Graph-based Retrieval-Augmented Generation (RAG) has shown great capability in enhancing Large Language Model (LLM)'s answer with an external knowledge base. Compared to traditional RAG, it introduces a graph as an intermediate representation to capture better structured relational knowledge in the corpus, elevating the precision and comprehensiveness of generation results. However, developers usually face challenges in analyzing the effectiveness of GraphRAG on their dataset due to GraphRAG's complex information processing pipeline and the overwhelming amount of LLM invocations involved during graph construction and query, which limits GraphRAG interpretability and accessibility. This research proposes a visual analysis framework that helps RAG developers identify critical recalls of GraphRAG and trace these recalls through the GraphRAG pipeline. Based on this framework, we develop XGraphRAG, a prototype system incorporating a set of interactive visualizations to facilitate users' analysis process, boosting failure cases collection and improvement opportunities identification. Our evaluation demonstrates the effectiveness and usability of our approach. Our work is open-sourced and available at https://github.com/Gk0Wk/XGraphRAG.
Graph Neural Networks (GNNs) have recently been found to excel in histopathology. However, an important histopathological task, where GNNs have not been extensively explored, is the classification of glomeruli health as an important indicator in nephropathology. This task presents unique difficulties, particularly for the graph construction, i.e., the identification of nodes, edges, and informative features. In this work, we propose a pipeline composed of different traditional and machine learning-based computer vision techniques to identify nodes, edges, and their corresponding features to form a heterogeneous graph. We then proceed to propose a novel heterogeneous GNN architecture for glomeruli classification, called HIEGNet, that integrates both glomeruli and their surrounding immune cells. Hence, HIEGNet is able to consider the immune environment of each glomerulus in its classification. Our HIEGNet was trained and tested on a dataset of Whole Slide Images from kidney transplant patients. Experimental results demonstrate that HIEGNet outperforms several baseline models and generalises best between patients among all baseline models. Our implementation is publicly available at https://github.com/nklsKrmnn/HIEGNet.git.
Graph-based learning provides a powerful framework for modeling complex relational structures; however, its application within the domain of wireless security remains significantly underexplored. In this work, we introduce the first application of graph-based learning for jamming source localization, addressing the imminent threat of jamming attacks in wireless networks. Unlike geometric optimization techniques that struggle under environmental uncertainties and dense interference, we reformulate the localization as an inductive graph regression task. Our approach integrates structured node representations that encode local and global signal aggregation, ensuring spatial coherence and adaptive signal fusion. To enhance robustness, we incorporate an attention-based \ac{GNN} that adaptively refines neighborhood influence and introduces a confidence-guided estimation mechanism that dynamically balances learned predictions with domain-informed priors. We evaluate our approach under complex \ac{RF} environments with various sampling densities, network topologies, jammer characteristics, and signal propagation conditions, conducting comprehensive ablation studies on graph construction, feature selection, and pooling strategies. Results demonstrate that our novel graph-based learning framework significantly outperforms established localization baselines, particularly in challenging scenarios with sparse and obfuscated signal information. Our code is available at https://github.com/tiiuae/gnn-jamming-source-localization.
Causality detection and mining are important tasks in information retrieval due to their enormous use in information extraction, and knowledge graph construction. To solve these tasks, in existing literature there exist several solutions -- both unsupervised and supervised. However, the unsupervised methods suffer from poor performance and they often require significant human intervention for causal rule selection, leading to poor generalization across different domains. On the other hand, supervised methods suffer from the lack of large training datasets. Recently, large language models (LLMs) with effective prompt engineering are found to be effective to overcome the issue of unavailability of large training dataset. Yet, in existing literature, there does not exist comprehensive works on causality detection and mining using LLM prompting. In this paper, we present several retrieval-augmented generation (RAG) based dynamic prompting schemes to enhance LLM performance in causality detection and extraction tasks. Extensive experiments over three datasets and five LLMs validate the superiority of our proposed RAG-based dynamic prompting over other static prompting schemes.
We present AutoSchemaKG, a framework for fully autonomous knowledge graph construction that eliminates the need for predefined schemas. Our system leverages large language models to simultaneously extract knowledge triples and induce comprehensive schemas directly from text, modeling both entities and events while employing conceptualization to organize instances into semantic categories. Processing over 50 million documents, we construct ATLAS (Automated Triple Linking And Schema induction), a family of knowledge graphs with 900+ million nodes and 5.9 billion edges. This approach outperforms state-of-the-art baselines on multi-hop QA tasks and enhances LLM factuality. Notably, our schema induction achieves 95\% semantic alignment with human-crafted schemas with zero manual intervention, demonstrating that billion-scale knowledge graphs with dynamically induced schemas can effectively complement parametric knowledge in large language models.
Large Language Models (LLMs) have achieved impressive progress in natural language processing, but their limited ability to retain long-term context constrains performance on document-level or multi-turn tasks. Retrieval-Augmented Generation (RAG) mitigates this by retrieving relevant information from an external corpus. However, existing RAG systems often rely on embedding-based retrieval trained on corpus-level semantic similarity, which can lead to retrieving content that is semantically similar in form but misaligned with the question's true intent. Furthermore, recent RAG variants construct graph- or hierarchy-based structures to improve retrieval accuracy, resulting in significant computation and storage overhead. In this paper, we propose an embedding-free retrieval framework. Our method leverages the logical inferencing ability of LLMs in retrieval using iterative search space refinement guided by our novel importance measure and extend our retrieval results with logically related information without explicit graph construction. Experiments on long-context QA benchmarks, including NovelQA and Marathon, show that our approach outperforms strong baselines while reducing storage and runtime by over an order of magnitude.
Recognizing biomedical concepts in the text is vital for ontology refinement, knowledge graph construction, and concept relationship discovery. However, traditional concept recognition methods, relying on explicit mention identification, often fail to capture complex concepts not explicitly stated in the text. To overcome this limitation, we introduce MA-COIR, a framework that reformulates concept recognition as an indexing-recognition task. By assigning semantic search indexes (ssIDs) to concepts, MA-COIR resolves ambiguities in ontology entries and enhances recognition efficiency. Using a pretrained BART-based model fine-tuned on small datasets, our approach reduces computational requirements to facilitate adoption by domain experts. Furthermore, we incorporate large language models (LLMs)-generated queries and synthetic data to improve recognition in low-resource settings. Experimental results on three scenarios (CDR, HPO, and HOIP) highlight the effectiveness of MA-COIR in recognizing both explicit and implicit concepts without the need for mention-level annotations during inference, advancing ontology-driven concept recognition in biomedical domain applications. Our code and constructed data are available at https://github.com/sl-633/macoir-master.
Multiview point cloud registration plays a crucial role in robotics, automation, and computer vision fields. This paper concentrates on pose graph construction and motion synchronization within multiview registration. Previous methods for pose graph construction often pruned fully connected graphs or constructed sparse graph using global feature aggregated from local descriptors, which may not consistently yield reliable results. To identify dependable pairs for pose graph construction, we design a network model that extracts information from the matching distance between point cloud pairs. For motion synchronization, we propose another neural network model to calculate the absolute pose in a data-driven manner, rather than optimizing inaccurate handcrafted loss functions. Our model takes into account geometric distribution information and employs a modified attention mechanism to facilitate flexible and reliable feature interaction. Experimental results on diverse indoor and outdoor datasets confirm the effectiveness and generalizability of our approach. The source code is available at https://github.com/Shi-Qi-Li/MDGD.
In recent years, graph neural networks (GNNs) have shown great potential in addressing various graph structure-related downstream tasks. However, recent studies have found that current GNNs are susceptible to malicious adversarial attacks. Given the inevitable presence of adversarial attacks in the real world, a variety of defense methods have been proposed to counter these attacks and enhance the robustness of GNNs. Despite the commendable performance of these defense methods, we have observed that they tend to exhibit a structural bias in terms of their defense capability on nodes with low degree (i.e., tail nodes), which is similar to the structural bias of traditional GNNs on nodes with low degree in the clean graph. Therefore, in this work, we propose a defense strategy by including hetero-homo augmented graph construction, $k$NN augmented graph construction, and multi-view node-wise attention modules to mitigate the structural bias of GNNs against adversarial attacks. Notably, the hetero-homo augmented graph consists of removing heterophilic links (i.e., links connecting nodes with dissimilar features) globally and adding homophilic links (i.e., links connecting nodes with similar features) for nodes with low degree. To further enhance the defense capability, an attention mechanism is adopted to adaptively combine the representations from the above two kinds of graph views. We conduct extensive experiments to demonstrate the defense and debiasing effect of the proposed strategy on benchmark datasets.
Textual data question answering has gained significant attention due to its growing applicability. Recently, a novel approach leveraging the Retrieval-Augmented Generation (RAG) method was introduced, utilizing the Prize-Collecting Steiner Tree (PCST) optimization for sub-graph construction. However, this method focused solely on node attributes, leading to incomplete contextual understanding. In this paper, we propose an enhanced approach that replaces the PCST method with an attention-based sub-graph construction technique, enabling more efficient and context-aware retrieval. Additionally, we encode both node and edge attributes, leading to richer graph representations. Our method also incorporates an improved projection layer and multi-head attention pooling for better alignment with Large Language Models (LLMs). Experimental evaluations on the WebQSP dataset demonstrate that our approach is competitive and achieves marginally better results compared to the original method, underscoring its potential for more accurate question answering.
With the rise of knowledge graph based retrieval-augmented generation (RAG) techniques such as GraphRAG and Pike-RAG, the role of knowledge graphs in enhancing the reasoning capabilities of large language models (LLMs) has become increasingly prominent. However, traditional Knowledge Graph Construction (KGC) methods face challenges like complex entity disambiguation, rigid schema definition, and insufficient cross-document knowledge integration. This paper focuses on the task of automatic document-level knowledge graph construction. It proposes the Document-level Retrieval Augmented Knowledge Graph Construction (RAKG) framework. RAKG extracts pre-entities from text chunks and utilizes these pre-entities as queries for RAG, effectively addressing the issue of long-context forgetting in LLMs and reducing the complexity of Coreference Resolution. In contrast to conventional KGC methods, RAKG more effectively captures global information and the interconnections among disparate nodes, thereby enhancing the overall performance of the model. Additionally, we transfer the RAG evaluation framework to the KGC field and filter and evaluate the generated knowledge graphs, thereby avoiding incorrectly generated entities and relationships caused by hallucinations in LLMs. We further developed the MINE dataset by constructing standard knowledge graphs for each article and experimentally validated the performance of RAKG. The results show that RAKG achieves an accuracy of 95.91 % on the MINE dataset, a 6.2 % point improvement over the current best baseline, GraphRAG (89.71 %). The code is available at https://github.com/LMMApplication/RAKG.
Machine learning is revolutionizing global weather forecasting, with models that efficiently produce highly accurate forecasts. Apart from global forecasting there is also a large value in high-resolution regional weather forecasts, focusing on accurate simulations of the atmosphere for a limited area. Initial attempts have been made to use machine learning for such limited area scenarios, but these experiments do not consider realistic forecasting settings and do not investigate the many design choices involved. We present a framework for building kilometer-scale machine learning limited area models with boundary conditions imposed through a flexible boundary forcing method. This enables boundary conditions defined either from reanalysis or operational forecast data. Our approach employs specialized graph constructions with rectangular and triangular meshes, along with multi-step rollout training strategies to improve temporal consistency. We perform systematic evaluation of different design choices, including the boundary width, graph construction and boundary forcing integration. Models are evaluated across both a Danish and a Swiss domain, two regions that exhibit different orographical characteristics. Verification is performed against both gridded analysis data and in-situ observations, including a case study for the storm Ciara in February 2020. Both models achieve skillful predictions across a wide range of variables, with our Swiss model outperforming the numerical weather prediction baseline for key surface variables. With their substantially lower computational cost, our findings demonstrate great potential for machine learning limited area models in the future of regional weather forecasting.
Knowledge graphs serve as critical resources supporting intelligent systems, but they can be noisy due to imperfect automatic generation processes. Existing approaches to noise detection often rely on external facts, logical rule constraints, or structural embeddings. These methods are often challenged by imperfect entity alignment, flexible knowledge graph construction, and overfitting on structures. In this paper, we propose to exploit the consistency between entity and relation type information for noise detection, resulting a novel self-supervised knowledge graph denoising method that avoids those problems. We formalize type inconsistency noise as triples that deviate from the majority with respect to type-dependent reasoning along the topological structure. Specifically, we first extract a compact representation of a given knowledge graph via an encoder that models the type dependencies of triples. Then, the decoder reconstructs the original input knowledge graph based on the compact representation. It is worth noting that, our proposal has the potential to address the problems of knowledge graph compression and completion, although this is not our focus. For the specific task of noise detection, the discrepancy between the reconstruction results and the input knowledge graph provides an opportunity for denoising, which is facilitated by the type consistency embedded in our method. Experimental validation demonstrates the effectiveness of our approach in detecting potential noise in real-world data.
The observations documented in Cyber Threat Intelligence (CTI) reports play a critical role in describing adversarial behaviors, providing valuable insights for security practitioners to respond to evolving threats. Recent advancements of Large Language Models (LLMs) have demonstrated significant potential in various cybersecurity applications, including CTI report understanding and attack knowledge graph construction. While previous works have proposed benchmarks that focus on the CTI extraction ability of LLMs, the sequential characteristic of adversarial behaviors within CTI reports remains largely unexplored, which holds considerable significance in developing a comprehensive understanding of how adversaries operate. To address this gap, we introduce AttackSeqBench, a benchmark tailored to systematically evaluate LLMs' capability to understand and reason attack sequences in CTI reports. Our benchmark encompasses three distinct Question Answering (QA) tasks, each task focuses on the varying granularity in adversarial behavior. To alleviate the laborious effort of QA construction, we carefully design an automated dataset construction pipeline to create scalable and well-formulated QA datasets based on real-world CTI reports. To ensure the quality of our dataset, we adopt a hybrid approach of combining human evaluation and systematic evaluation metrics. We conduct extensive experiments and analysis with both fast-thinking and slow-thinking LLMs, while highlighting their strengths and limitations in analyzing the sequential patterns in cyber attacks. The overarching goal of this work is to provide a benchmark that advances LLM-driven CTI report understanding and fosters its application in real-world cybersecurity operations. Our dataset and code are available at https://github.com/Javiery3889/AttackSeqBench .
Cybersecurity threats are growing, making network intrusion detection essential. Traditional machine learning models remain effective in resource-limited environments due to their efficiency, requiring fewer parameters and less computational time. However, handling short and highly imbalanced datasets remains challenging. In this study, we propose the fusion of a Contrastive Attentive Graph Network and Graph Attention Network (CAGN-GAT Fusion) and benchmark it against 15 other models, including both Graph Neural Networks (GNNs) and traditional ML models. Our evaluation is conducted on four benchmark datasets (KDD-CUP-1999, NSL-KDD, UNSW-NB15, and CICIDS2017) using a short and proportionally imbalanced dataset with a constant size of 5000 samples to ensure fairness in comparison. Results show that CAGN-GAT Fusion demonstrates stable and competitive accuracy, recall, and F1-score, even though it does not achieve the highest performance in every dataset. Our analysis also highlights the impact of adaptive graph construction techniques, including small changes in connections (edge perturbation) and selective hiding of features (feature masking), improving detection performance. The findings confirm that GNNs, particularly CAGN-GAT Fusion, are robust and computationally efficient, making them well-suited for resource-constrained environments. Future work will explore GraphSAGE layers and multiview graph construction techniques to further enhance adaptability and detection accuracy.
We present an agentic, autonomous graph expansion framework that iteratively structures and refines knowledge in situ. Unlike conventional knowledge graph construction methods relying on static extraction or single-pass learning, our approach couples a reasoning-native large language model with a continually updated graph representation. At each step, the system actively generates new concepts and relationships, merges them into a global graph, and formulates subsequent prompts based on its evolving structure. Through this feedback-driven loop, the model organizes information into a scale-free network characterized by hub formation, stable modularity, and bridging nodes that link disparate knowledge clusters. Over hundreds of iterations, new nodes and edges continue to appear without saturating, while centrality measures and shortest path distributions evolve to yield increasingly distributed connectivity. Our analysis reveals emergent patterns, such as the rise of highly connected 'hub' concepts and the shifting influence of 'bridge' nodes, indicating that agentic, self-reinforcing graph construction can yield open-ended, coherent knowledge structures. Applied to materials design problems, we present compositional reasoning experiments by extracting node-specific and synergy-level principles to foster genuinely novel knowledge synthesis, yielding cross-domain ideas that transcend rote summarization and strengthen the framework's potential for open-ended scientific discovery. We discuss other applications in scientific discovery and outline future directions for enhancing scalability and interpretability.
Large language models (LLMs) have achieved impressive performance on knowledge-intensive tasks, yet they often struggle with multi-step reasoning due to the unstructured nature of retrieved context. While retrieval-augmented generation (RAG) methods provide external information, the lack of explicit organization among retrieved passages limits their effectiveness, leading to brittle reasoning pathways. Recent interpretability studies highlighting the importance of structured intermediate reasoning further align with this perspective. We propose Retrieval-And-Structuring (RAS), a framework that dynamically constructs query-specific knowledge graphs through iterative retrieval and structured knowledge building. RAS interleaves targeted retrieval planning with incremental graph construction, enabling models to assemble and reason over evolving knowledge structures tailored to each query. On seven knowledge-intensive benchmarks, RAS consistently outperforms strong baselines, achieving up to 6.4% and 7.0% gains with open-source and proprietary LLMs, respectively. Our results demonstrate that dynamic, query-specific knowledge structuring offers a robust path to improving reasoning accuracy and robustness in language model generation. Our data and code can be found at https://github.com/pat-jj/RAS.
Whole Slide Imaging (WSI), which involves high-resolution digital scans of pathology slides, has become the gold standard for cancer diagnosis, but its gigapixel resolution and the scarcity of annotated datasets present challenges for deep learning models. Multiple Instance Learning (MIL), a widely-used weakly supervised approach, bypasses the need for patch-level annotations. However, conventional MIL methods overlook the spatial relationships between patches, which are crucial for tasks such as cancer grading and diagnosis. To address this, graph-based approaches have gained prominence by incorporating spatial information through node connections. Despite their potential, both MIL and graph-based models are vulnerable to learning spurious associations, like color variations in WSIs, affecting their robustness. In this dissertation, we conduct an extensive comparison of multiple graph construction techniques, MIL models, graph-MIL approaches, and interventional training, introducing a new framework, Graph-based Multiple Instance Learning with Interventional Training (GMIL-IT), for WSI classification. We evaluate their impact on model generalization through domain shift analysis and demonstrate that graph-based models alone achieve the generalization initially anticipated from interventional training. Our code is available here: github.com/ritamartinspereira/GMIL-IT
Federated learning has emerged as a key paradigm in privacy-preserving computing due to its "data usable but not visible" property, enabling users to collaboratively train models without sharing raw data. Motivated by this, federated recommendation systems offer a promising architecture that balances user privacy with recommendation accuracy through distributed collaborative learning. However, existing federated recommendation methods often neglect the underlying semantic or behavioral relationships between users during parameter aggregation, limiting their effectiveness. To address this, graph-based federated recommendation systems have been proposed to leverage neighborhood information. Yet, conventional graph construction methods usually require access to raw user data or explicit social links, which contradicts the strict privacy requirements of federated learning. In this work, we propose UFGraphFR (User Text-feature-based Graph Federated Recommendation), a personalized federated recommendation framework that constructs a user graph based on clients' locally embedded text features. Our core assumption is that users with similar textual descriptions exhibit similar preferences. UFGraphFR introduces two key components: a privacy-preserving user relationship graph built from the joint embedding layer's weight matrix without leaking raw user attributes, and a Transformer-based architecture to model temporal dependencies in user-item interaction sequences. Experimental results on benchmark datasets such as MovieLens and HetRec2011 demonstrate that UFGraphFR achieves competitive accuracy compared to centralized and state-of-the-art federated baselines while preserving user privacy. Code is available at https://github.com/trueWangSyutung/UFGraphFR
Superpixel segmentation is a foundation for many higher-level computer vision tasks, such as image segmentation, object recognition, and scene understanding. Existing graph-based superpixel segmentation methods typically concentrate on the relationships between a given pixel and its directly adjacent pixels while overlooking the influence of non-adjacent pixels. These approaches do not fully leverage the global information in the graph, leading to suboptimal segmentation quality. To address this limitation, we present SIT-HSS, a hierarchical superpixel segmentation method based on structural information theory. Specifically, we first design a novel graph construction strategy that incrementally explores the pixel neighborhood to add edges based on 1-dimensional structural entropy (1D SE). This strategy maximizes the retention of graph information while avoiding an overly complex graph structure. Then, we design a new 2D SE-guided hierarchical graph partitioning method, which iteratively merges pixel clusters layer by layer to reduce the graph's 2D SE until a predefined segmentation scale is achieved. Experimental results on three benchmark datasets demonstrate that the SIT-HSS performs better than state-of-the-art unsupervised superpixel segmentation algorithms. The source code is available at \url{https://github.com/SELGroup/SIT-HSS}.