knowledge graph engineers

Abstract: Link prediction on text-attributed graphs (TAGs) is a fundamental problem with applications in knowledge discovery, recommendation and beyond. Recent progress has highlighted the promise of combining Graph Neural Networks (GNNs) with Language Models (LMs) in order to leverage the complementary structural and semantic signals. However, due to the distinct inductive biases of GNNs and LMs, the design of an optimal fusion strategy remains an open research question. In this work, we present Bridge-LP, an intuitive, simple, efficient and theoretically grounded framework that unifies graph and language representations. It is built around three theoretically-justified design components: (D1) jumping connection of textual proximity, which enables robust LM training; (D2) compressed embedding, which encodes neighborhood information long exploited by classical link prediction heuristics, thereby enriching structural signals in a learnable way; and (D3) cache embedding training strategy, which reduces computational complexity. Together, these mechanisms establish an end-to-end cross-modal framework that scales to large graphs while capturing richer graph-text interactions. We conduct an extensive empirical evaluation, comparing against 40 existing models across 9 diverse datasets. Experiments show that Bridge-LP consistently outperforms state-of-the-art approaches, delivering up to a 43.06% improvement in Mean Reciprocal Rank (MRR) and setting a new benchmark for language-graph integration.

Abstract: Triple set prediction (TSP) is to recover missing relational triples in a knowledge graph by predicting the triple set instead of isolated links. Existing approaches predominantly rely on the subgraph-based completion paradigm, where the original graph is first partitioned into local subgraphs which are then independently completed. Such a paradigm suffers from fragmented structural reasoning, limited cross subgraph dependency modeling, and missing predictions across subgraphs. This paper proposes LatentDiff, a novel unified latent generative framework for TSP, which reformulates knowledge graph completion as latent space graph generation. LatentDiff first learns a compact latent representation using a relation-aware residual-quantized knowledge graph autoencoder, which encodes the whole graph into relation-aware latent embeddings, quantizes them with chunked residual codebooks, and reconstructs triples through a factorized decoder. On top of this latent space, we introduce an observation-anchored latent graph diffusion model, where the target latent graph representation is perturbed toward the observed latent. The reverse process recovers missing triples through progressive latent denoising. Experiments on three benchmark datasets show that LatentDiff outperforms the SOTA in terms of F_{tsp} by 5.4 percentage points on average. Code: https://anonymous.4open.science/r/LKGDiff-44A5.

Abstract: Complex Temporal Knowledge Graph Question Answering (TKGQA) involves more than retrieving facts: the timestamp or validity interval of one fact can constrain the search for another, while multiple intervals may jointly determine the answer. Existing single-agent TKGQA methods typically investigate these facts within a single reasoning context, where evidence from different event histories can become interleaved and distractors can misdirect subsequent retrieval. Distributing investigations across agents can separate event-specific evidence into distinct contexts, but effective collaboration must still be learned because question decomposition, subtask investigation, and evidence synthesis are interdependent. To address these limitations, we propose \textbf{Co}-Evolving \textbf{S}elf-Play \textbf{T}imeline \textbf{A}gents (CoSTA), which organizes facts into navigable timelines, delegates investigations to workers, and uses a coordinator to synthesize their original timestamped observations. CoSTA initializes a shared policy through role-conditioned distillation and jointly optimizes both roles through co-evolving self-play with final-answer rewards. Across three benchmarks, CoSTA achieves state-of-the-art overall performance, with particularly strong gains on complex multi-fact questions, while its compact variants outperform the evaluated closed-source LLM agents.

Abstract: Recent advances in large language models (LLMs) have spurred growing interest in temporal knowledge graph question answering (TKGQA). Most existing methods rely on semantic retrieval augmented generation (RAG), which suffers from fundamental limitations in complex temporal reasoning. On the one hand, semantic-based RAG methods struggle to capture the multi-hop causal knowledge required for complex temporal reasoning. On the other hand, these methods introduce excessive redundant knowledge, trapping LLMs in spurious reasoning chains that potentially result in erroneous answers. To address these problems, we propose a Temporal Causal Chain-guided RAG (TCC-RAG) to retrieve a concise yet sufficient set of causal knowledge to support complex temporal reasoning. Specifically, we reformulate the temporal knowledge graph into a multi-view causal cue graph, with causal cues inducing connections that explicitly encode temporal evolution and causal dynamics. Based on the causal cue graph, we construct a query-specific temporal causal chain to guide the retrieval process, enabling the model to focus on a concise set of causally relevant knowledge. Finally, we introduce a causal evidence filter to refine the retrieved knowledge, ensuring its causal consistency with the underlying temporal logic of the query. Experiments show that TCC-RAG achieves substantial performance gains of 10.72% and 8.40% on two TKGQA benchmarks, and delivers a remarkable 62.97% improvement for multi-step temporal reasoning.

Abstract: LLM agents that answer questions over Web knowledge graphs are increasingly wrapped in checks derived from the graph's ontology, on the assumption that a formal schema makes a reliable judge. Yet a checker can be wrong as well: it can miss errors, and it can flag correct answers and push the agent into "fixing" them. Whether a curated ontology is worth its cost as such a judge, and how it compares with an ontology an LLM writes or a schema mined from the data, is unknown. We make the checker itself the object of study. Across curated, LLM-generated and data-derived ontologies, used as prompt context, as a checker, or both, and across open-weight and proprietary agents on public graphs and a private graph of nearly $10^{9}$ triples, we account for what ontology-derived checks catch and what they wrongly flag. We show how each source trades caught errors against false alarms, how a curated schema used as published can contradict its own data, which errors structural checks miss, and whether combining sources or giving the agent the checker's specific feedback pays off. On UniProt, the curated ontology flags more correct answers than either an ontology derived from the data or one an LLM derives from a summary of the data with masked identifiers. On real agent answers, its flags are only marginally more precise than random flags.

Abstract: Relations compose through the entity they share - Alice is Bob's mother and Bob is Carol's father, so Alice is Carol's grandmother - and the order matters, since a father's mother is not a mother's father; verifying a composed relation means closing the loop. We show that if each entity's coordinate frame may be rotated independently (per-entity frame freedom), three things follow. In the pure-gauge sector, relations that share no cycle cannot interact at all. The only gauge-invariant score of a triangle is a class function of its holonomy $H = T_{ij} T_{jk} T_{ki}$ - a Wilson loop. And the only equivariant update of an edge is $U = Ψ(H)\, T_{ij}$ with $Ψ$ conjugation-equivariant. Edge attention by Wilson loops is therefore not one design among many but the unique form the symmetry permits. Three communities hold pieces of this form: the commuting-operator embeddings of knowledge graphs are its abelian (commuting) sector; AlphaFold's triangle update and the Edge Transformer have its shape - an edge updated through the third vertex - without its constraints; and lattice QCD builds it equivariantly on lattices. We instantiate the equivariant sub-family on general relational graphs as holonomy attention. With no training and composition alone, it infers unobserved $S_4$ relations on sparse graphs at 0.88 with a fifth of the edges corrupted, at or slightly below specialist synchronization algorithms, where every commutative architecture is capped at 0.083; its holonomy score flags corrupted triangles at AUC 0.99 where commuting scores are capped at 0.76 by a second selection rule, and it separates clusters without labels.

Abstract: Recent Sparse Autoencoders (SAEs) decompose the representations of large language models (LLMs) into interpretable features, enabling precise readout and control of encoded knowledge. However, existing SAEs treat each feature as a standalone unit, whereas real-world knowledge is often taxonomically organized. As a result, readout carries no guarantee of taxonomic consistency, and control lacks the granularity to specify the scope of an edit. We propose TaxoSAE, which explicitly encodes taxonomical information, built on is-a (hypernym-hyponym) relations, into the SAE feature space. TaxoSAE mirrors a taxonomy with a stack of SAEs, one per taxonomy level, and introduces a taxonomic alignment loss that trains each concept to be active whenever one of its hyponyms is. On two factual QA taxonomies, one over biographical relations and one over animals, TaxoSAE enables (1) more accurate readout through the taxonomy with concentrated activations, e.g., +31.3 points in reading out the hypernyms of abstract concepts never queried in training; (2) more precise control, with +25.5 points in swap success, while suppressing a concept removes only its own answers (0-2% accuracy vs. 91-100% on other concepts); and, more importantly, (3) readout of unseen concepts through their hypernyms, with up to +37.9 points in hypernym readout accuracy.

Abstract: Rule-based link prediction combines symbolic and statistical artificial intelligence methods by inductively learning a set of rules from a knowledge graph (KG), with the aim of completing the graph when a query cannot be answered from the KG alone. Several systems have been proposed, and while they perform well on classical benchmarks, even compared with embedding-based systems, many of them produce a large number of rules. This compromises scalability in the query-answering phase, especially under strong hardware constraints. In this work, we investigate the behavior of AnyBurl, a state-of-the-art rule learner for link prediction, to determine whether running it for a given time and then pruning the learned rules yields better query-answering performance at test time than a simpler approach that stops rule generation earlier.

Abstract: Large Language Models (LLMs) often struggle with temporally grounded reasoning because their static parametric memory is misaligned with the dynamic evolution of real-world knowledge. Although RAG and Parameter-Efficient Fine-Tuning (PEFT) provide practical ways to enhance LLMs, they remain insufficient for temporal reasoning. Existing retrieval methods typically prioritize semantic relevance while overlooking temporal validity, event order, and evolutionary dependencies, resulting in evidence that is relevant in isolation but temporally fragmented. Meanwhile, conventional PEFT methods usually employ fixed and input-agnostic low-rank updates, making it difficult to capture time-dependent entity semantics and relation drift. To address these limitations, we propose Temporal Evidence-Parameter Co-Alignment (TEPCA), a framework for LLM reasoning over TKGs. TEPCA aligns LLM reasoning with temporal knowledge at both the evidence and parameter levels. At the evidence level, it introduces time-constrained Dynamic Relevance-Guided Path (DRGP) pruning to preserve globally coherent temporal paths, together with Mutual-Information (MI)-based pruning to retain query-informative local facts under temporal constraints. At the parameter level, it integrates Dynamic-Gated LoRA (DG-LoRA), a timestamp-conditioned low-rank adaptation mechanism that dynamically modulates the effective adaptation subspace according to temporal context. This design enables LLMs to better capture fine-grained entity evolution and time-dependent relation semantics while preserving parameter efficiency. Experimental results on two TKG benchmarks demonstrate that TEPCA achieves state-of-the-art performance. Additional evaluations of DG-LoRA on eight commonsense QA datasets further verify its general input-adaptive capacity, scalability across LLM backbones, and interpretability.

Abstract: Multi-hop knowledge-graph question answering (KGQA) benchmarks are often treated as fixed language-and-reasoning tasks, but for navigation-based methods, difficulty also depends on the graph in which those tasks are instantiated. This makes graph construction a consequential but often entangled part of the navigation task. To isolate this effect, we audit PathQuestion (PQ) and PathQuestion-Large (PQL) as graph-navigation benchmarks under a controlled intervention: we hold questions, topic entities, released answers, released path annotations, and family-level splits fixed while replacing each released task-filtered graph with the larger source KG distributed with the benchmark. Source restoration expands the effective navigation search space and graph-consistent answer and path multiplicity while sharply reducing unguided reachability to released answers. We evaluate whether these structural changes persist across navigation policies using structural references, frozen small-language-model navigation policies, and trained MINERVA policies. Across both frozen and trained policies, restoration substantially reduces released-answer accuracy and trajectory fidelity, while graph-consistent evaluation recovers only part of the loss. These results show that benchmark graph construction is part of the navigation task specification rather than merely an implementation detail and can materially shape measured behavior even when the released QA task is held fixed.

Abstract: Dynamic edge classification on text-attributed Web graphs, such as review networks, community forums, and news-derived knowledge graphs, requires high quality, adaptive semantic representations in the context of network evolution. Existing dynamic graph architectures typically initialize text feature vectors with pretrained language models and hold them static during training to preserve their semantic structure, forgoing the potential benefits of allowing them to co-evolve with network topology. In this work, we investigate the effects of enabling such co-evolution with a unified text-graph alignment framework that integrates a lightweight Transformer adapter to update token-level text representations via spatio-temporal gradients from a contrastive pretraining objective. To prevent detrimental semantic distortion, a language model maintenance objective anchors the evolving text embeddings to their original semantic structure. Evaluations on the Dynamic Text-Attributed Graph Benchmark demonstrate that this anchored text-graph co-evolution consistently improves upon the edge classification performance of frozen-text baselines across diverse Web-related domains. Representational analyses reveal that the framework reduces anisotropy, improving the linear separability of text embeddings, and effectively encodes structural and temporal information into the semantic space. A computational efficiency analysis confirms that this beneficial semantic and spatio-temporal co-evolution is achieved without incurring the prohibitive computational overhead typical of end-to-end joint training.

Abstract: While hierarchical structures are intrinsic to organizing human knowledge, current representation learning on text-attributed graphs predominantly operates on flat semantic spaces, overlooking the rich coarse-to-fine granularity inherent in real-world data. To bridge this gap, we propose SHiFT, which synergizes the reasoning power of LLMs with the structural representation capability of GNNs within an Expectation-Maximization (EM) paradigm. In the E-step, we harness LLMs as expert taxonomists to induce an explicit semantic tree, introducing a lightweight Mapping & Diagnosis strategy that reduces inference costs by surgically updating the hierarchy only when anomalies are detected. In the M-step, we align the GNN encoder with this induced hierarchy from complementary perspectives, including clustering partition, topological skeleton, and semantic concepts. Theoretical analysis interprets SHiFT as a generalized Variational EM algorithm. Extensive experiments demonstrate that SHiFT not only achieves state-of-the-art performance but also uncovers high-quality, human-readable taxonomies. Our code can be found at https://github.com/Cloudy1225/SHiFT.

Abstract: Graph diffusion models are competitive approaches for generating complex graph-structured data. However, when such distributions have strict structural constraints, diffusion models may fail to capture them exactly, resulting in the generation of invalid graphs. In this paper, we propose a method for grounding graph diffusion models in domain-specific knowledge via First Order Logic (FOL), leveraging its expressive and interpretable formalism to impose structural constraints on the generative process. We incorporate domain knowledge using classifier guidance, a technique that conditions the diffusion model's distribution on external variables to exert control over the sampled data. During the generative process, classifier guidance steers the denoising trajectory to optimize an objective function, which we define as a fuzzy and differentiable relaxation of the logical rules. Our methodology requires only the specification of constraints in FOL, whose satisfaction is encouraged at inference time to guide a pre-trained generative model. We evaluate our approach by comparing the unconditional generation of knowledge graphs with our logic-guided framework, which incorporates domain ontologies as structural constraints during inference. This approach significantly increases the proportion of generated graphs that satisfy the ontological constraints.

Abstract: Knowledge graph link prediction involving unseen entities and relations requires learning transferable reasoning patterns from observed graph structure. Existing methods based on relation graphs primarily capture pairwise dependencies, limiting their ability to preserve the compositional semantics, relation ordering, and role information of complete path rules. To address this limitation, we propose QORH (Query-specific Ordered Rule Hypergraph), which jointly encodes rule heads and ordered rule bodies as hyperedges conditioned on the query relation, explicitly modeling joint dependencies among multiple relations. QORH performs learnable rule selection using statistical evidence, such as rule confidence and coverage, and enhances relation representations through role-aware hypergraph message passing to guide entity-level reasoning. The model's shared parameters are independent of specific entity or relation identifiers, enabling inductive prediction for unseen entities and relations. Extensive experiments on entity-inductive and fully inductive benchmarks demonstrate that QORH significantly outperforms the state-of-the-art baselines included in our evaluation, validating the effectiveness of rule hypergraph modeling for inductive link prediction.

Abstract: The ISO GQL standard introduces a rich value-type system for property graphs, including scalar, temporal, byte-string, list, record, and dynamic union datatypes. The vocabulary presented here additionally covers a vector extension. At the same time, RDF-based knowledge graph systems identify literal datatypes by IRIs and interpret typed literals through value spaces, lexical spaces, and lexical-to-value mappings. This paper presents the GQL Datatypes RDF Vocabulary, a lightweight RDF vocabulary that represents selected GQL datatypes and the vector extension as RDF datatype IRIs and describes their hierarchy, aliases, and selected constraints using RDF, RDFS, OWL, and XML Schema Datatypes vocabulary terms. The vocabulary is intended to support interoperability between GQL-oriented property graph systems and RDF-based knowledge graph systems. We describe its namespace and datatype model, summarize its datatype coverage, and show how the accompanying generator and validator use the vocabulary. In the reference implementation, RDF literals retain GQL datatype IRIs; XSD mappings declared in the vocabulary support scalar validation, while lists, records, and vectors are encoded directly as JSON lexical forms of vocabulary-typed literals.

Abstract: Multimodal entity alignment (MMEA) is fundamental to integrating heterogeneous knowledge graphs (KGs), yet existing paradigms remain critically vulnerable to incomplete modalities and cross-graph structural asymmetries. This paper exposes a fundamental oversight in current MMEA research: treating feature missingness and topological discrepancies as isolated preprocessing or denoising challenges, which overlooks their destructive coupling during multimodal fusion. We systematically formulate and evaluate two newly identified failure modes: 1) Detail Missing (DM)-induced overvaluation, where the absence of local modality details causes models to overemphasize uninformative, blurred representations; and 2) Context Imbalance (CI)-induced suppression, where topological discrepancies across KGs allow dense structural contexts to overwhelm weaker but highly discriminative modal signals, triggering high-level semantic drift. To break this cycle of degradation, we introduce ALMEA, a generative and calibration framework that establishes a bidirectional feedback loop between low-level feature reconstruction and high-level latent space alignment. Specifically, Cross-Modality Imputation (CMI) synthesizes missing modality details to mitigate overvaluation, while Latent Semantic Calibration (LSC) aligns cross-graph joint embeddings to suppress topology-driven semantic drift. Under sparse supervision, we develop Controlled Iterative Selection (CIS) to adaptively acquire representative and diverse pseudo-labeled pairs, optimizing latent calibration under constrained budgets. Extensive evaluations on standard benchmarks demonstrate that ALMEA consistently outperforms state-of-the-art baselines. At a 20% supervision rate, ALMEA yields substantial absolute improvements of up to 5.20% in MRR and 6.40% in Hits@1, maintaining robust gains across higher supervision thresholds.

Abstract: Knowledge graph (KG) foundation models (KGFMs) predict links on unseen graphs zero-shot. KGFMs have been pioneered by ULTRA which builds a relation graph from co-occurrences that match motif templates, and passes messages over it to obtain relation representations. More recent KGFMs such as MOTIF and TRIX increase the size of this relation graph, and FLOCK replaces message-passing with probabilistic random-walk ensembles. However, larger relation graphs mean more messages, and more walks mean more sequences to encode, so they improve performance at higher training and inference cost. This cost hinders their use in more complex reasoning tasks, such as complex query answering. To reverse this trend, we design MERIT, the first KGFM with a transformer relation encoder: every relation name attends to every other, and the motifs enter as a soft prior rather than as edges. Over 56 benchmarks, MERIT matches the zero-shot MRR of SoTA KGFMs while being 6x faster than TRIX and over 100x faster than FLOCK at inference. Fine-tuned for complex query answering like UltraQuery, MERITQuery improves over it at matched cost.

Abstract: Hypergraph Neural Networks (HNNs), designed to model higher-order relations beyond pairwise interactions, typically rely either on fixed structural weights or on normalised attention. Fixed weights can propagate misleading information in heterophilic settings, while normalisation makes attention coefficients competitive, in the sense that, in a message-passing framework, increasing the weight of one sender must reduce the weight of others in the same aggregation set. Our main contribution is the introduction of PANDA (Prior-guided AttentioNal Dual-path Architecture), a plug-in for two-stage message passing HNNs applicable to both undirected and directed settings. The main path interpolates between learned receiver-normalised attention and structural incidence priors, while a non-competitive (not normalised) auxiliary path lets each sender contribute its own transformed information. We also show that, with fixed structural coefficients, PANDA recovers a certain complex-valued convolution operator adopted in previous works. Across four HNNs spanning spatial and spectral methods in both directed and undirected settings, plugging PANDA in yields an average improvement of 5.18 percentage points across eight real-world benchmark datasets. The code is available at https://github.com/jainris/panda.

Abstract: This paper details our submission to KnowledgeGraphEval 2026 Subtask 2 on directed Arabic relation extraction. We explored encoder-based and large language model approaches for predicting one of 40 relations or no_relation from an Arabic sentence and a subject-object pair. Our encoder systems use typed entity markers and separate relation-existence and relation-classification heads, while our LLM systems fine-tune Yehia and Qwen3.5 with QLoRA and ontology-constrained prediction. Our best system, an ensemble of Yehia-RE, Qwen-RE, and TypedPair, achieved a micro-F1 score of 94.06 and ranked 1st in Subtask 2. Yehia-RE (full-vocabulary) achieved 92.98, while the best encoder and Qwen-RE achieved 92.69 and 91.94 respectively. Our results highlight the importance of constrained prediction and complementary modeling approaches for Arabic relation extraction.

Abstract: Graph foundation models aim to transfer across graphs, feature spaces, relational schemas, and prediction tasks, yet existing approaches typically generalize only within particular graph modalities or tasks. We propose Wander, a graph foundation model designed to operate across these settings within a single pretrained checkpoint. Following the prior-predictive perspective, we formulate graph learning as completion of a partially observed graph. We realize this task-general view through a common interface based on random walks, allowing the same model to operate across homogeneous and multi-relational graphs with varying features, labels, and relational schemas. Wander can increase its structural context at inference time without changing its learned parameters and, under suitable assumptions, universally approximates the corresponding Bayes-optimal predictor on bounded connected graphs. Empirically, a single pretrained checkpoint achieves state-of-the-art or highly competitive results across node classification, homogeneous link prediction, and knowledge-graph link prediction. Moreover, joint pretraining across graph modalities and tasks preserves performance in specialized settings while enabling positive transfer and the composition of separately learned capabilities at inference time.

Abstract: Long-horizon search requires agents to gather evidence across multiple steps and synthesize it into well-supported answers. The recent agent harnesses provide a natural and promising framework to support such long-running search processes. As interaction histories grow, one single agent in harnesses might get stuck and cause the policy to lose track of unresolved questions, overlook useful evidence, or terminate before sufficient support has been collected. One of promising way is to decouple three distinct responsibilities of proposing retrieval actions, updating persistent state, and deciding when to stop rather than concentrating them within a single policy. Targeted at it, we introduce Harness-Search, a multi-agent search harness to reduce the local errors propagating across subsequent exploration, evidence curation, and termination decisions. In particular, Harness-Search assigns these responsibilities to three permission-bounded authorities: a Retrieval Policy that proposes search operations, a Memory Operator that validates and commits persistent-state updates, and a Summary Auditor that accepts or rejects termination based on the sufficiency of the curated evidence. Together, these roles form a Propose-Commit-Audit loop in which actions are proposed, persistent evidence is selectively committed, and stopping decisions are subjected to an explicit sufficiency check. Across seven long-horizon search benchmarks, Harness-Search improves both retrieval and answer generation under the same policy backbone, increasing Recall by 4.60-27.92 points and Final-Answer Recall by 12.34-30.13 points over the strongest harness-based baseline on each evidence-retrieval benchmark. Moreover, trajectory-level analyses show that Harness-Search continues to accumulate useful evidence and expand evidence coverage with less redundant retrieval as the search history grows.

Abstract: Graph agents extend large language models (LLMs) with the ability to actively explore and reason over knowledge graphs through multi-step interactions with graph tools. However, training capable graph agents typically requires large collections of question-answer pairs and reasoning trajectories, whose manual construction is costly and difficult to scale. Moreover, employing proprietary LLMs to generate such supervision further risks exposing sensitive graph data to external services. Therefore, we propose GraphCert to bootstrap agentic graph reasoning with certified evidence rubrics during post-training. Specifically, the Bootstrapped Graph Quizzer guided by generation controls produces graph-grounded QA pairs and marks supporting evidence, which undergo execution certification and semantic curation. The accepted evidence is then canonicalized into certified evidence rubrics that later reward Graph Solver evidence alignment alongside answer correctness during GRPO training. Experiments on five graph reasoning domains in GRBENCH demonstrate that GraphCert consistently outperforms substantially larger LLM agents and post-training method. Furthermore, our analysis demonstrates that the learned policy transfers robustly across heterogeneous graph domains, suggesting that GraphCert acquires reusable graph-reasoning capabilities rather than domain-specific patterns. These results establish executable self-certification as an effective approach to self-training compact graph reasoning agents. Our code will be made publicly available.

Abstract: Structural reasoning, the ability to recognize and make inferences over the relational structure between objects and concepts, is a hallmark of human cognition, yet prevailing methods often collapse relational topology into flat embeddings, cannot discover hidden structure and lack interpretability. We introduce Neural Structural Reasoner (NSR), a brain-inspired network that preserves relational structure directly in the connectivity and dynamics of coupled neuronal populations. NSR draws inspiration from three biological mechanisms: multi-layered architecture for encoding hierarchical knowledge, stable representations of entity and concepts, and path integration for input-driven state inference. At query time, NSR parallelizes computation over candidate relational structures and leverages confidence-weighted scores to perform link prediction. Across standard knowledge-graph benchmarks, NSR achieves competitive accuracy without leading on every dataset, and has lower reported training times than several neural baselines. Because reasoning is implemented through sequences of human-readable neuron activations, NSR affords native interpretability by tracking intermediate inference steps. The model further extracts latent relational hierarchies and compositional rules, demonstrating the brain-inspired architecture as an effective, efficient, and highly interpretable substrate for structural reasoning.

Abstract: AI systems often feel brittle and fragmented. A large language model (LLM) may correctly explain a concept but fail to apply it, or follow safety instructions in one context but not another. This behavior suggests a general failure to lift local information to a global understanding. To gain fundamental insight, we frame "understanding" as learning constraints and propagating their consequences. We construct learning tasks on monoid worlds, sets of states connected by action transitions, where observed training transitions and an unseen constraint jointly determine held-out transitions. Measuring generalization tests whether models can learn global constraints from local transitions and propagate their consequences. We consider inverse, commutativity, composition, and periodicity constraints relevant to spatial and semantic structure. Across attention, recurrent, and state-space architectures, next-state training fits the data but fails to propagate non-trivial constraints. Compositional training, which uses identical paths but hides intermediate states from the input, achieves 96% accuracy on inverse, commutativity, and composition constraints across architectures, yields corresponding improvements in geometric generalization of world models trained on embodied environments and relational generalization in Wikidata-finetuned LLMs. How far do models propagate constraints when inferring an unseen fact may depend on first inferring others? We define proof depth d of a held-out transition, measuring the minimum number of inference rounds to infer the transition, and find that model generalization decreases sharply with proof depth. Increasing compositional path length T improves generalization. These results provide a formal way to investigate global understanding in language and world models and demonstrate that compositional training promotes information propagation and integration.

Abstract: A central limitation of current data-free self-evolution methods for training search agents is their reliance on difficulty-based proposer rewards. These methods reward a proposer for generating questions that challenge a co-evolving solver, using solver difficulty as a proxy for question quality. Yet difficulty alone is insufficient to distinguish questions that require cross-passage evidence from those that are answerable via simpler shortcuts. In addition, measuring difficulty demands repeated solver rollouts for every candidate question, leading to substantial computational costs. In this paper, we introduce \methodname, the first self-evolving search framework that eliminates difficulty-based proposer rewards and directly optimizes for evidence necessity relative to shortcut contexts. Dr. Free samples relational chains from a knowledge graph and pairs them with aligned passages, giving question generation an explicit multi-hop structure. A generated question receives a positive information-gain reward only when the likelihood of the target answer under the complete evidence passages exceeds the maximum likelihood under all evaluated shortcut contexts. Because this signal is computed from teacher-forced likelihoods, it removes the need for pass-rate estimation and reduces proposer training time by over $7\times$. Experiments on seven open-domain QA benchmarks show that Dr. Free outperforms prior data-free search agents and the supervised baseline, with large improvements on multi-hop QA benchmarks.

Abstract: Dynamic text-attributed graphs (DTAGs), where nodes, edges, and textual attributes evolve over time, are crucial in applications such as social networks, citation graphs, and knowledge graphs. However, existing approaches struggle to jointly model the temporal evolution of graph structures and the semantic richness of textual attributes. While Temporal Graph Neural Networks (TGNNs) capture evolving node relationships, they often lack contextual text reasoning. Conversely, Large Language Models (LLMs) excel in textual understanding but struggle with structured graph reasoning in temporal settings. To bridge this gap, we propose TemporalGraphLLM, a novel framework that can integrate any temporal GNN with an LLM for enhanced reasoning in DTAGs. Our approach fine-tunes LLMs using graph-time-aware instruction tuning and novel temporal GNNs injection to replace dedicated added tokens with graph embeddings. TemporalGraphLLM effectively leverages pretrained TGNNs within an LLM framework to achieve state-of-the-art performance on edge classification, link prediction, and edge-based text generation tasks. Extensive evaluation on real-world dynamic graph datasets demonstrates state-of-the-art performance. Our findings highlight the synergistic potential of LLMs and TGNNs, opening new directions for learning on evolving graphs.

Abstract: Structure-mapping forms analogies by aligning systems of relationally connected elements based on shared structure instead of surface features. We introduce a new structure-mapping algorithm: Structure-Mapping with Tight Bounds (SMTB) that is 5--15x faster than the structure-mapping engine (SME) and about 50\% better at finding mappings in large nested domains. SMTB is part of the broader Cognitive Rule Engine (CRE) project, a flexible multi-language-compatible framework with an accessible Python interface to state-of-the-art C++ implementations of core algorithms commonly used in cognitive systems such as pattern matching, planning, and structure-mapping. CRE and SMTB are designed to work with a wide range of representation choices. Unlike SME, which biases higher-order correspondences in tree-like predicate logic, SMTB maximizes relational connectivity without privileging higher-order relations. This allows SMTB to work just as well over arbitrary relational graphs as it does in tree-like domains of nested predicate logic. We discuss situations where privileging "higher-orderness" in structure-mapping can cause issues, and illustrate how SMTB avoids failure modes that SME would encounter in these situations. We also provide an evaluation comparing SMTB to SME v4 over 5845 domain pairs from the SME corpus.

Abstract: Because of its collaborative nature, Wikidata suffers from errors, in- consistencies, and excessive complexity, such as redundant classes, ambiguity between instances and classes, wrong taxonomic paths, and type constraint violations. The manual curation of these issues is infeasible at scale. To address these challenges, we introduce WiCleanData, a refined version of Wikidata with a consistent tax- onomy and free from type constraint violations. Specifically, we have designed an automated pipeline that first cleans the taxonomy with language model assistance, then simplifies type constraints by hierarchical aggregation, and finally filters facts accordingly. The resulting knowledge graph, free from any type violation, is made publicly available via a Web interface, enabling easy exploration and downstream applications.

Abstract: A large language model (LLM) agent can follow more graph paths without acquiring more independent evidence. GraphEcho tests whether agents mistake these repeated encounters for additional corroboration. The benchmark varies path counts and evidential origins while holding evidence content fixed, and evaluates both judgments and active exploration. Controlled synthetic experiments reveal model-dependent judgment shifts, but redundant supporting paths increase the share of repeated walks across all evaluated frozen agents. Provenance-aware post-training (PAPT) reduces revisits and improves synthetic accuracy, yet covers fewer distinct sources. On scientific claims, it continues to reduce repetition while accuracy declines. These findings expose a gap between efficient exploration and effective evidence use: an agent can learn to stop repeating itself while overlooking information it needs. GraphEcho provides a controlled way to evaluate both what graph agents conclude and whether their exploration reaches distinct evidential sources.

Abstract: Multi-Hop Knowledge Graph Question Answering (KGQA) tasks require models to assemble relational evidence along paths in a KG to answer natural-language questions. However, existing KGQA systems typically focus on predicting the final answer without explicitly modeling or validating the intermediate reasoning steps, obscuring whether the correct answers arise from faithful multi-hop reasoning. To address this limitation, we re-frame multi-hop KGQA as a question-conditioned graph navigation problem. We refer to this formulation as THESEUS - Traceable Hop-wise Evidence SEarch in a Unified Semantics. In this setting, an agent receives a KG, a question, and a topic entity, and traverses a sequence of relations towards the answer, making the reasoning path explicit. To systematically study this formulation, we provide three key contributions. (i) We augment the existing KINSHIP and MQuAKE resources into navigation-ready KGQA datasets with annotated evidence paths and paraphrased questions. (ii) We design evaluation protocols to measure path fidelity, robustness to linguistic variation, and performance across multi-hop and multi-answer questions. (iii) We adapt established path-based KG completion agents - MINERVA, MultiHopKG, and SQUIRE - to operate on full question embeddings rather than symbolic single-relation queries, enabling their trajectories to be guided by natural-language semantics. Together, these contributions advance KGQA research toward systems where traceability is fundamental: answers are accompanied by explicit reasoning paths whose agreement with reference evidence can be systematically evaluated.

Abstract: Structured knowledge fact checking aims to determine the truthfulness of natural language claims by reasoning over structured evidence. Recent program-generation approaches leverage large language models (LLMs) to generate executable graph reasoning programs, achieving strong performance on structured knowledge fact checking benchmarks. However, these methods remain limited by invalid relation generation, single-path reasoning that lacks self-correction, and biased evidence assessment that tends to overestimate supporting signals. We propose Dialectical Agentic Reasoning (DARE), a multi-agent framework that formulates structured knowledge fact checking as an iterative retrieve-reason-reflect process. DARE integrates relation-grounded evidence retrieval to constrain reasoning to valid structures, dialectical bidirectional verification to evaluate evidence from both supporting and refuting perspectives, and confidence-driven meta-reflection to dynamically determine whether additional evidence exploration is necessary. Extensive experiments demonstrate the effectiveness of DARE in structured knowledge fact checking, with an 8B backbone achieving 88.12% accuracy and matching or surpassing GPT-4o-based program-generation baselines, which attests to the efficacy of dialectical agentic reasoning in eliciting the latent reasoning capabilities of LLMs.

Abstract: SNAP-KG is a framework for assigning newly arriving entities to semantic communities in a growing knowledge graph (KG) using only their raw features, with no graph access and no retraining at inference time. It was evaluated on five multi-view benchmarks and a 2.4M-node OGB-WikiKG2 KG. In each of these datasets, at least one graph view is homophilous, meaning that connected nodes usually belong to the same class, and SNAP-KG performs well on all of them. This paper asks what happens outside that setting. We extend the evaluation to three heterophilous graphs (Texas, Wisconsin, Chameleon) and measure the edge homophily of every view. When no homophilous view is available, clustering quality drops sharply for both SNAP-KG and the transductive baselines used in its original evaluation. What decides this is the homophily of the relation, not the number of relations. Multi-view fusion still helps, but only when at least one homophilous relation provides a reliable foundation. The homophily assumption is therefore shared by the whole method family, not specific to SNAP-KG. We argue that heterophilous multi-view clustering is a separate research problem, outside the scope of this work. As future work, we outline how a heterophily-aware teacher could be distilled into SNAP-KG's projector to serve both homophilous and heterophilous KGs.

Abstract: Graph captions should help readers understand graph structure, rather than simply translate adjacency matrices into long textual edge lists. A useful graph caption abstracts connectivity into recognizable motifs, such as hubs, paths, cycles, cliques, and bridges, because these motifs provide compact structural units that are easier to read, compare, and recover. In this paper, we study motif-oriented graph captioning as a bidirectional graph-text translation task, where captions must both preserve enough topology for graph recovery and express the graph through concise motif-level descriptions. We show that direct prompting of GPT-5.1 often produces graph-recoverable captions by enumerating node-to-node connections, but these captions are verbose and can contain inconsistent motif interpretations. To address this gap, we introduce Structurally Speaking, a lightweight structured prompting protocol that guides translation between explicit connectivity and motif-level abstraction. Experiments on a synthetic motif-based dataset show that structured prompting produces shorter and more motif-consistent captions while maintaining comparable graph recovery. These results suggest that explicit topology-to-motif reasoning guidance can make LLM-generated graph captions more interpretable without model fine-tuning.

Abstract: Agentic graph learning (AGL) has recently achieved promising results on graph reasoning tasks, where an agent powered by a large language model (LLM) sequentially samples the graph as evidence to support its final prediction. Existing methods either employ a single agent or orchestrate multiple role-based agents to reason and learn over the entire graph, but both essentially rely on a shared reasoning policy across different graph regions, which can be suboptimal for graphs with heterogeneous structural and semantic patterns. Inspired by the progress of multi-agent collaboration on complex reasoning tasks, a natural remedy is to let multiple agents own different memory and collaborate; however, applying this paradigm to graphs directly faces two challenges. First, existing AGL methods typically verbalize graph structures into natural-language descriptions for LLM agents, making the reasoning process sensitive to the ordering of structural information and thereby breaking the permutation-invariant nature of graphs. Second, incorporating increasingly large sampled neighborhoods leads to rapidly growing contexts. To address these challenges, this paper introduces a multi-agent agentic graph learning (i.e., MAAGL) framework. MAAGL partitions the graph into communities and assigns an independent agent to each community for region-specific specialization. MAAGL represents structural and semantic evidence separately. Structural evidence is summarized by a dynamically updated structural signature that is permutation-invariant and fixed in size, while semantic evidence is filtered to the top-k nodes ranked by relevance. Based on historical trajectories with similar signatures, agents estimate their confidence and trigger debate-style collaboration when needed. Extensive experiments on four benchmark datasets show that MAAGL outperforms SOTA AGL methods.

Abstract: Knowledge graphs have become a key resource for integrating heterogeneous data and powering downstream tasks such as question answering, entity linking, and semantic search. They are built and maintained incrementally, either (i) fully automated, e.g., YAGO, (ii) semiautomatically with community oversight, e.g., DBpedia, or (iii) manually through collaborative editing, e.g., Wikidata. Understanding the evolution of knowledge graphs is essential as changes may reflect real-world updates, error corrections, or noise introduced by vandalism, all of which affect the reliability of downstream applications. Among openly available knowledge graphs, Wikidata is the most challenging case to study evolution, with over 120 million entities edited by humans and bots and an edit history spanning more than a decade. Although Wikidata exposes change data in various formats (e.g., periodic dumps and real-time event streams), none support analytical queries over the complete edit history. Therefore, we present WiDiff, a tool that extracts changes from Wikidata's complete edit history and provides a unified interface for large-scale analytical queries over it.

Abstract: In various data models, the classical triple is a typical semantic data model. However, due to the design of the triple as a simple structure for representing positive assertions, it cannot sufficiently express different forms of negation present in the triple and its elements. This paper conceptually proposes that there are three distinct forms of negation within triples and their elements: contradictory negation, opposite negation and intermediary negation. Based on the the set SCOI and the logic LCOI+PLCOI with three kinds of negation, we propose an extension of triple that can distinguish and express these three different negations in the triple and its elements, called the TCOI triple with contradictory negation, opposite negation and intermediary negation. The TCOI triple is a semantic and structural extension of the classical triple. While retaining the ability to express positive assertions, it systematically introduces the three semantic dimensions of three negations, allowing these negations to independently act on the elements of the triple and on the whole triple. This significantly enhances the triple model capability to represent and reasoning about complex negative information. This paper also explores the expressive power and reasoning of the TCOI triple, as well as the application of TCOI triple implication reasoning in counterfactuals and counterfactual reasoning. We propose a truth-value (continuous value) algorithm for TCOI triple implication reasoning and perform its calculation through an example of the counterfactuals and counterfactual reasoning.

Abstract: We demonstrate X-DigCheck, a domain-independent environment for building and maintaining application profiles as they co-evolve with the data they describe. Profiles developed against a fixed ontology quickly drift from the schema they were meant to capture. X-DigCheck treats profile construction as a continuous ontology-data co-evolution loop: data are lifted into RDF against the profile, checked through competency questions and SHACL, and the resulting reports jointly drive revisions of the ontology, mappings, constraints, and graph. The loop is agnostic to the domain and to the pipeline that produces the graph. We validate and demonstrate the tool in the cultural heritage domain, on the construction of RupeMagna-RTI, the first Reflectance Transformation Imaging (RTI) specialisation of the Cultural Heritage Survey ODP (CHS-ODP), aligned with CIDOC-CRM/CRMdig, ArCo, CHAD-KG, and Getty AAT, with semRTI as the lifting pipeline of this use case. The demonstration lets visitors run one full turn of the loop -on the shipped Rupe Magna (Grosio, Italy) RTI survey, or on a profile and graph of their own -executing the competency-question and SHACL checks live and reading the bidirectional coverage report that flags modelling gaps and stale assumptions. The result is a portable co-evolution environment for profile engineering, together with a reusable RTI application profile produced through it. A screencast of the demonstration is available at https://zenodo.org/records/22210609.