior into the sequence stream, preserving modality-specific modeling while enabling cross-modal enrichment. Built on a state space backbone, MuMo supports long-range dependency modeling and robust information propagation. Across 29 benchmark tasks from Therapeutics Data Commons (TDC) and MoleculeNet, MuMo achieves an average improvement of 2.7% over the best-performing baseline on each task, ranking first on 22 of them, including a 27% improvement on the LD50 task.