Knowledge Representation

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9 papers in the last four weeks, up 125% on the four weeks before. 0.1% of all new papers.

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Latest papers 83

Jul 27, 2026cs.AI

Making Mathematical Knowledge Explainable, Accessible and Interoperable Through Large Language Model Integration

Mathematical models are central to formalizing research problems, yet their documentation often falls short of FAIR principles. Knowledge bases such as the Mathematical Model Database (MathModDB) address this gap by providing curated, semantically rich representations of mathematical models. Built on Wikibase, the same open-source infrastructure underlying Wikidata, MathModDB utilizes Semantic Web technologies to support Linked Open Data, collaborative editing, and the storage of semantically enriched metadata, making it a domain-specific knowledge graph within the broader Wikidata ecosystem. However, access to MathModDB currently requires either navigating a complex web interface or proficiency in SPARQL and Wikibase APIs, posing significant barriers for potential users. In addition, the combination of such curated knowledge bases with actual research data stored, e.g., in Dataverse repository instances, remains a challenge. To overcome these limitations, we propose integrating Large Language Models (LLMs) with MathModDB via a Model Context Protocol (MCP) server that exposes a vector-indexed schema retrieval and Steiner-tree-based join planner, combining dialogue-based natural language interaction with curated, epistemically grounded knowledge. Although instantiated on MathModDB, the architecture can be applied to other Wikibase-based systems. We demonstrate that this approach enables epistemically grounded LLM usage, improves model explainability and accessibility beyond what the standard Wikibase interface offers, and simplifies interoperability with external databases and tools, such as Dataverse data repositories. We illustrate the benefits of combining the accessibility of an LLM with the epistemic safety of a curated knowledge base through the adaptability of the MCP protocol by two use cases involving mathematical models in the fields of continuum mechanics and enzyme kinetics.

Jan Range, Björn Schembera, Dominik Göddeke

Stuttgart Center for Simulation Science (SC SimTech), University of Stuttgart · Institute of Applied Analysis and Numerical Simulation, University of Stuttgart

LLM Grounding Knowledge Representation Knowledge Graph Question Answering Knowledge Graphs

Jul 23, 2026cs.AI

Representing Entity Importance in AI Knowledge Systems: A Dual-Signal Framework of Audience Evaluation and Structural Authority

AI knowledge systems require representations of entity importance for retrieval, recommendation, evidence selection, and knowledge-intensive reasoning. Yet importance is often reduced to a single score derived from either human response or graph structure. Such compression may discard distinctions that matter when an AI system must choose among entities for different tasks. This study introduces an interpretable dual-signal representation in which each entity is characterized by an audience-evaluation dimension and a structural-authority dimension. The framework is evaluated using movie entities as an empirical validation domain. IMDb non-commercial datasets provide a rating-based audience ranking, Wikidata supports entity alignment, and English Wikipedia hyperlinks form the knowledge network on which PageRank estimates structural authority. Experiments on 482 entities and 13,690 directed relationships reveal a statistically significant but weak association between the two dimensions (Spearman rho = 0.2275, p < 0.001). Their overlap is only 10% in the top 10 and 34% in the top 100, while entity-level divergence occurs in both directions. The results show that audience evaluation and structural authority are non-redundant signals and should not automatically be collapsed into a single scalar notion of importance. The contribution is not a new ranking algorithm or learned embedding, but a minimal knowledge-representation framework and an empirical test of its dimensional necessity. The findings support task-aware AI knowledge systems that preserve distinct importance signals before applying context-specific selection or aggregation.

Shen Xu

Independent Researcher

Knowledge Representation

Jul 22, 2026cs.AI

An Ontology-Guided, Deduplication-Aware Extraction Layer for Knowledge Graph Construction from Heterogeneous Documents

Large language models extract entities and relationships from unstructured documents fluently but inconsistently: type vocabularies fracture across documents, the same person surfaces under several name variants, relationships duplicate, and distinct individuals who share a name risk silent conflation. This paper presents the design, implementation, and empirical refinement of a production extraction layer that converts a live document stream into a validated knowledge graph aligned to a formal ontology. The system consumes document metadata from Kafka, routes PDF, spreadsheet, Office, and image content through handlers built for each format, and extracts entities and relationships in two passes using a locally hosted Qwen3.5-9B model tuned on the ontology. Its distinguishing component is ontology-guided extraction: the relevant slice of a curated ontology is retrieved live from a graph database by embedding similarity and injected into the extraction prompt, reducing catalog overhead by about 94 percent relative to static domain slices. Extracted results then pass through a refinement pipeline of five stages: deterministic cleaning, merging across chunks, a second pass for relationships, six deduplication algorithms that require no model inference, and an embedding resolution subsystem whose conflict guard no similarity score can override. Evaluation on intelligence corpora improved search recall from roughly 70 to 95 percent with no false merges, and corrected seven classes of silent quality defect, ranging from a bug that truncated source text by a single character to the systematic duplication of entities that carried title prefixes.

Vaibhav Dangaich, Kevin Lewis, Kundeshwar Pundalik

Relation Extraction KG Construction Entity Resolution Document Information Extraction Knowledge Representation LLM Information Extraction

Jul 22, 2026cs.CL

Are you Talking Logic to Me? Assessing Language Models Syllogistic Reasoning Capabilities

Language models (LMs) struggle with logical tasks like reasoning on syllogisms. It has been shown that Knowledge Representation (KR) plays a crucial role in expressing input information to help models solve tasks. This observation motivates our study of the impact of different formal KR notations on syllogistic reasoning by extending the FOLIO and P-FOLIO datasets. Our experiments on Small Language Models (SLMs) in Supervised Fine-Tuning (SFT) and Zero-Shot (ZS) settings show that the choice of input notation can yield performances competitive with natural language while enabling faster inference. We also propose a syllogistic categorization method (SEF) and use it to enrich ZS prompts with logical definitions, which boost reasoning in small models. We open-source our framework, Common Logic Grammar Construction (CLGC), as the first Python library for automatically generating syllogisms in KR notations and defining their SEF categories.

Hanna Abi Akl, Fabien Gandon, Catherine Faron +1

Université Côte d’Azur, Inria, CNRS, I3S, Sophia Antipolis, France · Data ScienceTech Institute, Paris, France

Knowledge Representation Structured Reasoning LLM Reasoning

Jul 20, 2026cs.DB

Natural Language Access to Domain-Specific Metadata: A Reusable Framework for LLM Query Generation

Researchers need to answer ad-hoc questions about the contents of domain-specific archives but often lack the expertise to write structured queries on the metadata. We show that when domain vocabulary and semantics are captured in a well-designed Web Ontology Language (OWL) ontology, Large Language Models (LLMs) can generate accurate structured queries zero-shot, without task-specific fine-tuning, retrieval augmentation, or multi-agent orchestration. We present the Natural Language Knowledge Graph Query (NLKGQ) system, a framework and development process that enables natural language access to metadata in such archives. The framework includes a web interface that helps researchers pose natural language questions, which a domain-agnostic harness translates to SPARQL via an LLM and executes against a knowledge graph. The development process begins with capturing domain vocabulary and semantics in a formal OWL ontology. Domain-specific code then extracts metadata from archive sources and imports it into a knowledge graph defined by the ontology. Both are designed for reuse across domains. We demonstrate the system on metadata derived from a large-scale neuroimaging research archive, evaluating multiple LLMs and ontology representations. The best configurations achieve 100% accuracy on a 21-question competency and regression test set developed with domain experts. An ablation study across eight ontology representations reveals that readable entity names and semantic annotations are the dominant factors in accuracy, more significant than model choice or prompt engineering. We also compare SPARQL to an auto-generated SQL database as query backends, showing that OWL's structural features provide a substantial advantage over SQL DDL for LLM-driven query generation. Our demonstration domain requires local LLMs on modest institutional hardware to address privacy concerns for human subject data.

Blake G. Fitch, Cato Elia Kurtz

Max Planck Institute for Biological Cybernetics Tübingen, Germany

Knowledge Representation Knowledge Graph Question Answering Natural Language to SPARQL

Jul 13, 2026cs.CL

RAGU: A Multi-Step GraphRAG Engine with a Compact Domain-Adapted LLM

Graph retrieval-augmented generation (GraphRAG) enhances large language models with structured knowledge, yet existing systems construct knowledge graphs in a single extraction pass, producing noisy entities and brittle retrieval. RAGU, an open-source modular GraphRAG engine, addresses this by separating extraction from consolidation: entities and relations pass through two-stage typed extraction, DBSCAN-backed deduplication, LLM summarization, and Leiden community detection. A key insight motivates a compact extractor: the skills an in-pipeline LLM needs - comprehension, extraction, reasoning over context - are language skills that grow only weakly with model size, unlike factual world knowledge. Accordingly, we train Meno-Lite-0.1, a 7B model optimized for language skills, which outperforms Qwen2.5-32B on knowledge-graph construction (+12.5% relative harmonic mean) and matches it on English GraphRAG tasks. On GraphRAG-Bench (Medical), RAGU retrieves the most complete context at every factoid level (evidence recall up to 0.84 vs.

\leq

0.76) and overtakes HippoRAG2 on synthesis tasks; on multi-hop factoid QA, the apparent HippoRAG2 advantage is shown to be largely an answer-format artifact. RAGU is installable via

\texttt{pip install graph_ragu}

, runs on a single GPU, and is released under MIT. The source code is publicly available at https://github.com/RaguTeam/RAGU, and the Meno-Lite-0.1 model can be obtained from https://huggingface.co/bond005/meno-lite-0.1.

Mikhail Komarov, Ivan Bondarenko, Stanislav Shtuka +5

1ITMO University · 2Novosibirsk State University · 3Far Eastern Federal University +1

KG Construction LLM Reasoning with Graphs Graph Retrieval-Augmented Generation Small Language Models Knowledge Representation LLM Information Extraction+1

Jul 9, 2026cs.AI

Towards Mechanistically Understanding Why Memorized Knowledge Fails to Generalize in Large Language Model Finetuning

Fine-tuning LLMs to inject new knowledge faces a critical challenge: LLMs can quickly memorize new facts, yet fail to use them for downstream reasoning tasks. We formalize this failure as the Knowing-Using Gap, characterized by an accuracy gap and a temporal lag between memorization and generalization. To understand this phenomenon, we fine-tune LLMs with unseen knowledge and monitor the spatial permeation dynamics of the knowledge internally with self-patching, an adaptation of activation patching that scans all layer pairs at every fine-tuning check-point. Self-patching identifies activation locations where relocating representations substantially improves failed generalization cases. These results are consistent with a knowledge-circuit misalignment hypothesis: memorized representations can exist internally but may not be routed to computation-effective layers. Experiments are done cross-domain for the robustness of this finding. Building on this diagnosis, we propose layer-wise representation self-distillation (LRSD) that aligns knowledge representation from late storage layer to middle layer. LRSD keeps improving generalization after fine-tuning saturates and nearly doubles multi-hop chaining accuracy on Qwen, while leaving memorization intact.

Lu Dai, Ziyang Rao, Yili Wang +3

HKUST · HKUST(GZ)

Memorization in Language Models LLM Fine-Tuning Neural Network Memorization Mechanistic Interpretability Knowledge Representation Factual Knowledge in Language Models+1

Jul 8, 2026cs.CL

Does Bielik Know What It Doesn't Know? Activation Dispersion Separates Entity Familiarity from Factual Reliability Across Model Scale

Large language models hallucinate most about entities they have never seen. We ask whether a model's activations betray entity familiarity before a single answer token is generated, and whether that signal predicts the factual reliability of the answers. On four Polish Bielik models (1.5B-11B parameters), we probe four entity domains (athletes, cities, writers, musicians), each with 42 well-known, 42 obscure-but-real, and 42 fabricated entities addressed by a one-sentence question (504 prompts per model). Two unsupervised, single-forward-pass dispersion measures over post-SwiGLU MLP activations, inverse participation ratio and spectral entropy, separate known from fabricated entities at AUROC 0.95-1.00 across all domains and scales; a supervised linear probe reaches 0.99-1.00. Both clear selection-aware permutation floors of about 0.70-0.74 (empirical p<=1e-3), survive held-out layer selection (0.93-0.99), and persist on real names (known vs. obscure-but-real: 0.96-1.00). The signal transfers across entity types (mean off-diagonal AUROC 0.92-0.99); a matched-template counterfactual shows the only large drops are template-caused, not entity-type effects, and the signal is diffuse across heads. This representational signal is already at ceiling at 1.5B, whereas behavioral factual reliability scales sharply: 0, 2, 10, and 19 of 42 known athletes are answered fully correctly by the 1.5B, 4.5B, 7B, and 11B models under a strict judge. Within known entities, separating correct from hallucinated answers is much harder (probe 0.93; dispersion no better than a first-token-entropy baseline). A five-sample semantic-entropy baseline reaches only 0.71-0.83 at 5x the inference cost. Despite this internal awareness, the models almost never abstain: an audit of 2,520 answers finds 2 refusals and 1 hedge. Entity familiarity and factual reliability are distinct phenomena on different scaling curves.

Grzegorz Brzezinka

Prosit AS

Hallucination in Language Models Knowledge Representation Factual Knowledge in Language Models Language Model Probing

Jul 6, 2026cs.AI

Narrative World Model: Narratology-Grounded Writer Memory for Long-Form Fiction

Long-form fiction writers need memory that answers multi-hop questions about evolving story state: who knows a secret and when they learned it, whether an event preceded the narration that revealed it, whether a setup paid off, and how a relationship shifted. General-purpose retrieval and agent-memory systems represent entities and facts but not the narratological structure these questions turn on, so they surface the wrong evidence or none at all. We introduce the Narrative World Model (NWM), a writer-memory system that pairs a narratology-grounded typed temporal-state graph with query-conditioned hybrid retrieval. To measure memory rather than the answerer, we read every system through a single held-constant Opus 4.8 reader over only that system's chapter-safe evidence, on a reproducible public corpus and a validated multi-hop benchmark, and we compare against the strongest existing temporal-knowledge-graph agent-memory framework, Graphiti/Zep (Rasmussen et al., 2025). NWM substantially and significantly outperforms this baseline on multi-hop narratological QA across both corpora, and far exceeds GraphRAG and flat retrieval. The advantage is representational rather than an artifact of extraction: it survives rebuilding the baseline with NWM's own extractor, and traces to its narratology-grounded structure and query-conditioned retrieval, not to graph size or extractor quality.

Mohammad Saifullah, Thomas Kornmaier, Taaha Kazi +3

PocketFM

Multi-Hop QA Question Answering Knowledge Representation Temporal KGs Temporal QA

Jul 2, 2026cs.AI

Verifiable Knowledge Expansion through Retrieval-Grounded Formal Concept Analysis

Ontology construction requires deciding which objects, attributes, and structural relations should be accepted as valid knowledge. Language models can propose such structures from text, but their outputs can still be unsupported or inconsistent. This paper proposes a retrieval-augmented small language model (SLM) framework that uses formal concept analysis (FCA) as a symbolic verification loop for knowledge expansion. Starting from seed attributes, FCA proposes implications over a growing formal context. A retrieval-grounded SLM oracle then validates each implication or returns a counterexample. The oracle also supports incidence judgments, consistency checks, and attribute proposals, making accepted implications, counterexamples, contradictions, and corrections inspectable. In a rare ataxia setting constructed from Orphadata resources, retrieval-grounded 10-seed runs obtain relation F1 of 0.29-0.52 and closure-based implication F1 of 0.22-0.30. Larger seed sets increase the number of evaluated implications and often improve implication F1. The lower implication scores reflect a stricter evaluation of derived implications, where one missed or extra relation can affect several implication judgments. Ablations show that incidence judgments in a fixed object-attribute setting can improve closure-based implication scores. However, identifying positive object-attribute pairs remains difficult even when the candidate objects and attributes are fixed.

Yujin Yang, Heejung Lee

Hanyang University Seoul, Korea

KG Construction LLM Grounding Knowledge Representation Formal Concept Analysis Ontology Learning

Jun 26, 2026cs.AI

JD Oxygen AI Item Center (Oxygen AIIC) V1: An Industrial-Scale LLM/VLM-Centric Solution for Item Understanding, Management, and Applications

JD

.

com, one of the world's largest e-commerce platforms, serves over 700 million active users and millions of merchants, with a catalog of tens of billions of SKUs. At this scale, high-quality, structured item knowledge underpins a better consumer experience, lower management costs, and higher operational efficiency-yet producing and serving it poses three industrial-scale challenges: fast-emerging concepts, high-quality knowledge production for massive SKUs, and diverse downstream requirements. To address these challenges, we present the JD Oxygen AI Item Center (Oxygen AIIC), an industrial-scale platform built on LLMs/VLMs for item-knowledge production and service. Oxygen AIIC is built around four core pillars: (i) ontology engineering driven by efficient human-AI collaboration, which supports the dynamic evolution and agile expansion of an ontology with millions of entries; (ii) a "Semantic Search then Discrimination"(S2D) knowledge identification architecture that, combined with throughput improvement strategies, enables scalable, extensible, and high-throughput AI Item Library production for tens of billions of SKUs; (iii) self-evolving item-understanding LLMs/VLMs that improve in a stable and controllable manner, enabling knowledge production with 94.2% precision and 82.8% recall; and (iv) a unified item tunnel that serves as the data and service hub. Oxygen AIIC now covers tens of thousands of JD categories and processes hundreds of millions of item updates per day on Huawei Ascend NPUs. It has accumulated hundreds of billions of item-knowledge assets. Deployed across core business scenarios-including search, recommendation, operations, category planning-Oxygen AIIC has delivered measurable gains at scale. Search-traffic coverage reaches 80.4%, item-information quality issues drop by 37%, the automated fill rate of core attributes during item listing exceeds 80%.

Oxygen AIIC, Chan Long, Chao Liu +52

Knowledge Representation E-Commerce

Jun 24, 2026cs.IR

TheoremGraph: Bridging Formal and Informal Mathematics

Mathematical knowledge is organized around statements and their dependencies, but this structure is exposed unevenly: informal papers cite mostly at the document level, while formal libraries record fine-grained dependencies over a much smaller body of mathematics. We introduce TheoremGraph, a unified statement-level dependency graph spanning both informal and formal mathematics. On the informal side, we parse 11.7M theorem-like environments from mathematics arXiv and recover 18.3M candidate directed dependencies, each labeled by the extractor that proposed it so downstream users can trade coverage for precision. On the formal side, we release LeanGraph, a Lean 4 elaborator-level extractor producing 388,105 declaration nodes and 11.3M typed edges across 25 Lean projects. We bridge the two graphs by embedding generated natural-language slogans into a shared semantic space, linking related statements across papers and across the informal/formal divide; an LLM judge affirms 47,952 such matches above a 0.8 cosine floor, with the judge-acceptance rate rising from 48% across the floor to 87% in the >=0.9 tier. On formal concept retrieval, our name-and-signature representation with graph expansion comes within 0.5pp of LeanSearch v2's reranked Recall@10 (0.775 vs. 0.780) without an LM reranker. We release the dataset, extractors, HTTP API, and MCP interface as infrastructure for mathematical search, attribution, and retrieval-augmented reasoning, available at theoremsearch.com and huggingface.co/datasets/uw-math-ai/theorem-matching.

Simon Kurgan, Evan Wang, Eric Leonen +6

University of Washington Math AI Lab

KG Construction Graph-Based Retrieval Knowledge Representation Information Retrieval

Jun 23, 2026cs.LG

Holographic Memory for Zero-Shot Compositional Reasoning in Knowledge Graphs: A Mechanistic Study of Where and Why It Fails

Knowledge graph embedding (KGE) models predict single-hop links well but have no mechanism for zero-shot compositional queries: multi-hop questions whose relation chains never appeared during training. Holographic Reduced Representations (HRR), which bind and unbind symbols via circular convolution, are a theoretically attractive candidate, since binding is approximately invertible and associative. We test whether this promise holds. We study two holographic memory variants, real-valued HRR and phase-only Fourier HRR (FHRR), each with a modern Hopfield cleanup, on FB15k-237 over five seeds. Four findings follow. First, both are competitive single-hop retrievers (filtered MRR 0.358 +/- 0.002 for HRR, 0.350 +/- 0.021 for FHRR). Second, neither composes zero-shot: accuracy stays at chance across all cleanup temperatures. Third, the main contribution, we localise the failure mechanistically. A hop-1 probe shows the memory recovers the correct intermediate entity with high fidelity (MRR 0.896 +/- 0.002 for HRR), yet composition still fails even with a verified-correct intermediate. A second probe shows why: posing the ground-truth second-hop fact as a standalone atomic query, bypassing composition entirely, already recovers it at only 0.26 to 0.48x average atomic accuracy, uniformly across relation fan-out. The bottleneck is not the bind-unbind algebra or the cleanup; it is that facts compositional chains pass through are intrinsically harder for the superposed memory to retrieve, a capacity and interference effect present already at a single hop. Fourth, we prove (Lemma 4.1) that FHRR's softmax cleanup is not phase-equivariant, compounding the primary failure on the minority of chains where hop-1 itself errs. Fixing zero-shot composition requires improving retrieval capacity under superposition, not just redesigning the cleanup.

Randhir Kumar

Independent Researcher

Compositional Reasoning KG Embedding Knowledge Representation Hyperdimensional Computing Multi-Hop Reasoning KG Completion

Jun 22, 2026cs.AI

The MMM Data Model -- A Normative Specification for Knowledge Interoperability in a Decentralisable Knowledge Commons

Many information systems are built around documents: self-contained units optimised for print production and linear reading. While effective for large-scale dissemination, the document-centric organisation constrains how knowledge can be structured, updated, shared, and reused. Formal approaches address some of these limitations but struggle to achieve widespread contribution and adoption due to their prioritisation of formal structure over other system properties such as human usability and scope. AI systems are reshaping document production, but without providing a unified portable alternative to traditional documents for humans' expression and exchange of knowledge. This paper presents MMM, a data model for knowledge documentation that emerged from the practical needs of interdisciplinary collaborative research, and positioned here within a comparative analysis of the design space of information systems. MMM combines a small set of normative constraints with the expressive freedom of free-text labels. It is designed for interoperability across disciplines, applications and deployments without requiring semantic convergence. A reference implementation and pilot deployment data demonstrate implementability and early usability.

Mathilde Noual

Aix Marseille Univ, CNRS, LIS, Marseille, france · Centre Européen de sociologie et de sciences politiques (CESSP) UMR8209. CNRS, Université Paris 1 Panthéon-Sorbonne

Knowledge Representation

Jun 15, 2026cs.AI

User as Code: Executable Memory for Personalized Agents

A personalized AI agent needs a user memory: a persistent model of who the user is, built across many conversations and consulted on each new one. Today this memory is almost always stored as unstructured text, a knowledge graph, or a flat store of facts, and consulted by retrieval -- fetching the entries most similar to the current request. Such "bag-of-facts" memory recalls individual facts well, but because storing a fact and acting on it are separate steps, it struggles to resolve contradictions, aggregate over many records, or enforce rules. We argue that user memory should instead be executable. We introduce User as Code (UaC), a paradigm in which an agent's model of a user is a living software project: typed Python objects hold the user's state and ordinary Python functions encode the rules that govern it, so representing and reasoning about the user happen in one medium an interpreter can run. The enabling mechanism is a two-phase pipeline: an append-only log that never discards a fact, periodically checkpointed into typed code. This changes what memory can do. On standard long-term conversation benchmarks, UaC matches both a full-context upper bound and the strongest prior memory systems on recall (78.8% on LOCOMO). Its advantage emerges where representation matters most. On aggregate questions over a user's history -- "how many international trips did I take last year?" -- retrieval-based memory collapses (6-43%) while UaC stays near-perfect (99%), because the answer is a one-line computation over typed state rather than a search over text. And because its rules execute deterministically whenever the state changes, UaC can surface unsolicited, safety-critical alerts -- such as a newly prescribed drug that conflicts with an allergy recorded months earlier -- a capability query-driven memory cannot provide.

Bojie Li

Pine AI

Persistent Memory for Language Models Knowledge Representation User Modeling Long-Term Conversational Memory Agent Memory Management Personal AI Agents

Jun 14, 2026cs.CL

Specific Domain Ontology Construction Using Large Language Models

Ontologies are useful structures to organize and maintain information that can be understood both by humans and systems. However, since their manual crafting is a laborious task, many specific domains lack reference ontologies. The outstanding ability for understanding natural language demonstrated by the Large Language Models (LLMs) has motivated their application to aid on a variety of fields, including on ontology development. This work presents the experimentation with a technique that uses LLMs in the role of domain experts to build conceptual hierarchies for a given initial concept. Twenty ontologies automatically constructed for the domain of the Brazilian maritime territory (a.k.a the Blue Amazon) using GPT-3.5 and GPT-4 were then evaluated by human experts. The models were able to construct overall coherent conceptualizations of the domain, but none of the outputs was completely satisfactory as a representation of the context without refinement.

Vivian Magri Alcaldi Soares, Renata Wassermann

University of SÃo Paulo (USP) · Center for Artificial Intelligence (C4AI)

Knowledge Representation Ontology Learning

Jun 14, 2026cs.MA

DeepRoot: A KG-Coordinated Multi-Agent System for Therapeutic Reasoning over Historical Medical Texts

Historical medical archives and traditional medicines hold immense potential for drug discovery and remain a primary source for current drug development. However, pre-ontological prose and idiosyncratic taxonomies prevent the standardization and medical modernization of the data for use in current biomedical pipelines. Furthermore, no existing LLM agent system, whether tool-calling, retrieval-augmented, or agentic deep-research, can convert such text into verifiable drug-discovery leads at scale. We close this gap with DeepRoot, a multi-agent LLM system that jointly builds and utilizes a verified knowledge graph, showing that grounding and reasoning -- often conflated -- are separable axes the system can compose for therapeutic reasoning. Applied to the Shen Nong Ben Cao Jing, DeepRoot recovers

10

of

21

held-out compound-disease treatment pairs at R@

20

(

47.6\%

vs

4.8\%

for a raw corpus LLM and

\sim\!2.4\%

random) and dominates an LLM-as-judge audit for reasoning quality over baseline LLMs and LLMs with direct tool-call access to the same APIs DeepRoot itself queries. Tool-using LLMs hallucinate evidence on

87\%

of claims, versus 7-10% for DeepRoot. Graph-only inference hallucinates

0\%

but ranks lowest on reasoning coherence; DeepRoot KG+LLM is the only condition to win on both axes, pointing toward a route for systematic mining and repurposing of historical medical knowledge.

Zijian Carl Ma, Sean J. Wang, Sijbren Kramer +1

Department of Bioengineering · Stanford University · Amazon AWS AI

Historical Document Analysis Multi-Agent LLM Systems AI Agents for Scientific Discovery Knowledge Representation Knowledge Graph Question Answering LLM Agent Reliability+2

Jun 14, 2026cs.CL

DYNA : Dynamic Episodic Memory Networks for Augmenting Large Language Models with Temporal Knowledge Graphs in Continuous Learning

Large Language Models (LLMs) struggle to incorporate new knowledge without forgetting or costly retraining. We propose DYNA, a lightweight framework that augments a frozen LLM with a temporal knowledge graph where events are nodes and temporal relations are directed, timestamped edges. The graph serves as an external, updatable memory. At query time, DYNA retrieves relevant nodes via random walks and centrality measures, then augments the LLM's response. Evaluated on three temporal recall tasks, DYNA reduces catastrophic forgetting by ~7% compared to fine-tuning and improves temporal ordering by ~5% over standard RAG. Higher graph clustering coefficients correlate with better retrieval, showing that graph structure matters. Contributions: (1) episodic memory as temporal KG, (2) retraining-free LLM augmentation, (3) graph properties as predictors of retrieval performance.

Ali Sarabadani, Mahtab Tajvidiyan

Department of Computer Engineering and Information Technology, University of Qom, Qom, Iran

Continual Learning for LLMs Memory-Augmented Language Models Graph Retrieval-Augmented Generation Temporal Reasoning in Language Models Persistent Memory for Language Models Temporal IR+2

Jun 13, 2026cs.AI

A Formal Framework for Declarative Agentic AI in Business Process Analysis

Agentic AI opens new opportunities for automating Business Process (BP), enabling autonomous decision-making and dynamic adaptation. However, realising this potential requires BP entities and their interactions to be defined with formal precision. This paper presents a formal framework for Agentic BP analysis through the AGO methodology. AGO captures the modelling perspective in terms of who is acting (Agents), why it is carried out (Goals), and what the relevant entities are (Objects). Grounded in set theory and mathematical logic, we formally define the AGO entity types and their interactions, organising all definitions into a BP Knowledge Base (BPKB). The resulting BPKB supports structured querying, incremental updates, and automatic generation of BP workflows, while ensuring soundness and completeness of the derived paths.

Mohammad Azarijafari, Luisa Mich, Michele Missikoff

Department of Industrial Engineering, University of Trento, Via Sommarive 9, 38123, Trento, Italy · Istituto di Analisi dei Sistemi ed Informatica (IASI) “Antonio Ruberti”, National Research Council (CNR), Via dei Taurini 19, 00185, Rome, Italy

Business Process Automation Knowledge Representation Agentic AI

Jun 13, 2026cs.LO

Provenance-Enhanced Statements in Knowledge Graphs

Provenance-enhanced statements of the form "according to

X

,

\varphi

" are pervasive in contemporary knowledge graphs, especially in domains where graph content primarily represents claims, interpretations, and hypotheses (\emph{capta}) rather than observer-independent facts (\emph{data}). Current provenance models can record who asserted what, but they typically treat provenance as semantically neutral, leaving underspecified how attributed claims relate to factual commitment, to one another, and to reasoning. In this paper we introduce DEC, a framework that interprets provenance predicates as indicators of epistemic stance and groups provenance-homogeneous sets of statements into \emph{cognitive worlds}. Drawing on cognitive modal logics (doxastic, epistemic, and conjectural), DEC characterizes locality, rationality, and controlled permeation between cognitive worlds and a distinguished factual core ("reality"), thereby enabling principled reasoning over attributed content without collapsing disagreements into inconsistencies. We formalize a DEC interpretation for RDF datasets that is conservative over RDF~1.2 semantics, clarify the role of intensionality and identity (including the Superman paradox), and illustrate the approach on common Semantic Web representations (named graphs, quoted triples/RDF-star, and reification). Finally, we describe our prototype DEC reasoner implemented as a Fuseki dataset module, supporting controlled factualisation and explicit detection of disagreements and delusions.

Fabio Vitali, Valentina Pasqual

University of Bologna, Italy

Logical Reasoning Data Provenance Knowledge Representation Graph Reasoning Knowledge Graphs Epistemic Logic

Jun 12, 2026cs.CL

The Holistic Storage of Verb+Up Phrases in Text-based and Audio-based Language Models

One of the most central aspects of language processing is the ability to trade off between stored representations and abstract knowledge: one must retrieve stored representations, but also generate novel ones by applying productive rules. While recent work has examined abstract knowledge in language models, holistic storage has received far less attention. We probe internal representations in both text-based LLMs and an ASR model, testing whether V+up phrasal verbs develop distinct representations as a function of frequency and predictability. All models show evidence of holistic storage driven by frequency and predictability, further supporting usage-based theories of language.

Zachary Nicholas Houghton, Yu Zhou, Dan Pluth +2

University of Oregon · Vail Systems, Inc

Memorization in Language Models Knowledge Representation Speech Language Models Representation Geometry in Language Models

Jun 11, 2026cs.AI

Agents-K1: Towards Agent-native Knowledge Orchestration

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.

Zongsheng Cao, Bihao Zhan, Jinxin Shi +23

Shanghai Artificial Intelligence Laboratory · East China Normal University · Fudan University

KG Construction AI for Science Document Information Extraction Knowledge Representation LLM Agents

Jun 7, 2026cs.AI

Extending Ontologies: From Dense Embeddings to Hybrid Quantum-Fuzzy Systems

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).

Angjelin Hila

KG Embedding Knowledge Representation Neuro-Symbolic Reasoning

Jun 6, 2026cs.CL

MechLens: Late Crystallization of Factual Knowledge Explains Intervention Effectiveness in Language Models

Understanding where LLMs store factual knowledge is critical for hallucination mitigation. We systematically quantify Late Crystallization: factual knowledge does not gradually emerge across layers but "crystallizes" abruptly at the final layers. Across five model families (Pythia, Gemma, Qwen2.5, Llama-3.1, Mistral; 0.5--14B), 26.8%--93.4% of correct answers never enter top-10 predictions at any intermediate layer, with late emergence (>80% depth) consistent across architectures. Cross-scale (Qwen2.5-14B) and cross-benchmark (MMLU: 98.2%) results confirm generality; tuned lens rules out probe artifacts. A sentiment-classification control (0.5% for Qwen vs. 85.9% factual; 2.0% for Mistral vs. 26.8%) confirms the phenomenon is specific to factual recall. Late Crystallization yields a crystallization-guided intervention principle: CAA outperforms DoLa on moderate-crystallization models (Llama, Mistral; p<0.001), with a directionally consistent reversal on high-crystallization Qwen (+25.4% vs. +15.5% MC1, p=0.069). LayerNorm ablation shows crystallization is intrinsic to the residual stream; LN scaling (x1.2) yields +11.8% MC1 with zero inference overhead. We further reveal a Computability-Memorization Spectrum: computable knowledge crystallizes earlier (layer 22.1/28) than memorized facts (28.0/28). We release MechLens supporting five model families.

Xueping Gao

Alibaba Cloud

Memorization in Language Models LLM Interpretability Knowledge Representation Factual Knowledge in Language Models Causal Interventions in Language Models

Jun 4, 2026cs.IR

Knowledge Manifold: A Riemannian Geometric Framework for Semantic Mapping and Geodesic Analysis of Scientific Literature

We present the knowledge manifold: a Riemannian geometric space in which a corpus of documents is arranged according to semantic positional relationships derived from character n-gram TF-IDF representations. The framework proceeds in five tightly coupled stages. First, each document is converted to a character-level n-gram TF-IDF vector (4-7 grams, up to 250,000 features, L2-normalized) and embedded in a two-dimensional knowledge map via constrained stress minimization with repulsion, variance, and centering regularizers. Second, knowledge at an arbitrary query point is estimated through Smoothed Particle Hydrodynamics (SPH) interpolation using a cubic-spline kernel, yielding an interpolated TF-IDF feature vector that can be linguistically characterized. Third, directional knowledge gradients at 0, 45, and 90 degrees are computed from the SPH interpolation map, and pairwise directional similarity is quantified via inner product and cosine similarity. Fourth, a Gaussian Process Regression (GPR) model, with a Constant x RBF + White kernel fitted on a 10-dimensional SVD projection, provides a Bayesian posterior mean, uncertainty estimate, and per-document contribution rate at the query point. Fifth, geodesics in the knowledge space are obtained by minimizing a discrete Riemannian path energy derived from the SPH-induced metric tensor, using L-BFGS-B with seven deterministic initial-path candidates. We apply the formulation to a corpus of 20 papers in fiber-reinforced composite materials and aerospace structural mechanics, showing that the semantic map recovers meaningful research clusters, geodesic paths reveal natural conceptual bridges between distant topics, and SPH/GPR interpolation enables the generation of virtual knowledge: hypothetical paper abstracts describing unstudied but geometrically predicted research directions.

Tomonaga Okabe, Kazuhiko Komatsu

Department of Aerospace Engineering, Tohoku University, 6-6-01, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan · Research Center for Green X-Tech, Tohoku University, 6-6-11, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan

Knowledge Representation Manifold Learning Semantic Mapping Riemannian Geometry

Jun 4, 2026cs.CL

Narrative Knowledge Weaver: Narrative-Centric Retrieval-Augmented Reasoning for Long-Form Text Understanding

Long-form narrative QA requires reasoning over evolving story worlds rather than isolated passages: answers may depend on earlier goals, changing character states, social relations, causal triggers, temporal position, and later consequences. Existing retrieval and graph-augmented generation methods improve evidence access, but their units--chunks, entities, relations, summaries, or tool actions--do not directly encode how evidence functions in a story. We introduce Narrative Knowledge Weaver(NKW), a source-grounded framework that aligns textual evidence, atomic facts, canonical graph structure, entity profiles, interactions, episodes, and storylines. At query time, NKW uses text, graph, and narrative tools with post-retrieval reading skills to assemble evidence and audit actor, scope, polarity, state, and temporal constraints. Across STAGE, FairytaleQA, and QuALITY, NKW is strongest on screenplay-level story-world QA while remaining competitive on more passage-centered benchmarks. Ablations, question-type analyses, graph-asset statistics, and case studies show complementary benefits for character, scene, temporal, causal, and narrative-progression reasoning.

Qiuyu Tian, Fengyi Chen, Yiding Li +9

Southeast University, Nanjing, China · Nanjing Normal University, Nanjing, China · ZhuiWen Technology Co., Ltd., Beijing, China +1

Retrieval-Augmented Generation Long-Context QA Question Answering Knowledge Representation Multi-Hop Reasoning

Jun 3, 2026cs.CL

Executable Schema Contracts: From Automatic Ingestion to Multi-Source Retrieval

Real-world data spans tables, documents, and semi-structured files with implicit semantics. Querying this data requires integrating evidence across inconsistent schemas and formats, yet existing approaches either demand costly manual engineering or bypass structure entirely. We present a system that automatically discovers an executable schema from raw multi-source data and uses it as a shared contract for knowledge graph construction and query-time retrieval. A closed-world field catalog constrains LLM-based schema discovery to attested fields; deterministic structural analysis infers identity keys, foreign keys, and source hierarchy; and the resulting schema drives extraction, deduplication, and cross-source linking into a provenance-aware knowledge graph. At query time the schema -- optionally extended via a monotonic protocol -- conditions a multi-tool agent routing retrieval across structured lookup, graph traversal, and vector search, returning grounded answers with traceable citations. In controlled zero-shot comparisons using the same LLM, data, and evaluation harness, the system improves over retrieval-only and decomposition-based baselines across four QA benchmarks, with ablations showing that schema-conditioned routing, structural intelligence, and schema-guided construction each contribute to the gains.

Padmaja Jonnalagedda, Yuguang Yao, Xiang Gao +2

Intuit AI Research

KG Construction Knowledge Representation Knowledge Graph Question Answering Hybrid Retrieval

May 29, 2026cs.IR

Reading Between the Citations: A Typed Claim Network for Scientific Literature

Knowledge graphs over corpora of inter-referencing documents - scholarly papers, legal opinions, policy briefs - encode the topology of reference but not its stance. The standard representation collapses a rich evaluative relation into an untyped edge, losing the very content that supports community-level queries about how one document is received by another. We propose the claim network: a representational pattern in which each cross-document reference is reified as a typed claim, carrying source, target, claim text, and a four-class stance label grounded in the citation-intent literature. We give a construction pipeline applicable to any corpus of scholarly inter-referencing documents and instantiate it on a corpus of 127 papers in 3D point cloud semantic segmentation, producing a network of 8,260 typed claims. Three downstream task families demonstrate what the network enables: retrieval signal augmentation, aggregated-stance summarisation, and topological analytics. Head-to-head evaluation against standard Retrieval-Augmented Generation (RAG) baselines shows that the gain over flat retrieval is the gain from the right intermediate representation rather than the wrong one.

Ning Ding, Sergio J. Rodríguez Méndez, Pouya G. Omran

Australian National University, Canberra ACT 2601, Australia

KG Construction Graph Retrieval-Augmented Generation Knowledge Representation

May 26, 2026cs.AI

Query Symbolically or Retrieve Semantically? A Dataset and Method for Semi-Structured Question Answering

Retrieval-Augmented Generation (RAG) systems for question answering typically retrieve evidence by semantic similarity between the query and document chunks. While effective for unstructured text, this approach is less reliable on semi-structured corpora where answering may require exact filtering, aggregation, or exhaustive retrieval over structured attributes across multiple documents. Symbolic approaches support such operations, but they are often brittle on noisy natural-language corpora. We address this gap with DualGraph, a RAG framework that represents documents through two complementary views: a Textual Knowledge Graph for semantic retrieval and a Symbolic Knowledge Graph for symbolic querying over typed subject--predicate--object triples. Building on these two components, we provide multiple strategies for selecting or combining semantic and symbolic evidence.We also introduce SpecsQA, a benchmark from a commercial shopping website with semi-structured product documents and manually curated questions spanning open-ended and specification-oriented retrieval. Experiments show that DualGraph consistently outperforms state-of-the-art dense-retrieval, GraphRAG, symbolic, and table-oriented baselines across question types.Code and data are available at https://github.com/corneliocristina/DualGraphRAG.

Mateusz Czyżnikiewicz, Ryszard Tuora, Adam Kozakiewicz +6

Samsung AI Warsaw · Samsung AI Cambridge

Graph Retrieval-Augmented Generation Question Answering Knowledge Representation Hybrid Retrieval Knowledge Graphs

May 22, 2026cs.LG

Generative Representation Learning on Hyper-relational Knowledge Graphs via Masked Discrete Diffusion

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

Jaejun Lee, Seheon Kim, Joyce Jiyoung Whang

School of Computing, KAIST, Daejeon, South Korea · Department of AI Computing, KAIST, Daejeon, South Korea

Graph Representation Learning Knowledge Representation Knowledge Graphs KG Completion Diffusion Models