Retrieval-Augmented Generation allows LLMs to access external knowledge, reducing hallucinations and ageing-data issues. However, it treats retrieved chunks independently and struggles with multi-hop or relational reasoning, especially across documents. Knowledge graphs enhance this by capturing the relationships between entities using triplets, enabling structured, multi-chunk reasoning. However, these tend to miss information that fails to conform to the triplet structure. We introduce BambooKG, a knowledge graph with frequency-based weights on non-triplet edges which reflect link strength, drawing on the Hebbian principle of "fire together, wire together". This decreases information loss and results in improved performance on single- and multi-hop reasoning, outperforming the existing solutions.

Uncertain knowledge graph embedding (UnKGE) methods learn vector representations that capture both structural and uncertainty information to predict scores of unseen triples. However, existing methods produce only point estimates, without quantifying predictive uncertainty-limiting their reliability in high-stakes applications where understanding confidence in predictions is crucial. To address this limitation, we propose \textsc{UnKGCP}, a framework that generates prediction intervals guaranteed to contain the true score with a user-specified level of confidence. The length of the intervals reflects the model's predictive uncertainty. \textsc{UnKGCP} builds on the conformal prediction framework but introduces a novel nonconformity measure tailored to UnKGE methods and an efficient procedure for interval construction. We provide theoretical guarantees for the intervals and empirically verify these guarantees. Extensive experiments on standard benchmarks across diverse UnKGE methods further demonstrate that the intervals are sharp and effectively capture predictive uncertainty.

Graph neural networks (GNNs) are powerful tools for learning from graph-structured data but often produce biased predictions with respect to sensitive attributes. Fairness-aware GNNs have been actively studied for mitigating biased predictions. However, no prior studies have evaluated fairness-aware GNNs on knowledge graphs, which are one of the most important graphs in many applications, such as recommender systems. Therefore, we introduce a benchmarking study on knowledge graphs. We generate new graphs from three knowledge graphs, YAGO, DBpedia, and Wikidata, that are significantly larger than the existing graph datasets used in fairness studies. We benchmark inprocessing and preprocessing methods in different GNN backbones and early stopping conditions. We find several key insights: (i) knowledge graphs show different trends from existing datasets; clearer trade-offs between prediction accuracy and fairness metrics than other graphs in fairness-aware GNNs, (ii) the performance is largely affected by not only fairness-aware GNN methods but also GNN backbones and early stopping conditions, and (iii) preprocessing methods often improve fairness metrics, while inprocessing methods improve prediction accuracy.

Uncertain knowledge graphs (UKGs) associate each triple with a confidence score to provide more precise knowledge representations. Recently, since real-world UKGs suffer from the incompleteness, uncertain knowledge graph (UKG) completion attracts more attention, aiming to complete missing triples and confidences. Current studies attempt to learn UKG embeddings to solve this problem, but they neglect the extremely imbalanced distributions of triple confidences. This causes that the learnt embeddings are insufficient to high-quality UKG completion. Thus, in this paper, to address the above issue, we propose a new semi-supervised Confidence Distribution Learning (ssCDL) method for UKG completion, where each triple confidence is transformed into a confidence distribution to introduce more supervision information of different confidences to reinforce the embedding learning process. ssCDL iteratively learns UKG embedding by relational learning on labeled data (i.e., existing triples with confidences) and unlabeled data with pseudo labels (i.e., unseen triples with the generated confidences), which are predicted by meta-learning to augment the training data and rebalance the distribution of triple confidences. Experiments on two UKG datasets demonstrate that ssCDL consistently outperforms state-of-the-art baselines in different evaluation metrics.

The effectiveness of artificial intelligence (AI) in healthcare is significantly hindered by unstructured clinical documentation, which results in noisy, inconsistent, and logically fragmented training data. To address this challenge, we present a knowledge-driven framework that integrates the standardized clinical terminology SNOMED CT with the Neo4j graph database to construct a structured medical knowledge graph. In this graph, clinical entities such as diseases, symptoms, and medications are represented as nodes, and semantic relationships such as ``caused by,'' ``treats,'' and ``belongs to'' are modeled as edges in Neo4j, with types mapped from formal SNOMED CT relationship concepts (e.g., \texttt{Causative agent}, \texttt{Indicated for}). This design enables multi-hop reasoning and ensures terminological consistency. By extracting and standardizing entity-relationship pairs from clinical texts, we generate structured, JSON-formatted datasets that embed explicit diagnostic pathways. These datasets are used to fine-tune large language models (LLMs), significantly improving the clinical logic consistency of their outputs. Experimental results demonstrate that our knowledge-guided approach enhances the validity and interpretability of AI-generated diagnostic reasoning, providing a scalable solution for building reliable AI-assisted clinical systems.

Heterogeneous graph neural networks have seen rapid progress in web applications such as social networks, knowledge graphs, and recommendation systems, driven by the inherent heterogeneity of web data. However, existing methods typically assume static graphs, while real-world graphs are continuously evolving. This dynamic nature requires models to adapt to new data while preserving existing knowledge. To this end, this work introduces HERO (HEterogeneous continual gRaph learning via meta-knOwledge distillation), a unified framework for continual learning on heterogeneous graphs. HERO employs meta-adaptation, a gradient-based meta-learning strategy that provides directional guidance for rapid adaptation to new tasks with limited samples. To enable efficient and effective knowledge reuse, we propose DiSCo (Diversity Sampling with semantic Consistency), a heterogeneity-aware sampling method that maximizes target node diversity and expands subgraphs along metapaths, retaining critical semantic and structural information with minimal overhead. Furthermore, HERO incorporates heterogeneity-aware knowledge distillation, which aligns knowledge at both the node and semantic levels to balance adaptation and retention across tasks. Extensive experiments on four web-related heterogeneous graph benchmarks demonstrate that HERO substantially mitigates catastrophic forgetting while achieving efficient and consistent knowledge reuse in dynamic web environments.

Current Retrieval-Augmented Generation (RAG) systems primarily operate on unimodal textual data, limiting their effectiveness on unstructured multimodal documents. Such documents often combine text, images, tables, equations, and graphs, each contributing unique information. In this work, we present a Modality-Aware Hybrid retrieval Architecture (MAHA), designed specifically for multimodal question answering with reasoning through a modality-aware knowledge graph. MAHA integrates dense vector retrieval with structured graph traversal, where the knowledge graph encodes cross-modal semantics and relationships. This design enables both semantically rich and context-aware retrieval across diverse modalities. Evaluations on multiple benchmark datasets demonstrate that MAHA substantially outperforms baseline methods, achieving a ROUGE-L score of 0.486, providing complete modality coverage. These results highlight MAHA's ability to combine embeddings with explicit document structure, enabling effective multimodal retrieval. Our work establishes a scalable and interpretable retrieval framework that advances RAG systems by enabling modality-aware reasoning over unstructured multimodal data.

Knowledge graphs represent information as structured triples and serve as the backbone for a wide range of applications, including question answering, link prediction, and recommendation systems. A prominent line of research for exploring knowledge graphs involves graph embedding methods, where entities and relations are represented in low-dimensional vector spaces that capture underlying semantics and structure. However, most existing methods rely on assumptions such as the Closed World Assumption or Local Closed World Assumption, treating missing triples as false. This contrasts with the Open World Assumption underlying many real-world knowledge graphs. Furthermore, while explicitly stated negative statements can help distinguish between false and unknown triples, they are rarely included in knowledge graphs and are often overlooked during embedding training. In this work, we introduce a novel approach that integrates explicitly declared negative statements into the knowledge embedding learning process. Our approach employs a dual-model architecture, where two embedding models are trained in parallel, one on positive statements and the other on negative statements. During training, each model generates negative samples by corrupting positive samples and selecting the most likely candidates as scored by the other model. The proposed approach is evaluated on both general-purpose and domain-specific knowledge graphs, with a focus on link prediction and triple classification tasks. The extensive experiments demonstrate that our approach improves predictive performance over state-of-the-art embedding models, demonstrating the value of integrating meaningful negative knowledge into embedding learning.

Deductive and abductive reasoning are two critical paradigms for analyzing knowledge graphs, enabling applications from financial query answering to scientific discovery. Deductive reasoning on knowledge graphs usually involves retrieving entities that satisfy a complex logical query, while abductive reasoning generates plausible logical hypotheses from observations. Despite their clear synergistic potential, where deduction can validate hypotheses and abduction can uncover deeper logical patterns, existing methods address them in isolation. To bridge this gap, we propose DARK, a unified framework for Deductive and Abductive Reasoning in Knowledge graphs. As a masked diffusion model capable of capturing the bidirectional relationship between queries and conclusions, DARK has two key innovations. First, to better leverage deduction for hypothesis refinement during abductive reasoning, we introduce a self-reflective denoising process that iteratively generates and validates candidate hypotheses against the observed conclusion. Second, to discover richer logical associations, we propose a logic-exploration reinforcement learning approach that simultaneously masks queries and conclusions, enabling the model to explore novel reasoning compositions. Extensive experiments on multiple benchmark knowledge graphs show that DARK achieves state-of-the-art performance on both deductive and abductive reasoning tasks, demonstrating the significant benefits of our unified approach.

Abstract--Recent breakthroughs in generative modeling have demonstrated remarkable capabilities in molecular generation, yet the integration of comprehensive biomedical knowledge into these models has remained an untapped frontier . In this study, we introduce K-DREAM (Knowledge-Driven Embedding-Augmented Model), a novel framework that leverages knowledge graphs to augment diffusion-based generative models for drug discovery. By embedding structured information from large-scale knowledge graphs, K-DREAM directs molecular generation toward candidates with higher biological relevance and therapeutic suitability. This integration ensures that the generated molecules are aligned with specific therapeutic targets, moving beyond traditional heuristic-driven approaches. In targeted drug design tasks, K-DREAM generates drug candidates with improved binding affinities and predicted efficacy, surpassing current state-of-the-art generative models. It also demonstrates flexibility by producing molecules designed for multiple targets, enabling applications to complex disease mechanisms. Impact Statement--We introduce K-DREAM, a new approach to drug discovery that combines knowledge graphs with AIdriven drug design. Unlike conventional methods that focus mainly on chemical properties, our framework incorporates biological relationships to create more medically relevant drug candidates.