Graph-based nearest neighbor search methods have seen a surge of popularity in recent years, offering state-of-the-art performance across a wide variety of applications. Central to these methods is the task of constructing a sparse navigable search graph for a given dataset endowed with a distance function. Unfortunately, doing so is computationally expensive, so heuristics are universally used in practice. In this work, we initiate the study of fast algorithms with provable guarantees for search graph construction. For a dataset with $n$ data points, the problem of constructing an optimally sparse navigable graph can be framed as $n$ separate but highly correlated minimum set cover instances. This yields a naive $O(n^3)$ time greedy algorithm that returns a navigable graph whose sparsity is at most $O(\log n)$ higher than optimal. We improve significantly on this baseline, taking advantage of correlation between the set cover instances to leverage techniques from streaming and sublinear-time set cover algorithms. Combined with problem-specific pre-processing techniques, we present an $\tilde{O}(n^2)$ time algorithm for constructing an $O(\log n)$-approximate sparsest navigable graph under any distance function. The runtime of our method is optimal up to logarithmic factors under the Strong Exponential Time Hypothesis via a reduction from Monochromatic Closest Pair. Moreover, we prove that, as with general set cover, obtaining better than an $O(\log n)$-approximation is NP-hard, despite the significant additional structure present in the navigable graph problem. Finally, we show that our techniques can also beat cubic time for the closely related and practically important problems of constructing $\alpha$-shortcut reachable and $\tau$-monotonic graphs, which are also used for nearest neighbor search. For such graphs, we obtain $\tilde{O}(n^{2.5})$ time or better algorithms.
Graph generation plays a pivotal role across numerous domains, including molecular design and knowledge graph construction. Although existing methods achieve considerable success in generating realistic graphs, their interpretability remains limited, often obscuring the rationale behind structural decisions. To address this challenge, we propose the Neural Graph Topic Model (NGTM), a novel generative framework inspired by topic modeling in natural language processing. NGTM represents graphs as mixtures of latent topics, each defining a distribution over semantically meaningful substructures, which facilitates explicit interpretability at both local and global scales. The generation process transparently integrates these topic distributions with a global structural variable, enabling clear semantic tracing of each generated graph. Experiments demonstrate that NGTM achieves competitive generation quality while uniquely enabling fine-grained control and interpretability, allowing users to tune structural features or induce biological properties through topic-level adjustments.
Human smuggling networks are increasingly adaptive and difficult to analyze. Legal case documents offer valuable insights but are unstructured, lexically dense, and filled with ambiguous or shifting references-posing challenges for automated knowledge graph (KG) construction. Existing KG methods often rely on static templates and lack coreference resolution, while recent LLM-based approaches frequently produce noisy, fragmented graphs due to hallucinations, and duplicate nodes caused by a lack of guided extraction. We propose CORE-KG, a modular framework for building interpretable KGs from legal texts. It uses a two-step pipeline: (1) type-aware coreference resolution via sequential, structured LLM prompts, and (2) entity and relationship extraction using domain-guided instructions, built on an adapted GraphRAG framework. CORE-KG reduces node duplication by 33.28%, and legal noise by 38.37% compared to a GraphRAG-based baseline-resulting in cleaner and more coherent graph structures. These improvements make CORE-KG a strong foundation for analyzing complex criminal networks.
Spatial transcriptomics (ST) technologies enable gene expression profiling with spatial resolution, offering unprecedented insights into tissue organization and disease heterogeneity. However, current analysis methods often struggle with noisy data, limited scalability, and inadequate modelling of complex cellular relationships. We present SemanticST, a biologically informed, graph-based deep learning framework that models diverse cellular contexts through multi-semantic graph construction. SemanticST builds multiple context-specific graphs capturing spatial proximity, gene expression similarity, and tissue domain structure, and learns disentangled embeddings for each. These are fused using an attention-inspired strategy to yield a unified, biologically meaningful representation. A community-aware min-cut loss improves robustness over contrastive learning, particularly in sparse ST data. SemanticST supports mini-batch training, making it the first graph neural network scalable to large-scale datasets such as Xenium (500,000 cells). Benchmarking across four platforms (Visium, Slide-seq, Stereo-seq, Xenium) and multiple human and mouse tissues shows consistent 20 percentage gains in ARI, NMI, and trajectory fidelity over DeepST, GraphST, and IRIS. In re-analysis of breast cancer Xenium data, SemanticST revealed rare and clinically significant niches, including triple receptor-positive clusters, spatially distinct DCIS-to-IDC transition zones, and FOXC2 tumour-associated myoepithelial cells, suggesting non-canonical EMT programs with stem-like features. SemanticST thus provides a scalable, interpretable, and biologically grounded framework for spatial transcriptomics analysis, enabling robust discovery across tissue types and diseases, and paving the way for spatially resolved tissue atlases and next-generation precision medicine.
Static analysis plays a key role in finding bugs, including security issues. A critical step in static analysis is building accurate call graphs that model function calls in a program. However, due to hard-to-analyze language features, existing call graph construction algorithms for JavaScript are neither sound nor complete. Prior work shows that even advanced solutions produce false edges and miss valid ones. In this work, we assist these tools by identifying missed call edges. Our main idea is to frame the problem as link prediction on full program graphs, using a rich representation with multiple edge types. Our approach, GRAPHIA, leverages recent advances in graph neural networks to model non-local relationships between code elements. Concretely, we propose representing JavaScript programs using a combination of syntactic- and semantic-based edges. GRAPHIA can learn from imperfect labels, including static call edges from existing tools and dynamic edges from tests, either from the same or different projects. Because call graphs are sparse, standard machine learning metrics like ROC are not suitable. Instead, we evaluate GRAPHIA by ranking function definitions for each unresolved call site. We conduct a large-scale evaluation on 50 popular JavaScript libraries with 163K call edges (150K static and 13K dynamic). GRAPHIA builds program graphs with 6.6M structural and 386K semantic edges. It ranks the correct target as the top candidate in over 42% of unresolved cases and within the top 5 in 72% of cases, reducing the manual effort needed for analysis. Our results show that learning-based methods can improve the recall of JavaScript call graph construction. To our knowledge, this is the first work to apply GNN-based link prediction to full multi-file program graphs for interprocedural analysis.
The core challenge in learning has shifted from knowledge acquisition to effective Self-Regulated Learning (SRL): planning, monitoring, and reflecting on one's learning. Existing digital tools, however, inadequately support metacognitive reflection. Spaced Repetition Systems (SRS) use de-contextualized review, overlooking the role of context, while Personal Knowledge Management (PKM) tools require high manual maintenance. To address these challenges, this paper introduces "Insight Recall," a novel paradigm that conceptualizes the context-triggered retrieval of personal past insights as a metacognitive scaffold to promote SRL. We formalize this paradigm using the Just-in-Time Adaptive Intervention (JITAI) framework and implement a prototype system, Irec, to demonstrate its feasibility. At its core, Irec uses a dynamic knowledge graph of the user's learning history. When a user faces a new problem, a hybrid retrieval engine recalls relevant personal "insights." Subsequently, a large language model (LLM) performs a deep similarity assessment to filter and present the most relevant scaffold in a just-in-time manner. To reduce cognitive load, Irec features a human-in-the-loop pipeline for LLM-based knowledge graph construction. We also propose an optional "Guided Inquiry" module, where users can engage in a Socratic dialogue with an expert LLM, using the current problem and recalled insights as context. The contribution of this paper is a solid theoretical framework and a usable system platform for designing next-generation intelligent learning systems that enhance metacognition and self-regulation.
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 neural networks (GNNs), as topology/structure-aware models within deep learning, have emerged as powerful tools for AI-aided drug discovery (AIDD). By directly operating on molecular graphs, GNNs offer an intuitive and expressive framework for learning the complex topological and geometric features of drug-like molecules, cementing their role in modern molecular modeling. This review provides a comprehensive overview of the methodological foundations and representative applications of GNNs in drug discovery, spanning tasks such as molecular property prediction, virtual screening, molecular generation, biomedical knowledge graph construction, and synthesis planning. Particular attention is given to recent methodological advances, including geometric GNNs, interpretable models, uncertainty quantification, scalable graph architectures, and graph generative frameworks. We also discuss how these models integrate with modern deep learning approaches, such as self-supervised learning, multi-task learning, meta-learning and pre-training. Throughout this review, we highlight the practical challenges and methodological bottlenecks encountered when applying GNNs to real-world drug discovery pipelines, and conclude with a discussion on future directions.
Large Language Model (LLM)-driven Multi-agent systems (Mas) have recently emerged as a powerful paradigm for tackling complex real-world tasks. However, existing Mas construction methods typically rely on manually crafted interaction mechanisms or heuristic rules, introducing human biases and constraining the autonomous ability. Even with recent advances in adaptive Mas construction, existing systems largely remain within the paradigm of semi-autonomous patterns. In this work, we propose MasHost, a Reinforcement Learning (RL)-based framework for autonomous and query-adaptive Mas design. By formulating Mas construction as a graph search problem, our proposed MasHost jointly samples agent roles and their interactions through a unified probabilistic sampling mechanism. Beyond the accuracy and efficiency objectives pursued in prior works, we introduce component rationality as an additional and novel design principle in Mas. To achieve this multi-objective optimization, we propose Hierarchical Relative Policy Optimization (HRPO), a novel RL strategy that collaboratively integrates group-relative advantages and action-wise rewards. To our knowledge, our proposed MasHost is the first RL-driven framework for autonomous Mas graph construction. Extensive experiments on six benchmarks demonstrate that MasHost consistently outperforms most competitive baselines, validating its effectiveness, efficiency, and structure rationality.
Design rule checking (DRC) is of great significance for cost reduction and design efficiency improvement in integrated circuit (IC) designs. Machine-learning-based DRC has become an important approach in computer-aided design (CAD). In this paper, we propose MAGNet, a hybrid deep learning model that integrates an improved U-Net with a graph neural network for DRC violation prediction. The U-Net backbone is enhanced with a Dynamic Attention Module (DAM) and a Multi-Scale Convolution Module (MSCM) to strengthen its capability in extracting fine-grained and multi-scale spatial features. In parallel, we construct a pixel-aligned graph structure based on chip layout tiles, and apply a specialized GNN to model the topological relationships among pins. During graph construction, a graph-to-grid mapping is generated to align GNN features with the layout image. In addition, a label amplification strategy is adopted during training to enhance the model's sensitivity to sparse violation patterns. Overall, MAGNet effectively combines spatial, semantic, and structural information, achieving improved prediction accuracy and reduced false positive rates in DRC hotspot detection. Subsequently, through incremental training, we achieve a more sensitive discrimination ability for hotspots. The results demonstrate that, in comparison with ibUnet, RouteNet, and J-Net, MAGnet significantly outperforms these models, achieving substantial improvements in overall performance.
Entity structure extraction, which aims to extract entities and their associated attribute-value structures from text, is an essential task for text understanding and knowledge graph construction. Existing methods based on large language models (LLMs) typically rely heavily on predefined entity attribute schemas or annotated datasets, often leading to incomplete extraction results. To address these challenges, we introduce Zero-Shot Open-schema Entity Structure Discovery (ZOES), a novel approach to entity structure extraction that does not require any schema or annotated samples. ZOES operates via a principled mechanism of enrichment, refinement, and unification, based on the insight that an entity and its associated structure are mutually reinforcing. Experiments demonstrate that ZOES consistently enhances LLMs' ability to extract more complete entity structures across three different domains, showcasing both the effectiveness and generalizability of the method. These findings suggest that such an enrichment, refinement, and unification mechanism may serve as a principled approach to improving the quality of LLM-based entity structure discovery in various scenarios.
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.
Integrating Large Language Models (LLMs) with Knowledge Graphs (KGs) results in complex systems with numerous hyperparameters that directly affect performance. While such systems are increasingly common in retrieval-augmented generation, the role of systematic hyperparameter optimization remains underexplored. In this paper, we study this problem in the context of Cognee, a modular framework for end-to-end KG construction and retrieval. Using three multi-hop QA benchmarks (HotPotQA, TwoWikiMultiHop, and MuSiQue) we optimize parameters related to chunking, graph construction, retrieval, and prompting. Each configuration is scored using established metrics (exact match, F1, and DeepEval's LLM-based correctness metric). Our results demonstrate that meaningful gains can be achieved through targeted tuning. While the gains are consistent, they are not uniform, with performance varying across datasets and metrics. This variability highlights both the value of tuning and the limitations of standard evaluation measures. While demonstrating the immediate potential of hyperparameter tuning, we argue that future progress will depend not only on architectural advances but also on clearer frameworks for optimization and evaluation in complex, modular systems.
Knowledge Graphs (KGs) structure real-world entities and their relationships into triples, enhancing machine reasoning for various tasks. While domain-specific KGs offer substantial benefits, their manual construction is often inefficient and requires specialized knowledge. Recent approaches for knowledge graph construction (KGC) based on large language models (LLMs), such as schema-guided KGC and reference knowledge integration, have proven efficient. However, these methods are constrained by their reliance on manually defined schema, single-document processing, and public-domain references, making them less effective for domain-specific corpora that exhibit complex knowledge dependencies and specificity, as well as limited reference knowledge. To address these challenges, we propose LKD-KGC, a novel framework for unsupervised domain-specific KG construction. LKD-KGC autonomously analyzes document repositories to infer knowledge dependencies, determines optimal processing sequences via LLM driven prioritization, and autoregressively generates entity schema by integrating hierarchical inter-document contexts. This schema guides the unsupervised extraction of entities and relationships, eliminating reliance on predefined structures or external knowledge. Extensive experiments show that compared with state-of-the-art baselines, LKD-KGC generally achieves improvements of 10% to 20% in both precision and recall rate, demonstrating its potential in constructing high-quality domain-specific KGs.
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.
We study the task of panoptic symbol spotting, which involves identifying both individual instances of countable things and the semantic regions of uncountable stuff in computer-aided design (CAD) drawings composed of vector graphical primitives. Existing methods typically rely on image rasterization, graph construction, or point-based representation, but these approaches often suffer from high computational costs, limited generality, and loss of geometric structural information. In this paper, we propose VecFormer, a novel method that addresses these challenges through line-based representation of primitives. This design preserves the geometric continuity of the original primitive, enabling more accurate shape representation while maintaining a computation-friendly structure, making it well-suited for vector graphic understanding tasks. To further enhance prediction reliability, we introduce a Branch Fusion Refinement module that effectively integrates instance and semantic predictions, resolving their inconsistencies for more coherent panoptic outputs. Extensive experiments demonstrate that our method establishes a new state-of-the-art, achieving 91.1 PQ, with Stuff-PQ improved by 9.6 and 21.2 points over the second-best results under settings with and without prior information, respectively, highlighting the strong potential of line-based representation as a foundation for vector graphic understanding.
Large language models (LLMs) have revolutionized natural language processing, yet their practical utility is often limited by persistent issues of hallucinations and outdated parametric knowledge. Although post-training model editing offers a pathway for dynamic updates, existing methods frequently suffer from overfitting and catastrophic forgetting. To tackle these challenges, we propose a novel framework that leverages hyperbolic geometry and graph neural networks for precise and stable model edits. We introduce HYPE (HYperbolic Parameter Editing), which comprises three key components: (i) Hyperbolic Graph Construction, which uses Poincar\'e embeddings to represent knowledge triples in hyperbolic space, preserving hierarchical relationships and preventing unintended side effects by ensuring that edits to parent concepts do not inadvertently affect child concepts; (ii) M\"obius-Transformed Updates, which apply hyperbolic addition to propagate edits while maintaining structural consistency within the hyperbolic manifold, unlike conventional Euclidean updates that distort relational distances; and (iii) Dual Stabilization, which combines gradient masking and periodic GNN parameter resetting to prevent catastrophic forgetting by focusing updates on critical parameters and preserving long-term knowledge. Experiments on CounterFact, CounterFact+, and MQuAKE with GPT-J and GPT2-XL demonstrate that HYPE significantly enhances edit stability, factual accuracy, and multi-hop reasoning.
The automatic analysis of document layouts in digital-born PDF documents remains a challenging problem due to the heterogeneous arrangement of textual and nontextual elements and the imprecision of the textual metadata in the Portable Document Format. In this work, we benchmark Graph Neural Network (GNN) architectures for the task of fine-grained layout classification of text blocks from digital native documents. We introduce two graph construction structures: a k-closest-neighbor graph and a fully connected graph, and generate node features via pre-trained text and vision models, thus avoiding manual feature engineering. Three experimental frameworks are evaluated: single-modality (text or visual), concatenated multimodal, and dual-branch multimodal. We evaluated four foundational GNN models and compared them with the baseline. Our experiments are specifically conducted on a rich dataset of public affairs documents that includes more than 20 sources (e.g., regional and national-level official gazettes), 37K PDF documents, with 441K pages in total. Our results demonstrate that GraphSAGE operating on the k-closest-neighbor graph in a dual-branch configuration achieves the highest per-class and overall accuracy, outperforming the baseline in some sources. These findings confirm the importance of local layout relationships and multimodal fusion exploited through GNNs for the analysis of native digital document layouts.