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.

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.

Since the seminal work of TabPFN [16], research on tabular foundation models (TFMs) based on in-context learning (ICL) has challenged long-standing paradigms in machine learning. Without seeing any real-world data, models pretrained on purely synthetic datasets generalize remarkably well across diverse datasets, often using only a moderate number of in-context examples. This shifts the focus in tabular machine learning from model architecture design to the design of synthetic datasets, or, more precisely, to the prior distributions that generate them. Yet the guiding principles for prior design remain poorly understood. This work marks the first attempt to address the gap. We systematically investigate and identify key properties of synthetic priors that allow pretrained TFMs to generalize well. Based on these insights, we introduce MITRA 1, a TFM trained on a curated mixture of synthetic priors selected for their diversity, distinctiveness, and performance on real-world tabular data. MITRA consistently outperforms state-of-the-art TFMs, such as TabPFNv2 [17] and TabICL [29], across both classification and regression benchmarks, with better sample efficiency.

Large-scale pre-trained models have revolutionized Natural Language Processing (NLP) and Computer Vision (CV), showcasing remarkable cross-domain generalization abilities. However, in graph learning, models are typically trained on individual graph datasets, limiting their capacity to transfer knowledge across different graphs and tasks. This approach also heavily relies on large volumes of annotated data, which presents a significant challenge in resource-constrained settings. Unlike NLP and CV, graph-structured data presents unique challenges due to its inherent heterogeneity, including domain-specific feature spaces and structural diversity across various applications. To address these challenges, we propose a novel structure-aware self-supervised learning method for Text-Attributed Graphs (SSTAG).

A phenomenon known as ``Neural Collapse (NC)'' in deep classification tasks, in which the penultimate-layer features and the final classifiers exhibit an extremely simple geometric structure, has recently attracted considerable attention, with the expectation that it can deepen our understanding of how deep neural networks behave. The Unconstrained Feature Model (UFM) has been proposed to explain NC theoretically, and there emerges a growing body of work that extends NC to tasks other than classification and leverages it for practical applications. In this study, we investigate whether a similar phenomenon arises in deep Ordinal Regression (OR) tasks, via combining the cumulative link model for OR and UFM. We show that a phenomenon we call Ordinal Neural Collapse (ONC) indeed emerges and is characterized by the following three properties: (ONC1) all optimal features in the same class collapse to their within-class mean when regularization is applied; (ONC2) these class means align with the classifier, meaning that they collapse onto a one-dimensional subspace; (ONC3) the optimal latent variables (corresponding to logits or preactivations in classification tasks) are aligned according to the class order, and in particular, in the zero-regularization limit, a highly local and simple geometric relationship emerges between the latent variables and the threshold values. We prove these properties analytically within the UFM framework with fixed threshold values and corroborate them empirically across a variety of datasets. We also discuss how these insights can be leveraged in OR, highlighting the use of fixed thresholds.