Ontology-Guided Information Extraction

We present SNO-PI, the top-performing submission on SNOMED International's SNOMED CT Entity Linking Benchmark as of 18 October 2026. SNO-PI achieves a macro character IoU of 0.5387, outperforming the organisers' reference system (0.4582; based on the 2024 challenge winner's approach) by 18% relative. Linking clinical mentions to SNOMED CT is a zero- and few-shot problem over a very large label space: the 272 annotated MIMIC-IV discharge summaries cover only 6,595 of the roughly 219,000 eligible concepts, and a third of those occur only once. This motivates a design built on transfer from pre-trained models and human-curated knowledge. SNO-PI combines high-recall span proposal, SapBERT candidate retrieval and listwise ensemble reranking with three BERT-family encoders, each further pre-trained with masked language modelling on unlabelled MIMIC-IV notes and then on SNOMED CT synonyms and hierarchy before task fine-tuning. We find that curated knowledge helps most on concepts never seen in training, yet these concepts remain the main source of error.

Scientific papers keep much of their quantitative content in tables and supplementary files, where a number means something only through its header, caption, unit, analytical method, and the conventions of its field. Recovering the rows and columns of a table is therefore not the same as recovering the scientific fact it reports. Most semantic table-interpretation methods assume that a clean table is already available and subsequently map its cells or columns to ontology terms, whereas most publication-level extraction systems are designed for a single domain. We study a middle path: a shared process that reads a paper and its supplementary files, gathers evidence from several parsers and a language model, and reconciles that evidence, while a bounded human-authored task module for each task supplies the domain meaning. The module lists the canonical names the graph may use, the surface forms that map to them, a small set of derivation rules and validity constraints, an identity key, and the bindings used to write RDF. It defines what a task is allowed to emit; it does not try to list every convention of a field. We build four such modules (for drug-discovery chemistry, materials science, machine learning, and mineral geochemistry) in the ArticleMiner framework, and evaluate them on 163 papers, including a new geochemistry benchmark with expert-curated ground truth. In comparisons against a same-LLM few-shot baseline, the point estimates favor ArticleMiner on all four tasks, with uncertainty on the two smaller benchmarks. The geochemistry comparison also includes access to supplementary files, so its improvement cannot be attributed to domain guidance alone.

Academic reviews, scholarly commentaries, and book reviews serve as sources of evaluative statements about theories, methods, literature, institutions, and policies, providing valuable evidence for scholarly evaluation. Existing scientific entity extraction methods mainly target research articles and are less effective for evaluation objects, which are often abstract, context-dependent, and characterized by ambiguous type boundaries. This study proposes an ontology-guided multi-agent framework for evaluation object extraction. The framework combines candidate discovery, ontology-constrained classification, and domain review. Experimental results show that it achieves a Precision of 90.33%, Recall of 84.55%, Entity-level F1 of 87.34%, Strict Typed F1 of 79.78%, and Type Accuracy of 91.35%, substantially outperforming rule-based and zero-shot baselines. Ablation results indicate that the multi-agent workflow improves recall and stability, while ontology-based boundary constraints enhance fine-grained classification and reduce category confusion. The framework supports the structured utilization of evaluative scholarly texts and provides methodological support for evidence-based research evaluation and STI mining.

Retrieval-Augmented Generation (RAG) enables large language models to incorporate external knowledge during generation, improving factual grounding and domain adaptability. However, existing RAG pipelines assume that evidence retrieved from multiple repositories can be ranked globally using a single similarity function. While suitable for open-domain retrieval, this assumption breaks down in enterprise document generation, where heterogeneous knowledge bases (such as policies, regulations, technical documentation, and departmental guidelines) serve distinct roles and must be jointly represented in the generated document. As a result, global ranking often produces unbalanced context dominated by a subset of sources, leading to incomplete enterprise drafts. To address this limitation, we propose W-RAG, a source-aware retrieval framework that performs ontology-guided retrieval, local ranking within each knowledge base, and source-level weighting to regulate evidence composition. We further introduce a new dataset for retrieval-grounded enterprise document generation spanning multiple document types and industry domains. Experiments show that standard RAG pipelines struggle on this task, while W-RAG significantly improves document coverage and generation quality.

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.

The NIS-2 Directive increases the need for continuous, auditable compliance evidence and motivates a shift from document-based compliance toward machine-readable compliance artifacts. The Open Security Controls Assessment Language (OSCAL) is a standard for this purpose, which the German Federal Office for Information Security (BSI) is adapting with Grundschutz++. However, companies are still managing extensive legacy IT security concepts (IT-SCs), and migrating them without verification could transfer outdated assets into the new format. While existing research primarily addresses the generation of new concepts, there is a lack of a verification framework that extracts legacy IT-SCs into an auditable intermediate representation, deterministically compares the extracted graph with an independently constructed reference state, and exports schema-valid OSCAL artifacts. This paper introduces the Automated Security Concept Structure Extraction and Reverse Topology-checking (ASSERT) Framework, which addresses this gap by using ontology-based extraction of legacy documents into formal document graphs, a five-class graph difference against a verified reference graph, and the export into schema-valid OSCAL outputs for system description and assessment evidence. Using the BSI's RecPlast dataset, we compare a local open-weight model and a commercial model across three configurations with different levels of reference-ontology exposure. The evaluation shows that ASSERT makes document-infrastructure inconsistencies measurable, but reveals a trade-off between discovering undocumented entities and enforcing a schema.

AI pipelines that reason quantitatively over technical text depend on input where physical quantities, numbers, units, and symbolic expressions arrive intact; when these entities fragment at tokenization, errors propagate downstream. Byte-Pair Encoding, optimized for vocabulary compression, is blind to such entities and fragments them into arbitrary subwords -- a problem aggravated in technical Brazilian Portuguese. We present TOTEN, a knowledge-based system whose input representation preserves each technical entity as a whole, typed unit: vocabulary is not derived statistically but classified declaratively under a formal ontology of engineering entities (OEE). The core is the triple <O, classify, {inst_tau}>: types, principles, and invariants; a classifier mapping raw text into typed regions; and instantiators yielding a self-descriptive representation. Integrity rests on deterministic coupling to three external authorities: Pint (dimensional), Unicode Character Database (typographic), and RSLP (Portuguese morphology). We evaluate four properties verifiable by construction -- atomicity, dimensional equivalence, typographic robustness, numerical reconstruction -- on an internal benchmark (EngQuant, N=800) and four Brazilian Portuguese external corpora (N=1771 eligible cases), and report detection recall. Against eight state-of-the-art baselines, TOTEN reaches unit atomicity in all contrasts and reconstruction of 0.775-0.904 externally vs. 0.627-0.703 for the best (Quantulum3); on EngQuant, 0.780 vs. 0.340. Differences are significant (McNemar, Holm-corrected). Spearman correlation between internal and external rankings confirms concurrent validity of the control benchmark. TOTEN shows statistical parity with Pint in dimensional equivalence. The result is a structurally faithful, auditable, low-cost input layer for intelligent systems on technical knowledge, without generative models.

Fragmentation is common in interdisciplinary fields with diverse methods and theoretical commitments. Predictive coding neuroscience is a clear example: its literature spans computational theory, electrophysiology, imaging, behavior, and modeling, creating a synthesis problem that conventional meta-analysis cannot easily resolve. Here, we describe a local multi-LLM pipeline for ontology-constrained literature synthesis. The pipeline reads papers, extracts evidence, incorporates figure descriptions, assembles constrained prompts, and validates outputs against an expert glossary. We manually defined a predictive-coding glossary of thirty-six concepts grouped into three hypotheses: predictive suppression, feedforward error propagation, and ubiquity. A council of ten local language models scored 31 studies according to their agreement or disagreement with each glossary factor across local and global oddball contexts. This enabled pairwise study-agreement analysis, cross-model comparison, and three-dimensional hypothesis-space mapping. Agreement was high for some hypotheses but weaker for others, revealing structured disagreement, particularly across local versus global oddball paradigms. We further define hypothesis-space temperature, a geometric dispersion metric measuring how compactly studies occupy the hypothesis space. Temperature was lower for local oddball contexts and higher for global oddball contexts, indicating greater dispersion in the latter. The scoring geometry also allowed us to estimate vectors of change between experimental contexts. These results demonstrate that local multi-LLM councils can produce auditable disagreement measurements that map heterogeneous literatures into quantitative evidence spaces. This framework may generalize to cross-study hypothesis mapping where conventional meta-analysis lacks a common comparison space.

Retrieval-Augmented Generation (RAG) systems face significant challenges in complex reasoning, multi-hop queries, and domain-specific QA. While existing GraphRAG frameworks have made progress in structural knowledge organization, they still have limitations in knowledge extraction precision, community report integrity, and retrieval performance. This paper proposes OMD-GraphRAG, an enhanced framework built upon open-source GraphRAG. The framework introduces three core innovations: (1) Ontology-Guided Knowledge Extraction that uses predefined Schema to guide LLMs in accurately identifying domain-specific entities and relations; (2) Multi-Dimensional Community Clustering Strategy that improves community completeness through alignment completion, attribute-based clustering, and multi-hop relationship clustering; (3) Dual-Channel Graph Retrieval Fusion that balances QA accuracy and performance through hybrid graph and community retrieval. Evaluation results on MultiHop-RAG benchmark show that OMD-GraphRAG outperforms mainstream open source solutions (e.g., LightRAG) in comprehensive F1 scores, particularly in inference and temporal queries.