Daily Papers

We present a node-based storytelling system for multimodal content generation. The system represents stories as graphs of nodes that can be expanded, edited, and iteratively refined through direct user edits and natural-language prompts. Each node can integrate text, images, audio, and video, allowing creators to compose multimodal narratives. A task selection agent routes between specialized generative tasks that handle story generation, node structure reasoning, node diagram formatting, and context generation. The interface supports targeted editing of individual nodes, automatic branching for parallel storylines, and node-based iterative refinement. Our results demonstrate that node-based editing supports control over narrative structure and iterative generation of text, images, audio, and video. We report quantitative outcomes on automatic story outline generation and qualitative observations of editing workflows. Finally, we discuss current limitations such as scalability to longer narratives and consistency across multiple nodes, and outline future work toward human-in-the-loop and user-centered creative AI tools.

Creative coding tasks are often exploratory in nature. When producing digital artwork, artists usually begin with a high-level semantic construct such as a "stained glass filter" and programmatically implement it by varying code parameters such as shape, color, lines, and opacity to produce visually appealing results. Based on interviews with artists, it can be effortful to translate semantic constructs to program syntax, and current programming tools don't lend well to rapid creative exploration. To address these challenges, we introduce Spellburst, a large language model (LLM) powered creative-coding environment. Spellburst provides (1) a node-based interface that allows artists to create generative art and explore variations through branching and merging operations, (2) expressive prompt-based interactions to engage in semantic programming, and (3) dynamic prompt-driven interfaces and direct code editing to seamlessly switch between semantic and syntactic exploration. Our evaluation with artists demonstrates Spellburst's potential to enhance creative coding practices and inform the design of computational creativity tools that bridge semantic and syntactic spaces.

Contrastive learning has recently achieved remarkable success in many domains including graphs. However contrastive loss, especially for graphs, requires a large number of negative samples which is unscalable and computationally prohibitive with a quadratic time complexity. Sub-sampling is not optimal and incorrect negative sampling leads to sampling bias. In this work, we propose a meta-node based approximation technique that can (a) proxy all negative combinations (b) in quadratic cluster size time complexity, (c) at graph level, not node level, and (d) exploit graph sparsity. By replacing node-pairs with additive cluster-pairs, we compute the negatives in cluster-time at graph level. The resulting Proxy approximated meta-node Contrastive (PamC) loss, based on simple optimized GPU operations, captures the full set of negatives, yet is efficient with a linear time complexity. By avoiding sampling, we effectively eliminate sample bias. We meet the criterion for larger number of samples, thus achieving block-contrastiveness, which is proven to outperform pair-wise losses. We use learnt soft cluster assignments for the meta-node constriction, and avoid possible heterophily and noise added during edge creation. Theoretically, we show that real world graphs easily satisfy conditions necessary for our approximation. Empirically, we show promising accuracy gains over state-of-the-art graph clustering on 6 benchmarks. Importantly, we gain substantially in efficiency; up to 3x in training time, 1.8x in inference time and over 5x in GPU memory reduction.

Mapping is crucial for spatial reasoning, planning and robot navigation. Existing approaches range from metric, which require precise geometry-based optimization, to purely topological, where image-as-node based graphs lack explicit object-level reasoning and interconnectivity. In this paper, we propose a novel topological representation of an environment based on "image segments", which are semantically meaningful and open-vocabulary queryable, conferring several advantages over previous works based on pixel-level features. Unlike 3D scene graphs, we create a purely topological graph with segments as nodes, where edges are formed by a) associating segment-level descriptors between pairs of consecutive images and b) connecting neighboring segments within an image using their pixel centroids. This unveils a "continuous sense of a place", defined by inter-image persistence of segments along with their intra-image neighbours. It further enables us to represent and update segment-level descriptors through neighborhood aggregation using graph convolution layers, which improves robot localization based on segment-level retrieval. Using real-world data, we show how our proposed map representation can be used to i) generate navigation plans in the form of "hops over segments" and ii) search for target objects using natural language queries describing spatial relations of objects. Furthermore, we quantitatively analyze data association at the segment level, which underpins inter-image connectivity during mapping and segment-level localization when revisiting the same place. Finally, we show preliminary trials on segment-level `hopping' based zero-shot real-world navigation. Project page with supplementary details: oravus.github.io/RoboHop/

Graphs are a fundamental data structure for representing relationships in real-world scenarios. With the success of Large Language Models (LLMs) across various natural language processing (NLP) tasks, there has been growing interest in integrating LLMs for graph learning. However, applying LLMs to graph-related tasks poses significant challenges, as these models are not inherently designed to capture the complex structural information present in graphs. Existing approaches address this challenge through two strategies: the chain of tasks approach, which uses Graph Neural Networks (GNNs) to encode the graph structure so that LLMs are relieved from understanding spatial positions; and Graph-to-Text Conversion, which translates graph structures into semantic text representations that LLMs can process. Despite their progress, these methods often struggle to fully preserve the topological information of graphs or require extensive computational resources, limiting their practical applicability. In this work, we introduce Node Tokenizer for Large Language Models (NT-LLM), a novel framework that efficiently encodes graph structures by selecting key nodes as anchors and representing each node based on its relative distance to these anchors. This position-anchored encoding effectively captures the graph topology, enabling enhanced reasoning capabilities in LLMs over graph data. Additionally, we implement a task-specific tuning procedure to further improve structural understanding within LLMs. Through extensive empirical evaluations, NT-LLM demonstrates significant performance improvements across a variety of graph-related tasks.

Acceleration of graph applications on GPUs has found large interest due to the ubiquitous use of graph processing in various domains. The inherent irregularity in graph applications leads to several challenges for parallelization. A key challenge, which we address in this paper, is that of load-imbalance. If the work-assignment to threads uses node-based graph partitioning, it can result in skewed task-distribution, leading to poor load-balance. In contrast, if the work-assignment uses edge-based graph partitioning, the load-balancing is better, but the memory requirement is relatively higher. This makes it unsuitable for large graphs. In this work, we propose three techniques for improved load-balancing of graph applications on GPUs. Each technique brings in unique advantages, and a user may have to employ a specific technique based on the requirement. Using Breadth First Search and Single Source Shortest Paths as our processing kernels, we illustrate the effectiveness of each of the proposed techniques in comparison to the existing node-based and edge-based mechanisms.

In the past years, predictive process monitoring (PPM) techniques based on artificial neural networks have evolved as a method to monitor the future behavior of business processes. Existing approaches mostly focus on interpreting the processes as sequences, so-called traces, and feeding them to neural architectures designed to operate on sequential data such as recurrent neural networks (RNNs) or transformers. In this study, we investigate an alternative way to perform PPM: by transforming each process in its directly-follows-graph (DFG) representation we are able to apply graph neural networks (GNNs) for the prediction tasks. By this, we aim to develop models that are more suitable for complex processes that are long and contain an abundance of loops. In particular, we present different ways to create DFG representations depending on the particular GNN we use. The tested GNNs range from classical node-based to novel edge-based architectures. Further, we investigate the possibility of using multi-graphs. By these steps, we aim to design graph representations that minimize the information loss when transforming traces into graphs.

Creative AI is moving from single-step asset generation toward long-horizon multimodal production. Although recent generative models can synthesize high-quality images, videos, audio clips, UI elements, storyboards, slides, and other creative assets, real-world creative work requires more than isolated prompt-output interactions. It involves references, drafts, alternatives, edits, failed attempts, version relations, tool actions, evaluation signals, and human feedback, which together form an evolving project state. Existing prompt-based, chat-based, and node-based generation systems only partially support this state, as they often discard intermediate context, rely on linear conversations, or require manually specified workflows. Recent commercial systems indicate a shift toward agent-assisted creative production, but their closed architectures make it difficult to study how agents represent context, choose tools, revise artifacts, recover from failures, and maintain consistency over time. To address this gap, we introduce JarvisHub, a canvas-native creative agent harness for long-horizon multimodal creation. JarvisHub treats an editable canvas as the user workspace, the agent's external memory, action space, and shared project state, representing multimodal artifacts, dependencies, versions, and feedback as typed canvas nodes and links. Through a three-layer architecture of canvas state, protocol bridge, and agent runtime, JarvisHub enables agents to act within an inspectable and editable creative state. This design moves creative agents beyond isolated tool use toward sustained, human-steerable creative automation, where agents can progressively plan, generate, revise, and organize multimodal projects while users remain able to inspect, guide, and intervene throughout the process.

We present a novel edge-level ego-network encoding for learning on graphs that can boost Message Passing Graph Neural Networks (MP-GNNs) by providing additional node and edge features or extending message-passing formats. The proposed encoding is sufficient to distinguish Strongly Regular Graphs, a family of challenging 3-WL equivalent graphs. We show theoretically that such encoding is more expressive than node-based sub-graph MP-GNNs. In an empirical evaluation on four benchmarks with 10 graph datasets, our results match or improve previous baselines on expressivity, graph classification, graph regression, and proximity tasks -- while reducing memory usage by 18.1x in certain real-world settings.

Recently, subgraph GNNs have emerged as an important direction for developing expressive graph neural networks (GNNs). While numerous architectures have been proposed, so far there is still a limited understanding of how various design paradigms differ in terms of expressive power, nor is it clear what design principle achieves maximal expressiveness with minimal architectural complexity. To address these fundamental questions, this paper conducts a systematic study of general node-based subgraph GNNs through the lens of Subgraph Weisfeiler-Lehman Tests (SWL). Our central result is to build a complete hierarchy of SWL with strictly growing expressivity. Concretely, we prove that any node-based subgraph GNN falls into one of the six SWL equivalence classes, among which SSWL achieves the maximal expressive power. We also study how these equivalence classes differ in terms of their practical expressiveness such as encoding graph distance and biconnectivity. Furthermore, we give a tight expressivity upper bound of all SWL algorithms by establishing a close relation with localized versions of WL and Folklore WL (FWL) tests. Our results provide insights into the power of existing subgraph GNNs, guide the design of new architectures, and point out their limitations by revealing an inherent gap with the 2-FWL test. Finally, experiments demonstrate that SSWL-inspired subgraph GNNs can significantly outperform prior architectures on multiple benchmarks despite great simplicity.

Generative artificial intelligence (GenAI) has ushered in a new era for storytellers, providing a powerful tool to ignite creativity and explore uncharted narrative territories. As technology continues to advance, the synergy between human creativity and AI-generated content holds the potential to redefine the landscape of storytelling. In this work, we propose SARD, a drag-and-drop visual interface for generating a multi-chapter story using large language models. Our evaluation of the usability of SARD and its creativity support shows that while node-based visualization of the narrative may help writers build a mental model, it exerts unnecessary mental overhead to the writer and becomes a source of distraction as the story becomes more elaborated. We also found that AI generates stories that are less lexically diverse, irrespective of the complexity of the story. We identified some patterns and limitations of our tool that can guide the development of future human-AI co-writing tools.

ComfyUI provides a widely-adopted, workflow-based interface that enables users to customize various image generation tasks through an intuitive node-based architecture. However, the intricate connections between nodes and diverse modules often present a steep learning curve for users. In this paper, we introduce ComfyGPT, the first self-optimizing multi-agent system designed to generate ComfyUI workflows based on task descriptions automatically. ComfyGPT comprises four specialized agents: ReformatAgent, FlowAgent, RefineAgent, and ExecuteAgent. The core innovation of ComfyGPT lies in two key aspects. First, it focuses on generating individual node links rather than entire workflows, significantly improving generation precision. Second, we proposed FlowAgent, a LLM-based workflow generation agent that uses both supervised fine-tuning (SFT) and reinforcement learning (RL) to improve workflow generation accuracy. Moreover, we introduce FlowDataset, a large-scale dataset containing 13,571 workflow-description pairs, and FlowBench, a comprehensive benchmark for evaluating workflow generation systems. We also propose four novel evaluation metrics: Format Validation (FV), Pass Accuracy (PA), Pass Instruct Alignment (PIA), and Pass Node Diversity (PND). Experimental results demonstrate that ComfyGPT significantly outperforms existing LLM-based methods in workflow generation.

We propose DyGFormer, a new Transformer-based architecture for dynamic graph learning. DyGFormer is conceptually simple and only needs to learn from nodes' historical first-hop interactions by: (1) a neighbor co-occurrence encoding scheme that explores the correlations of the source node and destination node based on their historical sequences; (2) a patching technique that divides each sequence into multiple patches and feeds them to Transformer, allowing the model to effectively and efficiently benefit from longer histories. We also introduce DyGLib, a unified library with standard training pipelines, extensible coding interfaces, and comprehensive evaluating protocols to promote reproducible, scalable, and credible dynamic graph learning research. By performing exhaustive experiments on thirteen datasets for dynamic link prediction and dynamic node classification tasks, we find that DyGFormer achieves state-of-the-art performance on most of the datasets, demonstrating its effectiveness in capturing nodes' correlations and long-term temporal dependencies. Moreover, some results of baselines are inconsistent with previous reports, which may be caused by their diverse but less rigorous implementations, showing the importance of DyGLib. All the used resources are publicly available at https://github.com/yule-BUAA/DyGLib.

Generating a consistent whole-house VR tour from a floorplan and style reference requires both photorealistic panoramas and cross-view spatial coherence. Pure 2D generators produce appealing single panoramas but re-imagine geometry and materials when the viewpoint changes, whereas monolithic 3D generation becomes expensive and loses fine texture at multi-room scale. We introduce PanoWorld, a generative spatial world model that treats whole-house synthesis as autoregressive generation of node-based 360-degree panoramas, matching the discrete navigation used by real VR tour products. PanoWorld uses a floorplan-derived 3D shell as a global geometric proxy and a dynamic 3D Gaussian Splatting cache as renderable spatial memory. A feed-forward panoramic LRM designed for metric-scale multi-room 360-degree inputs lifts generated panoramas into local 3DGS updates, while Room-aware Group Attention suppresses cross-room feature interference. A topology-aware progressive caching strategy fuses these local updates without repeatedly reconstructing the full history. By decoupling shell-based geometry guidance from cache-rendered visual memory, PanoWorld preserves high-frequency 2D synthesis quality while improving cross-node layout and material consistency. The project link is https://jjrcn.github.io/PanoWorld-project-home/

Proximity preserving and structural role-based node embeddings have become a prime workhorse of applied graph mining. Novel node embedding techniques are often tested on a restricted set of benchmark datasets. In this paper, we propose a new diverse social network dataset called Twitch Gamers with multiple potential target attributes. Our analysis of the social network and node classification experiments illustrate that Twitch Gamers is suitable for assessing the predictive performance of novel proximity preserving and structural role-based node embedding algorithms.

Attention-based graph neural networks (GNNs), such as graph attention networks (GATs), have become popular neural architectures for processing graph-structured data and learning node embeddings. Despite their empirical success, these models rely on labeled data and the theoretical properties of these models have yet to be fully understood. In this work, we propose a novel attention-based node embedding framework for graphs. Our framework builds upon a hierarchical kernel for multisets of subgraphs around nodes (e.g. neighborhoods) and each kernel leverages the geometry of a smooth statistical manifold to compare pairs of multisets, by "projecting" the multisets onto the manifold. By explicitly computing node embeddings with a manifold of Gaussian mixtures, our method leads to a new attention mechanism for neighborhood aggregation. We provide theoretical insights into generalizability and expressivity of our embeddings, contributing to a deeper understanding of attention-based GNNs. We propose both efficient unsupervised and supervised methods for learning the embeddings. Through experiments on several node classification benchmarks, we demonstrate that our proposed method outperforms existing attention-based graph models like GATs. Our code is available at https://github.com/BorgwardtLab/fisher_information_embedding.

Stock market prediction presents considerable challenges for investors, financial institutions, and policymakers operating in complex market environments characterized by noise, non-stationarity, and behavioral dynamics. Traditional forecasting methods, including fundamental analysis and technical indicators, often fail to capture the intricate patterns and cross-sectional dependencies inherent in financial markets. This paper presents an integrated framework combining a node transformer architecture with BERT-based sentiment analysis for stock price forecasting. The proposed model represents the stock market as a graph structure where individual stocks form nodes and edges capture relationships including sectoral affiliations, correlated price movements, and supply chain connections. A fine-tuned BERT model extracts sentiment information from social media posts and combines it with quantitative market features through attention-based fusion mechanisms. The node transformer processes historical market data while capturing both temporal evolution and cross-sectional dependencies among stocks. Experiments conducted on 20 S&P 500 stocks spanning January 1982 to March 2025 demonstrate that the integrated model achieves a mean absolute percentage error (MAPE) of 0.80% for one-day-ahead predictions, compared to 1.20% for ARIMA and 1.00% for LSTM. The inclusion of sentiment analysis reduces prediction error by 10% overall and 25% during earnings announcements, while the graph-based architecture contributes an additional 15% improvement by capturing inter-stock dependencies. Directional accuracy reaches 65% for one-day forecasts. Statistical validation through paired t-tests confirms the significance of these improvements (p < 0.05 for all comparisons). The model maintains lower error during high-volatility periods, achieving MAPE of 1.50% while baseline models range from 1.60% to 2.10%.

Graph neural networks (GNNs) achieve strong performance on homophilic graphs but often struggle under heterophily, where adjacent nodes frequently belong to different classes. We propose an interpretable and adaptive framework for semi-supervised node classification based on explicit combinatorial inference rather than deep message passing. Our method assigns labels using a confidence-ordered greedy procedure driven by an additive scoring function that integrates class priors, neighborhood statistics, feature similarity, and training-derived label-label compatibility. A small set of transparent hyperparameters controls the relative influence of these components, enabling smooth adaptation between homophilic and heterophilic regimes. We further introduce a validation-gated hybrid strategy in which combinatorial predictions are optionally injected as priors into a lightweight neural model. Hybrid refinement is applied only when it improves validation performance, preserving interpretability when neuralization is unnecessary. All adaptation signals are computed strictly from training data, ensuring a leakage-free evaluation protocol. Experiments on heterophilic and transitional benchmarks demonstrate competitive performance with modern GNNs while offering advantages in interpretability, tunability, and computational efficiency.

Graph unlearning has emerged as a pivotal method to delete information from a pre-trained graph neural network (GNN). One may delete nodes, a class of nodes, edges, or a class of edges. An unlearning method enables the GNN model to comply with data protection regulations (i.e., the right to be forgotten), adapt to evolving data distributions, and reduce the GPU-hours carbon footprint by avoiding repetitive retraining. Existing partitioning and aggregation-based methods have limitations due to their poor handling of local graph dependencies and additional overhead costs. More recently, GNNDelete offered a model-agnostic approach that alleviates some of these issues. Our work takes a novel approach to address these challenges in graph unlearning through knowledge distillation, as it distills to delete in GNN (D2DGN). It is a model-agnostic distillation framework where the complete graph knowledge is divided and marked for retention and deletion. It performs distillation with response-based soft targets and feature-based node embedding while minimizing KL divergence. The unlearned model effectively removes the influence of deleted graph elements while preserving knowledge about the retained graph elements. D2DGN surpasses the performance of existing methods when evaluated on various real-world graph datasets by up to 43.1% (AUC) in edge and node unlearning tasks. Other notable advantages include better efficiency, better performance in removing target elements, preservation of performance for the retained elements, and zero overhead costs. Notably, our D2DGN surpasses the state-of-the-art GNNDelete in AUC by 2.4%, improves membership inference ratio by +1.3, requires 10.2times10^6 fewer FLOPs per forward pass and up to 3.2times faster.

Automatic Multi-Agent Systems (MAS) generation has emerged as a promising paradigm for solving complex reasoning tasks. However, existing frameworks are fundamentally bottlenecked when applied to knowledge-intensive domains (e.g., healthcare and law). They either rely on a static library of general nodes like Chain-of-Thought, which lack specialized expertise, or attempt to generate nodes on the fly. In the latter case, the orchestrator is not only bound by its internal knowledge limits but must also simultaneously generate domain-specific logic and optimize high-level topology, leading to a severe architectural coupling that degrades overall system efficacy. To bridge this gap, we propose Unified-MAS that decouples granular node implementation from topological orchestration via offline node synthesis. Unified-MAS operates in two stages: (1) Search-Based Node Generation retrieves external open-world knowledge to synthesize specialized node blueprints, overcoming the internal knowledge limits of LLMs; and (2) Reward-Based Node Optimization utilizes a perplexity-guided reward to iteratively enhance the internal logic of bottleneck nodes. Extensive experiments across four specialized domains demonstrate that integrating Unified-MAS into four Automatic-MAS baselines yields a better performance-cost trade-off, achieving up to a 14.2% gain while significantly reducing costs. Further analysis reveals its robustness across different designer LLMs and its effectiveness on conventional tasks such as mathematical reasoning.

With the rapid growth of the low-altitude economy, UAVs have become crucial for measurement and tracking in patrol systems. However, in GNSS-denied areas, satellite-based localization methods are prone to failure. This paper presents a cross-view UAV localization framework that performs map matching via object detection, aimed at effectively addressing cross-temporal, cross-view, heterogeneous aerial image matching. In typical pipelines, UAV visual localization is formulated as an image-retrieval problem: features are extracted to build a localization map, and the pose of a query image is estimated by matching it to a reference database with known poses. Because publicly available UAV localization datasets are limited, many approaches recast localization as a classification task and rely on scene labels in these datasets to ensure accuracy. Other methods seek to reduce cross-domain differences using polar-coordinate reprojection, perspective transformations, or generative adversarial networks; however, they can suffer from misalignment, content loss, and limited realism. In contrast, we leverage modern object detection to accurately extract salient instances from UAV and satellite images, and integrate a graph neural network to reason about inter-image and intra-image node relationships. Using a fine-grained, graph-based node-similarity metric, our method achieves strong retrieval and localization performance. Extensive experiments on public and real-world datasets show that our approach handles heterogeneous appearance differences effectively and generalizes well, making it applicable to scenarios with larger modality gaps, such as infrared-visible image matching. Our dataset will be publicly available at the following URL: https://github.com/liutao23/ODGNNLoc.git.

Influence maximization (IM) is formulated as selecting a set of initial users from a social network to maximize the expected number of influenced users. Researchers have made great progress in designing various traditional methods, and their theoretical design and performance gain are close to a limit. In the past few years, learning-based IM methods have emerged to achieve stronger generalization ability to unknown graphs than traditional ones. However, the development of learning-based IM methods is still limited by fundamental obstacles, including 1) the difficulty of effectively solving the objective function; 2) the difficulty of characterizing the diversified underlying diffusion patterns; and 3) the difficulty of adapting the solution under various node-centrality-constrained IM variants. To cope with the above challenges, we design a novel framework DeepIM to generatively characterize the latent representation of seed sets, and we propose to learn the diversified information diffusion pattern in a data-driven and end-to-end manner. Finally, we design a novel objective function to infer optimal seed sets under flexible node-centrality-based budget constraints. Extensive analyses are conducted over both synthetic and real-world datasets to demonstrate the overall performance of DeepIM. The code and data are available at: https://github.com/triplej0079/DeepIM.

Graph representation learning is crucial for many real-world applications (e.g. social relation analysis). A fundamental problem for graph representation learning is how to effectively learn representations without human labeling, which is usually costly and time-consuming. Graph contrastive learning (GCL) addresses this problem by pulling the positive node pairs (or similar nodes) closer while pushing the negative node pairs (or dissimilar nodes) apart in the representation space. Despite the success of the existing GCL methods, they primarily sample node pairs based on the node-level proximity yet the community structures have rarely been taken into consideration. As a result, two nodes from the same community might be sampled as a negative pair. We argue that the community information should be considered to identify node pairs in the same communities, where the nodes insides are semantically similar. To address this issue, we propose a novel Graph Communal Contrastive Learning (gCooL) framework to jointly learn the community partition and learn node representations in an end-to-end fashion. Specifically, the proposed gCooL consists of two components: a Dense Community Aggregation (DeCA) algorithm for community detection and a Reweighted Self-supervised Cross-contrastive (ReSC) training scheme to utilize the community information. Additionally, the real-world graphs are complex and often consist of multiple views. In this paper, we demonstrate that the proposed gCooL can also be naturally adapted to multiplex graphs. Finally, we comprehensively evaluate the proposed gCooL on a variety of real-world graphs. The experimental results show that the gCooL outperforms the state-of-the-art methods.

Graph Neural Networks (GNNs) excel at learning from structured data, yet fairness in regression tasks remains underexplored. Existing approaches mainly target classification and representation-level debiasing, which cannot fully address the continuous nature of node-level regression. We propose FnRGNN, a fairness-aware in-processing framework for GNN-based node regression that applies interventions at three levels: (i) structure-level edge reweighting, (ii) representation-level alignment via MMD, and (iii) prediction-level normalization through Sinkhorn-based distribution matching. This multi-level strategy ensures robust fairness under complex graph topologies. Experiments on four real-world datasets demonstrate that FnRGNN reduces group disparities without sacrificing performance. Code is available at https://github.com/sybeam27/FnRGNN.

Graph Neural Networks (GNNs) have shown exceptional performance in the task of link prediction. Despite their effectiveness, the high latency brought by non-trivial neighborhood data dependency limits GNNs in practical deployments. Conversely, the known efficient MLPs are much less effective than GNNs due to the lack of relational knowledge. In this work, to combine the advantages of GNNs and MLPs, we start with exploring direct knowledge distillation (KD) methods for link prediction, i.e., predicted logit-based matching and node representation-based matching. Upon observing direct KD analogs do not perform well for link prediction, we propose a relational KD framework, Linkless Link Prediction (LLP), to distill knowledge for link prediction with MLPs. Unlike simple KD methods that match independent link logits or node representations, LLP distills relational knowledge that is centered around each (anchor) node to the student MLP. Specifically, we propose rank-based matching and distribution-based matching strategies that complement each other. Extensive experiments demonstrate that LLP boosts the link prediction performance of MLPs with significant margins, and even outperforms the teacher GNNs on 7 out of 8 benchmarks. LLP also achieves a 70.68x speedup in link prediction inference compared to GNNs on the large-scale OGB dataset.

How would randomly shuffling feature vectors among nodes from the same class affect graph neural networks (GNNs)? The feature shuffle, intuitively, perturbs the dependence between graph topology and features (A-X dependence) for GNNs to learn from. Surprisingly, we observe a consistent and significant improvement in GNN performance following the feature shuffle. Having overlooked the impact of A-X dependence on GNNs, the prior literature does not provide a satisfactory understanding of the phenomenon. Thus, we raise two research questions. First, how should A-X dependence be measured, while controlling for potential confounds? Second, how does A-X dependence affect GNNs? In response, we (i) propose a principled measure for A-X dependence, (ii) design a random graph model that controls A-X dependence, (iii) establish a theory on how A-X dependence relates to graph convolution, and (iv) present empirical analysis on real-world graphs that align with the theory. We conclude that A-X dependence mediates the effect of graph convolution, such that smaller dependence improves GNN-based node classification.

With the emergence of data marketplaces, the demand for methods to assess the value of data has increased significantly. While numerous techniques have been proposed for this purpose, none have specifically addressed graphs as the main data modality. Graphs are widely used across various fields, ranging from chemical molecules to social networks. In this study, we break down graphs into two main components: structural and featural, and we focus on evaluating data without relying on specific task-related metrics, making it applicable in practical scenarios where validation requirements may be lacking. We introduce a novel framework called blind message passing, which aligns the seller's and buyer's graphs using a shared node permutation based on graph matching. This allows us to utilize the graph Wasserstein distance to quantify the differences in the structural distribution of graph datasets, called the structural disparities. We then consider featural aspects of buyers' and sellers' graphs for data valuation and capture their statistical similarities and differences, referred to as relevance and diversity, respectively. Our approach ensures that buyers and sellers remain unaware of each other's datasets. Our experiments on real datasets demonstrate the effectiveness of our approach in capturing the relevance, diversity, and structural disparities of seller data for buyers, particularly in graph-based data valuation scenarios.

As a telecom provider, our company has a critical mission to maintain telecom services even during power outages. To accomplish the mission, it is essential to maintain the power of the telecom base stations. Here we consider a solution where electric vehicles (EVs) directly supply power to base stations by traveling to their locations. The goal is to find EV routes that minimize both the total travel distance of all EVs and the number of downed base stations. In this paper, we formulate this routing problem as a new variant of the Electric Vehicle Routing Problem (EVRP) and propose a solver that combines a rule-based vehicle selector and a reinforcement learning (RL)-based node selector. The rule of the vehicle selector ensures the exact environmental states when the selected EV starts to move. In addition, the node selection by the RL model enables fast route generation, which is critical in emergencies. We evaluate our solver on both synthetic datasets and real datasets. The results show that our solver outperforms baselines in terms of the objective value and computation time. Moreover, we analyze the generalization and scalability of our solver, demonstrating the capability toward unseen settings and large-scale problems. Check also our project page: https://ntt-dkiku.github.io/rl-evrpeps.

With the rapid development of fashion market, the customers' demands of customers for fashion recommendation are rising. In this paper, we aim to investigate a practical problem of fashion recommendation by answering the question "which item should we select to match with the given fashion items and form a compatible outfit". The key to this problem is to estimate the outfit compatibility. Previous works which focus on the compatibility of two items or represent an outfit as a sequence fail to make full use of the complex relations among items in an outfit. To remedy this, we propose to represent an outfit as a graph. In particular, we construct a Fashion Graph, where each node represents a category and each edge represents interaction between two categories. Accordingly, each outfit can be represented as a subgraph by putting items into their corresponding category nodes. To infer the outfit compatibility from such a graph, we propose Node-wise Graph Neural Networks (NGNN) which can better model node interactions and learn better node representations. In NGNN, the node interaction on each edge is different, which is determined by parameters correlated to the two connected nodes. An attention mechanism is utilized to calculate the outfit compatibility score with learned node representations. NGNN can not only be used to model outfit compatibility from visual or textual modality but also from multiple modalities. We conduct experiments on two tasks: (1) Fill-in-the-blank: suggesting an item that matches with existing components of outfit; (2) Compatibility prediction: predicting the compatibility scores of given outfits. Experimental results demonstrate the great superiority of our proposed method over others.

We present an end-to-end deep learning segmentation method by combining a 3D UNet architecture with a graph neural network (GNN) model. In this approach, the convolutional layers at the deepest level of the UNet are replaced by a GNN-based module with a series of graph convolutions. The dense feature maps at this level are transformed into a graph input to the GNN module. The incorporation of graph convolutions in the UNet provides nodes in the graph with information that is based on node connectivity, in addition to the local features learnt through the downsampled paths. This information can help improve segmentation decisions. By stacking several graph convolution layers, the nodes can access higher order neighbourhood information without substantial increase in computational expense. We propose two types of node connectivity in the graph adjacency: i) one predefined and based on a regular node neighbourhood, and ii) one dynamically computed during training and using the nearest neighbour nodes in the feature space. We have applied this method to the task of segmenting the airway tree from chest CT scans. Experiments have been performed on 32 CTs from the Danish Lung Cancer Screening Trial dataset. We evaluate the performance of the UNet-GNN models with two types of graph adjacency and compare it with the baseline UNet.

As multimodal LLM-driven agents continue to advance in autonomy and generalization, evaluation based on static datasets can no longer adequately assess their true capabilities in dynamic environments and diverse tasks. Existing LLM-based synthetic data methods are largely designed for LLM training and evaluation, and thus cannot be directly applied to agent tasks that require tool use and interactive capabilities. While recent studies have explored automatic agent task generation with LLMs, most efforts remain limited to text or image analysis, without systematically modeling multi-step interactions in web environments. To address these challenges, we propose Graph2Eval, a knowledge graph-based framework that automatically generates both multimodal document comprehension tasks and web interaction tasks, enabling comprehensive evaluation of agents' reasoning, collaboration, and interactive capabilities. In our approach, knowledge graphs constructed from multi-source external data serve as the task space, where we translate semantic relations into structured multimodal tasks using subgraph sampling, task templates, and meta-paths. A multi-stage filtering pipeline based on node reachability, LLM scoring, and similarity analysis is applied to guarantee the quality and executability of the generated tasks. Furthermore, Graph2Eval supports end-to-end evaluation of multiple agent types (Single-Agent, Multi-Agent, Web Agent) and measures reasoning, collaboration, and interaction capabilities. We instantiate the framework with Graph2Eval-Bench, a curated dataset of 1,319 tasks spanning document comprehension and web interaction scenarios. Experiments show that Graph2Eval efficiently generates tasks that differentiate agent and model performance, revealing gaps in reasoning, collaboration, and web interaction across different settings and offering a new perspective for agent evaluation.

Generating new molecules is fundamental to advancing critical applications such as drug discovery and material synthesis. Flows can generate molecules effectively by inverting the encoding process, however, existing flow models either require artifactual dequantization or specific node/edge orderings, lack desiderata such as permutation invariance, or induce discrepancy between the encoding and the decoding steps that necessitates post hoc validity correction. We circumvent these issues with novel continuous normalizing E(3)-equivariant flows, based on a system of node ODEs coupled as a graph PDE, that repeatedly reconcile locally toward globally aligned densities. Our models can be cast as message-passing temporal networks, and result in superlative performance on the tasks of density estimation and molecular generation. In particular, our generated samples achieve state-of-the-art on both the standard QM9 and ZINC250K benchmarks.

We present FastRP, a scalable and performant algorithm for learning distributed node representations in a graph. FastRP is over 4,000 times faster than state-of-the-art methods such as DeepWalk and node2vec, while achieving comparable or even better performance as evaluated on several real-world networks on various downstream tasks. We observe that most network embedding methods consist of two components: construct a node similarity matrix and then apply dimension reduction techniques to this matrix. We show that the success of these methods should be attributed to the proper construction of this similarity matrix, rather than the dimension reduction method employed. FastRP is proposed as a scalable algorithm for network embeddings. Two key features of FastRP are: 1) it explicitly constructs a node similarity matrix that captures transitive relationships in a graph and normalizes matrix entries based on node degrees; 2) it utilizes very sparse random projection, which is a scalable optimization-free method for dimension reduction. An extra benefit from combining these two design choices is that it allows the iterative computation of node embeddings so that the similarity matrix need not be explicitly constructed, which further speeds up FastRP. FastRP is also advantageous for its ease of implementation, parallelization and hyperparameter tuning. The source code is available at https://github.com/GTmac/FastRP.

To bridge the gaps between topology-aware Graph Neural Networks (GNNs) and inference-efficient Multi-Layer Perceptron (MLPs), GLNN proposes to distill knowledge from a well-trained teacher GNN into a student MLP. Despite their great progress, comparatively little work has been done to explore the reliability of different knowledge points (nodes) in GNNs, especially their roles played during distillation. In this paper, we first quantify the knowledge reliability in GNN by measuring the invariance of their information entropy to noise perturbations, from which we observe that different knowledge points (1) show different distillation speeds (temporally); (2) are differentially distributed in the graph (spatially). To achieve reliable distillation, we propose an effective approach, namely Knowledge-inspired Reliable Distillation (KRD), that models the probability of each node being an informative and reliable knowledge point, based on which we sample a set of additional reliable knowledge points as supervision for training student MLPs. Extensive experiments show that KRD improves over the vanilla MLPs by 12.62% and outperforms its corresponding teacher GNNs by 2.16% averaged over 7 datasets and 3 GNN architectures.

The rapid expansion of genomic sequence data calls for new methods to achieve robust sequence representations. Existing techniques often neglect intricate structural details, emphasizing mainly contextual information. To address this, we developed k-mer embeddings that merge contextual and structural string information by enhancing De Bruijn graphs with structural similarity connections. Subsequently, we crafted a self-supervised method based on Contrastive Learning that employs a heterogeneous Graph Convolutional Network encoder and constructs positive pairs based on node similarities. Our embeddings consistently outperform prior techniques for Edit Distance Approximation and Closest String Retrieval tasks.

Multiprotocol Label Switching (MPLS) is a high-performance telecommunications technology that directs data from one network node to another based on short path labels rather than long network addresses. Its efficiency and scalability have made it a popular choice for large-scale and enterprise networks. However, as MPLS networks grow and evolve, they encounter various security challenges. This paper explores the security implications associated with MPLS networks, including risks such as label spoofing, traffic interception, and denial of service attacks. Additionally, it evaluates advanced mitigation strategies to address these vulnerabilities, leveraging mathematical models and security protocols to enhance MPLS network resilience. By integrating theoretical analysis with practical solutions, this paper aims to provide a comprehensive understanding of MPLS security and propose effective methods for safeguarding network infrastructure.

Heterogeneous graph contrastive learning has received wide attention recently. Some existing methods use meta-paths, which are sequences of object types that capture semantic relationships between objects, to construct contrastive views. However, most of them ignore the rich meta-path context information that describes how two objects are connected by meta-paths. Further, they fail to distinguish negative samples, which could adversely affect the model performance. To address the problems, we propose MEOW, which considers both meta-path contexts and weighted negative samples. Specifically, MEOW constructs a coarse view and a fine-grained view for contrast. The former reflects which objects are connected by meta-paths, while the latter uses meta-path contexts and characterizes details on how the objects are connected. Then, we theoretically analyze the InfoNCE loss and recognize its limitations for computing gradients of negative samples. To better distinguish negative samples, we learn hard-valued weights for them based on node clustering and use prototypical contrastive learning to pull close embeddings of nodes in the same cluster. In addition, we propose a variant model AdaMEOW that adaptively learns soft-valued weights of negative samples to further improve node representation. Finally, we conduct extensive experiments to show the superiority of MEOW and AdaMEOW against other state-of-the-art methods.

Text-attributed graphs integrate semantic information of node texts with topological structure, offering significant value in various applications such as document classification and information extraction. Existing approaches typically encode textual content using language models (LMs), followed by graph neural networks (GNNs) to process structural information. However, during the LM-based text encoding phase, most methods not only perform semantic interaction solely at the word-token granularity, but also neglect the structural dependencies among texts from different nodes. In this work, we propose DuConTE, a dual-granularity text encoder with topology-constrained attention. The model employs a cascaded architecture of two pretrained LMs, encoding semantics first at the word-token granularity and then at the node granularity. During the self-attention computation in each LM, we dynamically adjust the attention mask matrix based on node connectivity, guiding the model to learn semantic correlations informed by the graph structure. Furthermore, when composing node representations from word-token embeddings, we separately evaluate the importance of tokens under the center-node context and the neighborhood context, enabling the capture of more contextually relevant semantic information. Extensive experiments on multiple benchmark datasets demonstrate that DuConTE achieves state-of-the-art performance on the majority of them.

Recent studies show that Large Language Models (LLMs) achieve strong reasoning capabilities through supervised fine-tuning or reinforcement learning. However, a key approach, the Process Reward Model (PRM), suffers from reward hacking, making it unreliable in identifying the best intermediate steps. In this paper, we propose a novel reward model approach, Hierarchical Reward Model (HRM), which evaluates both individual and consecutive reasoning steps from fine-grained and coarse-grained level. HRM performs better in assessing reasoning coherence and self-reflection, particularly when the previous reasoning step is incorrect. Furthermore, to address the inefficiency of autonomous generating PRM training data via Monte Carlo Tree Search (MCTS), we introduce a lightweight and effective data augmentation strategy called Hierarchical Node Compression (HNC) based on node merging (combining two consecutive reasoning steps into one step) in the tree structure. This approach diversifies MCTS results for HRM with negligible computational overhead, enhancing label robustness by introducing noise. Empirical results on the PRM800K dataset demonstrate that HRM, in conjunction with HNC, achieves superior stability and reliability in evaluation compared to PRM. Furthermore, cross-domain evaluations on MATH500 and GSM8K confirm HRM's superior generalization and robustness across diverse reasoning tasks. The code for all experiments will be released at https: //github.com/tengwang0318/hierarchial_reward_model.

Transformers often fail to learn generalizable algorithms, instead relying on brittle heuristics. Using graph connectivity as a testbed, we explain this phenomenon both theoretically and empirically. We consider a simplified Transformer architecture, the disentangled Transformer, and prove that an L-layer model has capacity to solve for graphs with diameters up to exactly 3^L, implementing an algorithm equivalent to computing powers of the adjacency matrix. We analyze the training-dynamics, and show that the learned strategy hinges on whether most training instances are within this model capacity. Within-capacity graphs (diameter leq 3^L) drive the learning of a correct algorithmic solution while beyond-capacity graphs drive the learning of a simple heuristic based on node degrees. Finally, we empirically demonstrate that restricting training data within a model's capacity leads to both standard and disentangled transformers learning the exact algorithm rather than the degree-based heuristic.

The identification of heterogeneous treatment effects (HTE) across subgroups is of significant interest in clinical trial analysis. Several state-of-the-art HTE estimation methods, including causal forests, apply recursive partitioning for non-parametric identification of relevant covariates and interactions. However, the partitioning criterion is typically based on differences in absolute risk. This can dilute statistical power by masking variation in the relative risk, which is often a more appropriate quantity of clinical interest. In this work, we propose and implement a methodology for modifying causal forests to target relative risk, using a novel node-splitting procedure based on exhaustive generalized linear model comparison. We present results from simulated data that suggest relative risk causal forests can capture otherwise undetected sources of heterogeneity. We implement our method on real-world trial data to explore HTEs for liraglutide in patients with type 2 diabetes.

Graph Neural Networks (GNNs) have achieved state-of-the-art performance in various graph-based learning tasks. However, enabling privacy-preserving GNNs in encrypted domains, such as under Fully Homomorphic Encryption (FHE), typically incurs substantial computational overhead, rendering real-time and privacy-preserving inference impractical. In this work, we propose DESIGN (EncrypteD GNN Inference via sErver-Side Input Graph pruNing), a novel framework for efficient encrypted GNN inference. DESIGN tackles the critical efficiency limitations of existing FHE GNN approaches, which often overlook input data redundancy and apply uniform computational strategies. Our framework achieves significant performance gains through a hierarchical optimization strategy executed entirely on the server: first, FHE-compatible node importance scores (based on encrypted degree statistics) are computed from the encrypted graph. These scores then guide a homomorphic partitioning process, generating multi-level importance masks directly under FHE. This dynamically generated mask facilitates both input graph pruning (by logically removing unimportant elements) and a novel adaptive polynomial activation scheme, where activation complexity is tailored to node importance levels. Empirical evaluations demonstrate that DESIGN substantially accelerates FHE GNN inference compared to state-of-the-art methods while maintaining competitive model accuracy, presenting a robust solution for secure graph analytics. Our implementation is publicly available at https://github.com/LabRAI/DESIGN.

Machine-learning interatomic potentials (MLIPs) have advanced rapidly, with many top models relying on strong physics-based inductive biases. However, as models scale to larger systems like biomolecules and electrolytes, they struggle to accurately capture long-range (LR) interactions, leading current approaches to rely on explicit physics-based terms or components. In this work, we propose AllScAIP, a straightforward, attention-based, and energy-conserving MLIP model that scales to O(100 million) training samples. It addresses the long-range challenge using an all-to-all node attention component that is data-driven. Extensive ablations reveal that in low-data/small-model regimes, inductive biases improve sample efficiency. However, as data and model size scale, these benefits diminish or even reverse, while all-to-all attention remains critical for capturing LR interactions. Our model achieves state-of-the-art energy/force accuracy on molecular systems, as well as a number of physics-based evaluations (OMol25), while being competitive on materials (OMat24) and catalysts (OC20). Furthermore, it enables stable, long-timescale MD simulations that accurately recover experimental observables, including density and heat of vaporization predictions.

Video action segmentation have been widely applied in many fields. Most previous studies employed video-based vision models for this purpose. However, they often rely on a large receptive field, LSTM or Transformer methods to capture long-term dependencies within videos, leading to significant computational resource requirements. To address this challenge, graph-based model was proposed. However, previous graph-based models are less accurate. Hence, this study introduces a graph-structured approach named Semantic2Graph, to model long-term dependencies in videos, thereby reducing computational costs and raise the accuracy. We construct a graph structure of video at the frame-level. Temporal edges are utilized to model the temporal relations and action order within videos. Additionally, we have designed positive and negative semantic edges, accompanied by corresponding edge weights, to capture both long-term and short-term semantic relationships in video actions. Node attributes encompass a rich set of multi-modal features extracted from video content, graph structures, and label text, encompassing visual, structural, and semantic cues. To synthesize this multi-modal information effectively, we employ a graph neural network (GNN) model to fuse multi-modal features for node action label classification. Experimental results demonstrate that Semantic2Graph outperforms state-of-the-art methods in terms of performance, particularly on benchmark datasets such as GTEA and 50Salads. Multiple ablation experiments further validate the effectiveness of semantic features in enhancing model performance. Notably, the inclusion of semantic edges in Semantic2Graph allows for the cost-effective capture of long-term dependencies, affirming its utility in addressing the challenges posed by computational resource constraints in video-based vision models.

Node clustering is a powerful tool in the analysis of networks. We introduce a graph neural network framework, named DIGRAC, to obtain node embeddings for directed networks in a self-supervised manner, including a novel probabilistic imbalance loss, which can be used for network clustering. Here, we propose directed flow imbalance measures, which are tightly related to directionality, to reveal clusters in the network even when there is no density difference between clusters. In contrast to standard approaches in the literature, in this paper, directionality is not treated as a nuisance, but rather contains the main signal. DIGRAC optimizes directed flow imbalance for clustering without requiring label supervision, unlike existing graph neural network methods, and can naturally incorporate node features, unlike existing spectral methods. Extensive experimental results on synthetic data, in the form of directed stochastic block models, and real-world data at different scales, demonstrate that our method, based on flow imbalance, attains state-of-the-art results on directed graph clustering when compared against 10 state-of-the-art methods from the literature, for a wide range of noise and sparsity levels, graph structures, and topologies, and even outperforms supervised methods.

Part-of-Speech (POS) tagging is an important component of the NLP pipeline, but many low-resource languages lack labeled data for training. An established method for training a POS tagger in such a scenario is to create a labeled training set by transferring from high-resource languages. In this paper, we propose a novel method for transferring labels from multiple high-resource source to low-resource target languages. We formalize POS tag projection as graph-based label propagation. Given translations of a sentence in multiple languages, we create a graph with words as nodes and alignment links as edges by aligning words for all language pairs. We then propagate node labels from source to target using a Graph Neural Network augmented with transformer layers. We show that our propagation creates training sets that allow us to train POS taggers for a diverse set of languages. When combined with enhanced contextualized embeddings, our method achieves a new state-of-the-art for unsupervised POS tagging of low-resource languages.

Fair machine learning seeks to identify and mitigate biases in predictions against unfavorable populations characterized by demographic attributes, such as race and gender. Recently, a few works have extended fairness to graph data, such as social networks, but most of them neglect the causal relationships among data instances. This paper addresses the prevalent challenge in fairness-aware ML algorithms, which typically assume Independent and Identically Distributed (IID) data. We tackle the overlooked domain of non-IID, graph-based settings where data instances are interconnected, influencing the outcomes of fairness interventions. We base our research on the Network Structural Causal Model (NSCM) framework and posit two main assumptions: Decomposability and Graph Independence, which enable the computation of interventional distributions in non-IID settings using the do-calculus. Based on that, we develop the Message Passing Variational Autoencoder for Causal Inference (MPVA) to compute interventional distributions and facilitate causally fair node classification through estimated interventional distributions. Empirical evaluations on semi-synthetic and real-world datasets demonstrate that MPVA outperforms conventional methods by effectively approximating interventional distributions and mitigating bias. The implications of our findings underscore the potential of causality-based fairness in complex ML applications, setting the stage for further research into relaxing the initial assumptions to enhance model fairness.

Approximate Nearest Neighbor Search (ANNS), as the core of vector databases (VectorDBs), has become widely used in modern AI and ML systems, powering applications from information retrieval to bio-informatics. While graph-based ANNS methods achieve high query efficiency, their scalability is constrained by the available host memory. Recent disk-based ANNS approaches mitigate memory usage by offloading data to Solid-State Drives (SSDs). However, they still suffer from issues such as long I/O traversal path, misalignment with storage I/O granularity, and high in-memory indexing overhead, leading to significant I/O latency and ultimately limiting scalability for large-scale vector search. In this paper, we propose PageANN, a disk-based approximate nearest neighbor search (ANNS) framework designed for high performance and scalability. PageANN introduces a page-node graph structure that aligns logical graph nodes with physical SSD pages, thereby shortening I/O traversal paths and reducing I/O operations. Specifically, similar vectors are clustered into page nodes, and a co-designed disk data layout leverages this structure with a merging technique to store only representative vectors and topology information, avoiding unnecessary reads. To further improve efficiency, we design a memory management strategy that combines lightweight indexing with coordinated memory-disk data allocation, maximizing host memory utilization while minimizing query latency and storage overhead. Experimental results show that PageANN significantly outperforms state-of-the-art (SOTA) disk-based ANNS methods, achieving 1.85x-10.83x higher throughput and 51.7%-91.9% lower latency across different datasets and memory budgets, while maintaining comparable high recall accuracy.

Detecting which nodes in graphs are outliers is a relatively new machine learning task with numerous applications. Despite the proliferation of algorithms developed in recent years for this task, there has been no standard comprehensive setting for performance evaluation. Consequently, it has been difficult to understand which methods work well and when under a broad range of settings. To bridge this gap, we present--to the best of our knowledge--the first comprehensive benchmark for unsupervised outlier node detection on static attributed graphs called BOND, with the following highlights. (1) We benchmark the outlier detection performance of 14 methods ranging from classical matrix factorization to the latest graph neural networks. (2) Using nine real datasets, our benchmark assesses how the different detection methods respond to two major types of synthetic outliers and separately to "organic" (real non-synthetic) outliers. (3) Using an existing random graph generation technique, we produce a family of synthetically generated datasets of different graph sizes that enable us to compare the running time and memory usage of the different outlier detection algorithms. Based on our experimental results, we discuss the pros and cons of existing graph outlier detection algorithms, and we highlight opportunities for future research. Importantly, our code is freely available and meant to be easily extendable: https://github.com/pygod-team/pygod/tree/main/benchmark

Graph measures that express closeness or distance between nodes can be employed for graph nodes clustering using metric clustering algorithms. There are numerous measures applicable to this task, and which one performs better is an open question. We study the performance of 25 graph measures on generated graphs with different parameters. While usually measure comparisons are limited to general measure ranking on a particular dataset, we aim to explore the performance of various measures depending on graph features. Using an LFR graph generator, we create a dataset of 11780 graphs covering the whole LFR parameter space. For each graph, we assess the quality of clustering with k-means algorithm for each considered measure. Based on this, we determine the best measure for each area of the parameter space. We find that the parameter space consists of distinct zones where one particular measure is the best. We analyze the geometry of the resulting zones and describe it with simple criteria. Given particular graph parameters, this allows us to recommend a particular measure to use for clustering.

While most network embedding techniques model the relative positions of nodes in a network, recently there has been significant interest in structural embeddings that model node role equivalences, irrespective of their distances to any specific nodes. We present PhUSION, a proximity-based unified framework for computing structural and positional node embeddings, which leverages well-established methods for calculating node proximity scores. Clarifying a point of contention in the literature, we show which step of PhUSION produces the different kinds of embeddings and what steps can be used by both. Moreover, by aggregating the PhUSION node embeddings, we obtain graph-level features that model information lost by previous graph feature learning and kernel methods. In a comprehensive empirical study with over 10 datasets, 4 tasks, and 35 methods, we systematically reveal successful design choices for node and graph-level machine learning with embeddings.

The activations of Facial Action Units (AUs) mutually influence one another. While the relationship between a pair of AUs can be complex and unique, existing approaches fail to specifically and explicitly represent such cues for each pair of AUs in each facial display. This paper proposes an AU relationship modelling approach that deep learns a unique graph to explicitly describe the relationship between each pair of AUs of the target facial display. Our approach first encodes each AU's activation status and its association with other AUs into a node feature. Then, it learns a pair of multi-dimensional edge features to describe multiple task-specific relationship cues between each pair of AUs. During both node and edge feature learning, our approach also considers the influence of the unique facial display on AUs' relationship by taking the full face representation as an input. Experimental results on BP4D and DISFA datasets show that both node and edge feature learning modules provide large performance improvements for CNN and transformer-based backbones, with our best systems achieving the state-of-the-art AU recognition results. Our approach not only has a strong capability in modelling relationship cues for AU recognition but also can be easily incorporated into various backbones. Our PyTorch code is made available.

This paper reports Deep LOGISMOS approach to 3D tumor segmentation by incorporating boundary information derived from deep contextual learning to LOGISMOS - layered optimal graph image segmentation of multiple objects and surfaces. Accurate and reliable tumor segmentation is essential to tumor growth analysis and treatment selection. A fully convolutional network (FCN), UNet, is first trained using three adjacent 2D patches centered at the tumor, providing contextual UNet segmentation and probability map for each 2D patch. The UNet segmentation is then refined by Gaussian Mixture Model (GMM) and morphological operations. The refined UNet segmentation is used to provide the initial shape boundary to build a segmentation graph. The cost for each node of the graph is determined by the UNet probability maps. Finally, a max-flow algorithm is employed to find the globally optimal solution thus obtaining the final segmentation. For evaluation, we applied the method to pancreatic tumor segmentation on a dataset of 51 CT scans, among which 30 scans were used for training and 21 for testing. With Deep LOGISMOS, DICE Similarity Coefficient (DSC) and Relative Volume Difference (RVD) reached 83.2+-7.8% and 18.6+-17.4% respectively, both are significantly improved (p<0.05) compared with contextual UNet and/or LOGISMOS alone.

Humans describe complex scenes with compositionality, using simple text descriptions enriched with links and relationships. While vision-language research has aimed to develop models with compositional understanding capabilities, this is not reflected yet in existing datasets which, for the most part, still use plain text to describe images. In this work, we propose a new annotation strategy, graph-based captioning (GBC) that describes an image using a labelled graph structure, with nodes of various types. The nodes in GBC are created using, in a first stage, object detection and dense captioning tools nested recursively to uncover and describe entity nodes, further linked together in a second stage by highlighting, using new types of nodes, compositions and relations among entities. Since all GBC nodes hold plain text descriptions, GBC retains the flexibility found in natural language, but can also encode hierarchical information in its edges. We demonstrate that GBC can be produced automatically, using off-the-shelf multimodal LLMs and open-vocabulary detection models, by building a new dataset, GBC10M, gathering GBC annotations for about 10M images of the CC12M dataset. We use GBC10M to showcase the wealth of node captions uncovered by GBC, as measured with CLIP training. We show that using GBC nodes' annotations -- notably those stored in composition and relation nodes -- results in significant performance boost on downstream models when compared to other dataset formats. To further explore the opportunities provided by GBC, we also propose a new attention mechanism that can leverage the entire GBC graph, with encouraging experimental results that show the extra benefits of incorporating the graph structure. Our datasets are released at https://huggingface.co/graph-based-captions.

Graph anomaly detection (GAD) has become an increasingly important task across various domains. With the rapid development of graph neural networks (GNNs), GAD methods have achieved significant performance improvements. However, fairness considerations in GAD remain largely underexplored. Indeed, GNN-based GAD models can inherit and amplify biases present in training data, potentially leading to unfair outcomes. While existing efforts have focused on developing fair GNNs, most approaches target node classification tasks, where models often rely on simple layer architectures rather than autoencoder-based structures, which are the most widely used architecturs for anomaly detection. To address fairness in autoencoder-based GAD models, we propose DisEntangled Counterfactual Adversarial Fair (DECAF)-GAD, a framework that alleviates bias while preserving GAD performance. Specifically, we introduce a structural causal model (SCM) to disentangle sensitive attributes from learned representations. Based on this causal framework, we formulate a specialized autoencoder architecture along with a fairness-guided loss function. Through extensive experiments on both synthetic and real-world datasets, we demonstrate that DECAF-GAD not only achieves competitive anomaly detection performance but also significantly enhances fairness metrics compared to baseline GAD methods. Our code is available at https://github.com/Tlhey/decaf_code.

Generating explanations for graph neural networks (GNNs) has been studied to understand their behavior in analytical tasks such as graph classification. Existing approaches aim to understand the overall results of GNNs rather than providing explanations for specific class labels of interest, and may return explanation structures that are hard to access, nor directly queryable.We propose GVEX, a novel paradigm that generates Graph Views for EXplanation. (1) We design a two-tier explanation structure called explanation views. An explanation view consists of a set of graph patterns and a set of induced explanation subgraphs. Given a database G of multiple graphs and a specific class label l assigned by a GNN-based classifier M, it concisely describes the fraction of G that best explains why l is assigned by M. (2) We propose quality measures and formulate an optimization problem to compute optimal explanation views for GNN explanation. We show that the problem is Σ^2_P-hard. (3) We present two algorithms. The first one follows an explain-and-summarize strategy that first generates high-quality explanation subgraphs which best explain GNNs in terms of feature influence maximization, and then performs a summarization step to generate patterns. We show that this strategy provides an approximation ratio of 1/2. Our second algorithm performs a single-pass to an input node stream in batches to incrementally maintain explanation views, having an anytime quality guarantee of 1/4 approximation. Using real-world benchmark data, we experimentally demonstrate the effectiveness, efficiency, and scalability of GVEX. Through case studies, we showcase the practical applications of GVEX.

Feedforward neural networks are widely used as universal predictive models to fit data distribution. Common gradient-based learning, however, suffers from many drawbacks making the training process ineffective and time-consuming. Alternative randomized learning does not use gradients but selects hidden node parameters randomly. This makes the training process extremely fast. However, the problem in randomized learning is how to determine the random parameters. A recently proposed method uses autoencoders for unsupervised parameter learning. This method showed superior performance on classification tasks. In this work, we apply this method to regression problems, and, finding that it has some drawbacks, we show how to improve it. We propose a learning method of autoencoders that controls the produced random weights. We also propose how to determine the biases of hidden nodes. We empirically compare autoencoder based learning with other randomized learning methods proposed recently for regression and find that despite the proposed improvement of the autoencoder based learning, it does not outperform its competitors in fitting accuracy. Moreover, the method is much more complex than its competitors.

With an ever-growing zoo of LLMs and benchmarks, the need to orchestrate multiple models for improved task performance has never been more pressing. While frameworks like Mixture-of-Agents (MoA) attempt to coordinate LLMs, they often fall short in terms of (1) selecting relevant agents, (2) facilitating effective intra-agent communication, and (3) integrating responses efficiently. In this work, we propose Graph-of-Agents (GoA), a new graph-based framework for modeling multi-agent LLM communication. Our approach begins with node sampling, selecting only the most relevant agents by leveraging model cards that summarize each model's domain, task specialization, and other characteristics. Next, we construct edges between the selected agents by evaluating their responses against one another to determine relevance ordering. Directed message passing is then performed from highly relevant agents to less relevant ones to enhance their responses, followed by reverse message passing to refine the original responses of the more relevant agents. Finally, the updated responses are aggregated via graph-based pooling (e.g., max or mean pooling) to produce a single, unified answer. We evaluate GoA on diverse multi-domain benchmarks (MMLU, MMLU-Pro, GPQA) and domain-specific benchmarks (MATH, HumanEval, MedMCQA), with an agent pool of 6 LLMs spanning multiple domains. Surprisingly, GoA achieves superior performance using only 3 selected agents, outperforming recent multi-agent LLM baselines that utilize all 6 agents simultaneously. By adopting a graph structure, GoA offers both scalability and effectiveness through structured message passing-positioning it as a strong candidate for navigating the challenges of the ever-growing LLM zoo. Code is available at: https://github.com/UNITES-Lab/GoA.

Financial transaction fraud prevention faces challenges such as complex relationship structures, concealed behavioral patterns, and dynamically changing data distribution. Discrimination models relying solely on independent sample features are insufficient to fully characterize the risks of group collaboration and chain transfers within transaction networks. This paper proposes a graph neural network representation learning and risk discrimination framework for financial transaction fraud prevention. It integrates transaction records and identity information into node attributes and constructs a transaction graph based on shared attributes and interaction consistency to explicitly model inter-transaction relationships. In model design, a multi-layer message passing mechanism is employed to aggregate neighborhood information, learn node embedding representations containing structural context semantics, and output transaction-level fraud probability and risk scores through a lightweight risk discrimination head. A weighted supervision objective is introduced to mitigate training bias caused by class imbalance, and structural consistency regularization constraints are combined to suppress the impact of noisy edges on representation drift, thereby improving the stability and usability of risk characterization. Experiments are conducted on a publicly available financial transaction dataset, comparing various methods in the same direction and comprehensively evaluating them under a unified evaluation protocol. The results show that the proposed method outperforms other methods in risk ranking and probability calibration quality, validating the effectiveness of graph structure modeling and representation learning collaboration in financial transaction fraud prevention.

Decision trees can make vision-language model (VLM) classification interpretable by replacing a single prediction with a sequence of root-to-leaf questions. However, the accuracy cost of this greedy, non-backtracking procedure remains unclear. We introduce MYOPIA, a benchmark comprising four LLM-generated, human-refined decision trees for GTSRB, MNIST, CIFAR-10, and MSCOCO, together with matched prompts, diagnostic protocols, and an evaluation harness. Across GPT-4o, Qwen-VL Max, and LLaMA-3.2 11B Vision, tree traversal underperforms zero-shot prompting in all 12 dataset--model pairs; paired bootstrap analyses consistently favor zero-shot. Our diagnostics characterize interacting failure modes associated with this gap. Models often recall tree-encoded class attributes more accurately than they ground the same attributes in images: the mean label--image accuracy gaps are 9.5, 13.8, and 12.6 points for GPT-4o, Qwen-VL Max, and LLaMA, respectively. Incorrect local decisions then irreversibly exclude the correct class, while answer extraction introduces additional model-dependent loss. A node-level audit of the four trees finds that split entropy is weakly but consistently associated with lower node accuracy, whereas depth, branching factor, and within-node grounding differences are less stable. MYOPIA therefore provides a framework for diagnosing hierarchical visual classification and motivates testing tree designs that prioritize perceptual answerability and recovery from early errors. Code is available at https://github.com/islammesabah/VLM_Classification.

We consider a project (model) owner that would like to train a model by utilizing the local private data and compute power of interested data owners, i.e., trainers. Our goal is to design a data marketplace for such decentralized collaborative/federated learning applications that simultaneously provides i) proof-of-contribution based reward allocation so that the trainers are compensated based on their contributions to the trained model; ii) privacy-preserving decentralized model training by avoiding any data movement from data owners; iii) robustness against malicious parties (e.g., trainers aiming to poison the model); iv) verifiability in the sense that the integrity, i.e., correctness, of all computations in the data market protocol including contribution assessment and outlier detection are verifiable through zero-knowledge proofs; and v) efficient and universal design. We propose a blockchain-based marketplace design to achieve all five objectives mentioned above. In our design, we utilize a distributed storage infrastructure and an aggregator aside from the project owner and the trainers. The aggregator is a processing node that performs certain computations, including assessing trainer contributions, removing outliers, and updating hyper-parameters. We execute the proposed data market through a blockchain smart contract. The deployed smart contract ensures that the project owner cannot evade payment, and honest trainers are rewarded based on their contributions at the end of training. Finally, we implement the building blocks of the proposed data market and demonstrate their applicability in practical scenarios through extensive experiments.

Along with the rapid development of real-world applications, higher requirements on the accuracy and efficiency of image super-resolution (SR) are brought forward. Though existing methods have achieved remarkable success, the majority of them demand plenty of computational resources and large amount of RAM, and thus they can not be well applied to mobile device. In this paper, we aim at designing efficient architecture for 8-bit quantization and deploy it on mobile device. First, we conduct an experiment about meta-node latency by decomposing lightweight SR architectures, which determines the portable operations we can utilize. Then, we dig deeper into what kind of architecture is beneficial to 8-bit quantization and propose anchor-based plain net (ABPN). Finally, we adopt quantization-aware training strategy to further boost the performance. Our model can outperform 8-bit quantized FSRCNN by nearly 2dB in terms of PSNR, while satisfying realistic needs at the same time. Code is avaliable at https://github.com/NJU- Jet/SR_Mobile_Quantization.

Graph Neural Networks (GNNs) have shown great promise in learning node embeddings for link prediction (LP). While numerous studies aim to improve the overall LP performance of GNNs, none have explored its varying performance across different nodes and its underlying reasons. To this end, we aim to demystify which nodes will perform better from the perspective of their local topology. Despite the widespread belief that low-degree nodes exhibit poorer LP performance, our empirical findings provide nuances to this viewpoint and prompt us to propose a better metric, Topological Concentration (TC), based on the intersection of the local subgraph of each node with the ones of its neighbors. We empirically demonstrate that TC has a higher correlation with LP performance than other node-level topological metrics like degree and subgraph density, offering a better way to identify low-performing nodes than using cold-start. With TC, we discover a novel topological distribution shift issue in which newly joined neighbors of a node tend to become less interactive with that node's existing neighbors, compromising the generalizability of node embeddings for LP at testing time. To make the computation of TC scalable, We further propose Approximated Topological Concentration (ATC) and theoretically/empirically justify its efficacy in approximating TC and reducing the computation complexity. Given the positive correlation between node TC and its LP performance, we explore the potential of boosting LP performance via enhancing TC by re-weighting edges in the message-passing and discuss its effectiveness with limitations. Our code is publicly available at https://github.com/YuWVandy/Topo_LP_GNN.

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

Generating graph-structured data requires learning the underlying distribution of graphs. Yet, this is a challenging problem, and the previous graph generative methods either fail to capture the permutation-invariance property of graphs or cannot sufficiently model the complex dependency between nodes and edges, which is crucial for generating real-world graphs such as molecules. To overcome such limitations, we propose a novel score-based generative model for graphs with a continuous-time framework. Specifically, we propose a new graph diffusion process that models the joint distribution of the nodes and edges through a system of stochastic differential equations (SDEs). Then, we derive novel score matching objectives tailored for the proposed diffusion process to estimate the gradient of the joint log-density with respect to each component, and introduce a new solver for the system of SDEs to efficiently sample from the reverse diffusion process. We validate our graph generation method on diverse datasets, on which it either achieves significantly superior or competitive performance to the baselines. Further analysis shows that our method is able to generate molecules that lie close to the training distribution yet do not violate the chemical valency rule, demonstrating the effectiveness of the system of SDEs in modeling the node-edge relationships. Our code is available at https://github.com/harryjo97/GDSS.

The internet is undergoing a historical transformation from the "Internet of Websites" to the "Internet of AgentSites." While traditional Websites served as the foundation for information hosting and dissemination, a new frontier is emerging where AgentSites serve as the hubs of the internet, where each AgentSite hosts one or more AI agents that receive tasks, address them, and deliver actionable solutions, marking a significant shift in the digital landscape and representing the next generation of online ecosystems. Under this vision, AIOS, the AI Agent Operating System, serves as the server for the development, deployment and execution of AI agents, which is a fundamental infrastructure for the Internet of Agentsites. In this paper, we introduce AIOS Server, a runtime framework to host agents and enable global-scale collaboration among decentralized agents. AIOS Server provides a communication protocol leveraging the Model Context Protocol (MCP) and JSON-RPC to enable agent-agent or human-agent interactions. Each AIOS node operates as a server to host and execute agents, while supporting peer-to-peer coordination without reliance on centralized orchestration. Based on AIOS Server, we further present the world's first practically deployed Internet of Agentsites (AIOS-IoA), including AgentHub for agent registration and discovery and AgentChat for interactive communication, at https://planet.aios.foundation. The agent discovery mechanism based on Distributed Hash Tables (DHT) and a Gossip protocol serves as the search engine for the internet of agentsites. This work provides a practical foundation for building the Internet of Agentsites-a new paradigm where autonomous agents become first-class citizens of the web. The implementation is available at https://github.com/agiresearch/AIOS.Server and is integrated into the AIOS main branch at https://github.com/agiresearch/AIOS.

We present DYMAG, a graph neural network based on a novel form of message aggregation. Standard message-passing neural networks, which often aggregate local neighbors via mean-aggregation, can be regarded as convolving with a simple rectangular waveform which is non-zero only on 1-hop neighbors of every vertex. Here, we go beyond such local averaging. We will convolve the node features with more sophisticated waveforms generated using dynamics such as the heat equation, wave equation, and the Sprott model (an example of chaotic dynamics). Furthermore, we use snapshots of these dynamics at different time points to create waveforms at many effective scales. Theoretically, we show that these dynamic waveforms can capture salient information about the graph including connected components, connectivity, and cycle structures even with no features. Empirically, we test DYMAG on both real and synthetic benchmarks to establish that DYMAG outperforms baseline models on recovery of graph persistence, generating parameters of random graphs, as well as property prediction for proteins, molecules and materials. Our code is available at https://github.com/KrishnaswamyLab/DYMAG.

Knowledge graphs have been proposed as a structured alternative to flat retrieval-augmented generation for long-term agent memory, on the assumption that representing conversations as entities and relations improves recall. We evaluate that assumption directly. Our framework extracts each conversational turn into typed nodes and attributed edges, answers questions from a two-hop subgraph, and periodically prunes nodes that score low on a weighted combination of recency, access frequency, degree centrality, and age. On LongMemEval, the graph does not outperform a flat vector baseline at a matched candidate-generation budget of five retrieval roots: token F1 is 0.417 against 0.468, and a paired bootstrap over 500 questions gives Δ= -0.050 (95\% CI [-0.085, -0.016]). The gap is widest on questions that require recalling a specific prior assistant turn, where judged correctness falls from 0.911 to 0.607, suggesting that decomposing a turn into entities discards the surface form these questions depend on. The forgetting module is more successful. Applied once to a persistent 27{,}021-node graph, it removes 9.8\% of nodes and 9.5\% of stored bytes; token F1 is unchanged (+0.001, 95\% CI [-0.015, +0.016]) and judged correctness falls by 1.6 points, with the 95\% interval bounding any loss at 3.8 points ([-0.038, +0.006]). Because our extractor is a single small model evaluated on one benchmark, these results characterise this extraction-based pipeline rather than graph-structured memory in general. Code: https://github.com/skhanzad/Selective-Amnesia

In node classification using graph neural networks (GNNs), a typical model generates logits for different class labels at each node. A softmax layer often outputs a label prediction based on the largest logit. We demonstrate that it is possible to infer hidden graph structural information from the dataset using these logits. We introduce the key notion of label non-uniformity, which is derived from the Wasserstein distance between the softmax distribution of the logits and the uniform distribution. We demonstrate that nodes with small label non-uniformity are harder to classify correctly. We theoretically analyze how the label non-uniformity varies across the graph, which provides insights into boosting the model performance: increasing training samples with high non-uniformity or dropping edges to reduce the maximal cut size of the node set of small non-uniformity. These mechanisms can be easily added to a base GNN model. Experimental results demonstrate that our approach improves the performance of many benchmark base models.

Graph generation is integral to various engineering and scientific disciplines. Nevertheless, existing methodologies tend to overlook the generation of edge attributes. However, we identify critical applications where edge attributes are essential, making prior methods potentially unsuitable in such contexts. Moreover, while trivial adaptations are available, empirical investigations reveal their limited efficacy as they do not properly model the interplay among graph components. To address this, we propose a joint score-based model of nodes and edges for graph generation that considers all graph components. Our approach offers two key novelties: (i) node and edge attributes are combined in an attention module that generates samples based on the two ingredients; and (ii) node, edge and adjacency information are mutually dependent during the graph diffusion process. We evaluate our method on challenging benchmarks involving real-world and synthetic datasets in which edge features are crucial. Additionally, we introduce a new synthetic dataset that incorporates edge values. Furthermore, we propose a novel application that greatly benefits from the method due to its nature: the generation of traffic scenes represented as graphs. Our method outperforms other graph generation methods, demonstrating a significant advantage in edge-related measures.

Long-context capabilities are essential for large language models (LLMs) to tackle complex and long-input tasks. Despite numerous efforts made to optimize LLMs for long contexts, challenges persist in robustly processing long inputs. In this paper, we introduce GraphReader, a graph-based agent system designed to handle long texts by structuring them into a graph and employing an agent to explore this graph autonomously. Upon receiving a question, the agent first undertakes a step-by-step analysis and devises a rational plan. It then invokes a set of predefined functions to read node content and neighbors, facilitating a coarse-to-fine exploration of the graph. Throughout the exploration, the agent continuously records new insights and reflects on current circumstances to optimize the process until it has gathered sufficient information to generate an answer. Experimental results on the LV-Eval dataset reveal that GraphReader, using a 4k context window, consistently outperforms GPT-4-128k across context lengths from 16k to 256k by a large margin. Additionally, our approach demonstrates superior performance on four challenging single-hop and multi-hop benchmarks.

The abundance of intestinal flora is closely related to human diseases, but diseases are not caused by a single gut microbe. Instead, they result from the complex interplay of numerous microbial entities. This intricate and implicit connection among gut microbes poses a significant challenge for disease prediction using abundance information from OTU data. Recently, several methods have shown potential in predicting corresponding diseases. However, these methods fail to learn the inner association among gut microbes from different hosts, leading to unsatisfactory performance. In this paper, we present a novel architecture, Unsupervised Multi-graph Merge Adversarial Network (UMMAN). UMMAN can obtain the embeddings of nodes in the Multi-Graph in an unsupervised scenario, so that it helps learn the multiplex association. Our method is the first to combine Graph Neural Network with the task of intestinal flora disease prediction. We employ complex relation-types to construct the Original-Graph and disrupt the relationships among nodes to generate corresponding Shuffled-Graph. We introduce the Node Feature Global Integration (NFGI) module to represent the global features of the graph. Furthermore, we design a joint loss comprising adversarial loss and hybrid attention loss to ensure that the real graph embedding aligns closely with the Original-Graph and diverges from the Shuffled-Graph. Comprehensive experiments on five classical OTU gut microbiome datasets demonstrate the effectiveness and stability of our method. (We will release our code soon.)

Effective treatment for rectal cancer relies on accurate lymph node metastasis (LNM) staging. However, radiological criteria based on lymph node (LN) size, shape and texture morphology have limited diagnostic accuracy. In this work, we investigate applying a Variational Autoencoder (VAE) as a feature encoder model to replace the large pre-trained Convolutional Neural Network (CNN) used in existing approaches. The motivation for using a VAE is that the generative model aims to reconstruct the images, so it directly encodes visual features and meaningful patterns across the data. This leads to a disentangled and structured latent space which can be more interpretable than a CNN. Models are deployed on an in-house MRI dataset with 168 patients who did not undergo neo-adjuvant treatment. The post-operative pathological N stage was used as the ground truth to evaluate model predictions. Our proposed model 'VAE-MLP' achieved state-of-the-art performance on the MRI dataset, with cross-validated metrics of AUC 0.86 +/- 0.05, Sensitivity 0.79 +/- 0.06, and Specificity 0.85 +/- 0.05. Code is available at: https://github.com/benkeel/Lymph_Node_Classification_MIUA.

Energy in Wireless Sensor Networks (WSNs) is critical to network lifetime and data delivery. However, the primary impediment to the durability and dependability of these sensor nodes is their short battery life. Currently, power-saving algorithms such as clustering and routing algorithms have improved energy efficiency in standard protocols. This paper proposes a clustering-based routing approach for creating an adaptive, energy-efficient mechanism. Our system employs a multi-step clustering strategy to select dynamic cluster heads (CH) with optimal energy distribution. We use Game Theory (GT) and Reinforcement Learning (RL) to optimize resource utilization. Modeling the network as a multi-agent RL problem using GT principles allows for self-clustering while optimizing sensor lifetime and energy balance. The proposed AI-powered CH-Finding algorithm improves network efficiency by preventing premature energy depletion in specific nodes while also ensuring uniform energy usage across the network. Our solution enables controlled power consumption, resulting in a deterministic network lifetime. This predictability lowers maintenance costs by reducing the need for node replacement. Furthermore, our proposed method prevents sensor nodes from disconnecting from the network by designating the sensor with the highest charge as an intermediary and using single-hop routing. This approach improves the energy efficiency and stability of Wireless Sensor Network (WSN) deployments.

Graph retrieval based on subgraph isomorphism has several real-world applications such as scene graph retrieval, molecular fingerprint detection and circuit design. Roy et al. [35] proposed IsoNet, a late interaction model for subgraph matching, which first computes the node and edge embeddings of each graph independently of paired graph and then computes a trainable alignment map. Here, we present IsoNet++, an early interaction graph neural network (GNN), based on several technical innovations. First, we compute embeddings of all nodes by passing messages within and across the two input graphs, guided by an injective alignment between their nodes. Second, we update this alignment in a lazy fashion over multiple rounds. Within each round, we run a layerwise GNN from scratch, based on the current state of the alignment. After the completion of one round of GNN, we use the last-layer embeddings to update the alignments, and proceed to the next round. Third, IsoNet++ incorporates a novel notion of node-pair partner interaction. Traditional early interaction computes attention between a node and its potential partners in the other graph, the attention then controlling messages passed across graphs. In contrast, we consider node pairs (not single nodes) as potential partners. Existence of an edge between the nodes in one graph and non-existence in the other provide vital signals for refining the alignment. Our experiments on several datasets show that the alignments get progressively refined with successive rounds, resulting in significantly better retrieval performance than existing methods. We demonstrate that all three innovations contribute to the enhanced accuracy. Our code and datasets are publicly available at https://github.com/structlearning/isonetpp.

Precision in identifying nanometer-scale device-killer defects is crucial in both semiconductor research and development as well as in production processes. The effectiveness of existing ML-based approaches in this context is largely limited by the scarcity of data, as the production of real semiconductor wafer data for training these models involves high financial and time costs. Moreover, the existing simulation methods fall short of replicating images with identical noise characteristics, surface roughness and stochastic variations at advanced nodes. We propose a method for generating synthetic semiconductor SEM images using a diffusion model within a limited data regime. In contrast to images generated through conventional simulation methods, SEM images generated through our proposed DL method closely resemble real SEM images, replicating their noise characteristics and surface roughness adaptively. Our main contributions, which are validated on three different real semiconductor datasets, are: i) proposing a patch-based generative framework utilizing DDPM to create SEM images with intended defect classes, addressing challenges related to class-imbalance and data insufficiency, ii) demonstrating generated synthetic images closely resemble real SEM images acquired from the tool, preserving all imaging conditions and metrology characteristics without any metadata supervision, iii) demonstrating a defect detector trained on generated defect dataset, either independently or combined with a limited real dataset, can achieve similar or improved performance on real wafer SEM images during validation/testing compared to exclusive training on a real defect dataset, iv) demonstrating the ability of the proposed approach to transfer defect types, critical dimensions, and imaging conditions from one specified CD/Pitch and metrology specifications to another, thereby highlighting its versatility.

Graph Foundation Models (GFMs) have achieved remarkable success in generalizing across diverse domains. However, they mainly focus on Text-Attributed Graphs (TAGs), leaving Multimodal-Attributed Graphs (MAGs) largely untapped. Developing Multimodal Graph Foundation Models (MGFMs) allows for leveraging the rich multimodal information in MAGs, and extends applicability to broader types of downstream tasks. While recent MGFMs integrate diverse modality information, our empirical investigation reveals two fundamental limitations of existing MGFMs: (1)they fail to explicitly model modality interaction, essential for capturing intricate cross-modal semantics beyond simple aggregation, and (2)they exhibit sub-optimal modality alignment, which is critical for bridging the significant semantic disparity between distinct modal spaces. To address these challenges, we propose PLANET (graPh topoLogy-aware modAlity iNteraction and alignmEnT), a novel framework employing a Divide-and-Conquer strategy to decouple modality interaction and alignment across distinct granularities. At the embedding granularity, (1)Embedding-wise Domain Gating (EDG) performs local semantic enrichment by adaptively infusing topology-aware cross-modal context, achieving modality interaction. At the node granularity, (2)Node-wise Discretization Retrieval (NDR) ensures global modality alignment by constructing a Discretized Semantic Representation Space (DSRS) to bridge modality gaps. Extensive experiments demonstrate that PLANET significantly outperforms state-of-the-art baselines across diverse graph-centric and multimodal generative tasks.

Scientific paper evaluation often involves not only assessing a manuscript itself, but also relating it to contemporaneous research and prior literature. However, existing LLM-based methods typically model these signals separately and lack a unified mechanism for aggregating review evidence across papers. We propose GraphReview, a graph-based LLM framework that formulates paper evaluation as inference-time graph evidence expansion over a semantic paper graph. The graph jointly captures intrinsic quality, synchronic links among contemporaneous papers, and diachronic links to prior work. LLMs are used to estimate node-level quality priors and generate edge-level comparative evidence through pairwise paper comparisons, while Personalized PageRank integrates these structured signals for quality ranking, decision prediction, and review generation. To produce higher-quality graph evidence, we propose reward-induced maximum likelihood objectives for training the LLM backbones. Experiments show that GraphReview consistently outperforms the strongest baseline, achieving average improvements of 29.7% on decision and ranking metrics, including gains of 23.7% in Accuracy and 57.6% in Spearman's ρ. It also produces higher-quality review texts and generalizes effectively across time periods and conference venues.

Devriendt and Lambiotte recently introduced the node resistance curvature, a notion of graph curvature based on the effective resistance matrix. In this paper, we begin the study of the behavior of the node resistance curvature under the operation of the Cartesian graph product. We study the natural question of global positivity of node resistance curvature of the Cartesian product of positively-curved graphs, and prove that, whenever m,nge3, the node resistance curvature of the interior vertices of a mtimes n grid is always nonpositive, while it is always nonnegative on the boundary of such grids. For completeness, we also prove a number of results on node resistance curvature in 2times n grids and exhibit a counterexample to a generalization. We also give generic bounds and suggest several further questions for future study.

Knowledge graph (KG) embedding has been used to benefit the diagnosis of animal diseases by analyzing electronic medical records (EMRs), such as notes and veterinary records. However, learning representations to capture entities and relations with literal information in KGs is challenging as the KGs show heterogeneous properties and various types of literal information. Meanwhile, the existing methods mostly aim to preserve graph structures surrounding target nodes without considering different types of literals, which could also carry significant information. In this paper, we propose a knowledge graph embedding model for the efficient diagnosis of animal diseases, which could learn various types of literal information and graph structure and fuse them into unified representations, namely LiteralKG. Specifically, we construct a knowledge graph that is built from EMRs along with literal information collected from various animal hospitals. We then fuse different types of entities and node feature information into unified vector representations through gate networks. Finally, we propose a self-supervised learning task to learn graph structure in pretext tasks and then towards various downstream tasks. Experimental results on link prediction tasks demonstrate that our model outperforms the baselines that consist of state-of-the-art models. The source code is available at https://github.com/NSLab-CUK/LiteralKG.

Familial amyloid-β (Aβ) variants alter aggregation kinetics, but their interaction with structural brain connectivity remains incompletely understood. We developed a mutation-aware mechanistic model coupling a coarse-grained monomer--oligomer--fibril aggregation--fragmentation system to graph diffusion on the 540-node Budapest Reference Connectome component. Experimental Aβ_{42} nucleation scores scaled primary nucleation rates for seven variants relative to wild type. Robustness was examined using mutation-score uncertainty, alternative kinetic mappings, global sensitivity analysis, seed and edge-weight perturbations, degree-preserving randomized connectomes, spatial propagation analysis, synthetic ABC-SMC parameter recovery, posterior prediction, and Chemical Langevin simulations. E22G showed the earliest threshold crossing and greatest cumulative oligomer burden, whereas A2V was delayed under the selected mapping. Mutation rankings persisted across tested network perturbations, although regional burden patterns depended on topology. Connectome distance from seed regions was associated with later oligomer arrival (Spearman ρapprox0.92). Under inferred parameter uncertainty, the mean timing-rank correlation was 0.990 and cumulative-burden ordering was preserved in every posterior draw, while exact peak-amplitude ordering was less stable. Stochastic ensemble medians retained the deterministic ordering despite overlap among trajectories. Within this proof-of-concept framework, mutation-dependent kinetics primarily influence aggregation timing and cumulative burden, while connectivity shapes spatial propagation. Nominal background rates, model-time units, and synthetic parameter recovery limit interpretation to mechanistic comparisons rather than clinically calibrated prediction.

Recent studies on Graph Convolutional Networks (GCNs) reveal that the initial node representations (i.e., the node representations before the first-time graph convolution) largely affect the final model performance. However, when learning the initial representation for a node, most existing work linearly combines the embeddings of node features, without considering the interactions among the features (or feature embeddings). We argue that when the node features are categorical, e.g., in many real-world applications like user profiling and recommender system, feature interactions usually carry important signals for predictive analytics. Ignoring them will result in suboptimal initial node representation and thus weaken the effectiveness of the follow-up graph convolution. In this paper, we propose a new GCN model named CatGCN, which is tailored for graph learning when the node features are categorical. Specifically, we integrate two ways of explicit interaction modeling into the learning of initial node representation, i.e., local interaction modeling on each pair of node features and global interaction modeling on an artificial feature graph. We then refine the enhanced initial node representations with the neighborhood aggregation-based graph convolution. We train CatGCN in an end-to-end fashion and demonstrate it on semi-supervised node classification. Extensive experiments on three tasks of user profiling (the prediction of user age, city, and purchase level) from Tencent and Alibaba datasets validate the effectiveness of CatGCN, especially the positive effect of performing feature interaction modeling before graph convolution.

This paper studies the online node classification problem under a transductive learning setting. Current methods either invert a graph kernel matrix with O(n^3) runtime and O(n^2) space complexity or sample a large volume of random spanning trees, thus are difficult to scale to large graphs. In this work, we propose an improvement based on the online relaxation technique introduced by a series of works (Rakhlin et al.,2012; Rakhlin and Sridharan, 2015; 2017). We first prove an effective regret O(n^{1+gamma}) when suitable parameterized graph kernels are chosen, then propose an approximate algorithm FastONL enjoying O(kn^{1+gamma}) regret based on this relaxation. The key of FastONL is a generalized local push method that effectively approximates inverse matrix columns and applies to a series of popular kernels. Furthermore, the per-prediction cost is O(vol({S})log 1/epsilon) locally dependent on the graph with linear memory cost. Experiments show that our scalable method enjoys a better tradeoff between local and global consistency.

Skeleton-based action recognition has attracted considerable attention due to its compact representation of the human body's skeletal sructure. Many recent methods have achieved remarkable performance using graph convolutional networks (GCNs) and convolutional neural networks (CNNs), which extract spatial and temporal features, respectively. Although spatial and temporal dependencies in the human skeleton have been explored separately, spatio-temporal dependency is rarely considered. In this paper, we propose the Spatio-Temporal Curve Network (STC-Net) to effectively leverage the spatio-temporal dependency of the human skeleton. Our proposed network consists of two novel elements: 1) The Spatio-Temporal Curve (STC) module; and 2) Dilated Kernels for Graph Convolution (DK-GC). The STC module dynamically adjusts the receptive field by identifying meaningful node connections between every adjacent frame and generating spatio-temporal curves based on the identified node connections, providing an adaptive spatio-temporal coverage. In addition, we propose DK-GC to consider long-range dependencies, which results in a large receptive field without any additional parameters by applying an extended kernel to the given adjacency matrices of the graph. Our STC-Net combines these two modules and achieves state-of-the-art performance on four skeleton-based action recognition benchmarks.

Graph convolutional networks (GCNs) are the most commonly used methods for skeleton-based action recognition and have achieved remarkable performance. Generating adjacency matrices with semantically meaningful edges is particularly important for this task, but extracting such edges is challenging problem. To solve this, we propose a hierarchically decomposed graph convolutional network (HD-GCN) architecture with a novel hierarchically decomposed graph (HD-Graph). The proposed HD-GCN effectively decomposes every joint node into several sets to extract major structurally adjacent and distant edges, and uses them to construct an HD-Graph containing those edges in the same semantic spaces of a human skeleton. In addition, we introduce an attention-guided hierarchy aggregation (A-HA) module to highlight the dominant hierarchical edge sets of the HD-Graph. Furthermore, we apply a new six-way ensemble method, which uses only joint and bone stream without any motion stream. The proposed model is evaluated and achieves state-of-the-art performance on four large, popular datasets. Finally, we demonstrate the effectiveness of our model with various comparative experiments.

Graph generation with Machine Learning is an open problem with applications in various research fields. In this work, we propose to cast the generative process of a graph into a sequential one, relying on a node ordering procedure. We use this sequential process to design a novel generative model composed of two recurrent neural networks that learn to predict the edges of graphs: the first network generates one endpoint of each edge, while the second network generates the other endpoint conditioned on the state of the first. We test our approach extensively on five different datasets, comparing with two well-known baselines coming from graph literature, and two recurrent approaches, one of which holds state of the art performances. Evaluation is conducted considering quantitative and qualitative characteristics of the generated samples. Results show that our approach is able to yield novel, and unique graphs originating from very different distributions, while retaining structural properties very similar to those in the training sample. Under the proposed evaluation framework, our approach is able to reach performances comparable to the current state of the art on the graph generation task.

Node features and structural information of a graph are both crucial for semi-supervised node classification problems. A variety of graph neural network (GNN) based approaches have been proposed to tackle these problems, which typically determine output labels through feature aggregation. This can be problematic, as it implies conditional independence of output nodes given hidden representations, despite their direct connections in the graph. To learn the direct influence among output nodes in a graph, we propose the Explicit Pairwise Factorized Graph Neural Network (EPFGNN), which models the whole graph as a partially observed Markov Random Field. It contains explicit pairwise factors to model output-output relations and uses a GNN backbone to model input-output relations. To balance model complexity and expressivity, the pairwise factors have a shared component and a separate scaling coefficient for each edge. We apply the EM algorithm to train our model, and utilize a star-shaped piecewise likelihood for the tractable surrogate objective. We conduct experiments on various datasets, which shows that our model can effectively improve the performance for semi-supervised node classification on graphs.

We present MOFA, an open-source generative AI (GenAI) plus simulation workflow for high-throughput generation of metal-organic frameworks (MOFs) on large-scale high-performance computing (HPC) systems. MOFA addresses key challenges in integrating GPU-accelerated computing for GPU-intensive GenAI tasks, including distributed training and inference, alongside CPU- and GPU-optimized tasks for screening and filtering AI-generated MOFs using molecular dynamics, density functional theory, and Monte Carlo simulations. These heterogeneous tasks are unified within an online learning framework that optimizes the utilization of available CPU and GPU resources across HPC systems. Performance metrics from a 450-node (14,400 AMD Zen 3 CPUs + 1800 NVIDIA A100 GPUs) supercomputer run demonstrate that MOFA achieves high-throughput generation of novel MOF structures, with CO_2 adsorption capacities ranking among the top 10 in the hypothetical MOF (hMOF) dataset. Furthermore, the production of high-quality MOFs exhibits a linear relationship with the number of nodes utilized. The modular architecture of MOFA will facilitate its integration into other scientific applications that dynamically combine GenAI with large-scale simulations.

In recent years, graph representation learning has undergone a paradigm shift, driven by the emergence and proliferation of graph neural networks (GNNs) and their heterogeneous counterparts. Heterogeneous GNNs have shown remarkable success in extracting low-dimensional embeddings from complex graphs that encompass diverse entity types and relationships. While meta-path-based techniques have long been recognized for their ability to capture semantic affinities among nodes, their dependence on manual specification poses a significant limitation. In contrast, matrix-focused methods accelerate processing by utilizing structural cues but often overlook contextual richness. In this paper, we challenge the current paradigm by introducing ontology as a fundamental semantic primitive within complex graphs. Our goal is to integrate the strengths of both matrix-centric and meta-path-based approaches into a unified framework. We propose perturbation Ontology-based Graph Attention Networks (POGAT), a novel methodology that combines ontology subgraphs with an advanced self-supervised learning paradigm to achieve a deep contextual understanding. The core innovation of POGAT lies in our enhanced homogeneous perturbing scheme designed to generate rigorous negative samples, encouraging the model to explore minimal contextual features more thoroughly. Through extensive empirical evaluations, we demonstrate that POGAT significantly outperforms state-of-the-art baselines, achieving a groundbreaking improvement of up to 10.78\% in F1-score for the critical task of link prediction and 12.01\% in Micro-F1 for the critical task of node classification.

Despite Graph Neural Networks (GNNs) have achieved prominent success in many graph-based learning problem, such as credit risk assessment in financial networks and fake news detection in social networks. However, the trained GNNs still make errors and these errors may cause serious negative impact on society. Model editing, which corrects the model behavior on wrongly predicted target samples while leaving model predictions unchanged on unrelated samples, has garnered significant interest in the fields of computer vision and natural language processing. However, model editing for graph neural networks (GNNs) is rarely explored, despite GNNs' widespread applicability. To fill the gap, we first observe that existing model editing methods significantly deteriorate prediction accuracy (up to 50% accuracy drop) in GNNs while a slight accuracy drop in multi-layer perception (MLP). The rationale behind this observation is that the node aggregation in GNNs will spread the editing effect throughout the whole graph. This propagation pushes the node representation far from its original one. Motivated by this observation, we propose Editable Graph Neural Networks (EGNN), a neighbor propagation-free approach to correct the model prediction on misclassified nodes. Specifically, EGNN simply stitches an MLP to the underlying GNNs, where the weights of GNNs are frozen during model editing. In this way, EGNN disables the propagation during editing while still utilizing the neighbor propagation scheme for node prediction to obtain satisfactory results. Experiments demonstrate that EGNN outperforms existing baselines in terms of effectiveness (correcting wrong predictions with lower accuracy drop), generalizability (correcting wrong predictions for other similar nodes), and efficiency (low training time and memory) on various graph datasets.

The problem of predicting node properties (e.g., node classes) in graphs has received significant attention due to its broad range of applications. Graphs from real-world datasets often evolve over time, with newly emerging edges and dynamically changing node properties, posing a significant challenge for this problem. In response, temporal graph neural networks (TGNNs) have been developed to predict dynamic node properties from a stream of emerging edges. However, our analysis reveals that most TGNN-based methods are (a) far less effective without proper node features and, due to their complex model architectures, (b) vulnerable to distribution shifts. In this paper, we propose SPLASH, a simple yet powerful method for predicting node properties on edge streams under distribution shifts. Our key contributions are as follows: (1) we propose feature augmentation methods and an automatic feature selection method for edge streams, which improve the effectiveness of TGNNs, (2) we propose a lightweight MLP-based TGNN architecture that is highly efficient and robust under distribution shifts, and (3) we conduct extensive experiments to evaluate the accuracy, efficiency, generalization, and qualitative performance of the proposed method and its competitors on dynamic node classification, dynamic anomaly detection, and node affinity prediction tasks across seven real-world datasets.

Graph Neural Networks (GNNs) have shown great promise in tasks like node and graph classification, but they often struggle to generalize, particularly to unseen or out-of-distribution (OOD) data. These challenges are exacerbated when training data is limited in size or diversity. To address these issues, we introduce a theoretical framework using Rademacher complexity to compute a regret bound on the generalization error and then characterize the effect of data augmentation. This framework informs the design of GRATIN, an efficient graph data augmentation algorithm leveraging the capability of Gaussian Mixture Models (GMMs) to approximate any distribution. Our approach not only outperforms existing augmentation techniques in terms of generalization but also offers improved time complexity, making it highly suitable for real-world applications.

Large language model (LLM) based agentic workflows have become a popular paradigm for coordinating multiple specialized agents to solve complex tasks. To improve serving efficiency, existing LLM systems employ prefix caching to reuse key-value (KV) tensors corresponding to agents' fixed prompts, thereby avoiding redundant computation across repeated invocations. However, current systems typically evict KV caches using a Least Recently Used (LRU) policy, which fails to anticipate future agent usage and often discards KV caches shortly before their reuse. This leads to frequent cache misses and substantial recomputation or swapping overhead. We present KVFlow, a workflow-aware KV cache management framework tailored for agentic workloads. KVFlow abstracts the agent execution schedule as an Agent Step Graph and assigns each agent a steps-to-execution value that estimates its temporal proximity to future activation. These values guide a fine-grained eviction policy at the KV node level, allowing KVFlow to preserve entries likely to be reused and efficiently manage shared prefixes in tree-structured caches. Moreover, KVFlow introduces a fully overlapped KV prefetching mechanism, which proactively loads required tensors from CPU to GPU in background threads for agents scheduled in the next step, thereby avoiding cache miss stalls during generation. Compared to SGLang with hierarchical radix cache, KVFlow achieves up to 1.83times speedup for single workflows with large prompts, and up to 2.19times speedup for scenarios with many concurrent workflows.

Recent advancements in graph neural networks (GNNs) have significantly enhanced the prediction of material properties by modeling crystal structures as graphs. However, GNNs often struggle to capture global structural characteristics, such as crystal systems, limiting their predictive performance. To overcome this issue, we propose CAST, a cross-attention-based multimodal model that integrates graph representations with textual descriptions of materials, effectively preserving critical structural and compositional information. Unlike previous approaches, such as CrysMMNet and MultiMat, which rely on aggregated material-level embeddings, CAST leverages cross-attention mechanisms to combine fine-grained graph node-level and text token-level features. Additionally, we introduce a masked node prediction pretraining strategy that further enhances the alignment between node and text embeddings. Our experimental results demonstrate that CAST outperforms existing baseline models across four key material properties-formation energy, band gap, bulk modulus, and shear modulus-with average relative MAE improvements ranging from 10.2% to 35.7%. Analysis of attention maps confirms the importance of pretraining in effectively aligning multimodal representations. This study underscores the potential of multimodal learning frameworks for developing more accurate and globally informed predictive models in materials science.

Subgraph-based graph representation learning (SGRL) has recently emerged as a powerful tool in many prediction tasks on graphs due to its advantages in model expressiveness and generalization ability. Most previous SGRL models face computational challenges associated with the high cost of subgraph extraction for each training or test query. Recently, SUREL was proposed to accelerate SGRL, which samples random walks offline and joins these walks online as a proxy of subgraph for representation learning. Thanks to the reusability of sampled walks across different queries, SUREL achieves state-of-the-art performance in terms of scalability and prediction accuracy. However, SUREL still suffers from high computational overhead caused by node duplication in sampled walks. In this work, we propose a novel framework SUREL+ that upgrades SUREL by using node sets instead of walks to represent subgraphs. This set-based representation eliminates repeated nodes by definition but can also be irregular in size. To address this issue, we design a customized sparse data structure to efficiently store and access node sets and provide a specialized operator to join them in parallel batches. SUREL+ is modularized to support multiple types of set samplers, structural features, and neural encoders to complement the structural information loss after the reduction from walks to sets. Extensive experiments have been performed to validate SUREL+ in the prediction tasks of links, relation types, and higher-order patterns. SUREL+ achieves 3-11times speedups of SUREL while maintaining comparable or even better prediction performance; compared to other SGRL baselines, SUREL+ achieves sim20times speedups and significantly improves the prediction accuracy.

Prime Video regularly conducts load tests to simulate the viewer traffic spikes seen during live events such as Thursday Night Football as well as video-on-demand (VOD) events such as Rings of Power. While these stress tests validate system capacity, they can sometimes miss service behaviors unique to real event traffic. We present a graph-based anomaly detection system that identifies under-represented services using unsupervised node-level graph embeddings. Built on a GCN-GAE, our approach learns structural representations from directed, weighted service graphs at minute-level resolution and flags anomalies based on cosine similarity between load test and event embeddings. The system identifies incident-related services that are documented and demonstrates early detection capability. We also introduce a preliminary synthetic anomaly injection framework for controlled evaluation that show promising precision (96%) and low false positive rate (0.08%), though recall (58%) remains limited under conservative propagation assumptions. This framework demonstrates practical utility within Prime Video while also surfacing methodological lessons and directions, providing a foundation for broader application across microservice ecosystems.

The robustness of a model for real-world deployment is decided by how well it performs on unseen data and distinguishes between in-domain and out-of-domain samples. Visual document classifiers have shown impressive performance on in-distribution test sets. However, they tend to have a hard time correctly classifying and differentiating out-of-distribution examples. Image-based classifiers lack the text component, whereas multi-modality transformer-based models face the token serialization problem in visual documents due to their diverse layouts. They also require a lot of computing power during inference, making them impractical for many real-world applications. We propose, GVdoc, a graph-based document classification model that addresses both of these challenges. Our approach generates a document graph based on its layout, and then trains a graph neural network to learn node and graph embeddings. Through experiments, we show that our model, even with fewer parameters, outperforms state-of-the-art models on out-of-distribution data while retaining comparable performance on the in-distribution test set.

Planning with a learned model is arguably a key component of intelligence. There are several challenges in realizing such a component in large-scale reinforcement learning (RL) problems. One such challenge is dealing effectively with continuous action spaces when using tree-search planning (e.g., it is not feasible to consider every action even at just the root node of the tree). In this paper we present a method for selecting affordances useful for planning -- for learning which small number of actions/options from a continuous space of actions/options to consider in the tree-expansion process during planning. We consider affordances that are goal-and-state-conditional mappings to actions/options as well as unconditional affordances that simply select actions/options available in all states. Our selection method is gradient based: we compute gradients through the planning procedure to update the parameters of the function that represents affordances. Our empirical work shows that it is feasible to learn to select both primitive-action and option affordances, and that simultaneously learning to select affordances and planning with a learned value-equivalent model can outperform model-free RL.

Code pre-trained models (CodePTMs) have recently demonstrated significant success in code intelligence. To interpret these models, some probing methods have been applied. However, these methods fail to consider the inherent characteristics of codes. In this paper, to address the problem, we propose a novel probing method CAT-probing to quantitatively interpret how CodePTMs attend code structure. We first denoise the input code sequences based on the token types pre-defined by the compilers to filter those tokens whose attention scores are too small. After that, we define a new metric CAT-score to measure the commonality between the token-level attention scores generated in CodePTMs and the pair-wise distances between corresponding AST nodes. The higher the CAT-score, the stronger the ability of CodePTMs to capture code structure. We conduct extensive experiments to integrate CAT-probing with representative CodePTMs for different programming languages. Experimental results show the effectiveness of CAT-probing in CodePTM interpretation. Our codes and data are publicly available at https://github.com/nchen909/CodeAttention.

Parse graphs of the human body can be obtained in the human brain to help humans complete the human pose estimation (HPE). It contains a hierarchical structure, like a tree structure, and context relations among nodes. Many researchers pre-design the parse graph of body structure, and then design framework for HPE. However, these frameworks are difficulty adapting when encountering situations that differ from the preset human structure. Different from them, we regard the feature map as a whole, similarly to human body, so the feature map can be optimized based on parse graphs and each node feature is learned implicitly instead of explicitly, which means it can flexibly respond to different human body structure. In this paper, we design the Refinement Module based on the Parse Graph of feature map (RMPG), which includes two stages: top-down decomposition and bottom-up combination. In the top-down decomposition stage, the feature map is decomposed into multiple sub-feature maps along the channel and their context relations are calculated to obtain their respective context information. In the bottom-up combination stage, the sub-feature maps and their context information are combined to obtain refined sub-feature maps, and then these refined sub-feature maps are concatenated to obtain the refined feature map. Additionally ,we design a top-down framework by using multiple RMPG modules for HPE, some of which are supervised to obtain context relations among body parts. Our framework achieves excellent results on the COCO keypoint detection, CrowdPose and MPII human pose datasets. More importantly, our experiments also demonstrate the effectiveness of RMPG on different methods, including SimpleBaselines, Hourglass, and ViTPose.

Document retrieval is a core component of question-answering systems, as it enables conditioning answer generation on new and large-scale corpora. While effective, the standard practice of encoding documents into high-dimensional embeddings for similarity search entails large memory and compute footprints, and also makes it hard to inspect the inner workings of the system. In this paper, we propose a tree-based method for organizing and representing reference documents at various granular levels, which offers the flexibility to balance cost and utility, and eases the inspection of the corpus content and retrieval operations. Our method, called ReTreever, jointly learns a routing function per internal node of a binary tree such that query and reference documents are assigned to similar tree branches, hence directly optimizing for retrieval performance. Our evaluations show that ReTreever generally preserves full representation accuracy. Its hierarchical structure further provides strong coarse representations and enhances transparency by indirectly learning meaningful semantic groupings. Among hierarchical retrieval methods, ReTreever achieves the best retrieval accuracy at the lowest latency, proving that this family of techniques can be viable in practical applications.

With the rapid advancement of generative models, general-purpose generation has gained increasing attention as a promising approach to unify diverse tasks across modalities within a single system. Despite this progress, existing open-source frameworks often remain fragile and struggle to support complex real-world applications due to the lack of structured workflow planning and execution-level feedback. To address these limitations, we present ComfyMind, a collaborative AI system designed to enable robust and scalable general-purpose generation, built on the ComfyUI platform. ComfyMind introduces two core innovations: Semantic Workflow Interface (SWI) that abstracts low-level node graphs into callable functional modules described in natural language, enabling high-level composition and reducing structural errors; Search Tree Planning mechanism with localized feedback execution, which models generation as a hierarchical decision process and allows adaptive correction at each stage. Together, these components improve the stability and flexibility of complex generative workflows. We evaluate ComfyMind on three public benchmarks: ComfyBench, GenEval, and Reason-Edit, which span generation, editing, and reasoning tasks. Results show that ComfyMind consistently outperforms existing open-source baselines and achieves performance comparable to GPT-Image-1. ComfyMind paves a promising path for the development of open-source general-purpose generative AI systems. Project page: https://github.com/LitaoGuo/ComfyMind

Cross-View Geo-Localisation within urban regions is challenging in part due to the lack of geo-spatial structuring within current datasets and techniques. We propose utilising graph representations to model sequences of local observations and the connectivity of the target location. Modelling as a graph enables generating previously unseen sequences by sampling with new parameter configurations. To leverage this newly available information, we propose a GNN-based architecture, producing spatially strong embeddings and improving discriminability over isolated image embeddings. We outline SpaGBOL, introducing three novel contributions. 1) The first graph-structured dataset for Cross-View Geo-Localisation, containing multiple streetview images per node to improve generalisation. 2) Introducing GNNs to the problem, we develop the first system that exploits the correlation between node proximity and feature similarity. 3) Leveraging the unique properties of the graph representation - we demonstrate a novel retrieval filtering approach based on neighbourhood bearings. SpaGBOL achieves state-of-the-art accuracies on the unseen test graph - with relative Top-1 retrieval improvements on previous techniques of 11%, and 50% when filtering with Bearing Vector Matching on the SpaGBOL dataset.

Graph Neural Networks (GNNs) are widely used today in recommendation systems, fraud detection, and node/link classification tasks. Real world GNNs continue to scale in size and require a large memory footprint for storing graphs and embeddings that often exceed the memory capacities of the target GPUs used for training. To address limited memory capacities, traditional GNN training approaches use graph partitioning and sharding techniques to scale up across multiple GPUs within a node and/or scale out across multiple nodes. However, this approach suffers from the high computational costs of graph partitioning algorithms and inefficient communication across GPUs. To address these overheads, we propose Large-scale Storage-based Multi-GPU GNN framework (LSM-GNN), a storagebased approach to train GNN models that utilizes a novel communication layer enabling GPU software caches to function as a system-wide shared cache with low overheads.LSM-GNN incorporates a hybrid eviction policy that intelligently manages cache space by using both static and dynamic node information to significantly enhance cache performance. Furthermore, we introduce the Preemptive Victim-buffer Prefetcher (PVP), a mechanism for prefetching node feature data from a Victim Buffer located in CPU pinned-memory to further reduce the pressure on the storage devices. Experimental results show that despite the lower compute capabilities and memory capacities, LSM-GNN in a single node with two GPUs offers superior performance over two-node-four-GPU Dist-DGL baseline and provides up to 3.75x speed up on end-to-end epoch time while running large-scale GNN training

The recent surge in contrast-based graph self-supervised learning has prominently featured an intensified exploration of spectral cues. Spectral augmentation, which involves modifying a graph's spectral properties such as eigenvalues or eigenvectors, is widely believed to enhance model performance. However, an intriguing paradox emerges, as methods grounded in seemingly conflicting assumptions regarding the spectral domain demonstrate notable enhancements in learning performance. Through extensive empirical studies, we find that simple edge perturbations - random edge dropping for node-level and random edge adding for graph-level self-supervised learning - consistently yield comparable or superior performance while being significantly more computationally efficient. This suggests that the computational overhead of sophisticated spectral augmentations may not justify their practical benefits. Our theoretical analysis of the InfoNCE loss bounds for shallow GNNs further supports this observation. The proposed insights represent a significant leap forward in the field, potentially refining the understanding and implementation of graph self-supervised learning.

In the conventional cellular system, devices are not allowed to communicate directly with each other in the licensed cellular bandwidth and all communications take place through the base stations. The users requirements has led the technology to become fast and faster. Multimedia rich data exchange, fast service, high quality voice calls, newer and more demanding applications, information at fingertips, everything requires technology and communication between devices. A constant need to increase network capacity for meeting the users growing demands has led to the growth of cellular communication networks from the first generation(1G) to the fifth generation(5G). There will be crores of connected devices in the coming future . A large number of connections are going to be heterogeneous, demanding lesser delays, higher data rates, superior throughput and enhanced system capacity. The available spectrum resources are limited and has to be flexibly used by mobile network operators to cope with the rising demands. An emerging facilitator of the upcoming high data rate demanding next-generation networks are device-to-device(D2D) communication. This paper has developed a model that establishes Device-to-Device (D2D) communication between two end-users without involving the eNB (evolved Node B). We have sharded the UEs and CUs based on the criteria of DISTANCE. To do so, we used the K-means clustering method.

Graph representation learning is a fundamental task in various applications that strives to learn low-dimensional embeddings for nodes that can preserve graph topology information. However, many existing methods focus on static graphs while ignoring evolving graph patterns. Inspired by the success of graph convolutional networks(GCNs) in static graph embedding, we propose a novel k-core based temporal graph convolutional network, the CTGCN, to learn node representations for dynamic graphs. In contrast to previous dynamic graph embedding methods, CTGCN can preserve both local connective proximity and global structural similarity while simultaneously capturing graph dynamics. In the proposed framework, the traditional graph convolution is generalized into two phases, feature transformation and feature aggregation, which gives the CTGCN more flexibility and enables the CTGCN to learn connective and structural information under the same framework. Experimental results on 7 real-world graphs demonstrate that the CTGCN outperforms existing state-of-the-art graph embedding methods in several tasks, including link prediction and structural role classification. The source code of this work can be obtained from https://github.com/jhljx/CTGCN.

We present H-Node Adversarial Noise Cancellation (H-Node ANC), a mechanistic framework that identifies, exploits, and defends hallucination representations in transformer-based large language models (LLMs) at the level of individual hidden-state dimensions. A logistic regression probe trained on last-token hidden states localizes hallucination signal to a small set of high-variance dimensions -- termed Hallucination Nodes (H-Nodes) -- with probe AUC reaching 0.90 across four architectures. A white-box adversarial attack amplifies these dimensions at inference time via a real-time forward hook, achieving a selectivity of 3.02x with less than 10% visibility to the defender. Adaptive ANC defense suppresses H-Node excess in-pass using confidence-weighted cancellation, reducing grounded activation drift by 33-42% over static cancellation. A dynamic iterative extension that re-ranks cancellation targets across successive passes recovers up to 0.69 robustness from a single-pass baseline of 8%. All contributions are validated on OPT-125M, Phi-3-mini-4k-instruct, LLaMA-3-8B-Instruct, and Mistral-7B-Instruct-v0.3 (125M-8B parameters). Perplexity impact is surgical (<5%) and MMLU degradation is at most 3%, confirming that the defense does not impair general reasoning capability.

Factorisation-based Models (FMs), such as DistMult, have enjoyed enduring success for Knowledge Graph Completion (KGC) tasks, often outperforming Graph Neural Networks (GNNs). However, unlike GNNs, FMs struggle to incorporate node features and generalise to unseen nodes in inductive settings. Our work bridges the gap between FMs and GNNs by proposing ReFactor GNNs. This new architecture draws upon both modelling paradigms, which previously were largely thought of as disjoint. Concretely, using a message-passing formalism, we show how FMs can be cast as GNNs by reformulating the gradient descent procedure as message-passing operations, which forms the basis of our ReFactor GNNs. Across a multitude of well-established KGC benchmarks, our ReFactor GNNs achieve comparable transductive performance to FMs, and state-of-the-art inductive performance while using an order of magnitude fewer parameters.

Recent progress in Graph Neural Networks has resulted in wide adoption by many applications, including recommendation systems. The reason for Graph Neural Networks' superiority over other approaches is that many problems in recommendation systems can be naturally modeled as graphs, where nodes can be either users or items and edges represent preference relationships. In current Graph Neural Network approaches, nodes are represented with a static vector learned at training time. This static vector might only be suitable to capture some of the nuances of users or items they define. To overcome this limitation, we propose using a recently proposed model inspired by category theory: Sheaf Neural Networks. Sheaf Neural Networks, and its connected Laplacian, can address the previous problem by associating every node (and edge) with a vector space instead than a single vector. The vector space representation is richer and allows picking the proper representation at inference time. This approach can be generalized for different related tasks on graphs and achieves state-of-the-art performance in terms of F1-Score@N in collaborative filtering and Hits@20 in link prediction. For collaborative filtering, the approach is evaluated on the MovieLens 100K with a 5.1% improvement, on MovieLens 1M with a 5.4% improvement and on Book-Crossing with a 2.8% improvement, while for link prediction on the ogbl-ddi dataset with a 1.6% refinement with respect to the respective baselines.

For supervised learning with tabular data, decision tree ensembles produced via boosting techniques generally dominate real-world applications involving iid training/test sets. However for graph data where the iid assumption is violated due to structured relations between samples, it remains unclear how to best incorporate this structure within existing boosting pipelines. To this end, we propose a generalized framework for iterating boosting with graph propagation steps that share node/sample information across edges connecting related samples. Unlike previous efforts to integrate graph-based models with boosting, our approach is anchored in a principled meta loss function such that provable convergence can be guaranteed under relatively mild assumptions. Across a variety of non-iid graph datasets with tabular node features, our method achieves comparable or superior performance than both tabular and graph neural network models, as well as existing hybrid strategies that combine the two. Beyond producing better predictive performance than recently proposed graph models, our proposed techniques are easy to implement, computationally more efficient, and enjoy stronger theoretical guarantees (which make our results more reproducible).

In this work, we explore the use of a novel neural network architecture, the Kolmogorov-Arnold Networks (KANs) as feature extractors for sensor-based (specifically IMU) Human Activity Recognition (HAR). Where conventional networks perform a parameterized weighted sum of the inputs at each node and then feed the result into a statically defined nonlinearity, KANs perform non-linear computations represented by B-SPLINES on the edges leading to each node and then just sum up the inputs at the node. Instead of learning weights, the system learns the spline parameters. In the original work, such networks have been shown to be able to more efficiently and exactly learn sophisticated real valued functions e.g. in regression or PDE solution. We hypothesize that such an ability is also advantageous for computing low-level features for IMU-based HAR. To this end, we have implemented KAN as the feature extraction architecture for IMU-based human activity recognition tasks, including four architecture variations. We present an initial performance investigation of the KAN feature extractor on four public HAR datasets. It shows that the KAN-based feature extractor outperforms CNN-based extractors on all datasets while being more parameter efficient.

Criminals have become increasingly experienced in using cryptocurrencies, such as Bitcoin, for money laundering. The use of cryptocurrencies can hide criminal identities and transfer hundreds of millions of dollars of dirty funds through their criminal digital wallets. However, this is considered a paradox because cryptocurrencies are goldmines for open-source intelligence, giving law enforcement agencies more power when conducting forensic analyses. This paper proposed Inspection-L, a graph neural network (GNN) framework based on a self-supervised Deep Graph Infomax (DGI) and Graph Isomorphism Network (GIN), with supervised learning algorithms, namely Random Forest (RF), to detect illicit transactions for anti-money laundering (AML). To the best of our knowledge, our proposal is the first to apply self-supervised GNNs to the problem of AML in Bitcoin. The proposed method was evaluated on the Elliptic dataset and shows that our approach outperforms the state-of-the-art in terms of key classification metrics, which demonstrates the potential of self-supervised GNN in the detection of illicit cryptocurrency transactions.

We propose a filtering feature selection framework that considers subsets of features as paths in a graph, where a node is a feature and an edge indicates pairwise (customizable) relations among features, dealing with relevance and redundancy principles. By two different interpretations (exploiting properties of power series of matrices and relying on Markov chains fundamentals) we can evaluate the values of paths (i.e., feature subsets) of arbitrary lengths, eventually go to infinite, from which we dub our framework Infinite Feature Selection (Inf-FS). Going to infinite allows to constrain the computational complexity of the selection process, and to rank the features in an elegant way, that is, considering the value of any path (subset) containing a particular feature. We also propose a simple unsupervised strategy to cut the ranking, so providing the subset of features to keep. In the experiments, we analyze diverse settings with heterogeneous features, for a total of 11 benchmarks, comparing against 18 widely-known comparative approaches. The results show that Inf-FS behaves better in almost any situation, that is, when the number of features to keep are fixed a priori, or when the decision of the subset cardinality is part of the process.

Electronic Health Records (EHR) are high-dimensional data with implicit connections among thousands of medical concepts. These connections, for instance, the co-occurrence of diseases and lab-disease correlations can be informative when only a subset of these variables is documented by the clinician. A feasible approach to improving the representation learning of EHR data is to associate relevant medical concepts and utilize these connections. Existing medical ontologies can be the reference for EHR structures, but they place numerous constraints on the data source. Recent progress on graph neural networks (GNN) enables end-to-end learning of topological structures for non-grid or non-sequential data. However, there are problems to be addressed on how to learn the medical graph adaptively and how to understand the effect of the medical graph on representation learning. In this paper, we propose a variationally regularized encoder-decoder graph network that achieves more robustness in graph structure learning by regularizing node representations. Our model outperforms the existing graph and non-graph based methods in various EHR predictive tasks based on both public data and real-world clinical data. Besides the improvements in empirical experiment performances, we provide an interpretation of the effect of variational regularization compared to standard graph neural network, using singular value analysis.

Physically Based Rendering (PBR) materials play a crucial role in modern graphics, enabling photorealistic rendering across diverse environment maps. Developing an effective and efficient algorithm that is capable of automatically generating high-quality PBR materials rather than RGB texture for 3D meshes can significantly streamline the 3D content creation. Most existing methods leverage pre-trained 2D diffusion models for multi-view image synthesis, which often leads to severe inconsistency between the generated textures and input 3D meshes. This paper presents TexGaussian, a novel method that uses octant-aligned 3D Gaussian Splatting for rapid PBR material generation. Specifically, we place each 3D Gaussian on the finest leaf node of the octree built from the input 3D mesh to render the multi-view images not only for the albedo map but also for roughness and metallic. Moreover, our model is trained in a regression manner instead of diffusion denoising, capable of generating the PBR material for a 3D mesh in a single feed-forward process. Extensive experiments on publicly available benchmarks demonstrate that our method synthesizes more visually pleasing PBR materials and runs faster than previous methods in both unconditional and text-conditional scenarios, exhibiting better consistency with the given geometry. Our code and trained models are available at https://3d-aigc.github.io/TexGaussian.

Ear biometrics offer a stable and contactless modality for identity recognition, yet their effectiveness remains limited by the scarcity of annotated data and significant intra-class variability. Existing methods typically extract identity features from individual impressions in isolation, restricting their ability to capture consistent and discriminative representations. To overcome these limitations, a few-shot learning framework, ProtoN, is proposed to jointly process multiple impressions of an identity using a graph-based approach. Each impression is represented as a node in a class-specific graph, alongside a learnable prototype node that encodes identity-level information. This graph is processed by a Prototype Graph Neural Network (PGNN) layer, specifically designed to refine both impression and prototype representations through a dual-path message-passing mechanism. To further enhance discriminative power, the PGNN incorporates a cross-graph prototype alignment strategy that improves class separability by enforcing intra-class compactness while maintaining inter-class distinction. Additionally, a hybrid loss function is employed to balance episodic and global classification objectives, thereby improving the overall structure of the embedding space. Extensive experiments on five benchmark ear datasets demonstrate that ProtoN achieves state-of-the-art performance, with Rank-1 identification accuracy of up to 99.60% and an Equal Error Rate (EER) as low as 0.025, showing the effectiveness for few-shot ear recognition under limited data conditions.

Monte Carlo Tree Search (MCTS)-based algorithms, such as MuZero and its derivatives, have achieved widespread success in various decision-making domains. These algorithms employ the reanalyze process to enhance sample efficiency from stale data, albeit at the expense of significant wall-clock time consumption. To address this issue, we propose a general approach named ReZero to boost tree search operations for MCTS-based algorithms. Specifically, drawing inspiration from the one-armed bandit model, we reanalyze training samples through a backward-view reuse technique which uses the value estimation of a certain child node to save the corresponding sub-tree search time. To further adapt to this design, we periodically reanalyze the entire buffer instead of frequently reanalyzing the mini-batch. The synergy of these two designs can significantly reduce the search cost and meanwhile guarantee or even improve performance, simplifying both data collecting and reanalyzing. Experiments conducted on Atari environments, DMControl suites and board games demonstrate that ReZero substantially improves training speed while maintaining high sample efficiency. The code is available as part of the LightZero MCTS benchmark at https://github.com/opendilab/LightZero.

The presence of unhealthy nodes in cloud infrastructure signals the potential failure of machines, which can significantly impact the availability and reliability of cloud services, resulting in negative customer experiences. Effectively addressing unhealthy node mitigation is therefore vital for sustaining cloud system performance. This paper introduces Deoxys, a causal inference engine tailored to recommending mitigation actions for unhealthy node in cloud systems to minimize virtual machine downtime and interruptions during unhealthy events. It employs double machine learning combined with causal forest to produce precise and reliable mitigation recommendations based solely on limited observational data collected from the historical unhealthy events. To enhance the causal inference model, Deoxys further incorporates a policy fallback mechanism based on model uncertainty and action overriding mechanisms to (i) improve the reliability of the system, and (ii) strike a good tradeoff between downtime reduction and resource utilization, thereby enhancing the overall system performance. After deploying Deoxys in a large-scale cloud infrastructure at Microsoft, our observations demonstrate that Deoxys significantly reduces average VM downtime by 53% compared to a legacy policy, while leading to 49.5% lower VM interruption rate. This substantial improvement enhances the reliability and stability of cloud platforms, resulting in a seamless customer experience.

Transformer-based models have demonstrated significant success in various source code representation tasks. Nonetheless, traditional positional embeddings employed by these models inadequately capture the hierarchical structure intrinsic to source code, typically represented as Abstract Syntax Trees (ASTs). To address this, we propose a novel tree-based positional embedding approach that explicitly encodes hierarchical relationships derived from ASTs, including node depth and sibling indices. These hierarchical embeddings are integrated into the transformer architecture, specifically enhancing the CodeBERTa model. We thoroughly evaluate our proposed model through masked language modeling (MLM) pretraining and clone detection fine-tuning tasks. Experimental results indicate that our Tree-Enhanced CodeBERTa consistently surpasses the baseline model in terms of loss, accuracy, F1 score, precision, and recall, emphasizing the importance of incorporating explicit structural information into transformer-based representations of source code.