Knowledge Graphs

LLM-based agents for industrial asset operations show limited accuracy when reasoning over flat document stores. AssetOpsBench (KDD 2026) establishes that GPT-4 agents achieve 65% on 139 industrial maintenance scenarios, and compares LLM orchestration paradigms (Agent-As-Tool vs. Plan-Execute) on a fixed data layer. We ask the orthogonal question: how much does the data model behind the tools matter? We treat a typed knowledge graph as a grounding substrate and route each question by how it is best answered: (i) LLM-generated Cypher for structured retrieval, which lifts the same GPT-4 model from 65% to 82-83%; (ii) native graph and optimization primitives, with no LLM, reaching 99% on graph-answerable scenarios; and (iii) generation-augmented knowledge (GAK) for answers absent from the data -- the engine's agent materializes the missing facts as provenance-tagged graph nodes, then answers. A recurring theme is inverted LLM usage: we constrain the LLM to query generation or one-shot enrichment from a typed schema and let the graph execute deterministically. On the 88 real AssetOpsBench failure-mode scenarios the benchmark itself flags non-deterministic -- ten equipment types absent from the graph -- GAK lifts answerability from zero to 100% of equipment types and answers 81.8% of scenarios, every materialized fact tagged source:LLM-derived for auditability. We also contribute 40 graph-native scenarios. For structured operational domains the data layer -- not the LLM orchestration -- is the primary lever, and a typed knowledge graph serves as a grounding substrate between raw industrial data and LLM reasoning.

LLM-based multi-agent systems have been widely adopted for knowledge retrieval and report generation, synthesizing known information through web search and textual reasoning. However, many critical information tasks in supply chains are not simple one-shot queries: they are structural inference problems requiring multi-hop reasoning across complex, fragmented web resources. Questions such as \textit{``Which Tesla components use lithium from Australian mines?''} have no answer in any single document; answers must be computationally synthesized through the autonomous construction and analysis of dynamic knowledge graphs assembled from fragmented, heterogeneous sources. Moreover, such discovery processes must be uncertainty-aware: decisions depend not only on answers but on calibrated confidence in their reliability, traceable to source quality and reasoning consistency. To address this capability gap, we propose \textit{Helicase}, an autonomous multi-agent LLM system for uncertainty-guided supply chain knowledge graph construction. \textit{Helicase} decomposes high-level supply-chain queries into executable investigation plans, coordinates specialized web-search, reasoning, and coding agents through iterative verification loops, and incrementally constructs query-specific supply chain knowledge graphs with per-fact uncertainty annotations. Its three-layer uncertainty framework tracks uncertainty at the action, trajectory, and memory layers, enabling both structural inference and calibrated confidence assessment. To evaluate autonomous reasoning across the full complexity spectrum, we introduce SCQA (Supply Chain Query Assessment), a benchmark of 80 supply chain queries organized into four quadrants spanning single-hop to multi-hop inference under both high and low data visibility.

Synthetic data offers a promising solution to two persistent barriers in supply chain analytics: data scarcity and data privacy. However, for synthetic data to support operational simulation and decision-making, it must do more than reproduce the statistical distributions of real records, and also preserve the \emph{operational logic} that governs supply chain processes, including the temporal orderings, mathematical dependencies, hierarchical taxonomies, and conditional rules that make a record operationally plausible. We consider this logic as the ``physics'' of supply chain data. Existing tabular generative models are primarily optimized for distributional fidelity and downstream predictive utility, and therefore often generate records that appear statistically realistic but violate fundamental operational constraints. This paper introduces \textbf{\textit{TabKG}}, a knowledge-graph-guided framework for logically consistent synthetic supply chain tabular data generation. TabKG constructs a \textbf{\textit{Column Relationship Knowledge Graph (CR-KG)}} to represent data operational dependencies. It uses a multi-LLM ensemble with majority voting to propose candidate relationships from column metadata, validates these relationships against real data to remove hallucinated or unsupported edges, and then uses the validated CR-KG to guide generation. Specifically, TabKG compresses the original table into independent columns, generates these columns using a latent diffusion model, and deterministically reconstructs dependent columns according to the validated relationships, enforcing logical consistency by construction with respect to the discovered operational rules.

We present RAGEAR (Retrieval-Augmented Graph-Enhanced Academic Recommender), a neurosymbolic recommender system for academic course recommendation. RAGEAR combines dense retrieval over full lecture transcripts with a symbolic Knowledge Graph modelling courses, lessons, transcript chunks, credits, study plans, and curricular information. The Knowledge Graph supports symbolic filtering and contextualisation based on structured constraints, such as credits, academic disciplines, study plans, and prerequisites. Unlike metadata-based approaches, it exploits fine-grained instructional content by retrieving transcript chunks semantically aligned with a student's query. The main contribution is a graph-aware aggregation function that propagates chunk-level evidence to course-level recommendations. The score combines three factors: the share of retrieved similarity associated with a course, the rank-based strength of its relevant chunks, and the distribution of evidence across lessons. We evaluate RAGEAR on 152 student-like queries through a human evaluation sample and a large-scale LLM-based relevance assessment. Results show that lecture transcripts improve over metadata-only retrieval, and that RAGEAR further improves ranking quality over a transcript-based normalized SumP baseline, especially for top-ranked recommendations.

LLM-based knowledge-graph question answering (KGQA) delegates graph traversal to language models, turning each question into a sequence of local relation-selection decisions repeated across beams and hops. A common but untested default is to serialize the complete partial path into every routing prompt, even though the controller already maintains this path as exact symbolic state. Bounded Path Context (BPC) decouples these two roles: the controller retains full paths in symbolic memory for answer extraction and audit, while the relation-selection prompt exposes only the question, the current entity, outgoing relation candidates, and at most the last K hops. A controlled sweep over K -- fixing graph neighborhoods, beam budget, depth, decoding, and answer-extraction format -- shows that bounded histories match or exceed full-history prompting on complete WebQSP and CWQ test sets with Qwen3.5-9B-AWQ: K=1 achieves 0.487 answer-set F1 on WebQSP versus 0.472 for full history, and K=0 reaches 0.287 on CWQ versus 0.274, with 9.7% and 12.1% fewer input tokens respectively. At the 4B scale, K=1 remains the strongest setting on both benchmarks. Per-example analysis reveals that 71-84% of examples are unaffected by history length, while the affected cases expose when prior hops disambiguate versus distract. These results suggest that path serialization length is better treated as a tunable interface variable than as a default assumption in LLM-based graph controllers.

We test the standard RLVR tool-use recipe -- GRPO on Qwen2.5-7B-Instruct -- on a deliberately minimal knowledge-graph tool API: four Freebase navigation verbs over Complex WebQuestions. Under a self-verifiable retrieval reward, the policy's tool-grounded answer rate climbs from $3.8\%$ to $9.6\%$ over 250 steps, then collapses to $0\%$ within a single 50-step window -- a \emph{peak-then-collapse} pattern replicated across four seeds. Across seven reward designs, we find four recurring failure modes: adding denser or more targeted proxy rewards shifts the failure mode rather than eliminating it. We argue that a key difference from Python interpreters, web search, and JSON APIs is interface feedback: their failures often leak natural-language signal the model saw in pretraining. A Python traceback names the failing line; an empty Freebase result \texttt{[]} does not. Stripping away that surface exposes a degradation regime that same-family reward redesigns do not fix. A direct oracle ablation rules out relation selection: injecting gold relations at every retrieval call lifts exact-match accuracy by only $+0.20$~pp, and $95.4\%$ of retrieval-dependent errors are retrieval-composition failures rather than answer-extraction failures. As a mitigation, one-iteration self-distillation reaches $40.0\%$ EM at 7B and is capacity-invariant: doubling capacity to 14B improves EM by only $0.25$~pp, and initialization barely matters -- the ceiling appears interface-bound within the 7B--14B range tested.

Complex Query Answering (CQA) is a fundamental knowledge representation and reasoning task over incomplete knowledge graphs (KGs). Answering existential first-order queries with $k$ free variables (i.e., $\text{EFO}_k$ queries) is a crucial yet challenging problem, as it requires ranking answer tuples in $\mathcal{E}^k$, where $\mathcal{E}$ denotes the entity set of a KG. This quickly becomes intractable as $k$ grows. Consequently, existing benchmarks and methods rely on marginal rankings over individual variables; however, marginal rankings are a poor proxy for the true joint ranking of tuples. Building on neural symbolic search for $\text{EFO}_1$ queries, we propose Neural Scalable Symbolic Search (NS3), a budgeted framework that approximates joint ranking without enumerating $\mathcal{E}^k$. NS3 (i) answers marginalized sub-queries to obtain necessary candidate sets, (ii) merges multiple free variables into hypernodes whose domains are pruned and controlled by a dynamic budget $B$, and (iii) progressively reduces an $\text{EFO}_k$ query to an $\text{EFO}_{k-1}$ query over a budgeted reduced domain. Across three standard KG datasets, NS3 substantially improves joint ranking performance while retaining strong marginal accuracy. We further release a joint-ranking benchmark that extends existing $\text{EFO}_1$ datasets to $k=3$, enabling systematic evaluation of multi-variable queries. Our code is provided in https://github.com/HKUST-KnowComp/NS3_KDD2026.

Dirty entity resolution (ER), which identifies records referring to the same real-world entity from a single, messy dataset, is a fundamental task in data management and mining. However, the dominant blocking-matching-clustering paradigm for ER suffers from critical flaws. Its cascaded, decoupled workflow essentially produces a static, sparse graph plagued by missing edges (due to blocking failures) and noisy links (due to matching errors), causing error propagation and yielding suboptimal clusters, particularly when rigid transitivity is imposed in the clustering. We contend that matching and clustering are fundamentally synergistic, both optimizing for the construction of an ideal entity graph. Building upon this insight, we propose Alper, a unified framework that integrates these steps into an iterative probabilistic label propagation process over a global, evolving graph. Unlike disjoint blocking, Alper refines the graph structure and labels dynamically by adaptively integrating "weak but cheap" signals from graph propagation with "strong but expensive" LLM-based pairwise queries. For higher cost-effectiveness, we formulate the signal selection as a constrained optimization problem maximizing cumulative marginal gain under a query budget, solved via our greedy algorithm with provable theoretical guarantees. Our extensive experiments over eight benchmark datasets demonstrate that Alper is consistently superior to state-of-the-art cascaded pipelines.

Metaphorical videos are prevalent across various real-world scenarios to convey complex ideas, and understanding them typically requires high-order cognitive capabilities. The lack of systematic studies on metaphorical video understanding not only constrains the real-world applicability of MLLMs but also impedes the thorough assessment of their high-order cognitive capabilities. To bridge this gap, we propose MetaphorVU-Bench, the first systematic and comprehensive benchmark dedicated to metaphorical video understanding. Through experiments, we find current MLLMs struggle with accurate metaphorical video understanding, lagging far behind human level, primarily due to defective cross-domain mapping. Motivated by this finding, we construct a metaphor knowledge graph as mapping augmentation and propose MetaphorBoost, an inference-time enhancement framework achieving consistent performance improvement. Our benchmark, analysis, and method provide useful insights and a foundation for future research on advancing MLLMs.

Knowledge graph (KG) is an abstraction that can be extracted from text corpora and used for in-depth reasoning. Prior work has leveraged KGs to fine-tune language models (LMs), enabling domain-specific superintelligence. In this work, we explore whether KG-driven in-depth reasoning capabilities can emerge in neuroscience using only information contained within a single authoritative textbook. The central hypothesis is that structured knowledge, when distilled into a high-quality KG and converted into KG-grounded question-answer (QA) supervision, is sufficient to produce expert-level reasoning through a fine-tuned LM that surpasses large language models (LLMs) in accuracy, while employing orders of magnitude fewer parameters. We construct a textbook-derived KG via a dual-LLM validation pipeline, expand it with a masked LM trained on the KG topology, generate multi-hop QA items, which include QA pairs and reasoning traces, to fine-tune an LM exclusively on KG-derived supervision, and apply reinforcement learning using path-derived KG signals as implicit reward models. Our results demonstrate that deep, mechanistic neuroscience understanding can be induced in the model without reliance on large, heterogeneous web-scale corpora. The KG-based synthetic neuroscience curriculum that readers can quiz themselves on, and the fine-tuned LM, are available at the following GitHub location: https://kg-bottom-up-superintelligence.github.io/neuro-bench.

Biological systems are governed by structured molecular interactions, where pathways, regulatory circuits, and functional gene relationships shape cellular behavior and disease progression. Much of this knowledge is naturally represented as graphs. However, most biomedical AI models cannot directly use graph-encoded biological knowledge and instead require compressed low-dimensional representations, which can lose important structure and reduce performance, especially in limited-sample clinical studies. Here, we introduce Graph-in-Graph (GiG), a knowledge graph-modulated deep learning framework for data-efficient clinical prediction. GiG represents each patient as a standalone modular graph, in which curated biological knowledge graphs define edges and patient-specific measurements, such as gene expression, define node features. This design allows multiple biological knowledge graphs to be integrated while preserving gene-gene interactions and pathway topology during patient-level representation learning. Across cohorts comprising nearly 9,700 patients and five clinical tasks, including liquid biopsy cancer detection, prostate cancer diagnosis, and 32-class pan-cancer classification, GiG consistently outperforms traditional and state-of-the-art methods, with the largest gains in limited-sample settings. On the challenging prostate cancer diagnosis task, GiG improves macro-F1 by up to 49 percentage points relative to competing methods. Control experiments replacing real pathway graphs with random topologies confirm that these gains arise from biologically grounded knowledge graph structure rather than graph modeling alone. These findings show that knowledge graph-modulated deep learning can improve robustness, interpretability, and sample efficiency in clinical data analysis, and provide a principled framework for integrating biological knowledge graphs into predictive modeling.

Knowledge graphs (KGs) offer a rich representation for relational knowledge, but their irregular structure makes retrieval challenging: ego-graph expansion grows rapidly, and dense embedding methods struggle with multi-hop compositional queries. Existing agent-based graph exploration approaches, while expressive, are often too expensive for large-scale retrieval. We introduce SeedER (Seed-and-Expand Retrieval), a retrieval framework that explicitly leverages KG structure through iterative, low-cost expansion. SeedER first seeds a compact set of core nodes using lightweight dense and entity-based retrieval, then selectively expands this set via a learned graph-aware policy trained with reinforcement learning. This design decomposes global reasoning into reusable local decisions, enabling efficient discovery of query-relevant nodes while tightly controlling expansion cost. We show theoretical limitations of dense retrieval on compositional graph queries, and establish advantages of SeedER from both compositional generalization and graph-constrained submodular optimization perspectives. Empirically, SeedER substantially improves recall with compact candidate sets over strong dense and graph-augmented baselines, making it an effective first-stage retriever for knowledge-intensive reasoning systems.

Hyper-relational knowledge graphs (HKGs) effectively represent complex facts. While inferring new knowledge in HKGs is a critical problem, current methods cast it as a simple link prediction, assuming that nearly all entities and relations within a fact are known, leaving only a single blank to be filled. However, this restricted assumption may not hold in real-world scenarios in which multiple, or even all, constituent components of a fact may be missing simultaneously. To bridge this gap, we introduce a task called fact generation: generating a valid hyper-relational fact from an arbitrarily masked query, i.e., completing a partially observed fact or generating a fact from scratch. We propose KREPE, the first generative representation learning method for HKGs that learns to model the probability distributions of missing components conditioned on the local fact components and global structure of HKGs via a masked discrete diffusion. KREPE models both the intra-fact dependencies by contextual message passing and inter-fact correlations by aggregating stochastically sampled contexts. KREPE seamlessly unifies link prediction and fact generation within a single training framework, achieving state-of-the-art performance on standard HKG link prediction benchmarks and outperforming LLM-based baselines in generating novel and correct facts.

Generative text-to-video systems can produce visually fluent educational clips, but they rarely encode the pedagogical content knowledge (PCK) needed for effective instruction, including prerequisite-aware sequencing, learner-adaptive depth, and sustained cognitive engagement. We present CourseBlueprint, a course-grounded pipeline for adaptive pedagogical video generation. Given a topic and learner persona, the system generates a structured teaching blueprint in a single forward pass over an undergraduate biomedical-imaging corpus (BMED 2300; twenty-three lectures, 1,116 slides). Instead of ad-hoc prompt chaining, the pipeline uses typed intermediate representations with validation: a scaffolding module builds a stage-labeled prerequisite concept graph with deterministic cycle removal, an adaptive controller assigns per-concept style specifications, and an engagement generator produces narration following a fixed hook->retrieval->core->analogy->forward contract. A deterministic slide-image override further grounds the rendered video by reusing instructor slides whenever retrieval confidence is high. We also release a reusable benchmark corpus and an evaluation harness combining repeated LLM-judge scoring with regex-grounded objective metrics. In a five-topic ablation, removing the engagement contract reduces the engagement score from 5.00 to 1.20, the adaptive score from 4.80 to 3.40, Flesch readability from 38.0 to 19.8, and analogy and retrieval-prompt counts to near zero. The slide-image override converts a 0/9 corpus-grounding failure into 9/10 successful slide matches on the same topic. These results show that pedagogical video quality depends less on surface fluency than on explicit, typed instructional contracts that make scaffolding, adaptation, engagement, and grounding auditable.

Deep learning has brought significant progress to medical image classification, yet most existing methods still rely on isolated visual evidence and cannot effectively leverage similar cases or external knowledge. In clinical practice, diagnosis is typically supported by similar historical cases and their associated symptoms. To explicitly model this evidence-based diagnostic process, we propose a case-aware reasoning framework driven by multimodal knowledge graphs for medical image classification. Specifically, we construct a case-aware multimodal knowledge graph as a structured diagnostic memory, where diseases, images, and symptoms are hierarchically organized. Given an input image, our method adaptively retrieves similar cases from this memory and extracts their corresponding case-centered subgraphs. We further introduce a knowledge propagation and injection mechanism, in which an image-centric Graph Attention Network aggregates heterogeneous semantics into case-based features, followed by a bidirectional cross-modal attention mechanism that injects these features into visual representations for cross-modal alignment. To mitigate noisy retrieval, we design a confidence-calibrated decision refinement scheme that estimates the reliability of each retrieved case by jointly considering prediction confidence and sample similarity, and reweights its contribution to the final prediction, providing interpretable case-level evidence. Extensive experiments on multiple medical imaging datasets demonstrate that our approach consistently outperforms strong baselines, while ablation and qualitative analyses validate its effectiveness and interpretability. The code is available at https://anonymous.4open.science/r/MKG-CARE-8B7B.

We present Epicure, a family of three sibling skip-gram ingredient embeddings retrained from scratch on a multilingual recipe corpus. We aggregate 4.14M recipes from 11 sources spanning seven languages, English, Chinese, Russian, Vietnamese, Spanish, Turkish, Indonesian, German, and Indian-English, and normalise the raw ingredient strings to 1,790 canonical entries via an LLM-augmented pipeline. A 203,508-edge ingredient-ingredient NPMI graph and an 80,019-edge typed FlavorDB ingredient-compound graph, 2,247 typed compound nodes across 15 categories, seed three Metapath2Vec variants that share architecture and hyperparameters and differ only in the random-walk schema: Cooc walks the co-occurrence graph only, Chem walks the typed compound metapaths only, and Core blends both via injected ingredient-ingredient walks at controlled mixing, placing each model at a distinct point on the chemistry-vs-recipe-context spectrum.

Integrating new data into knowledge graphs (KG) typically involves different tasks that are executed within workflows or pipelines There are many possible pipelines for a specific integration problem but there is not yet a general approach to evaluate the overall quality and performance of such pipelines to be able to determine the best choices. We therefore propose a new benchmark KGI-Bench to evaluate integration pipelines that ingest different kinds of input data into an existing KG. We evaluate pipelines by analyzing their output, i.e., the updated KG, with the three complementary quality metrics coverage, correctness and consistency. We also provide benchmark datasets (seed KG, overlapping input data of three formats, reference KG as a ground truth) for the movie domain. To demonstrate the applicability and usefulness of the proposed benchmark, we comparatively evaluate 12 pipelines and analyze their behavior across different input data formats and design choices.

Reinforcement learning under partial observability requires deciding what information to retain, yet most memory-based approaches do not explicitly model short-term-to-long-term transfer of symbolic observations. We study this transfer process in a temporal knowledge-graph memory setting and cast it as a neuro-symbolic value-based decision problem: for each observed triple, the agent chooses whether to keep or drop it before long-term insertion. To handle variable-sized short-term buffers, we use a per-item Q-learning design with shared parameters and a practical temporal-difference update over matched items across consecutive steps. On the RoomKG benchmark at long-term memory capacity 128, learned transfer decisions outperform symbolic and neural baselines, including symbolic baselines with temporal annotations and history-based LSTM/Transformer baselines. Across transfer-policy ablations, a lightweight local short-term-only variant performs best, and step-level behavior shows that the policy keeps navigation- and query-relevant facts while discarding lower-value candidate facts, supporting explicit and interpretable memory decisions under memory constraints.

Knowledge graphs have become the primary vehicle for data integration and are critical to the success of modern AI, but the diversity of KG modelling practices, from lightweight vocabularies to richly axiomatised ontologies, makes integration and reuse expensive and brittle. This challenge is particularly acute in neuro-symbolic AI, where bridging neural and symbolic components depends on the ability to reengineer KGs to fit new requirements; GenAI now offers unprecedented automation capability, but without a principled understanding of the KG space, such automation remains conceptually ungrounded. We introduce the ontological continuum as that missing conceptualisation, a theoretical construct a theoretical construct whose characterisation framework is defined by two orthogonal distinctions: semantics vs pragmatics, and properties vs affordances; together these define a vocabulary to describe, compare, navigate, and transform KGs across the full range of modelling practices. The methodological stance is empirical: rather than prescribing how KGs should be modelled, the continuum aims to define a theory of the existent, derived from observation of real-world KG engineering practices and whose structure can be made formally explicit, for example, through Formal Concept Analysis (FCA). We ground the vision through a case study on provenance knowledge, showing how a single concern manifests differently across the continuum. We articulate five open research challenges and invite the community to develop the ontological continuum as a shared research agenda.

An extraction schema should not reduce knowledge graph fidelity. On statistical CSV, however, it can. We study country-by-year time-series matrices, a common layout on open-data portals. In this setting, serialization format and schema constraints interact super-additively. Their joint effect exceeds the sum of independent effects by up to +1.180 (2x2 factorial, 6 datasets). Bootstrap 95% CIs are strictly positive on 4/6 datasets, with strongest evidence on wide Type-II matrices. More critically, a schema applied to a mismatched format can trigger catastrophic mismatch. Fact coverage falls below the unconstrained baseline on 4/6 datasets through entity inflation or extraction refusal. We call this observed pattern format-constraint coupling. Probing and token ablation support a surface-form anchoring explanation centred on column-name references. Controlled variants across format-schema pairings, GraphRAG hosts, and LLM families show the same direction within the measured scope; one LLM family shows only partial activation. The observation also has a diagnostic consequence. Three standard retrieval modes largely mask construction quality (delta <= 1pp), whereas direct graph access exposes gaps up to +47.6pp (p < 0.0001). To support fidelity-aware evaluation, we release CSVFidelity-Bench. It contains 15 datasets, 11 Type-II matrices, 4 Type-III tables, and 1,892 Gold Standard facts across 6 domains.

The exponential growth of global academic output has confronted researchers and AI agents with an unprecedented information explosion,'' where fragmented and unstructured knowledge organization impedes deep interdisciplinary integration. Current academic retrieval tools predominantly rely on superficial keyword matching or vector-space semantic retrieval, which lack the topological reasoning capabilities required to navigate complex logical connections. Agentic deep-research-based frameworks are often prone to logical hallucinations and consuming high inference costs. To bridge this gap, in this report, we introduce SciAtlas, a large-scale, multi-disciplinary, heterogeneous academic resource knowledge graph designed as a panoramic scientific evolution network. By integrating over 43M papers from 26 disciplines, and a total of 157M entities and 3B triplets, SciAtlas provides a structured topological cognitive substrate that dismantles disciplinary barriers and furnishes AI agents with a global perspective. Furthermore, we develop a neuro-symbolic retrieval algorithm featuring tri-path collaborative recall and graph reranking, achieving a seamless transition from simple semantic matching to deterministic association discovery. We also present key application directions of SciAtlas, including literature review, automated research trend synthesis, idea positioning, and academic trajectory exploration, to demonstrate that SciAtlas can serve as an effective cognitive map'' to empower the full loop of automated scientific research while significantly reducing reasoning costs. We have released the interfaces for KG retrieval and various downstream tasks in our GitHub repo.

Graph-based Retrieval Augmented Generation (GraphRAG) extends retrieval-augmented generation to support structured reasoning over complex corpora, but its reliability under resource-constrained, privacy-sensitive deployments remains unclear. In healthcare, where Electronic Health Record (EHR) data is complex and strictly regulated, reliance on cloud-based large language models (LLMs) introduces challenges in cost, latency, and compliance. In this work, we present a systematic evaluation of GraphRAG for EHR schema retrieval using locally deployed open-source LLMs. We implement the Microsoft GraphRAG pipeline on real-world EHR schema documentation and benchmark four models, including Llama 3.1 (8B), Mistral (7B), Qwen 2.5 (7B), and Phi-4-mini (3.8B), each deployed via Ollama on a single consumer GPU (8 GB VRAM). We evaluate indexing efficiency, knowledge graph construction, query latency, answer quality, and hallucination under both global and local retrieval modes. Our results reveal substantial differences: Llama 3.1 produces the richest knowledge graph (1,172 entities), Qwen 2.5 achieves the best answer quality (3.3/5), Phi-4-mini fails to complete the pipeline due to structured-output errors, and Mistral exhibits degenerate repetition behavior. We further show that GraphRAG exhibits a practical capacity threshold, where models below approximately 7B parameters fail to reliably produce valid structured outputs and cannot complete the pipeline. In addition, indexing and answer quality are decoupled across models, and local retrieval consistently outperforms global summarization in both latency and factual grounding, with reduced hallucination. These findings demonstrate that GraphRAG is feasible on consumer hardware while highlighting the importance of model selection and retrieval design for robust deployment in regulated settings.

Modern Large Language Models (LLMs) have shown impressive performances in user-facing tasks such as question answering, as well as consistent improvements in reasoning capabilities. Still, the way these models encode knowledge seems inherently flawed: by design, LLMs encode world-knowledge within their parameters. This way of representing knowledge is inherently opaque, difficult to debug and update, and prone to hallucinations. On the other hand, Knowledge Graphs can provide human-readable and easily editable world knowledge representations, and their application in knowledge-intensive tasks has consistently proven beneficial to downstream performance. Nonetheless, current integration techniques require extensive retraining or finetuning. To overcome this issue, we introduce KoRe, a methodology to encode 1-hop sub-graphs into compact discrete knowledge tokens and inject them into a LLM backbone. We test the proposed approach on three established benchmarks, and report competitive performances coupled with a significant reduction (up to 10x) in token usage. Our results show that compact discrete KG representations can efficiently and effectively be used to ground modern LLMs.

Graph Anomaly Detection (GAD) aims to identify atypical graph entities, such as nodes, edges, or substructures, that deviate significantly from the majority. While existing text-rich approaches typically integrate structural context into the data representation pipeline using raw textual features, they often neglect the structural context of nodes. This limitation hinders their ability to detect sophisticated anomalies arising from inconsistencies between a node's inherent content and its topological role. To bridge this gap, we propose TERGAD (Structure-aware Text-enhanced Representations for Graph Anomaly Detection), A novel data augmentation framework that enriches structural semantics for GAD via the semantic reasoning capabilities of Large Language Models (LLMs). Specifically, TERGAD translates node-level topological properties into descriptive natural language narratives, which are subsequently processed by an LLM to derive high-level semantic embeddings. These embeddings are then adaptively fused with original node attributes through a gated dual-branch autoencoder to jointly reconstruct both graph structure and node features. The anomaly score is computed based on the integrated reconstruction error, effectively capturing deviations in both observable attributes and LLM-informed semantic expectations. Extensive experiments on six real-world datasets demonstrate that TERGAD consistently outperforms state-of-the-art baselines. Furthermore, our ablation studies validate the indispensable role of structural semantic guidance and the efficacy of the gated fusion mechanism. Code is available at https://github.com/Kantorakitty/TERGAD-main.

Knowledge Graphs (KGs) are a powerful representation of linked data, offering flexibility, semantic richness, and support for knowledge enrichment and reasoning. They help data owners organize and exploit heterogeneous data to provide insightful services (e.g., recommendations), yet real-world KGs are often incomplete, hiding true facts or missing valuable insights. Knowledge graph embedding techniques are commonly used to infer valuable missing information. However, reasoning over KGs can inadvertently expose sensitive user information, even when such data is not explicitly stored. In this work, we investigate the privacy risks associated with KGE-based reasoning, focusing on attribute inference attacks where adversaries attempt to deduce sensitive user attributes from seemingly non-sensitive outputs. We propose and evaluate a framework that mitigates these privacy risks by applying post processing sanitization techniques to KGE outputs. Preliminary results demonstrate the effectiveness of these attacks on the outputs of KGE models, and explore the trade-off between recommendation quality and privacy protection when applying randomization based approaches, highlighting the need to experiment with more advanced techniques in future work to address this issue.

Cross-domain knowledge alignment is essential for integrating heterogeneous medical systems, yet existing approaches typically treat entity alignment as a static matching problem, ignoring query context and cross-system asymmetry. This limitation is particularly critical in integrative medical settings, where correspondence between concepts is inherently context-dependent, non-bijective, and direction-sensitive. In this paper, we propose Query-Conditioned Entity Alignment (QCEA), which reformulates entity alignment as a query-conditioned correspondence problem. Instead of learning a fixed mapping between entity representations, QCEA treats the textual description of a source entity as a query and ranks candidate entities in the target graph, enabling context-dependent alignment. The framework integrates semantic encoding, graph-based representation learning, and a direction-aware transformation module to capture asymmetric and many-to-many correspondence across heterogeneous knowledge systems. We evaluate QCEA on TCM--WM knowledge graphs derived from SymMap, covering both symptom alignment and herb--molecule alignment tasks. Experimental results show consistent improvements over representative baselines, particularly on rank-sensitive metrics such as Hit@K and MRR. Furthermore, downstream retrieval-augmented generation (RAG) experiments demonstrate that improved alignment leads to better evidence retrieval, stronger grounding, and higher answer accuracy. These findings highlight that alignment is not merely a data integration step, but a key factor that shapes knowledge accessibility and reliability in cross-system medical reasoning.

Software repositories accumulate large amounts of unstructured knowledge in commit messages, pull-request discussions, and issue threads, but developers and AI coding assistants rarely reuse this history effectively. Recent work on typed-memory architectures for LLM agents (MemGPT, generative agents, and the PlugMem module of Yang et al.) argues that agent memory should be distilled, typed knowledge rather than raw interaction text. We adapt that stance to a software repository's own git history under a constrained regime: deterministic, dependency-free, local-only, no embeddings. We present CommitDistill, an open-source Python prototype that mines a local git history into typed knowledge units (Facts, Skills, Patterns) using deterministic regex and surfaces them through a TF-IDF retriever with a calibrated silence threshold (theta = 2.5) that abstains on out-of-distribution queries. The artefact is a trust-instrumented memory substrate: deterministic, no external service, inspectable plain-JSON store, tunable abstention. A case study on five public repositories spanning Python, JavaScript, C, and Java (25,000 commits, 1,167 extracted units) reports useful-precision 0.525 at Cohen's kappa = 0.633 on 40 dual-annotated Python units. The decisive finding is budget-constrained retrieval: at a 256-character per-query budget, CommitDistill reaches 0.750 hit-rate on a 12-query benchmark against BM25's 0.333 and git log --grep's 0.083. On a four-arm paired LLM-as-judge evaluation (n=200 time-travel bug-fixes, two judges) covering control, CommitDistill, a body-budget-matched CD-Hybrid, and BM25, no condition produces a statistically detectable lift over control on the headline mean and CD-Hybrid is indistinguishable from BM25 head-to-head. Extraction over 10,000 commits completes in under 4 seconds on a laptop. Source, annotations, baselines, and a reproducibility script accompany this paper.

We introduce Graph-Augmented Sequence-to-Sequence (GA-S2S), a novel framework that integrates a T5-small encoder-decoder with a Relational Graph Attention Network (RGAT) to improve link prediction in knowledge graphs. While existing Seq2Seq models rely solely on surface-level textual descriptions of entities and relations and at best, flatten the neighborhoods of a query entity into a single linear sequence, thereby discarding the inherent graph structure, GA-S2S jointly encodes both textual features and the full $k$-hop subgraph topology surrounding the query entity. By integrating raw encoder outputs with RGAT's relation-aware embeddings, our model captures and leverages richer multi-hop relational patterns and textual information. Our preliminary experiments on the CoDEx dataset demonstrate that GA-S2S outperforms competitive Seq2Seq-based baseline models, achieving up to a 19% relative gain in link prediction accuracy.

The preservation and interpretation of cultural heritage increasingly rely on digital technologies, among which Knowledge Graphs (KGs) stand out for their ability to structure vast amounts of data. However, the construction and expansion of these KGs often face challenges due to the diverse and complex nature of cultural heritage information. In this paper, we propose a novel approach for extending KG resources in the domain of cultural heritage, which we applied to French data. First, we introduce a new knowledge graph in the domain of French cultural heritage, WJoconde, which is distinguished by its multimodality as it integrates both textual and image information of the entities. We further introduce three variants of WJoconde to facilitate downstream research, such as Knowledge Graph Completion (KGC). We also built a comprehensive benchmark for KGC methods on our dataset. Second, we propose a new framework for extending cultural heritage KGs using multi-modal approaches leveraging Large Language Models (LLMs) and Vision-Language Models (VLMs), which includes automated data extraction from unstructured resources combined with a special validation pipeline for grounding the output of both models, to further extend WJoconde. Our results show that by integrating the rich text and image information in cultural heritage data, we can efficiently enhance KGs with high reliability. We open-source all code and benchmark datasets with text and images, as well as the original data with an interactive access point

Existing LLM-driven knowledge graph (KG) construction methods predominantly employ stateless batch processing pipelines, exhibiting structural deficiencies in cross-chunk semantic relation capture, entity disambiguation, and construction process interpretability. These limitations undermine KG quality, retrieval precision, and deployment trust in high-stakes domains. We propose RAGA (Reading And Graph-building Agent), an LLM-based autonomous KG construction and retrieval fusion framework. RAGA provides an atomic toolset supporting full KG lifecycle CRUD operations and embeds a Read-Search-Verify-Construct cognitive constraint into a ReAct tool loop. A KG-vector synchronization mechanism enables hybrid symbolic-vector retrieval, while evidence-anchored verification links every knowledge entry to its source text for auditable provenance. Preliminary experiments on a subset of the QASPER scientific QA dataset indicate that RAGA's fusion retrieval outperforms zero-shot baselines, with KG integration providing measurable gains in both answer and evidence quality. The framework design and experimental baseline serve as a reference for agent-driven autonomous KG construction.

Security knowledge graphs can provide computable external memory for security agents, but constructing them from long-form cyber threat intelligence (CTI) remains difficult: LLMs often lack grounded security-domain knowledge, and end-to-end document-to-graph training is hard to supervise with cheap, stable rewards. We present GRID (Graph Representation of Intelligence Data), an end-to-end framework for security text knowledge graph construction. GRID first builds security-domain supervision from CTI articles by creating traceable article-graph alignments through graph extraction and knowledge-graph-conditioned text revision. It then turns document-to-graph learning into a scripted task bank combining four-option multi-select questions with triple-level regex matching targets, yielding more stable task-specific rewards than repeatedly scoring full graph outputs with an LLM judge. Using this supervision pipeline, we train two Qwen3-4B-Instruct-2507-based 4B extractors: a primary Task-bank Reward model and a secondary End2End Reward model with LLM-as-judge precision/recall rewards. On 249 CTI articles from GRID, CASIE, CTINexus, MalKG, and SecureNLP, the Task-bank Reward model with the ontology-guided GRID extraction pipeline reaches 84.62% source-averaged precision, 64.91% source-averaged recall, and 68.53% Avg F1, achieving the best source-averaged recall and near-top Avg F1 with lower token usage and deployment cost. The End2End Reward model reaches 76.91% precision, 53.85% recall, and 58.06% Avg F1. Further analyses show that task-bank rewards can be built once offline and reused across later post-training runs, outperforming online End2End LLM-as-judge reward and weaker alternatives such as Choice-only Reward and End2End SFT without RL.

Metacognition-the ability to monitor one's own knowledge state, spot gaps, and autonomously fill them--remains largely absent from modern AI. Here, we present MetaKGEnrich, a fully automated pipeline that endows large language model (LLM) applications with self-directed knowledge repair. The system (i) builds knowledge graphs from a seed query, (ii) detects sparse regions via seven graph metrics, (iii) has GPT-4o generate targeted questions, (iv) retrieves web evidence with Tavily and ingests it into Neo4j, and (v) re-answers the query with GraphRAG for GPT-4 to evaluate improvement. Tested on 30 queries from each of three widely-used datasets: Google Research Natural Questions, MS MARCO, and Hot-potQA. MetaKGEnrich improved answer quality in 80% of HotpotQA questions, 87% of Google Research Natural Questions and 83% of MS MARCO questions, while preserving well-supported regions. This proof of concept demonstrates how topological self-diagnosis plus targeted retrieval can advance AI toward humanlike metacognitive learning.

Evaluating multi-turn dialogue systems remains challenging because response quality depends not only on the current prompt, but also on previously established entities, claims, and conversational commitments. Existing automatic evaluators, including LLM-as-a-judge frameworks and embedding-based metrics, largely rely on flat or turn-isolated representations, making them less effective at detecting long-range issues such as contradiction, topic drift, and entity inconsistency. To address this, we propose SKG-Eval, a quasi-deterministic and interpretable framework that models dialogue as an evolving Semantic Knowledge Graph (SKG) of entities, relations, and commitments across turns. The framework incrementally updates the graph through structured triple extraction and computes three complementary signals: (i) local relevance, measuring alignment with the current prompt and optional reference; (ii) historical consistency, evaluating how newly introduced information connects to prior conversational context using graph-based and embedding-driven signals; and (iii) logical coherence, assessed by a geometric contradiction engine that detects cross-turn conflicts without relying on NLI models or LLM judges. These signals are adaptively fused and aggregated into a length-invariant session score via recency-weighted trend analysis. Across multiple benchmarks, SKG-Eval achieves higher correlation with human judgments and substantially improves detection of long-range inconsistencies in extended conversations. In addition, the framework produces explicit contradiction certificates and deterministic scores for fixed inputs, enabling reproducible and auditable evaluation. Overall, our results suggest that structured externalized state tracking through semantic knowledge graphs provides a scalable alternative to implicit reasoning in LLM-based dialogue evaluators.

Knowledge Graphs are pivotal for semantic data integration. The real-world data they model is often inherently uncertain. Within knowledge graphs, uncertainty manifests in three distinct levels: imprecise attribute values, probabilistic triple existence, and incomplete schema knowledge. However, current Semantic Web standards lack native support for reasoning over such uncertainty, and naïve extensions often incur computational intractability. In this thesis, I aim to develop a modular framework that addresses each level through tailored techniques: (1) defining probabilistic literals and a corresponding query algebra for continuous attributes; (2) a compilation-based framework transforming SPARQL provenance into tractable probabilistic circuits for uncertain triples; and (3) topology-aware geometric embeddings for statistical schema reasoning. The central hypothesis is that specialized reasoning mechanisms, namely algebraic, logical, and geometric approaches, can reconcile semantic precision with computational tractability.

Knowledge graph (KG) foundation models aim to generalize across graphs with unseen entities and relations by learning transferable relational structure. However, most existing methods primarily emphasize relation-level universality, while in-context learning, the other pillar of foundation models remains under-explored for KG reasoning. In KGs, context is inherently structured and heterogeneous: effective prediction requires conditioning on the local context around the query entities as well as the global context that summarizes how a relation behaves across many instances. We propose KGPFN, a KG foundation model using Prior-data Fitted Network that unifies transferable relational regularities with inference-time in-context learning from structured context. KGPFN first learns relation representations via message passing on relation graphs to capture cross-graph relational invariances. For query-specific reasoning, it encodes local neighborhoods using a multi-layer NBFNet as local context. To enable ICL at global scale, it constructs relation-specific global context by retrieving a large set of instances of the query relation together with their local neighborhoods, and aggregates them within a Prior-Data Fitted Network framework that combines feature-level and sample-level attention. Through multi-graph pretraining on diverse KGs, KGPFN learns when to instantiate reusable patterns and when to override them using contextual evidence. Experiments on 57 KG benchmarks demonstrate that KGPFN achieves strong adaptation to previously unseen graphs through in-context learning alone, consistently outperforming competitive fine-tuned KG foundation models. Our code is available at https://github.com/HKUST-KnowComp/KGPFN.

Knowledge Graphs (KGs) are extensively used across different domains and in several applications. Often, these KGs are very large in size. Such KGs become unwieldy for tasks such as question answering and visualization. Summarization of KGs offers a viable alternative in such cases. Furthermore, personalized KG summarization is crucial in the current data-driven world as it captures the specific requirements of users based on their query patterns. Since it only maintains relevant information, the personalized summaries of KG are small, resulting in significantly smaller storage requirements and query runtime. In this work, we adapt the coreset theory to create personalized KG summaries. For a given dataset and a user-specific query workload, we present an approach that samples a relevant subset of triples using sensitivity-based importance sampling. We ensure that the subset approximates the characteristics of the full dataset with bounded approximation error. We define sensitivity scores that measure the importance of a triple with respect to a user's query workload, which are then used by our coreset construction algorithm. We explicitly focus on personalized knowledge graph summarization by constructing summaries independently for each user based on their query behaviour. Our evaluation on Freebase, WikiData, and DBpedia shows that COREKG delivers higher query-answering accuracy and structural coverage than the state-of-the-art methods, such as GLIMPSE, PPR, iSummary, PEGASUS and APEX$^2$ while requiring only a tiny fraction of the original graph.

Multilingual knowledge editing (MKE) remains challenging because language-specific edits interfere with one another, even when locate-then-edit methods work well in monolingual settings. This paper focuses on three issues: the effectiveness of vector merging methods for MKE, the extent to which Task Singular Vectors for Merging (TSVM) can reduce multilingual interference, and the influence of the weight scaling factor and rank compression ratio on performance. We evaluate six merging variants with two popular backbone large language models, two base knowledge editing methods, and 12 languages on the MzsRE benchmark under a large-scale batch-editing setting. Our results show that vector summation with shared covariance is the most reliable overall strategy, whereas simple summation without shared covariance performs poorly. TSVM improves performance in some settings, but its ability to mitigate multilingual interference is limited. We also find that performance is sensitive to both weight scale and rank ratio, with larger-than-default scaling and relatively low rank often yielding better results. These findings clarify the practical strengths and limits of current vector merging methods for MKE and provide guidance for future multilingual knowledge editing research.

We introduce PersonalAI 2.0 (PAI-2), a novel framework designed to enhance LLM-based systems through integration of external knowledge graphs (KGs). The proposed approach addresses key limitations of existing Graph Retrieval-Augmented Generation (GraphRAG) methods by incorporating a dynamic, multistage query-processing pipeline. The central point of the PAI-2 design is its ability to perform adaptive, iterative information search, guided by extracted entities, matched graph vertices, and generated clue-queries. An evaluation conducted on five benchmarks (Natural Questions, TriviaQA, HotpotQA, 2WikiMultihopQA, and MuSiQue) demonstrates an improvement in the factual correctness of generated answers compared to analogue methods (LightRAG, RAPTOR, HippoRAG 2, and PAI-1). PAI-2 achieves a 9% average gain by LLM-as-a-Judge on the 2WikiMultihopQA and MuSiQue benchmarks, and attains accuracy comparable to HippoRAG 2 on the TriviaQA and HotpotQA benchmarks, reflecting its effectiveness in reducing hallucination rates and increasing precision. We show that enabled search plan enhancement mechanism gain 18% boost compared to disabled one by LLM-as-a-Judge across five benchmarks. In addition, an ablation study reveals that PAI-2 achieves SOTA result on the MINE-1 benchmark, obtaining an 89% information-retention score with LLMs in the 7--15B tiers. Collectively, these findings underscore the potential of PAI-2 to serve as a reusable component for personalized AI applications, which require scalable, context-aware knowledge-representation and reasoning capabilities. The source code of PAI-2 is available at the following link: https://github.com/Dzigen/PersonalAI.

We introduce KadiAssistant, a privacy-by-design AI assistant integrated into the Kadi research data ecosystem, enabling researchers to efficiently access, aggregate, and synthesize information from heterogeneous, privacy-sensitive research data. Interdisciplinary fields such as materials science bring together disciplines with their own terminology and standards. While this convergence fuels innovation, it also makes it increasingly difficult to connect and access knowledge, as data are distributed across disciplines, organizations, and individuals. For example, battery research combines electrochemical measurements, materials characterization data, physics-based simulations, and manufacturing parameters, each using different formats, vocabularies, and standards. Efficiently storing and sharing such heterogeneous data via research data platforms, such as Kadi4Mat, demands domain knowledge, technical expertise, and familiarity with metadata schemas and interfaces. Research data also vary in sensitivity: newly generated 'warm' data are often private, whereas published 'cold' data are usually openly accessible. The Kadi ecosystem offers fine-grained access control needed for sensitive data. A solution for efficient information retrieval in Kadi must therefore respect the fine-grained access permissions. To address these intertwined challenges of information retrieval, strong data privacy, and complex access control, KadiAssistant combines a self-hosted large language model (LLM) with a privacy-preserving semantic search, inspired by retrieval-augmented generation, that can access files and record metadata on Kadi. This allows the assistant to screen, aggregate, and structure information into a highly informative answer. KadiAssistant therefore bridges terminology and standards, lowers access barriers for researchers, and strengthens the Findable pillar of FAIR data principles.

To effectively interact with the real world, Large Language Models (LLMs) require entity-based commonsense reasoning, a challenging task that necessitates integrating factual knowledge about specific entities with commonsense inference. Existing datasets for evaluating LLM entity-based commonsense reasoning have largely focused on True/False or multiple-choice questions, leaving the explicit assessment of the model's ability in abductive reasoning about causes and effects and generating explanations largely unexamined. In this work, we introduce CommonWhy, a dataset of 15,000 why questions designed to evaluate entity-based commonsense reasoning about causal relationships in LLMs. CommonWhy also serves as a Knowledge Graph Question Answering (KGQA) benchmark, as all supporting knowledge required to answer its queries is available in the Wikidata knowledge graph. Unlike existing KGQA datasets, which primarily test fact retrieval, CommonWhy targets causal commonsense reasoning, establishing a new paradigm for KGQA evaluation. Experiments with state-of-the-art LLMs and LLM-based KGQA methods reveal their significant shortcomings, including frequent factual hallucinations and failures in causal reasoning.

Automated data quality assessment is crucial for managing big data, but existing solutions face challenges in achieving accurate context-aware assessment. This paper presents a novel knowledge-based approach to enhance automated data quality assessment. Our approach utilizes knowledge graph embeddings to predict missing edges between the input dataset's context representation and the relevant quality rules and dimensions within a knowledge graph representing contextual data characteristics and the required quality assessment operations. We surpass conventional practices by integrating diverse representations within the knowledge graph, drawing insights from contextual information from a thorough literature investigation. This integration allows us to develop a comprehensive and context-specific data quality assessment plan tailored to each context. Leveraging the knowledge graph improves our understanding of the input dataset's context, overcoming the limitations of traditional methods that rely solely on strict matching and overlook contextual characteristics. By injecting numerical edge attributes, we assign corresponding weights to each predicted quality measurement, providing a comprehensive data quality assessment plan for the input dataset. To evaluate our approach, we leverage AmpliGraph, a framework developed and benchmarked by AccentureLabs. The evaluation involves employing a real-world radiation sensors dataset provided by the Lebanese Atomic Energy Commission (LAEC-CNRS). The results obtained from this evaluation demonstrate the capability of our solution to generate a comprehensive data quality assessment plan for the given input dataset.

Modern GUI agents typically rely on a model-centric and step-wise interaction paradigm, where LLMs must re-interpret the UI and re-decide actions at every screen, which is fragile in long-horizon tasks. In this paper, we propose Executable Agentic Memory (EAM), a structured Knowledge Graph (KG) that shifts GUI planning from free-form generation to a robust retrieval-and-execution process. Our approach includes a sample-efficient memory construction pipeline using state-aware DFS and action-group mining to compress multi-step routines. To ensure efficient planning, we introduce a value-guided graph search where a lightweight Q-function model steers Monte Carlo Tree Search (MCTS) over the KG. We theoretically establish bias-consistency for the Q-model and derive sample complexity bounds for path recovery. Empirically, EAM outperforms state-of-the-art baselines like UI-TARS-7B by up to $19.6\%$ on AndroidWorld, while reducing token costs $6\times$ relative to GPT-4o. With a $2.8$s average latency, EAM enables reliable, quick, and long-horizon GUI automation.

We propose graph-grounded optimization: a paradigm in which the decision variables, constraints, and objective coefficients of a real-world optimization problem are sourced from a property knowledge graph (KG) via Cypher queries, rather than supplied as free-form natural-language text or static tabular input. We motivate the paradigm by surveying recent LLM/SLM-driven optimization systems -- OptiMUS, Chain-of-Experts, LLMOPT, OPRO, FunSearch, Eureka -- none of which consume property graphs as the primary input modality. We instantiate the paradigm in the open-source samyama-graph database and evaluate seven real-world public-domain KG-backed problems spanning drug repurposing (245K-node biomedical KG), clinical-trial site selection (7.78M-node trial registry), Indian supply-chain rerouting (5.34M-node OSM road graph), healthcare equity allocation (WHO/GAVI/IHME KG), economic-environmental grid dispatch, antimicrobial-resistance stewardship (NCBI AMRFinderPlus, 10.4K resistance genes), and wildfire evacuation routing (OSM Paradise, CA). We compare a portfolio of Rao-family metaheuristics (BMWR, Jaya, SAMP-Jaya, EHR-Jaya, Rao-1) against Google OR-tools (CP-SAT and GLOP) reference solvers. We find that (i) no single Rao variant dominates: BMWR wins on discrete-with-tradeoff and high-dim-with-hard-constraint problems while Rao-1 wins on continuous low-/mid-dim problems, empirically supporting a portfolio approach; (ii) OR-tools dominates on small linear/MILP-friendly sub-problems but cannot encode the non-linear objectives that emerge in several of the real-world settings; (iii) graph-grounded formulations surface data-quality issues (missing properties, degenerate aggregates) that purely text-formulated optimizations would silently mask

Graph Neural Networks (GNNs) have emerged as a powerful paradigm in Knowledge Graphs (KGs) due to their intrinsic ability to model graph-structured data. However, there remains a lack of a systematic review about GNN-based methodologies across the entire knowledge graph technologies pipeline. To address this gap, we first propose a novel two-level taxonomy framework for GNN-based knowledge graph technologies: the KG technologies pipeline and GNN-based perspective. Specifically, the knowledge graph technologies pipeline covers knowledge graph construction, knowledge graph embedding, knowledge reasoning and knowledge graph applications. Meanwhile, the GNN-based perspective provides a new categorization of knowledge graph technologies with GNN models, such as GCN, GAT, and HGNN. Then, we analyze the advantages of GNN technology based on the characteristics of different tasks in the knowledge graph lifecycle. Furthermore, we detailed review various GNN-based models for knowledge graph following the proposed taxonomy, and summarize strengths and limitations. Finally, we discuss unresolved challenges and outline promising directions for future research.

Knowledge Graph Question Answering (KGQA) aims to answer user questions by reasoning over Knowledge Graphs (KGs). Recent KGQA methods mainly follow the retrieval-augmented generation paradigm to ground Large Language Models~(LLMs) with structured knowledge from KGs. However, training effective models to retrieve question-relevant evidence from KGs typically requires high-quality intermediate supervision signals, such as question-relevant paths or subgraphs, which are time- and resource-intensive to obtain. We propose PathISE, a novel framework for learning high-quality intermediate supervision from answer-level labels. PathISE introduces a lightweight transformer-based estimator that estimates the informativeness of relation paths to construct pseudo path-level supervision. This supervision is then distilled into an LLM path generator, whose generated paths are grounded in the KG to provide compact evidence for inductive answer reasoning. ExtensiveISE experiments on three KGQA benchmarks show that PathISE achieves competitive or state-of-the-art KGQA performance, and provides reusable supervision signals that can enhance existing KGQA models, without relying on costly LLM-refined supervision signals. Our source code is available at https://anonymous.4open.science/r/PathISE-2F87.

Biomedical knowledge graphs are increasingly large, dynamic, and multimodal, driven by rapid advances in biotechnology such as high-throughput sequencing. Machine learning models can infer previously unobserved biomedical relationships and characterize biomedical entities in these graphs, but existing knowledge graph embedding methods and their continual learning extensions either assume static graph structure or fail to exploit multimodal information under evolving data distributions. They also apply uniform regularization across all model parameters, ignoring that different modalities may exhibit distinct forgetting dynamics as the graph evolves. We propose the Continual Multimodal Knowledge Graph Learner (CMKL), a CL framework for biomedical KGs that natively encodes structure, text, and molecules, fuses them through a Mixture-of-Experts (MoE) router, and protects previously learned knowledge with standard EWC regularization and a K-means-diverse multimodal replay buffer. We evaluate CMKL on a 129K-entity biomedical continual benchmark with 10 tasks. On continual biomedical entity classification, CMKL reaches AP 0.591 versus 0.370 for the strongest structural baseline, a 60% gain that is driven by access to multimodal features and preserved across the sequence with near-zero forgetting (AF 0.008). On continual relationship prediction, CMKL reaches AP $0.062$, matching Naive Sequential and EWC (0.058) within seed noise and outperforming Joint Training (0.047, p=0.045) and LKGE (0.039). A frozen-text ablation reaches AP 0.136, more than double any jointly trained model, yet that signal is unreachable by margin-ranking gradients: the greedy-modality asymmetry lives at the representation level, not the fusion level, and MoE routing manages it by suppressing the unreachable modality without forcing it through a learned bottleneck. Code: github.com/yradwan147/cmkl-neurips2026

Agent-compiled knowledge bases provide persistent external knowledge for large language model (LLM) agents in open-ended, knowledge-intensive downstream tasks. Yet their quality is systematically limited by \emph{incompleteness}, \emph{incorrectness}, and \emph{redundancy}, manifested as missing evidence or cross-document links, low-confidence or imprecise claims, and ambiguous or coreference resolution issues. Such defects compound under iterative use, degrading retrieval fidelity and downstream task performance. We present \textbf{DeepRefine}, a general LLM-based reasoning model for \emph{agent-compiled knowledge refinement} that improves the quality of any pre-constructed knowledge bases with user queries to make it more suitable for the downstream tasks. DeepRefine performs multi-turn interactions with the knowledge base and conducts abductive diagnosis over interaction history, localizes likely defects, and executes targeted refinement actions for incremental knowledge base updates. To optimize refinement policies of DeepRefine without gold references, we introduce a Gain-Beyond-Draft (GBD) reward and train the reasoning process end-to-end via reinforcement learning. Extensive experiments demonstrate consistent downstream gains over strong baselines.

Large language models have significantly improved natural language interfaces to databases by translating user questions into executable queries. In particular, Text2Cypher focuses on generating Cypher queries for graph databases, enabling users to access graph data without query language expertise. Most existing Text2Cypher systems assume a single preselected graph database, where queries are generated over a known schema. However, real-world systems are often distributed across multiple independent graph databases organized by domain or system boundaries, where relevant information may span multiple sources. To address this limitation, we propose a shift from single-database query generation to multi-database query reasoning. Instead of assuming a fixed execution context, the system must reason about (i) relevant databases, (ii) how to decompose a question across them, and (iii) how to integrate partial results. We formalize this setting through a three-phase roadmap: database routing, multi-database decomposition, and heterogeneous query reasoning across database types and query languages. This work provides a structured formulation of multi-database reasoning for Text2Cypher and identifies challenges in source selection, query decomposition, and result integration, aiming to support more realistic and scalable natural language interfaces to graph databases.

Knowledge graph embedding (KGE) models typically represent each relation as an operator on entity embeddings. In this work, we identify three structural axioms that any principled relation operator must satisfy, linearity, trace preservation, and complete positivity, and show that they characterize a Kraus channel structure via the Kraus representation theorem. The completeness constraint defining this family is equivalent to these axioms, providing a principled foundation rather than an externally imposed condition. Under this formulation, most existing operator-based KGE models are recoverable as special cases with Kraus rank $κ= 1$ under specific embedding choices. We further generalize this characterization to arbitrary metric geometries by introducing \mbox{w-Kraus} channels, which satisfy completeness by construction within their respective spaces. Building on this theory, we propose \textsc{KrausKGE}, a principled KGE model that naturally handles $1$-to-$N$ and $N$-to-$N$ relations, supports $k$-hop reasoning without requiring explicit path encoders, and eliminates the need for norm constraints on entity embeddings. Additionally, our framework yields the first theoretically grounded per-relation complexity measure in the KGE literature, with a provable lower bound in terms of the empirical relation matrix rank. Empirical evaluation demonstrates that \textsc{KrausKGE} consistently outperforms strong baselines on $N$-to-$N$ relations, with performance gains that increase monotonically with relation fan-out, in alignment with theoretical predictions.

Multimodal large language models (MLLMs) show remarkable potential for scientific reasoning, yet their performance in specialized domains such as microscopy remains limited by the scarcity of domain-specific training data and the difficulty of encoding fine-grained expert knowledge into model parameters. To bridge the gap, we introduce MicroWorld, a framework that constructs a multimodal attributed property graph (MAPG) from large-scale scientific image--caption corpora and leverages it to augment MLLM reasoning at inference time without any domain-specific fine-tuning. MicroWorld extracts biomedical entities and relations via scispaCy or LLM-based triplet mining, aligns images and entities in a shared embedding space using Qwen3-VL-Embedding, and assembles a knowledge graph comprising approximately 111K nodes and 346K typed edges spanning eight relation categories. At inference time, a graph-augmented retrieval pipeline matches query entities to the MAPG and injects structured knowledge context into the MLLM prompt. On the MicroVQA benchmark, MicroWorld improves the reasoning performance of Qwen3-VL-8B-Instruct by 37.5%, outperforming GPT-5 by 13.0% to achieve a new state-of-the-art. Furthermore, it yields a 6.0% performance gain on the MicroBench benchmark. Extensive experiments demonstrate the enhanced generalization capability introduced by MicroWorld. A qualitative case study further reveals both the mechanisms through which structured knowledge improves reasoning and the failure modes that point to promising future directions. Code and data are available at https://github.com/ieellee/MicroWorld.

Self-evolving language-model agents must decide what to learn next and how to preserve what they have learned across iterations. Existing systems typically carry this cross-iteration knowledge as natural-language feedback, flat episodic memory, or implicit reinforcement signals, none of which cleanly supports a frozen weak backbone at inference time. This paper introduces MAGE (Multi-Agent Graph-guided Evolution), a framework that externalizes self-knowledge into a four-subgraph co-evolutionary knowledge graph. Its experience subgraph stores both teacher-written failure corrections and the learner's own past correct reasoning traces, which are retrieved as task-conditioned guidance for a frozen execution model. During evolution, the graph, a task-level search bandit, and a skill-level routing bandit are updated from the same reward stream, while the learner's backbone remains unchanged. We further provide structural analysis showing how append-only memory growth, bounded curriculum coverage, and task-filtered retrieval together support stable improvement of the retrieval substrate for frozen-learner evolution. Across nine benchmarks spanning mathematical reasoning, multi-hop and open-domain question answering, spatio-temporal analysis, financial numerical reasoning, medical multiple-choice, an open-world survival game, and web navigation, MAGE achieves strong performance against prompt-based frozen-backbone baselines. Ablations show that self-harvested success traces and teacher-written corrections are complementary, with success memories contributing most on reasoning-template-heavy tasks and corrective memories supporting harder composition and interaction settings.

We define Oracle Poisoning, an attack class in which an adversary corrupts a structured knowledge graph that AI agents query at runtime via tool-use protocols, causing incorrect conclusions through correct reasoning. Unlike prompt injection, Oracle Poisoning manipulates the data agents reason over, not their instructions. We demonstrate six attack scenarios against a production 42-million-node code knowledge graph, providing the first empirical demonstration of knowledge graph poisoning against a production-scale agentic system, distinct from CTI embedding poisoning. Primary evaluation uses real SDK tool-use across nine models from three providers (N=30 per model), where models autonomously invoke a graph query tool and reason from results. The result is unambiguous: every tested model trusts poisoned data at 100% at moderate attacker sophistication(L2), with 269 valid trials (of 270) accepting fabricated security claims under directed queries. Under open-ended prompts, trust drops to 3-55%, confirming prompt framing as a confound; we report both conditions. An attacker sophistication gradient reveals discrete break points, a minimum skill at which trust flips from 0% to 100%, reframing the attack as a question not of whether but of how much. A controlled delivery-mode comparison shows that inline evaluation produces false negatives: GPT-5.1 shows 0% trust inline but 100% under both simulated and real agentic tool-use, demonstrating that delivery mode is a first-order confound. We evaluate five defences; read-only access control eliminates the direct mutation vector, while the remaining four are partial and model-dependent. Analysis of four additional platforms suggests the attack may generalise across the knowledge-graph ecosystem.

Large language models (LLMs) are increasingly used in K-12 education, yet existing benchmarks such as C-Eval, CMMLU, GaokaoBench, and EduEval mainly evaluate factual recall through exam-style question answering. Effective educational AI additionally requires curriculum cognition: understanding how knowledge is structured through prerequisite chains, concept taxonomies, experiment-concept links, and pedagogical sequencing. To address this gap, we introduce K12-KGraph, a curriculum-aligned knowledge graph extracted from official People's Education Press textbooks across mathematics, physics, chemistry, and biology from primary to high school. The graph contains seven node types (Concept, Skill, Experiment, Exercise, Section, Chapter, Book) and nine relation types covering taxonomy, prerequisite, association, verification, assessment, location, and order. Based on this graph, we construct two resources: (1) K12-Bench, a 23,640-question multi-select benchmark spanning five graph-derived task families (Ground, Prereq, Neighbor, Evidence, and Locate); and (2) K12-Train, a KG-guided supervised fine-tuning corpus of approximately 2,300 QA pairs synthesized from graph structure and node attributes. Experiments reveal substantial deficiencies in curriculum cognition: on K12-Bench, Gemini-3-Flash achieves only 57% exact match, while the best open-source model, Gemma-4-31B-IT, reaches 46%. Under a strictly matched 2,300-sample SFT budget on Qwen3-4B-Base and Llama-3.1-8B-Base, K12-Train consistently outperforms equally sized subsets from eight mainstream instruction-tuning corpora on both GaokaoBench and EduEval, demonstrating that curriculum-structured supervision is highly sample-efficient for educational tuning. We release the graph, benchmark, training data, and full construction pipeline.

Extracting multi-step explanations from knowledge graphs poses a combinatorial challenge requiring both heuristic guidance (as candidates proliferate with depth) and credit assignment (as path quality emerges over extended sequences). Frontier LLMs, strong on knowledge/reasoning benchmarks, offer a compelling source of such heuristics, yet their knowledge comes sans guarantees and compositional performance degrades as chains lengthen. We thus present TESSERA, a 3-part neuro-symbolic framework that uses LLMs in a circumscribed role: for local discriminative judgement rather than autonomous multi-step generation; the knowledge graph then defines the hypothesis space enforcing hard structural constraints, and MCTS coordinates the long-horizon search with principled credit assignment via backpropagation. LLMs perform dual roles as a prior policy biasing exploration and a comparative state evaluator supplying reward signals. Evaluation on drug mechanism elucidation across two complementary knowledge graphs demonstrates fidelity to curated biology while surfacing coherent alternative mechanisms, with ablations confirming discriminative contribution from both LLM components. Beyond its current application, our framework offers a general paradigm for compositional reasoning over structured knowledge.

Epilepsy diagnosis and treatment require evidence-intensive reasoning across heterogeneous clinical knowledge, including biosignal patterns, genetic mechanisms, pharmacogenomics, treatment strategies, and patient outcomes. In this work, we present \textsc{EpiGraph}, a large-scale epilepsy knowledge graph and benchmark for evaluating knowledge-augmented clinical reasoning. \textsc{EpiGraph} integrates 48,166 peer-reviewed papers and seven clinical resources into a heterogeneous graph containing 24,324 entities and 32,009 evidence-grounded triplets across five clinical layers. Built upon this graph, \textsc{EpiBench} defines five clinically motivated tasks spanning clinical decision-making, EEG report generation, pharmacogenomic precision medicine, treatment recommendation, and deep research planning. We evaluate six LLMs under both standard and Graph-RAG settings. Results show that integrating \textsc{EpiGraph} consistently improves performance across all tasks, with the largest gains observed in pharmacogenomic reasoning (+30--41%). Our findings demonstrate that structured epilepsy knowledge substantially enhances evidence-grounded clinical reasoning and provides a practical benchmark framework for evaluating knowledge-augmented LLMs in real-world neurological settings. Our code is available at: https://github.com/LabRAI/EEG-KG.

Large Language Models (LLMs) provide flexible natural language processing capabilities, while knowledge graphs (KGs) offer explicit and structured knowledge. Integrating these two in a complementary manner enables the development of reliable and verifiable AI systems. In particular, knowledge graph question answering (KGQA) has attracted attention as a means to reduce LLM hallucinations and to leverage knowledge beyond the training data. However, existing KGQA benchmark datasets are biased toward encyclopedic knowledge, limited to a single modality, and lack fine-grained spatiotemporal data, which limits their applicability to real-world scenarios targeted by Embodied AI. We introduce HOME-KGQA, a novel KGQA benchmark dataset built on a multimodal KG of daily household activities. HOME-KGQA consists of complex, multi-hop natural language questions paired with graph database query languages. Compared to existing benchmarks, it includes more challenging questions that involve multi-level spatiotemporal reasoning, multimodal grounding, and aggregate functions. Experimental results show that the LLM-based KGQA methods fail to achieve performance comparable to that on existing datasets when evaluated on HOME-KGQA. This highlights significant challenges that should be addressed for the real-world deployment of KGQA systems. Our dataset is available at https://github.com/aistairc/home-kgqa

The emerging collaborative information-based knowledge tracing (KT) has been a promising way to enhance modeling of learners' knowledge states. The core idea is to extract the collaborative information from interaction sequences of other learners to assist the prediction on the target one. Despite effectiveness, existing methods are built on the raw interaction sequences with tailored modules, which inevitably limits their capacity in deeply capturing learning behavioral patterns and generalization. To this end, we propose a general meta-behavioral pattern-aware framework (MBP-KT) for KT. Specifically, MBP-KT introduces a novel meta-behavioral sequence construction to transform the raw interaction sequences into the combinations of different meta-behavioral patterns. In this way, the learning behavioral patterns of learners can be effectively preserved. Then, MBP-KT develops a parameter-free module to extract the global collaborative representations from the constructed meta-behavioral sequences. Moreover, MBP-KT provides general injection strategies to introduce the extracted global collaborative information into various downstream KT models, ensuring the universality of the collaborative information. Extensive results on real-world datasets demonstrate that MBP-KT can consistently boosts the performance of a wide range of KT models.

In recent years, the use of edge information provided by knowledge graphs together with the advantages of higher-order connectivity in graph neural networks for recommendation systems has become an important research direction. However, existing approaches are often limited by sparse labels, insufficient graph structure learning, and noisy entities in the knowledge graph, which reduce recommendation accuracy. To address these limitations, we propose a multi-view graph contrastive learning framework. The proposed method enhances user representations through multi-view knowledge graph distillation, enabling more accurate modeling of user preferences over entities and relations. The network aggregates neighborhood entity information to construct informative item representations. Furthermore, we design a multi-level self-supervised contrastive learning module that performs comparisons across three perspectives: Inter-Level, Intra-Level, and Interaction-Level. This design improves the model's ability to generalize across intra-class samples while increasing discrimination between inter-class samples, thereby enabling more effective multi-dimensional feature modeling. We conduct extensive experiments on three public datasets using both baseline and ablation settings. Experimental results demonstrate that the proposed framework consistently outperforms existing state-of-the-art methods. Ablation studies further verify the effectiveness of each module in the proposed model.

Knowledge Graph Question Answering (KGQA) offers grounded, interpretable reasoning, but existing methods often fail to provide reliable coverage guarantees over retrieved answers. While Conformal Prediction (CP) offers a principled framework for producing prediction sets with statistical guarantees, prior conformal KGQA methods suffer from two critical pitfalls: violated coverage guarantees due to invalid calibration, and weak score discriminability that yields excessively large prediction sets. We propose Conformal Path Reasoning (CPR), a novel trustworthy KGQA framework built on two key innovations. First, query-level conformal calibration over path-level scores preserves exchangeability to ensure valid coverage guarantees. Second, we introduce the Residual Conformal Value Network (RCVNet), a lightweight module trained via PUCT-guided exploration to learn discriminative path-level nonconformity scores. Extensive experiments show that CPR significantly improves the Empirical Coverage Rate by 45% while reducing prediction set size by 52% on average over conformal baselines across benchmark datasets, highlighting its effectiveness for reliable conformal reasoning over knowledge graphs.

Tacit knowledge plays a central role in human expertise, yet it remains difficult to capture, formalize, and reuse in machine-interpretable form. This challenge is especially relevant in procedural domains, where successful execution depends not only on explicit instructions, but also on implicit assumptions, contextual constraints, embodied skills, and experience-based judgments rarely documented. As a result, current knowledge engineering pipelines struggle to transform tacit and process-centric knowledge into formally specified, machine-interpretable representations that can be queried, validated, reasoned over, and reused. In this paper, we introduce a neuro-symbolic framework that combines Logic-Augmented Generation and an Active-Inference-inspired approach for ontology-grounded Knowledge Graph construction. We evaluate the approach in a knowledge transfer case study in manufacturing, using assembly-like repair procedures from instructional videos as a reproducible proxy domain. Results show that the proposed solution improves completeness and semantic quality, advancing neuro-symbolic knowledge engineering for industrial domains.