Biomedical knowledge graphs combine ontology-derived hierarchies with transversal associations among heterogeneous entities such as phenotypes, diseases, genes, proteins, and patients. This hybrid structure raises the question of whether hyperbolic embeddings, which naturally capture tree-like organization, remain useful beyond purely hierarchical graphs. We present a preliminary study of hyperbolic graph representation learning for Mendelian-disease differential diagnosis on a patient-integrated biomedical graph. Experiments on isolated ontology subgraphs show that hyperbolic models achieve strong performance in substantially lower dimensions than Euclidean baselines. We then evaluate the models on a link-prediction task that ranks candidate diseases for each patient. Results suggest that hyperbolic embeddings can exploit biomedical hierarchical structure while supporting diagnostic reasoning over heterogeneous patient-level graphs.
https://arxiv.org/abs/2609.18481
Large language models (LLMs) suffer from a long-tail deficit: culturally specific facts, particularly those concerning underrepresented regions such as Latin America, appear too rarely in pretraining corpora to be reliably memorized. Retrieval-Augmented Generation (RAG) addresses this by grounding generation in external text, but structured alternatives such as Knowledge Graphs (KGs) offer tighter control over what enters the context, along with potential gains in explainability and updatability. We benchmark Graph-RAG against standard RAG on LatamQA, a culturally grounded multiple-choice dataset spanning eight thematic categories. The graphs are built end-to-end from Wikipedia articles with KGGen, a recent open-domain extractor, without manual curation in our main setting. G-Retriever is competitive with RAG and reduces the error of the base LLM by 72\% with a standard KG and 78\% with a benchmark-aware variant, the gap to RAG narrowing further as the graph is oriented toward task-relevant content. The trained projection transfers zero-shot to Portuguese without target-language fine-tuning, indicating multilingual reach.
https://arxiv.org/abs/2609.18317
An advanced retrieval-augmented generation pipeline is typically assembled from three or four independently operated systems: an approximate nearest-neighbour index, a full-text search engine, a graph database, and a relational document store. Each contributes its own deployment surface, configuration model, and failure modes, and the integration logic that binds them is written anew in every project. In this work, we present \textsc{Quanta}, an open-source Python library, which unifies dense vector search over 4-bit quantised embeddings, BM25 full-text retrieval, and knowledge-graph traversal behind a single retrieval API. Quanta makes two design commitments, which distinguish it from existing hybrid retrieval stacks. First, signals are combined by \emph{weighted reciprocal rank fusion} rather than by normalising heterogeneous scores onto a shared range, which we argue is ill-posed because such normalisations are query-dependent. Second, the graph is a \emph{candidate expander and not a relevance scorer}: traversal widens the candidate pool, and the newly admitted documents are re-scored by the dense indexes under an identifier allowlist, so structural adjacency determines what is considered while content evidence determines how it ranks.
https://arxiv.org/abs/2609.18248
The quest for new materials increasingly relies on predictive models and comprehensive simulations that span scales from atomic to macroscopic levels. However, essential data necessary for these models and simulations are often embedded in scientific literature as unstructured text, limiting reusability and posing challenges for researchers seeking to leverage existing knowledge effectively. While extracting structured data from unstructured text using large language models is gaining popularity, traditional methods typically generate key-value pairs data with straightforward schemas. In contrast, we introduce eolas, a modular pipeline that uses large language models to automatically transform scientific documents into knowledge graphs aligned with a specified ontology. We demonstrate eolas effectiveness in extracting useful information for scientists studying materials designed to endure the extreme temperatures and radiation levels found in fusion reactors. While a human expert might spend between thirty to ninety minutes extracting relevant data from an article, eolas can generate high-quality knowledge graphs in just a few minutes. These are presented in a tabular format with faceted navigation for easy human validation. Additionally, we introduce the first benchmark dataset designed to assess large language models capabilities in constructing knowledge graphs within the domain of irradiated materials. The analysis of 168 experiments using our dataset, various large language models and prompting techniques provides key insights that we summarize into practical guidelines for effectively extracting knowledge graphs aligned with an input ontology.
https://arxiv.org/abs/2609.17291
Generative AI promises natural language access to the massive numerical telemetry of data centers and Industry 4.0 installations, yet text-to-query and tool-using agents stay unreliable: even frontier models answer little more than half of real-world database questions, and far fewer of the multi-step, operational ones, because the LLM must compose how heterogeneous sources relate and hallucinates the relations, not just the fields. We propose symbolic separation: a deep agent reasons freely but may act on data only through an ontology-constrained Virtual Knowledge Graph with deterministic pre-execution validation. Unlike a tool API's interface contract, this domain-semantic contract turns a complex question into one validated graph traversal instead of LLM-inferred joins. Instantiated as the Neurosymbolic Deep Analyst and evaluated on 49.9 TB of superconputer telemetry against a rigid workflow and a non-symbolic ablation, it raises end-to-end task success from 43% to 86%, prevents silent data-integrity errors that no syntactic check catches, and cuts token cost by 2.4x, letting a smaller on-premise model outperform a larger one.
https://arxiv.org/abs/2609.17107
This paper introduces NeuroSymbEAD, a large-scale neuro-symbolic caption dataset featuring an ego-centric knowledge graph (KG) of static and dynamic objects annotated with classes, categories, heading directions, orientations, and distances from the ego-vehicle. These annotations are used on the KITTI-360 dataset to generate multilevel textual captions representing a lightweight version of an ego-centric scene map. Outdoor scene-map reconstruction, visual recognition, and object grounding establish baselines for driving common sense and traffic/scene understanding. For these purposes, natural language-based grounded captioning of objects and their complex relationships is a widely adopted contextual representation for indoor scene tasks. Neuro-symbolic representations have proven effective in handling structured information for various computer vision and language applications. Our data annotation pipeline allows the generation of varied map segments, populating simulated or real objects within the bounding boxes predicted by any 3D object detection network, and building hierarchical text captions. We benchmark our neuro-symbolic and ontological caption generation using pre-trained grounding and learned auto-regressive captioning networks. By converting 3D driving scenes into structured ego-centric language, NeuroSymbEAD provides a benchmark for vision-language and foundation models for traffic-scene explanation, 3D reasoning, and interpretable autonomous-driving perception.
https://arxiv.org/abs/2609.16919
Puns are a challenging form of figurative language that exploit phonetic similarity and semantic ambiguity to convey multiple meanings. Although large language models (LLMs) demonstrate strong language understanding capabilities, they still struggle with pun reasoning due to limited phonetic modeling and uncontrolled end-to-end generation. We propose \textbf{PunGraph}, a retrieval-enhanced knowledge graph framework for pun understanding. PunGraph constructs a phonetic-semantic lexical graph using the Unisyn phonetic dictionary, IPA and G2P representations, and WordNet definitions, and retrieves candidate words or senses to constrain LLM reasoning within a structured candidate space. We further introduce \textbf{WebPun}, a new large-scale dataset containing 5,730 annotated heterographic and homographic puns. Experiments on SemEval-2017 and WebPun show that PunGraph consistently improves the performance of small-scale LLMs and achieves competitive results against strong proprietary models. Further analysis shows that retrieval-guided phonetic and semantic constraints effectively reduce common reasoning errors in pun interpretation, highlighting the benefits of integrating structured knowledge with LLMs. We release our code and dataset at this https URL.
https://arxiv.org/abs/2609.16557
Research data repositories are essential infrastructure for scientific inquiry and for ensuring that datasets follow FAIR (Findable, Accessible, Interoperable, and Reusable) principles. However, repository reuse depends on the quality and completeness of geospatial and thematic metadata, which researchers generally provide voluntarily. Given limited curation resources, it is unsurprising that even Harvard Dataverse, the world's largest general-purpose research repository, contains many incomplete metadata records. Missing fields represent lost information and reduce interoperability. We find that datasets with more missing metadata receive fewer downstream citations and have fewer resolvable connections to other datasets. The implications are particularly important for geospatial datasets: only 0.3% of research datasets include a bounding box, and most represent archival points rather than complete geographic shapes. Our analysis shows that geospatial metadata helps connect concepts across disciplines. After embedding Harvard Dataverse datasets in a metadata knowledge graph, we find that datasets are twice as likely to connect across scientific disciplines through shared geospatial metadata as through keywords. This suggests that geographic metadata is a more reliable basis for cross-disciplinary interoperability than keyword vocabularies, which often remain discipline-specific. We train and fine-tune a small language model using datasets from Harvard Dataverse. Through geospatial metadata enrichment, we increase the share of datasets from different disciplines connected through metadata elements from 58.5% to 63.2%.
https://arxiv.org/abs/2609.16498
Large Language Model (LLM) applications often transfer domain concepts into the model's context informally, through prompt prose, schema dumps, and examples. We show that for database queries, data model concepts pass to LLMs more effectively through representations whose vocabulary terms carry declared, machine-readable semantics (controlled semantics). NLKGQ is a working system and reusable framework that does this for data modeled in a knowledge graph. A formal OWL ontology serves as the transfer mechanism, concentrating the meaning of the data into semantically precise tokens the model can use directly. In a single LLM call, NLKGQ places in the context a system prompt instructing on SPARQL, the complete domain OWL ontology, and a domain-specific prompt addition, together with the user's natural language query. The model then generates the SPARQL query directly, zero-shot. Where the native vocabulary of an existing database or federation of databases is opaque, a wrapper ontology substitutes clean terms and a runtime rewriter restores the native forms. Evaluating on DBLP-QuAD 2.0 showed that its scores depend on the graph snapshot, the endpoint used, and the wording of its machine-generated questions, so we propose DBLP-QuAD 3.1, which maintains the intent of 2.0 while making reference results deterministic, revising reference SPARQL where needed, and rewriting the natural language questions, with a frontier model, to state each reference query's intent clearly and completely. We evaluate on the DBLP-QuAD 2.0 benchmark (57.6% Match under deterministic re-scoring), DBLP-QuAD 3.1 (89.9% Match on 1,000 questions), SemOpenAlex (98% Match against a published baseline's 86% on the identical test set), and neuroimaging metadata (100%).
https://arxiv.org/abs/2609.14652
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.
https://arxiv.org/abs/2609.14528
Temporal knowledge graph embedding (TKGE) models infer missing facts in knowledge graphs that evolve over time. Many existing models use a single geometric space, which can limit their ability to represent diverse relational patterns, or treat entity representations as static. We propose Biquaternionic Space with Complex-valued Attention (BSCA), a TKGE model that combines circular and hyperbolic rotations within a unified biquaternionic framework. A complex-valued attention mechanism adaptively fuses time-conditioned and relation-conditioned entity representations, allowing them to vary with temporal and relational context. Experiments on five benchmark datasets show competitive performance across datasets, with the largest improvement on GDELT: BSCA achieves an MRR of 52.1\%, compared with 38.1\% for the strongest baseline in our comparison.
https://arxiv.org/abs/2609.14279
Knowledge graphs are increasingly distributed across autonomous organizations that share an entity space but own disjoint subsets of relations, forming a vertical partition. Answering a multi-hop query may require combining facts from several silos, making the partitioning strategy a key data management decision that affects communication, indexing, load balance, and query latency. However, the costs associated with different partitioning strategies remain insufficiently studied. We formalize vertical partitioning as a design space and compare four strategies: semantic domain grouping, frequency-balanced partitioning, co-occurrence graph-cut partitioning, and random partitioning. We evaluate them using five metrics: communication cost, candidate index size, cross-silo path length, load balance, and end-to-end query latency. Three of the five prove to be determined by the graph and the silo count rather than by the partition, which reduces the design problem to two conflicting axes, cross-silo path length and load balance. Experiments on MetaQA and PathQuestion use a fixed federated knowledge graph question-answering architecture based on TransE embeddings and a frozen BERT encoder across three silo configurations. By keeping the learning model unchanged, we isolate the effect of partitioning and show that the trade-off between locality and balance holds only where each silo can hold several relations, weakening as the number of silos increases. The study provides practical guidance for deployments constrained by cross-silo reasoning or by silo load.
https://arxiv.org/abs/2609.13664
Knowledge graph question answering usually assumes that one system can reach the whole graph. In practice, facts are often held by organizations that share entity identifiers but own disjoint relation types, so no single party sees a complete reasoning chain. This poster presents the empirical findings of FedV-KGQA on multi-hop question answering over such vertically partitioned graphs. Each silo enriches its local graph and trains a knowledge graph embedding on its own triples. A server then concatenates the silo-specific entity views, anchors the projected question at the topic entity, and ranks candidates by similarity. Raw triples and relation embeddings never leave a silo. Comparing the FedV-KGQA experiments with one another yields three results. First, federated fusion recovers most of the centralized accuracy, while a single silo recovers little. Second, anchoring and enrichment matter more than the choice of embedding model. Third, the cheapest encoder depends on the target accuracy rather than on parameter count. This poster paper contributes that cross-experiment comparison, four design lessons drawn from it, and an interactive prototype that runs real inference and traces the full pipeline, per question, on released checkpoints.
https://arxiv.org/abs/2609.13661
Retrieval-Augmented Generation (RAG) has empowered Large Language Models (LLMs) to tackle knowledge-intensive tasks. However, navigating global, heterogeneous knowledge bases (large-scale knowledge graphs and text corpora) for complex reasoning remains a challenge. Existing methods typically employ reactive, graph-driven exploration strategies, which blindly follow graph topology without adapting to the question context or evolving exploration progress, and lack deep bidirectional synergy between graph and text. To address these limitations, we propose CoG (Cognition on Graph), a cognitive-inspired, training-free framework for adaptive knowledge exploration. Drawing inspiration from human problem-solving, CoG performs a continuous plan-explore-reflect cycle, where it proactively formulates investigation plans, performs dual-source retrieval, and dynamically reflects on progress to adjust strategies. Crucially, it establishes deep bidirectional synergy between structured graph and unstructured text, where entities extracted from text dynamically guide graph exploration to bridge knowledge gaps. Extensive experiments on seven multi-hop QA benchmarks demonstrate that CoG significantly outperforms state-of-the-art methods while achieving superior exploration efficiency. Our code and datasets are available at this https URL.
https://arxiv.org/abs/2609.12791
Sensitive attributes such as age, income, and occupation can be inferred from user-generated content by aggregating indirect cues across many ordinary posts. LLM-based profilers can perform this aggregation automatically and with high accuracy, which makes large-scale personal attribute inference a major privacy threat. Existing LLM-based profilers, however, offer limited insight into which specific posts, concepts, and relationships made an inference possible, which is key to targeted privacy mitigation, i.e., redacting or rewriting only the few posts that actually leak an attribute, rather than perturbing entire histories. We introduce GraphProfiler, an auditable LLM-based profiler that represents each user's post history as a source-linked personal knowledge graph where nodes and edges trace back to the originating post and resolves attribute predictions to cited graph records and source texts. GraphProfiler reaches 86.7% attack success rate on the eight-attribute SynthPAI benchmark, within two points of strong text-only baselines, and 84.6% on PANDORA, while citing supporting evidence for over 98% of predictions. Our controlled ablation experiments provide evidence that the cited posts contribute to attack success, as removing them reduces the attack success rate substantially more than removing an equal number of random posts.
https://arxiv.org/abs/2609.12448
Graph-RAG systems often assume pristine data quality, overlooking the severe impact of perturbations in cloud-native databases. This paper proposes a three-layer decoupled diagnostic framework to orthogonally attribute system errors to reasoning loss, Knowledge Graph (KG) defects, and Cypher generation errors. Evaluated on a spatio-temporal ecological KG of the Southeastern Tibet region with eight defect types, results reveal that data integrity, rather than algorithmic reasoning, is the dominant performance bottleneck, with structural defects degrading system accuracy from 0.93 to 0.39. Crucially, we observe a masking-like phenomenon termed the Parametric Knowledge Masking Effect (PKME), suggesting LLMs compensate for broken retrieval paths using internal memory. This shrinks apparent query generation errors by over 70 percent, obscuring actual storage deterioration and increasing the risk of false negatives for automated monitoring. This work provides a quantitative foundation for auditing and optimizing data integrity in cloud-based information fusion systems.
https://arxiv.org/abs/2609.13324
Large language models (LLMs) can generate biomedical hypotheses, but it remains unclear whether they truly reason from scientific evidence or simply produce convincing-sounding ideas. To study this, we combine three major biological databases: the Kyoto Encyclopedia of Genes and Genomes (KEGG), Rhea, and UniProt, into a unified biochemical knowledge graph and construct a benchmark of 550 paths connecting enzyme sources to rare disease endpoints, yielding 13,200 hypotheses from six LLMs under four conditions varying the biological information each model receives: source enzyme only, full biological path, or source and disease endpoint only. Hypotheses are scored using an expert-derived five-criterion rubric on a 1-5 scale per criterion. We find that models given both the source and disease endpoint often produce the highest-scoring hypotheses, showing that LLMs can generate compelling ideas from minimal information. However, these hypotheses are less grounded in the evidence. In contrast, models given the full biological path generate hypotheses more consistent with known mechanistic relationships. We call this evidence-disciplined reasoning. To confirm this effect, we shuffled intermediate path steps while keeping endpoints fixed. Evidence grounding dropped significantly (delta = -0.793, p < 0.001), confirming models genuinely used path structure during reasoning. Our findings show that knowledge graphs support hypothesis generation in two ways: they identify biological endpoint pairs absent from the literature, and their mechanistic paths guide how LLMs reason between them.
https://arxiv.org/abs/2609.12260
Question-answering often requires reasoning across multiple connected facts rather than retrieving a single isolated relation. Knowledge graphs (KGs) provide a structured way to represent such facts, but training large language models (LLMs) only on isolated KG head-relation-tail triples may limit their ability to learn the surrounding context needed for multi-hop reasoning. In this work, we propose a context-augmented training framework for multi-hop question-answering. Although generally applicable, we validate the framework in the context of disease-specific KGs, extracted using a reliable KG extraction framework called GraphMERT, for Gastroparesis and Diabetes. For each primary KG triple, we attach supporting triples extracted from the same source text chunk to form a context graph (CG). This creates two supervision settings: KG-grounded supervision, which uses only the target KG triple or path, and CG-grounded supervision, which uses the target KG triple or path together with supporting context triples. We train the Qwen3-14B model using supervised fine-tuning (SFT) under both settings, producing KGModel and CGModel variants. To strengthen the lower-hop factual foundation of the models, we introduce an LLM-judged, history-aware adaptive repair pipeline that identifies unresolved one-hop failures, continually fine-tunes on targeted repair examples, and removes or quarantines problematic noisy triples. This repair stage enables the models to reach 100% accuracy on the cleaned retained one-hop validation sets. Finally, we employ reinforcement learning (RL) using lower-hop question-answer items and evaluate generalization on harder 3-hop, 4-hop, and 5-hop tasks. Across both diseases, context-augmented supervision consistently improves multi-hop performance over KG-only supervision. RL initialized from repaired SFT checkpoints yields larger and more stable gains.
https://arxiv.org/abs/2609.12230
This paper details the Eloquence team's approach to Task 2 of the 2nd MLC-SLM challenge at Interspeech 2026, which involves multilingual Multiple-Choice Question Answering (MCQA) across 21 languages. Three approaches are explored. First, we fine-tune Voxtral-Mini-3B via LoRA with cross-lingual data augmentation, ASR transcript augmentation and timestamp-aware audio cropping, achieving 0.72 macro-accuracy on evaluation Phase 2. Second, we apply multimodal in-context learning (ICL) to the frozen Voxtral-24B model to correct a strong label bias, reaching 0.81, our best result. Third, a training-free retrieval system based on a three-layer voice-anchored memory combining acoustic identity, semantic content, and a knowledge graph achieves 0.68. All three systems substantially outperform the official baseline.
https://arxiv.org/abs/2609.11724
Harvard Dataverse hosts over 150,000 research datasets, but the geographic information those datasets carry is entered as free text by depositors and has never been assembled into a searchable structure. We construct a knowledge graph from the repository's public data and metadata, organizing 102,650 datasets within a 215,985-node network of 528,003 edges linking datasets to keywords, publications, subjects, journals, and locations. Of those datasets, 43,991 (42.9 percent) carry at least one geospatial field, geographic coverage, geographic unit, or a bounding box and 96.9 percent of all nodes sit in a single connected component, so datasets remain reachable from one another even when their geospatial metadata share nothing in common. A conservative keyword search identifies 7,654 geospatially tagged datasets (17.4 percent) as directly policy-relevant, with elections and legislatures the largest cluster, followed by government administration, health policy, transportation, and education. Five datasets illustrate how this metadata behaves across policy domains and spatial scales, and an extended use case shows how community language models, stance detection with geographic aggregation, and partisan language bridging tools can attach discourse to place. The central obstacle is place resolution: the same location appears as many disconnected nodes. We argue that the graph provides a concrete setting for developing AI-driven metadata enrichment and entity resolution, and we document its coverage skew toward American, city-level data.
https://arxiv.org/abs/2609.11674