Knowledge_Graph
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Knowledge Graph Enhanced Memory-Augmented Retrieval for Long Context Modeling
2026-06-12 02:48:45Ghadir Alselwi, Basem Suleiman, Hao Xue, Shoaib Jameel, Hakim Hacid, Flora D. Salim, Imran RazzakAbstract
Long-context language modeling requires not only extending context windows but maintaining coherent understanding of entity states and relationships across thousands of tokens -- a challenge that semantic similarity alone cannot address. KGERMAR addresses this by constructing dynamic, context-specific knowledge graphs from input text during inference, enabling domain-adaptive retrieval that leverages both semantic similarity and explicit entity relationships. The framework performs real-time entity and relation extraction to build contextual knowledge graphs, then integrates graph-structural embeddings with textual semantics through a multi-component memory architecture. Three memory banks -- contextual, semantic, and structural -- are maintained with retrieval signals fused via learned weights to capture both surface-level semantics and deeper relational patterns. Evaluated on SlimPajama (84.7K training examples), WikiText-103 (4,358 examples), PG-19 (100 examples), and Proof-pile (46.3K examples), KGERMAR achieves up to 8.5\% lower perplexity and 2--2.5x better memory efficiency than memory-augmented baselines across context lengths from 1K to 32K tokens, with superior in-context learning performance across five NLU tasks. The dynamic knowledge graph construction approach advances memory-augmented language modeling by enabling domain-specific knowledge representation that adapts to input contexts rather than relying on fixed knowledge bases.
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URL
https://arxiv.org/abs/2606.14047
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Knowledge-Based Zero-Replay Debugging of Multi-Agent LLM Traces
2026-06-11 22:34:39Dong Ho Kang, Hyeonjeong Cha, Daein WeonAbstract
Reliable operation of multi-agent large language model (LLM) systems depends on debugging long execution traces, where the few causally decisive events are buried in unstructured logs of messages, routes, memory writes, and tool calls. The standard tool is counterfactual replay (rewind, edit, and re-run the trajectory to measure each event's effect), but its cost grows linearly with the number of candidate events, making exhaustive replay infeasible at scale. We frame trace debugging as a knowledge-based decision-support problem. Each trace is compiled into a structured event knowledge graph over routing, memory, tool-use, uncertainty, and latent evidence, and a calibrated predictor decides where a scarce replay budget should be spent. We do not propose a new replay oracle; we propose a method to predict its results without paying the replay cost. We formulate zero-replay counterfactual-effect prediction: given a trace under a fixed budget, predict which events the oracle would mark high-effect before any replay is performed. BranchPoint-Latent is a lightweight predictor over observable, structural, uncertainty, and latent features of the knowledge graph. Calibrated against a deterministic replay oracle across 37 trace families, a single learning-to-rank gradient-boosted predictor raises per-trace localization (Branch Recall@5) from 0.73 to 0.93 on held-out families at zero oracle-replay cost. Rather than claiming universal dominance, we characterize when cheap graph centrality suffices and when learned evidence is necessary. The result is an auditable, cost-efficient decision-support system for AI-reliability debugging, positioned explicitly on the cost-accuracy frontier with reproducible artifacts.
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URL
https://arxiv.org/abs/2606.14805
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Agents-K1: Towards Agent-native Knowledge Orchestration
2026-06-11 17:58:35Zongsheng Cao, Bihao Zhan, Jinxin Shi, Jiong Wang, Fangchen Yu, Zhijie Zhong, Zijie Guo, Tianshuo Peng, Zhuo Liu, Yi Xie, Xiang Zhuang, Yue Fan, Runmin Ma, Shiyang Feng, Xiangchao Yan, Anran Liu, Peng Ye, Wenlong Zhang, Shufei Zhang, Chunfeng Song, Fenghua Ling, Jie Zhou, Liang He, Bo Zhang, Lei BaiAbstract
Current LLM-based research agents have advanced through agent orchestration, yet largely overlook scientific knowledge orchestration. Existing works often reduce papers to abstracts, surface mentions, and flat \texttt{cites} edges, omitting key entities, claims, evidence, mechanisms, and method lineages essential for scientific reasoning. To this end, we introduce \textbf{Agents-K1}, an end-to-end knowledge orchestration pipeline that converts raw documents into agent-native scientific knowledge graphs. Agents-K1 integrates three components under a unifying theoretical foundation: a multimodal parser whose five-module schema captures entities, multimodal evidence, citations, and typed inter-entity relations across the full paper rather than abstracts alone; a 4B information-extraction backbone trained with GRPO under a rule-based reward; and a graphanything CLI, a tri-source agent interface that unifies web search, multimodal graph retrieval, and cross-document traversal. On top of this, we process 2.46 million scientific papers across six subjects to produce \textbf{Scholar-KG}, of which we release a one-million-paper subset, and the full Scholar-KG is accessible via the SCP link below. The same pipeline can be extended to general-domain corpora and to schema-conformant data synthesis. Extensive experiments demonstrate that Agents-K1 achieves superior performance in scientific information extraction, knowledge graph construction, and multi-hop scientific reasoning.
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URL
https://arxiv.org/abs/2606.13669
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LoHoSearch: Benchmarking Long-Horizon Search Agents Beyond the Human Difficulty Ceiling
2026-06-11 03:04:32Jiarui Zhao, Rongzhi Zhang, Lingchuan Liu, Hao Yang, Xunliang Cai, Xi SuAbstract
Search agent benchmarks exemplified by BrowseComp have rapidly saturated over the past year, with the strongest models surpassing 90% accuracy. Since these benchmarks are predominantly human-authored, annotators lack a global perspective on entity statistics and cannot systematically maximize search space size and structural complexity. This creates a difficulty ceiling that is hard to break. To address this, we introduce LoHoSearch (Long-Horizon Search Agents), a challenging benchmark comprising 544 human-verified questions across 11 domains. LoHoSearch is constructed via an automated pipeline built upon a knowledge graph covering over 7 million Wikipedia entities, which selects relations with large search spaces and assembles them into structurally complex questions with KG-verified unique answers. Our evaluation demonstrates that even the strongest model achieves only 34.74% accuracy, and existing context management strategies (best +6.8%) yield far smaller gains than on prior benchmarks. LoHoSearch provides a more demanding standard for evaluating long-horizon reasoning and context management in search agents.
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https://arxiv.org/abs/2606.12837
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Automating Geometry-Intensive Compliance Checking in BIM: Graph-Based Semantic Reasoning Framework
2026-06-10 13:31:43Zixuan Xiao, Pei Troh Koh, Jun Ma, Jack C. P. ChengAbstract
Automating compliance check for geometry-intensive regulations remains a significant technical bottleneck in Building Information Modeling (BIM), primarily due to the semantic disparity between high-level regulatory logic and structured IFC data. Existing methods, often reliant on static rule templates, struggle to traverse multi-hop reasoning chains or resolve latent spatial dependencies across multiple building entities. To address these challenges, a Spatial-Geometric Reasoning System for Building Information Modeling (SGR-BIM) is proposed as an integrative graph-driven reasoning framework. SGR-BIM dynamically constructs a cross-modal knowledge graph that aligns user intent, regulatory semantics, and BIM geometry, enabling interpretable reasoning without rigid hard-coding. Validated on 679 expert-verified queries from fire safety codes, the framework achieves 84.3% accuracy, representing an 8.6% improvement over enhanced-tool single-agent baselines. This research provides a graph-based semantic reasoning paradigm, enhancing the transparency and flexibility of automated geometric compliance check workflows in the Architecture, Engineering, and Construction (AEC) industry.
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URL
https://arxiv.org/abs/2606.12065
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Hey Chat, Can You Teach Me? Structuring Socratic Dialogue for Human Learning in the Wild
2026-06-10 07:20:59Sidney Tio, Arunesh Sinha, Pradeep VarakanthamAbstract
Large language models are now widely used for everyday learning, but the underlying interactions are typically unstructured chats rather than following a curriculum. Unlike formal online learning systems, these interactions carry no prior record of the student, so any estimate of what the student already knows must be inferred from the dialogue itself. We show that this gap is not closed by scaling models alone. Frontier and education-tuned LLMs perform poorly when asked to tutor a student over an extended session, because doing so requires three things at once. The tutor must sequence a curriculum, conduct Socratic dialogue, and infer the student's knowledge state from that dialogue. We propose separating these responsibilities. Given a student query, our system constructs a prerequisite knowledge graph in which subtopics are nodes and dependencies are edges, and frames tutoring as deciding which node to teach next and how many dialogue turns to spend on it before moving on. A lightweight PPO policy handles this sequencing decision, while an LLM conducts the Socratic exchange at the chosen node and returns a signal of student progress. Across held-out STEM and non-STEM topics, our PPO-paired tutor outperforms heuristic baselines, frontier general-purpose models, and a model specialised for Socratic dialogue: on both the rate at which students reach full curriculum mastery and the number of turns required. Explicit curriculum structure delivers gains that scaling the underlying model does not.
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URL
https://arxiv.org/abs/2606.11744
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Lung-R1: A Knowledge Graph-Guided LLM for Pulmonary Diagnostic Reasoning
2026-06-10 05:39:08Haoyang Zeng, Yuanxi Fu, Rongzhen Li, Yuming Yang, Xiao Sun, Jingwang Huang, Gujie Shao, Guohui Xiang, Quan Lu, Dongfan Ye, Xuetao Chen, Jiang Zhong, Kaiwen Wei, Zhi XuAbstract
Diagnosing pulmonary diseases requires integrating heterogeneous evidence amid phenotypic variability and cross-disease overlap. Although large language models (LLMs) have shown progress on pulmonary knowledge question answering (QA) and information-processing tasks, reliable pulmonary diagnosis requires patient-specific, relation-aware reasoning over electronic medical record (EMR) evidence rather than isolated knowledge recall. We define this gap between pulmonary knowledge and case-level diagnostic reasoning as the Pulmonary Knowledge-to-Diagnosis Gap. To address it, we introduce LungKG, the first structured pulmonary knowledge graph for diagnostic knowledge organization and record-grounded reasoning. LungKG contains 59,038 nodes and 164,308 edges across 15 entity types and 112 relation types, serving as both a reusable pulmonary knowledge resource and the foundation for LungKG-guided model adaptation. Built on LungKG, we propose Lung-R1, a LungKG-guided pulmonary LLM trained through KG-constrained reasoning-chain construction and KG-guided reinforcement learning. In a 20-system evaluation, Lung-R1-14B achieves state-of-the-art performance across Choice, Pulmonary-QA, and EMR Diagnosis, reaching an EMR Diagnosis score of 4.3583 and surpassing the strongest non-Lung-R1 baseline by 0.1476 points. These results demonstrate the value of LungKG-guided training for EMR-based pulmonary diagnosis.
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URL
https://arxiv.org/abs/2606.11675
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LLMs+Graphs: Toward Graph-Native, Synergistic AI Systems
2026-06-10 01:39:41Arijit Khan, Longxu Sun, Xin HuangAbstract
Large Language Models (LLMs) have advanced rapidly, but their limitations in structured and multi-hop reasoning underscore the need for graph-native, synergistic artificial intelligence (AI) systems. Graph-structured data underpins critical applications across social, biological, financial, transportation, web, and knowledge domains, making it essential to understand how LLMs can leverage graph computation for grounded, context-rich inference. Three complementary synergies are emerging: LLMs augmented with graph computation for retrieval and reasoning; bidirectional integration between LLMs and knowledge graphs (KGs), where LLMs support KG construction and curation while KGs enforce semantic constraints and factual consistency; and AI agents strengthened by graph algorithms for planning, decision making, and multi-step reasoning. In parallel, LLMs introduce new capabilities for graph data management and graph machine learning (ML) through natural language interfaces and hybrid LLM-graph neural network (GNN) pipelines. This tutorial synthesizes the algorithms, systems, and design principles driving these converging directions, offering data science and data mining researchers a unified perspective on integrating LLMs, graph data management, graph mining, graph ML, and agentic computation into next-generation graph-native AI systems.
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https://arxiv.org/abs/2606.11560
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Towards a Bridge Layer Between Bibliographic and Formalized Mathematical Knowledge
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Mathematical knowledge is split between bibliographic databases (e.g., MathSciNet, zbMATH Open) and formal proof libraries (e.g., Lean mathlib), preventing unified access between published results and their formalizations. We propose a relational bridge-database that aligns publication metadata with formal artifacts, providing an interoperability layer between mathematical literature and machine-verifiable proofs. We introduce a paper-level formalization score that measures how much of a publication is covered in formal systems. As a feasibility study, we show how such scores can be estimated via cross-document alignment between informal texts and Lean formalizations, enabling large-scale analysis of formalization coverage. This framework is a first step toward integrating bibliographic and formal mathematical ecosystems into scalable, machine-actionable knowledge graphs linking publications to formal proof objects.
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URL
https://arxiv.org/abs/2606.11430
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Detecting Knowledge Gaps from Conversational AI Interactions Using Curriculum Prerequisite Graphs
2026-06-09 11:47:04Youssef Medhat, Junsoo Park, Ploy Thajchayapong, Ashok K. GoelAbstract
Large online courses generate thousands of student questions directed at conversational AI teaching assistants, yet these interaction logs remain largely untapped as diagnostic signals. We present a pipeline that maps student questions from a conversational AI teaching assistant to curriculum topics using a few-shot text classifier, grounded in a GPT-4-extracted prerequisite knowledge graph of course concepts. Evaluated on 1,340 question events from 164 students in a graduate-level AI course, our classifier achieves 80.0% accuracy across 43 labels (42 curriculum topics plus an "unknown" abstention class). Topic-level question volume correlates significantly with student self-reported difficulty from an independent mid-semester survey (rho = 0.491, p = 0.008, n = 28 topics), providing convergent evidence that the classified question stream reflects genuine topic difficulty. These results demonstrate that conversational AI interaction logs, mapped onto curriculum structure, carry actionable signals about topic-level knowledge gaps and provide instructors with a curriculum-grounded view of which topics warrant attention.
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https://arxiv.org/abs/2606.10736
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Benchmarking Knowledge Editing using Logical Rules
2026-06-09 08:21:56Tatiana Moteu Ngoli, NDah Jean Kouagou, Hamada M. Zahera, Axel-Cyrille Ngonga NgomoAbstract
Large Language Models (LLMs) are increasingly deployed in real-world applications that require access to up-to-date knowledge. However, retraining LLMs is computationally expensive. Therefore, knowledge editing techniques are crucial for maintaining current information and correcting erroneous assertions within pre-trained models. Current benchmarks for knowledge editing primarily focus on recalling edited facts, often neglecting their logical consequences. To address this limitation, we introduce a new benchmark designed to evaluate how knowledge editing methods handle the logical consequences of a single fact edit. Our benchmark extracts relevant logical rules from a knowledge graph for a given edit. Then, it generates multi-hop questions based on these rules to assess the impact on logical consequences. Our findings indicate that while existing knowledge editing approaches can accurately insert direct assertions into LLMs, they frequently fail to inject entailed knowledge. Specifically, experiments with popular methods like ROME and FT reveal a substantial performance gap, up to 24%, between evaluations on directly edited knowledge and on entailed knowledge. This highlights the critical need for semantics-aware evaluation frameworks in knowledge editing.
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URL
https://arxiv.org/abs/2606.10554
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Instruction Finetuning DeepSeek-R1-8B Model Using LoRA and NEFTune
2026-06-09 04:14:49Wu Yuerong, Mingni LuoAbstract
Financial named-entity recognition (NER) is essential for translating unstructured financial reports and news into structured knowledge graphs. However, general-purpose large language models (LLMs) often misclassify financial entities or ignore domain-specific patterns. This paper investigates the use of DeepSeek-R1-8B, a recent open-source large language model, combined with Low-Rank Adaptation (LoRA) and Noisy Embedding Fine-Tuning (NEFTune) for financial NER. Each annotated sentence in our corpus of 1693 samples is converted into an instruction-input-output triple. We insert lightweight LoRA matrices into the Transformer layers and apply NEFTune to improve generalisation by adding uniform noise to embedding vectors during training. Experiments show that the LoRA-adapted DeepSeek-R1-8B achieves a micro-F1 of 0.901 on seven entity types (Company, Date, Location, Money, Person, Product and Quantity), and adding NEFTune further boosts the micro-F1 to 0.912, outperforming Llama3-8B, Qwen3-8B, Baichuan2-7B, T5 and BERT-Base baselines.
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https://arxiv.org/abs/2606.10392
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KG-SoftMAP: Soft Knowledge-Graph Priors for Bayesian Network Structure Learning from Sparse Discrete Data
2026-06-09 03:14:50Guoliang Xu, James E. CorterAbstract
Learning Bayesian network (BN) structure from sparse discrete data is hard: when each instance records only a few variables, most variable pairs lack the joint observations needed for reliable scoring, and data-only methods recover little structure. Imperfect domain knowledge, expressible as a weighted directed knowledge graph (KG), is often available. We propose KG-SoftMAP, which encodes such a KG as a soft, confidence-weighted, data-overridable edge prior and maximizes a MAP objective combining the BDeu score with a logit-form prior; the KG may be expert-curated or LLM-extracted. On controlled synthetic benchmarks, the only setting with ground-truth DAGs, KG-SoftMAP recovers partial directed structure at $\rho=0.05$ (DF1 $0.14$ to $0.29$, versus near-zero baselines) and substantially more once $\rho\geq0.2$ (DF1 $0.46$ to $0.96$), when paired with an informative but imperfect KG; recovery degrades gracefully as KG quality drops. On real sparse educational data, which has no ground-truth DAG, we evaluate deployment-facing measures only: prediction, calibration, and KG-consistency. The learned BN is best read as a diagnostic model: on SAF it trails logistic regression by $0.03$ F1_FAIL while providing KG-consistent edges, calibrated joint probabilities, and inference from arbitrary observed concept subsets; when no meaningful KG exists, discriminative logistic regression is preferable.
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https://arxiv.org/abs/2606.10358
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When Metrics Disagree: A Meta-Analysis of Knowledge-Graph-Completion Model Benchmarking
2026-06-09 01:20:43Haji Gul, Ajaz Ahmad BhatAbstract
Evaluating Knowledge Graph Completion (KGC) models remains challenging because standard assessment relies on isolated rank-based metrics such as MRR, Hits$@$k, and Mean Rank, which often produce conflicting model orderings across datasets. A model that leads on MRR may trail on Hits@1, and strong performance on one dataset may not generalize to another. This fragmentation hinders comparison, enables selective reporting, and obscures real progress. We reframe KGC evaluation as a Multi-Criteria Decision-Making (MCDM) problem and present a meta-analysis of seven aggregators across five tests: consistency, cross-dataset stability, metric independence, robustness under noise, and generalizability. Each test is averaged over leave-one-model-out (LOMO) and leave-one-group-out (LOGO) removals so that reliability reflects aggregator behavior across diverse model subsets. Across tail $(h,r,?)$ and relation $(h,?,t)$ prediction, Pareto-optimal analysis identifies Z-score as the most balanced aggregator, which ranks DualE highest for tail prediction and FMS (Flow-Modulated Scoring) highest for relation prediction. A test-sensitivity analysis using the same removals shows that consistency and stability are largely removal-invariant, while generalizability and independence are the most sensitive. The framework resolves evaluation inconsistencies and offers evidence-based guidance for aggregator selection and model benchmarking in KGC.
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https://arxiv.org/abs/2606.10287
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XMedFusion: A Knowledge-Guided Multimodal Perception and Reasoning Framework for Autonomous Medical Systems
2026-06-08 20:26:32Hamza Riaz, Arham Haroon, Maha Baig, Muhammad Dawood Rizwan, Muhammad Naseer Bajwa, Muhammad Moazam FrazAbstract
Autonomous medical and robotic systems increasingly rely on intelligent perception and reasoning capabilities to interpret visual data and support clinical decision making. Radiology report generation represents a critical component of such automated diagnostic workflows, yet existing end-to-end multimodal models often suffer from weak visual grounding, resulting in unreliable interpretations and omission of subtle clinical findings. This paper presents XMedFusion, a modular AI framework designed as an intelligent perception and reasoning module for autonomous medical systems. The proposed framework decomposes visual information into coordinated functional components that emulate expert-driven analysis, including a visual perception agent that extracts image-grounded evidence, a knowledge graph construction agent that structures clinically relevant findings, and a retrieval-guided drafting process that ensures a consistent reporting structure. A synthesis agent iteratively integrates visual and structured evidence through reasoning-driven verification to produce reliable and interpretable diagnostic outputs. Experimental evaluation on a public chest radiograph dataset demonstrates significant improvements over baseline vision-language models, achieving gains from 0.0493 to 0.3359 in BLEU-1, 0.0863 to 0.2440 in ROUGE-L, and 0.0829 to 0.1708 in METEOR, along with substantial improvements in semantic evaluation metrics such as Consistency (2.38 to 7.80) and Accuracy (2.34 to 6.93). The results highlight the effectiveness of structured multi-agent perception and reasoning for enhancing robustness, transparency, and automation in intelligent medical imaging systems, enabling integration into autonomous healthcare and robotic diagnostic workflows.
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https://arxiv.org/abs/2606.14766
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Correlation Is Not Enough: Embedding Human Metadata for Individual Causal Discovery
2026-06-08 15:54:28Suraj Biswas, Saurabh Gupta, Pritam MukherjeeAbstract
Ask a pretrained biomedical language model whether "cortisol 28 ug/dL" and "stock-market volatility" are related, and it returns a cosine similarity of 0.83 on a scale where 1.0 means identical. The two share no mechanism. This is not a corner case: every off-the-shelf biomedical encoder we tested (BioBERT, PubMedBERT, BioM-ELECTRA) scores unrelated cross-domain pairs between 0.76 and 0.92 when the answer should be near zero. Accuracy on cross-domain discrimination is 0%. Retrieval systems survive this, because a language model downstream filters the noise. A Large Behavioural Model (LBM), a foundation model whose subject is a person rather than a sentence, does not: it reasons over a graph of a user's life and treats embedding proximity as evidence that two events are causally linked. False proximity writes a false causal edge, and everything downstream inherits the error. Here, embedding geometry is not a tuning knob; it is correctness. We report the fix. A contrastive pass over 72,034 pairs raises PubMedBERT BIOSSES correlation from 0.633 to 0.828 and within-vs-across-domain separation from 1.05x to 1.63x. A second pass, BODHI, mines hard negatives from edges absent in a biomedical knowledge graph and lifts separation to 2.30x and the discrimination gap to +0.392, at a 4.5% BIOSSES cost. On an Intel Xeon 6737P with AMX, OpenVINO cuts single-query latency from 1367 ms to 10 ms (133x) and reaches 555 sentences/sec. One finding contradicts standard advice: FP16 beats INT8 on this silicon at every serving batch size, and we explain why. The same model on a no-AMX Ice Lake instance runs 13-27x slower. We release the benchmark suite, training corpora, the BODHI generator, and the OpenVINO scripts.
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https://arxiv.org/abs/2606.09672
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From USD Scenes to Knowledge Graphs: Zero-Shot Ontology Grounding with LLMs
2026-06-08 07:32:06Jiangtao Shuai, Zongxiong Chen, Manfred Hauswirth, Sonja SchimmlerAbstract
Constructing knowledge graphs from 3D simulation scenes is essential for robot task reasoning, but the key bottleneck, grounding scene objects to formal ontology classes, still relies on manually curated dictionaries that are brittle and do not generalize across assets. We investigate whether large language models (LLMs) can automate this grounding step for Universal Scene Description (USD) scenes as a zero-shot, training-free alternative. On a kitchen scene (125 objects) with SOMA-HOME Ontology, LLMs achieve 90-96% exact-match accuracy with descriptive names and 49-89% with abbreviated names, substantially outperforming dictionary and embedding baselines. Under fully opaque names, context-augmented prompting recovers up to 48%. Feature ablation reveals that LLMs primarily exploit semantic cues in the scene graph (sibling names and parent paths); anonymizing these cues reduces accuracy to 0-6%, while geometry alone yields only 4-17%.
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https://arxiv.org/abs/2606.09134
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Graph2Idea:Retrieval-Augmented Scientific Idea Generation with Graph-Structured Contexts
2026-06-08 06:58:21Xu Li, Hanzhe Tu, Xun HanAbstract
Generating novel, feasible, and high-quality research ideas is an important yet challenging task in scientific this http URL Large Language Model (LLM)-based methods often ground idea generation with retrieved literature, but the retrieved evidence is usually provided as flat text, such as titles, abstracts, or summaries. Such flat contexts may contain redundant or weakly relevant information, while making cross-paper relations among problems, methods, mechanisms, and findings difficult to identify and this http URL address this challenge, we propose Graph2Idea, a knowledge graph-guided framework for retrieval-augmented scientific idea generation.Graph2Idea first retrieves papers according to the input topic, transforms them into structured knowledge triples, and dynamically constructs a target-centered knowledge graph to make literature relations this http URL then extracts compact graph-derived contexts that retain target-relevant relational evidence while reducing noisy textual this http URL on these contexts, a two-stage generation process first identifies promising research directions and then guides the LLM to synthesize candidate ideas from graph-grounded this http URL on a scientific idea generation benchmark show that Graph2Idea outperforms representative baselines under the automatic evaluation this http URL with the strongest baseline scores, it improves Novelty from 0.45 to 0.52, Quality from 0.24 to 0.29, and Feasibility from 0.22 to this http URL results suggest that graph-structured evidence helps LLMs generate research ideas through more explicit, compact, and traceable recombination of prior scientific knowledge.
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https://arxiv.org/abs/2606.09105
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Knowledge Graphs and Reasoning LLMs for Finding Simple Yet Effective Transcriptomic Perturbation Predictors
2026-06-07 20:09:30Jake Fawkes, Liam Hodgson, Jason HartfordAbstract
Predicting the effect of an unseen gene knockout perturbation on transcriptomic gene expression remains a highly challenging problem for virtual cell models. Recent progress has been made by leveraging biological knowledge graphs to provide a notion of similar perturbation, allowing for improved extrapolation beyond the set of training perturbations. In this work, we demonstrate that the simplest model to leverage these assumptions - a K-nearest neighbour from the knowledge graph - achieves highly competitive performance on this task, and that this can be improved further using LLMs optimised via reinforcement learning (RL) for predictive performance. Specifically, we find that the K-nearest neighbour approach beats almost all methods on out-of-distribution perturbation prediction, and when a reasoning LLM is trained via RL to make changes to the neighbourhood, it obtains equivalent performance to current state of the art methods on the cell lines from Replogle et al. (2022). We also demonstrate that the RL training improves the LLM's performance on the downstream task of differential expression prediction, despite not being trained on this directly. Overall, these findings demonstrate the efficacy of knowledge graphs as model priors, and show early signs that RL can refine LLMs into generalizable tools for predicting complex biological responses.
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https://arxiv.org/abs/2606.08816
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Extending Ontologies: From Dense Embeddings to Hybrid Quantum-Fuzzy Systems
2026-06-07 14:56:13Angjelin HilaAbstract
LLMs have revolutionized knowledge representation and retrieval, but lack the explicit modeling that knowledge ontologies possess. This paper surveys the ways that ontologies and knowledge graphs have been integrated with dense embedding algorithms. All hitherto attempts involve a trade-off between probabilistic and crisp inference. This paper proposes a novel frontier for devising knowledge representation systems that can simultaneously accommodate probabilistic and crisp inference in the same representation. To this effect, the paper proposes neuro-quantum-fuzzy systems as knowledge representation systems that accommodate both classical and contextual inference implemented through quantum-neural networks (QNN).
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https://arxiv.org/abs/2606.08658
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