Daily Papers

Automating ontology construction and curation is an important but challenging task in knowledge engineering and artificial intelligence. Prediction by machine learning techniques such as contextual semantic embedding is a promising direction, but the relevant research is still preliminary especially for expressive ontologies in Web Ontology Language (OWL). In this paper, we present a new subsumption prediction method named BERTSubs for classes of OWL ontology. It exploits the pre-trained language model BERT to compute contextual embeddings of a class, where customized templates are proposed to incorporate the class context (e.g., neighbouring classes) and the logical existential restriction. BERTSubs is able to predict multiple kinds of subsumers including named classes from the same ontology or another ontology, and existential restrictions from the same ontology. Extensive evaluation on five real-world ontologies for three different subsumption tasks has shown the effectiveness of the templates and that BERTSubs can dramatically outperform the baselines that use (literal-aware) knowledge graph embeddings, non-contextual word embeddings and the state-of-the-art OWL ontology embeddings.

OWL (Web Ontology Language) ontologies which are able to formally represent complex knowledge and support semantic reasoning have been widely adopted across various domains such as healthcare and bioinformatics. Recently, ontology embeddings have gained wide attention due to its potential to infer plausible new knowledge and approximate complex reasoning. However, existing methods face notable limitations: geometric model-based embeddings typically overlook valuable textual information, resulting in suboptimal performance, while the approaches that incorporate text, which are often based on language models, fail to preserve the logical structure. In this work, we propose a new ontology embedding method OnT, which tunes a Pretrained Language Model (PLM) via geometric modeling in a hyperbolic space for effectively incorporating textual labels and simultaneously preserving class hierarchies and other logical relationships of Description Logic EL. Extensive experiments on four real-world ontologies show that OnT consistently outperforms the baselines including the state-of-the-art across both tasks of prediction and inference of axioms. OnT also demonstrates strong potential in real-world applications, indicated by its robust transfer learning abilities and effectiveness in real cases of constructing a new ontology from SNOMED CT. Data and code are available at https://github.com/HuiYang1997/OnT.

Ontologies are widely used for representing domain knowledge and meta data, playing an increasingly important role in Information Systems, the Semantic Web, Bioinformatics and many other domains. However, logical reasoning that ontologies can directly support are quite limited in learning, approximation and prediction. One straightforward solution is to integrate statistical analysis and machine learning. To this end, automatically learning vector representation for knowledge of an ontology i.e., ontology embedding has been widely investigated. Numerous papers have been published on ontology embedding, but a lack of systematic reviews hinders researchers from gaining a comprehensive understanding of this field. To bridge this gap, we write this survey paper, which first introduces different kinds of semantics of ontologies and formally defines ontology embedding as well as its property of faithfulness. Based on this, it systematically categorizes and analyses a relatively complete set of over 80 papers, according to the ontologies they aim at and their technical solutions including geometric modeling, sequence modeling and graph propagation. This survey also introduces the applications of ontology embedding in ontology engineering, machine learning augmentation and life sciences, presents a new library mOWL and discusses the challenges and future directions.

A variety of knowledge graph embedding approaches have been developed. Most of them obtain embeddings by learning the structure of the knowledge graph within a link prediction setting. As a result, the embeddings reflect only the semantics of a single knowledge graph, and embeddings for different knowledge graphs are not aligned, e.g., they cannot be used to find similar entities across knowledge graphs via nearest neighbor search. However, knowledge graph embedding applications such as entity disambiguation require a more global representation, i.e., a representation that is valid across multiple sources. We propose to learn universal knowledge graph embeddings from large-scale interlinked knowledge sources. To this end, we fuse large knowledge graphs based on the owl:sameAs relation such that every entity is represented by a unique identity. We instantiate our idea by computing universal embeddings based on DBpedia and Wikidata yielding embeddings for about 180 million entities, 15 thousand relations, and 1.2 billion triples. Moreover, we develop a convenient API to provide embeddings as a service. Experiments on link prediction show that universal knowledge graph embeddings encode better semantics compared to embeddings computed on a single knowledge graph. For reproducibility purposes, we provide our source code and datasets open access at https://github.com/dice-group/Universal_Embeddings

Current methods for embedding-based query answering over incomplete Knowledge Graphs (KGs) only focus on inductive reasoning, i.e., predicting answers by learning patterns from the data, and lack the complementary ability to do deductive reasoning, which requires the application of domain knowledge to infer further information. To address this shortcoming, we investigate the problem of incorporating ontologies into embedding-based query answering models by defining the task of embedding-based ontology-mediated query answering. We propose various integration strategies into prominent representatives of embedding models that involve (1) different ontology-driven data augmentation techniques and (2) adaptation of the loss function to enforce the ontology axioms. We design novel benchmarks for the considered task based on the LUBM and the NELL KGs and evaluate our methods on them. The achieved improvements in the setting that requires both inductive and deductive reasoning are from 20% to 55% in HITS@3.

We introduce semantic towers, an extrinsic knowledge representation method, and compare it to intrinsic knowledge in large language models for ontology learning. Our experiments show a trade-off between performance and semantic grounding for extrinsic knowledge compared to a fine-tuned model intrinsic knowledge. We report our findings on the Large Language Models for Ontology Learning (LLMs4OL) 2024 challenge.

In many modern day systems such as information extraction and knowledge management agents, ontologies play a vital role in maintaining the concept hierarchies of the selected domain. However, ontology population has become a problematic process due to its nature of heavy coupling with manual human intervention. With the use of word embeddings in the field of natural language processing, it became a popular topic due to its ability to cope up with semantic sensitivity. Hence, in this study, we propose a novel way of semi-supervised ontology population through word embeddings as the basis. We built several models including traditional benchmark models and new types of models which are based on word embeddings. Finally, we ensemble them together to come up with a synergistic model with better accuracy. We demonstrate that our ensemble model can outperform the individual models.

Integrating deep learning techniques, particularly language models (LMs), with knowledge representation techniques like ontologies has raised widespread attention, urging the need of a platform that supports both paradigms. Although packages such as OWL API and Jena offer robust support for basic ontology processing features, they lack the capability to transform various types of information within ontologies into formats suitable for downstream deep learning-based applications. Moreover, widely-used ontology APIs are primarily Java-based while deep learning frameworks like PyTorch and Tensorflow are mainly for Python programming. To address the needs, we present DeepOnto, a Python package designed for ontology engineering with deep learning. The package encompasses a core ontology processing module founded on the widely-recognised and reliable OWL API, encapsulating its fundamental features in a more "Pythonic" manner and extending its capabilities to incorporate other essential components including reasoning, verbalisation, normalisation, taxonomy, projection, and more. Building on this module, DeepOnto offers a suite of tools, resources, and algorithms that support various ontology engineering tasks, such as ontology alignment and completion, by harnessing deep learning methods, primarily pre-trained LMs. In this paper, we also demonstrate the practical utility of DeepOnto through two use-cases: the Digital Health Coaching in Samsung Research UK and the Bio-ML track of the Ontology Alignment Evaluation Initiative (OAEI).

Scholarly data are largely fragmented across siloed databases with divergent metadata and missing linkages among them. We present the Science Data Lake, a locally-deployable infrastructure built on DuckDB and simple Parquet files that unifies eight open sources - Semantic Scholar, OpenAlex, SciSciNet, Papers with Code, Retraction Watch, Reliance on Science, a preprint-to-published mapping, and Crossref - via DOI normalization while preserving source-level schemas. The resource comprises approximately 960GB of Parquet files spanning ~293 million uniquely identifiable papers across ~22 schemas and ~153 SQL views. An embedding-based ontology alignment using BGE-large sentence embeddings maps 4,516 OpenAlex topics to 13 scientific ontologies (~1.3 million terms), yielding 16,150 mappings covering 99.8% of topics (geq 0.65 threshold) with F1 = 0.77 at the recommended geq 0.85 operating point, outperforming TF-IDF, BM25, and Jaro-Winkler baselines on a 300-pair gold-standard evaluation. We validate through 10 automated checks, cross-source citation agreement analysis (pairwise Pearson r = 0.76 - 0.87), and stratified manual annotation. Four vignettes demonstrate cross-source analyses infeasible with any single database. The resource is open source, deployable on a single drive or queryable remotely via HuggingFace, and includes structured documentation suitable for large language model (LLM) based research agents.

With the rapid development of IT operations, it has become increasingly crucial to efficiently manage and analyze large volumes of data for practical applications. The techniques of Natural Language Processing (NLP) have shown remarkable capabilities for various tasks, including named entity recognition, machine translation and dialogue systems. Recently, Large Language Models (LLMs) have achieved significant improvements across various NLP downstream tasks. However, there is a lack of specialized LLMs for IT operations. In this paper, we introduce the OWL, a large language model trained on our collected OWL-Instruct dataset with a wide range of IT-related information, where the mixture-of-adapter strategy is proposed to improve the parameter-efficient tuning across different domains or tasks. Furthermore, we evaluate the performance of our OWL on the OWL-Bench established by us and open IT-related benchmarks. OWL demonstrates superior performance results on IT tasks, which outperforms existing models by significant margins. Moreover, we hope that the findings of our work will provide more insights to revolutionize the techniques of IT operations with specialized LLMs.

In this paper we introduce the olog, or ontology log, a category-theoretic model for knowledge representation (KR). Grounded in formal mathematics, ologs can be rigorously formulated and cross-compared in ways that other KR models (such as semantic networks) cannot. An olog is similar to a relational database schema; in fact an olog can serve as a data repository if desired. Unlike database schemas, which are generally difficult to create or modify, ologs are designed to be user-friendly enough that authoring or reconfiguring an olog is a matter of course rather than a difficult chore. It is hoped that learning to author ologs is much simpler than learning a database definition language, despite their similarity. We describe ologs carefully and illustrate with many examples. As an application we show that any primitive recursive function can be described by an olog. We also show that ologs can be aligned or connected together into a larger network using functors. The various methods of information flow and institutions can then be used to integrate local and global world-views. We finish by providing several different avenues for future research.

Large language model (LLM) agents rely heavily on knowledge encoded in model parameters or presented as unstructured context. In domain-specific tasks, this leaves important semantic connections implicit. This often results in incomplete evidence use and brittle multi-step decisions. Ontologies offer a way to externalize domain concepts and relations as machine-interpretable structures, but constructing task-usable ontologies traditionally requires substantial effort from domain experts and is difficult to scale. Automatic construction is also challenging: an ontology that appears semantically plausible may not contain the relational structures needed for actual decision making. We present OaK, an ontology-as-a-kernel framework that dynamically constructs and refines task-oriented ontologies for LLM agents. Given task requirements and training data, OaK constructs an ontology and its knowledge graph, generates task-adaptation functions for graph reasoning, and uses judge feedback to iteratively refine both. By making relevant concepts and relations explicit, the ontology grounds knowledge retrieval and multi-step decision making. We evaluate OaK on TravelPlanner, CRMArenaPro, and ToolQA. Results show that OaK improves standard LLM agents, strengthens evidence grounding, and boosts the reliability of multi-step reasoning.

Investigating whether pre-trained language models (LMs) can function as knowledge bases (KBs) has raised wide research interests recently. However, existing works focus on simple, triple-based, relational KBs, but omit more sophisticated, logic-based, conceptualised KBs such as OWL ontologies. To investigate an LM's knowledge of ontologies, we propose OntoLAMA, a set of inference-based probing tasks and datasets from ontology subsumption axioms involving both atomic and complex concepts. We conduct extensive experiments on ontologies of different domains and scales, and our results demonstrate that LMs encode relatively less background knowledge of Subsumption Inference (SI) than traditional Natural Language Inference (NLI) but can improve on SI significantly when a small number of samples are given. We will open-source our code and datasets.

We propose the LLMs4OL approach, which utilizes Large Language Models (LLMs) for Ontology Learning (OL). LLMs have shown significant advancements in natural language processing, demonstrating their ability to capture complex language patterns in different knowledge domains. Our LLMs4OL paradigm investigates the following hypothesis: Can LLMs effectively apply their language pattern capturing capability to OL, which involves automatically extracting and structuring knowledge from natural language text? To test this hypothesis, we conduct a comprehensive evaluation using the zero-shot prompting method. We evaluate nine different LLM model families for three main OL tasks: term typing, taxonomy discovery, and extraction of non-taxonomic relations. Additionally, the evaluations encompass diverse genres of ontological knowledge, including lexicosemantic knowledge in WordNet, geographical knowledge in GeoNames, and medical knowledge in UMLS.

We investigate the task of inserting new concepts extracted from texts into an ontology using language models. We explore an approach with three steps: edge search which is to find a set of candidate locations to insert (i.e., subsumptions between concepts), edge formation and enrichment which leverages the ontological structure to produce and enhance the edge candidates, and edge selection which eventually locates the edge to be placed into. In all steps, we propose to leverage neural methods, where we apply embedding-based methods and contrastive learning with Pre-trained Language Models (PLMs) such as BERT for edge search, and adapt a BERT fine-tuning-based multi-label Edge-Cross-encoder, and Large Language Models (LLMs) such as GPT series, FLAN-T5, and Llama 2, for edge selection. We evaluate the methods on recent datasets created using the SNOMED CT ontology and the MedMentions entity linking benchmark. The best settings in our framework use fine-tuned PLM for search and a multi-label Cross-encoder for selection. Zero-shot prompting of LLMs is still not adequate for the task, and we propose explainable instruction tuning of LLMs for improved performance. Our study shows the advantages of PLMs and highlights the encouraging performance of LLMs that motivates future studies.

Selecting a representative vector for a set of vectors is a very common requirement in many algorithmic tasks. Traditionally, the mean or median vector is selected. Ontology classes are sets of homogeneous instance objects that can be converted to a vector space by word vector embeddings. This study proposes a methodology to derive a representative vector for ontology classes whose instances were converted to the vector space. We start by deriving five candidate vectors which are then used to train a machine learning model that would calculate a representative vector for the class. We show that our methodology out-performs the traditional mean and median vector representations.

Ontology alignment (a.k.a ontology matching (OM)) plays a critical role in knowledge integration. Owing to the success of machine learning in many domains, it has been applied in OM. However, the existing methods, which often adopt ad-hoc feature engineering or non-contextual word embeddings, have not yet outperformed rule-based systems especially in an unsupervised setting. In this paper, we propose a novel OM system named BERTMap which can support both unsupervised and semi-supervised settings. It first predicts mappings using a classifier based on fine-tuning the contextual embedding model BERT on text semantics corpora extracted from ontologies, and then refines the mappings through extension and repair by utilizing the ontology structure and logic. Our evaluation with three alignment tasks on biomedical ontologies demonstrates that BERTMap can often perform better than the leading OM systems LogMap and AML.

Since long, corporations are looking for knowledge sources which can provide structured description of data and can focus on meaning and shared understanding. Structures which can facilitate open world assumptions and can be flexible enough to incorporate and recognize more than one name for an entity. A source whose major purpose is to facilitate human communication and interoperability. Clearly, databases fail to provide these features and ontologies have emerged as an alternative choice, but corporations working on same domain tend to make different ontologies. The problem occurs when they want to share their data/knowledge. Thus we need tools to merge ontologies into one. This task is termed as ontology matching. This is an emerging area and still we have to go a long way in having an ideal matcher which can produce good results. In this paper we have shown a framework to matching ontologies using graphs.

We present KNOW--the Knowledge Navigator Ontology for the World--the first ontology designed to capture everyday knowledge to augment large language models (LLMs) in real-world generative AI use cases such as personal AI assistants. Our domain is human life, both its everyday concerns and its major milestones. We have limited the initial scope of the modeled concepts to only established human universals: spacetime (places, events) plus social (people, groups, organizations). The inclusion criteria for modeled concepts are pragmatic, beginning with universality and utility. We compare and contrast previous work such as Schema.org and Cyc--as well as attempts at a synthesis of knowledge graphs and language models--noting how LLMs already encode internally much of the commonsense tacit knowledge that took decades to capture in the Cyc project. We also make available code-generated software libraries for the 12 most popular programming languages, enabling the direct use of ontology concepts in software engineering. We emphasize simplicity and developer experience in promoting AI interoperability.

Ontologies and taxonomies of research fields are critical for managing and organising scientific knowledge, as they facilitate efficient classification, dissemination and retrieval of information. However, the creation and maintenance of such ontologies are expensive and time-consuming tasks, usually requiring the coordinated effort of multiple domain experts. Consequently, ontologies in this space often exhibit uneven coverage across different disciplines, limited inter-domain connectivity, and infrequent updating cycles. In this study, we investigate the capability of several large language models to identify semantic relationships among research topics within three academic domains: biomedicine, physics, and engineering. The models were evaluated under three distinct conditions: zero-shot prompting, chain-of-thought prompting, and fine-tuning on existing ontologies. Additionally, we assessed the cross-domain transferability of fine-tuned models by measuring their performance when trained in one domain and subsequently applied to a different one. To support this analysis, we introduce PEM-Rel-8K, a novel dataset consisting of over 8,000 relationships extracted from the most widely adopted taxonomies in the three disciplines considered in this study: MeSH, PhySH, and IEEE. Our experiments demonstrate that fine-tuning LLMs on PEM-Rel-8K yields excellent performance across all disciplines.

Ontology Alignment (OA) is fundamental for achieving semantic interoperability across diverse knowledge systems. We present OntoAligner, a comprehensive, modular, and robust Python toolkit for ontology alignment, designed to address current limitations with existing tools faced by practitioners. Existing tools are limited in scalability, modularity, and ease of integration with recent AI advances. OntoAligner provides a flexible architecture integrating existing lightweight OA techniques such as fuzzy matching but goes beyond by supporting contemporary methods with retrieval-augmented generation and large language models for OA. The framework prioritizes extensibility, enabling researchers to integrate custom alignment algorithms and datasets. This paper details the design principles, architecture, and implementation of the OntoAligner, demonstrating its utility through benchmarks on standard OA tasks. Our evaluation highlights OntoAligner's ability to handle large-scale ontologies efficiently with few lines of code while delivering high alignment quality. By making OntoAligner open-source, we aim to provide a resource that fosters innovation and collaboration within the OA community, empowering researchers and practitioners with a toolkit for reproducible OA research and real-world applications.

Knowledge graph embeddings are now a widely adopted approach to knowledge representation in which entities and relationships are embedded in vector spaces. In this chapter, we introduce the reader to the concept of knowledge graph embeddings by explaining what they are, how they can be generated and how they can be evaluated. We summarize the state-of-the-art in this field by describing the approaches that have been introduced to represent knowledge in the vector space. In relation to knowledge representation, we consider the problem of explainability, and discuss models and methods for explaining predictions obtained via knowledge graph embeddings.

This work investigates the applicability of recent generative Large Language Models (LLMs), such as the GPT series and Flan-T5, to ontology alignment for identifying concept equivalence mappings across ontologies. To test the zero-shot performance of Flan-T5-XXL and GPT-3.5-turbo, we leverage challenging subsets from two equivalence matching datasets of the OAEI Bio-ML track, taking into account concept labels and structural contexts. Preliminary findings suggest that LLMs have the potential to outperform existing ontology alignment systems like BERTMap, given careful framework and prompt design.

With the adoption of Semantic Web technologies, an increasing number of vocabularies and ontologies have been developed in different domains, ranging from Biology to Agronomy or Geosciences. However, many of these ontologies are still difficult to find, access and understand by researchers due to a lack of documentation, URI resolving issues, versioning problems, etc. In this chapter we describe guidelines and best practices for creating accessible, understandable and reusable ontologies on the Web, using standard practices and pointing to existing tools and frameworks developed by the Semantic Web community. We illustrate our guidelines with concrete examples, in order to help researchers implement these practices in their future vocabularies.

Knowledge Graph (KG) and its variant of ontology have been widely used for knowledge representation, and have shown to be quite effective in augmenting Zero-shot Learning (ZSL). However, existing ZSL methods that utilize KGs all neglect the intrinsic complexity of inter-class relationships represented in KGs. One typical feature is that a class is often related to other classes in different semantic aspects. In this paper, we focus on ontologies for augmenting ZSL, and propose to learn disentangled ontology embeddings guided by ontology properties to capture and utilize more fine-grained class relationships in different aspects. We also contribute a new ZSL framework named DOZSL, which contains two new ZSL solutions based on generative models and graph propagation models, respectively, for effectively utilizing the disentangled ontology embeddings. Extensive evaluations have been conducted on five benchmarks across zero-shot image classification (ZS-IMGC) and zero-shot KG completion (ZS-KGC). DOZSL often achieves better performance than the state-of-the-art, and its components have been verified by ablation studies and case studies. Our codes and datasets are available at https://github.com/zjukg/DOZSL.

Ontologies comprising of concepts, their attributes, and relationships are used in many knowledge based AI systems. While there have been efforts towards populating domain specific ontologies, we examine the role of document structure in learning ontological relationships between concepts in any document corpus. Inspired by ideas from hypernym discovery and explainability, our method performs about 15 points more accurate than a stand-alone R-GCN model for this task.

We present a comprehensive system for addressing Tasks A, B, and C of the LLMs4OL 2025 challenge, which together span the full ontology construction pipeline: term extraction, typing, and taxonomy discovery. Our approach combines retrieval-augmented prompting, zero-shot classification, and attention-based graph modeling -- each tailored to the demands of the respective task. For Task A, we jointly extract domain-specific terms and their ontological types using a retrieval-augmented generation (RAG) pipeline. Training data was reformulated into a document to terms and types correspondence, while test-time inference leverages semantically similar training examples. This single-pass method requires no model finetuning and improves overall performance through lexical augmentation Task B, which involves assigning types to given terms, is handled via a dual strategy. In the few-shot setting (for domains with labeled training data), we reuse the RAG scheme with few-shot prompting. In the zero-shot setting (for previously unseen domains), we use a zero-shot classifier that combines cosine similarity scores from multiple embedding models using confidence-based weighting. In Task C, we model taxonomy discovery as graph inference. Using embeddings of type labels, we train a lightweight cross-attention layer to predict is-a relations by approximating a soft adjacency matrix. These modular, task-specific solutions enabled us to achieve top-ranking results in the official leaderboard across all three tasks. Taken together these strategies showcase the scalability, adaptability, and robustness of LLM-based architectures for ontology learning across heterogeneous domains. Code is available at: https://github.com/BelyaevaAlex/LLMs4OL-Challenge-Alexbek

Organizing a large-scale knowledge graph into a typed property graph requires structural decisions -- which entities become nodes, which properties become edges, and what schema governs these choices. Existing approaches embed these decisions in pipeline code or extract relations ad hoc, producing schemas that are tightly coupled to their construction process and difficult to reuse for downstream ontology-level tasks. We present an ontology-oriented approach in which the schema is designed from the outset for ontology analysis, entity disambiguation, domain customization, and LLM-guided extraction -- not merely as a byproduct of graph building. The core mechanism is intrinsic-relational routing, which classifies every property as either intrinsic or relational and routes it to the corresponding schema module. This routing produces a declarative schema that is portable across storage backends and independently reusable. We instantiate the approach on the January 2026 Wikidata dump. A rule-based cleaning stage identifies a 34.6M-entity core set from the full dump, followed by iterative intrinsic-relational routing that assigns each property to one of 94 modules organized into 8 categories. With tool-augmented LLM support and human review, the schema reaches 93.3% category coverage and 98.0% module assignment among classified entities. Exporting this schema yields a property graph with 34.0M nodes and 61.2M edges across 38 relationship types. We validate the ontology-oriented claim through five applications that consume the schema independently of the construction pipeline: ontology structure analysis, benchmark annotation auditing, entity disambiguation, domain customization, and LLM-guided extraction.

Knowledge graph embedding involves learning representations of entities -- the vertices of the graph -- and relations -- the edges of the graph -- such that the resulting representations encode the known factual information represented by the knowledge graph and can be used in the inference of new relations. We show that knowledge graph embedding is naturally expressed in the topological and categorical language of cellular sheaves: a knowledge graph embedding can be described as an approximate global section of an appropriate knowledge sheaf over the graph, with consistency constraints induced by the knowledge graph's schema. This approach provides a generalized framework for reasoning about knowledge graph embedding models and allows for the expression of a wide range of prior constraints on embeddings. Further, the resulting embeddings can be easily adapted for reasoning over composite relations without special training. We implement these ideas to highlight the benefits of the extensions inspired by this new perspective.

Domain ontologies are important information sources for knowledge-based systems. Yet, building domain ontologies from scratch is known to be a very labor-intensive process. In this study, we present our semi-automatic approach to building an ontology for the domain of wind energy which is an important type of renewable energy with a growing share in electricity generation all over the world. Related Wikipedia articles are first processed in an automated manner to determine the basic concepts of the domain together with their properties and next the concepts, properties, and relationships are organized to arrive at the ultimate ontology. We also provide pointers to other engineering ontologies which could be utilized together with the proposed wind energy ontology in addition to its prospective application areas. The current study is significant as, to the best of our knowledge, it proposes the first considerably wide-coverage ontology for the wind energy domain and the ontology is built through a semi-automatic process which makes use of the related Web resources, thereby reducing the overall cost of the ontology building process.

Large Language Models (LLMs) demonstrate impressive capabilities in natural language processing but suffer from inaccuracies and logical inconsistencies known as hallucinations. This compromises their reliability, especially in domains requiring factual accuracy. We propose a neuro-symbolic approach integrating symbolic ontological reasoning and machine learning methods to enhance the consistency and reliability of LLM outputs. Our workflow utilizes OWL ontologies, a symbolic reasoner (e.g., HermiT) for consistency checking, and a lightweight machine learning model (logistic regression) for mapping natural language statements into logical forms compatible with the ontology. When inconsistencies between LLM outputs and the ontology are detected, the system generates explanatory feedback to guide the LLM towards a corrected, logically coherent response in an iterative refinement loop. We present a working Python prototype demonstrating this pipeline. Experimental results in a defined domain suggest significant improvements in semantic coherence and factual accuracy of LLM outputs, showcasing the potential of combining LLM fluency with the rigor of formal semantics.

We introduce the use of Poincar\'e embeddings to improve existing state-of-the-art approaches to domain-specific taxonomy induction from text as a signal for both relocating wrong hyponym terms within a (pre-induced) taxonomy as well as for attaching disconnected terms in a taxonomy. This method substantially improves previous state-of-the-art results on the SemEval-2016 Task 13 on taxonomy extraction. We demonstrate the superiority of Poincar\'e embeddings over distributional semantic representations, supporting the hypothesis that they can better capture hierarchical lexical-semantic relationships than embeddings in the Euclidean space.

Recent advances in Language Models (LMs) have failed to mask their shortcomings particularly in the domain of reasoning. This limitation impacts several tasks, most notably those involving ontology engineering. As part of a PhD research, we investigate the consequences of incorporating formal methods on the performance of Small Language Models (SLMs) on reasoning tasks. Specifically, we aim to orient our work toward using SLMs to bootstrap ontology construction and set up a series of preliminary experiments to determine the impact of expressing logical problems with different grammars on the performance of SLMs on a predefined reasoning task. Our findings show that it is possible to substitute Natural Language (NL) with a more compact logical language while maintaining a strong performance on reasoning tasks and hope to use these results to further refine the role of SLMs in ontology engineering.

Large language models (LLMs) increasingly underpin scientific AI applications that reason over structured knowledge, from biomedical question answering to materials informatics. However, their logical reasoning often falls short, producing factual inaccuracies unacceptable in these settings. Reliable evaluation remains challenging: manual dataset construction scales poorly, and LLM-based generation risks embedding the very flaws it aims to measure. High-quality benchmarks must ground both correct and incorrect labelled examples in explicit background knowledge, formally verifiable by a standard reasoner. We propose a pipeline that automatically generates ontology-grounded multiple-choice question (MCQ) benchmarks from any sufficiently axiomatised OWL 2 ontology, with correct answers grounded in the ontology by design. Distractors are generated by perturbing the right-hand-side class expressions of class definition axioms, and their incorrectness is formally verified by an OWL reasoner via entailment checks. We evaluate the pipeline on three ontologies: Pizza (small, academic), PMDco (complex, materials science), and DOID (large, biomedical), generating 112, 2,491, and 15,216 MCQs respectively. Distractors span four semantic categories from class unsatisfiability to weakened subsumptions, enabling diagnostic evaluation of specific reasoning failures. Items meet natural language quality standards: mean LLM judge scores of 4.02, 4.36, and 3.36 out of 5 confirm fluency, and correct-answer-to-distractor similarity above 0.8 shows that wrong options cannot be dismissed on surface form alone. Six LLMs evaluated zero-shot achieve 41.1-76.8% accuracy, well above the 25% random-guessing baseline, indicating the benchmarks are challenging and discriminative. This work is a step towards more reliable benchmarks for assessing logical reasoning in scientific AI.

Goal oriented dialogue systems were originally designed as a natural language interface to a fixed data-set of entities that users might inquire about, further described by domain, slots, and values. As we move towards adaptable dialogue systems where knowledge about domains, slots, and values may change, there is an increasing need to automatically extract these terms from raw dialogues or related non-dialogue data on a large scale. In this paper, we take an important step in this direction by exploring different features that can enable systems to discover realizations of domains, slots, and values in dialogues in a purely data-driven fashion. The features that we examine stem from word embeddings, language modelling features, as well as topological features of the word embedding space. To examine the utility of each feature set, we train a seed model based on the widely used MultiWOZ data-set. Then, we apply this model to a different corpus, the Schema-Guided Dialogue data-set. Our method outperforms the previously proposed approach that relies solely on word embeddings. We also demonstrate that each of the features is responsible for discovering different kinds of content. We believe our results warrant further research towards ontology induction, and continued harnessing of topological data analysis for dialogue and natural language processing research.

Embedding knowledge graphs (KGs) into continuous vector spaces is a focus of current research. Early works performed this task via simple models developed over KG triples. Recent attempts focused on either designing more complicated triple scoring models, or incorporating extra information beyond triples. This paper, by contrast, investigates the potential of using very simple constraints to improve KG embedding. We examine non-negativity constraints on entity representations and approximate entailment constraints on relation representations. The former help to learn compact and interpretable representations for entities. The latter further encode regularities of logical entailment between relations into their distributed representations. These constraints impose prior beliefs upon the structure of the embedding space, without negative impacts on efficiency or scalability. Evaluation on WordNet, Freebase, and DBpedia shows that our approach is simple yet surprisingly effective, significantly and consistently outperforming competitive baselines. The constraints imposed indeed improve model interpretability, leading to a substantially increased structuring of the embedding space. Code and data are available at https://github.com/iieir-km/ComplEx-NNE_AER.

Existing domain-specific Large Language Models (LLMs) are typically developed by fine-tuning general-purposed LLMs with large-scale domain-specific corpora. However, training on large-scale corpora often fails to effectively organize domain knowledge of LLMs, leading to fragmented understanding. Inspired by how humans connect concepts and organize knowledge through mind maps, we aim to emulate this approach by using ontology with hierarchical conceptual knowledge to reorganize LLM's domain knowledge. From this perspective, we propose an ontology-driven self-training framework called OntoTune, which aims to align LLMs with ontology through in-context learning, enabling the generation of responses guided by the ontology. We leverage in-context learning to identify whether the LLM has acquired the specific concept's ontology knowledge, and select the entries not yet mastered by LLM as the training set to further align the LLM with ontology. Compared to existing domain LLMs based on newly collected large-scale domain-specific corpora, our OntoTune, which relies on the existing, long-term developed ontology and LLM itself, significantly reduces data maintenance costs and offers improved generalization ability. We conduct our study in the medical domain to evaluate the effectiveness of OntoTune, utilizing a standardized medical ontology, SNOMED CT as our ontology source. Experimental results demonstrate that OntoTune achieves state-of-the-art performance in both in-ontology task hypernym discovery and out-of-ontology task medical domain QA. Moreover, compared to the latest direct ontology injection method TaxoLLaMA, our OntoTune better preserves original knowledge of LLM. The code and data are available at https://github.com/zjukg/OntoTune.

The recent advances in large language models (LLM) and foundation models with emergent capabilities have been shown to improve the performance of many NLP tasks. LLMs and Knowledge Graphs (KG) can complement each other such that LLMs can be used for KG construction or completion while existing KGs can be used for different tasks such as making LLM outputs explainable or fact-checking in Neuro-Symbolic manner. In this paper, we present Text2KGBench, a benchmark to evaluate the capabilities of language models to generate KGs from natural language text guided by an ontology. Given an input ontology and a set of sentences, the task is to extract facts from the text while complying with the given ontology (concepts, relations, domain/range constraints) and being faithful to the input sentences. We provide two datasets (i) Wikidata-TekGen with 10 ontologies and 13,474 sentences and (ii) DBpedia-WebNLG with 19 ontologies and 4,860 sentences. We define seven evaluation metrics to measure fact extraction performance, ontology conformance, and hallucinations by LLMs. Furthermore, we provide results for two baseline models, Vicuna-13B and Alpaca-LoRA-13B using automatic prompt generation from test cases. The baseline results show that there is room for improvement using both Semantic Web and Natural Language Processing techniques.

This paper presents OG-RAG, an Ontology-Grounded Retrieval Augmented Generation method designed to enhance LLM-generated responses by anchoring retrieval processes in domain-specific ontologies. While LLMs are widely used for tasks like question answering and search, they struggle to adapt to specialized knowledge, such as industrial workflows or knowledge work, without expensive fine-tuning or sub-optimal retrieval methods. Existing retrieval-augmented models, such as RAG, offer improvements but fail to account for structured domain knowledge, leading to suboptimal context generation. Ontologies, which conceptually organize domain knowledge by defining entities and their interrelationships, offer a structured representation to address this gap. OG-RAG constructs a hypergraph representation of domain documents, where each hyperedge encapsulates clusters of factual knowledge grounded using domain-specific ontology. An optimization algorithm then retrieves the minimal set of hyperedges that constructs a precise, conceptually grounded context for the LLM. This method enables efficient retrieval while preserving the complex relationships between entities. OG-RAG applies to domains where fact-based reasoning is essential, particularly in tasks that require workflows or decision-making steps to follow predefined rules and procedures. These include industrial workflows in healthcare, legal, and agricultural sectors, as well as knowledge-driven tasks such as news journalism, investigative research, consulting and more. Our evaluations demonstrate that OG-RAG increases the recall of accurate facts by 55% and improves response correctness by 40% across four different LLMs. Additionally, OG-RAG enables 30% faster attribution of responses to context and boosts fact-based reasoning accuracy by 27% compared to baseline methods.

Large language models can interpret natural-language chemistry questions, but their internal reasoning is difficult to inspect, constrain, and validate. This paper presents ChemOntoRule, a proof-of-concept symbolic core for AI-assisted school-level chemistry problem solving. The central design choice is task-centric ontology engineering: the ontology is constructed around the concepts, properties, relations, and executable procedures required by a defined collection of chemistry problems, rather than as a universal representation of chemistry. The implemented artifact combines a lightweight ontology serialized in JSON and RDF/Turtle with deterministic Python rules for electronic structure, periodic trends, oxidation states, oxide and hydride behavior, and related school-level reasoning patterns. A separate expert-coded fallback handles problem families not yet represented by general rules. The system was examined on 300 human-authored and manually validated chemistry problems. The complete system matched 296 of 300 reference answers (98.67%). The ontology-driven rule subset covered 269 problems and matched 266 references (98.88%); 31 problems were handled by task-specific expert-coded fallbacks, with 30 matches. Because the same collection informed ontology construction and evaluation, these results measure implemented coverage and internal consistency, not independent generalization. We analyze the four mismatches, distinguish structural validation from chemical correctness, and define a future architecture in which a language model acts primarily as a translator from user language into a normalized ontological task frame. Token efficiency is presented as a testable hypothesis for future controlled studies, not as a result of the current work.

Embeddings have become a pivotal means to represent complex, multi-faceted information about entities, concepts, and relationships in a condensed and useful format. Nevertheless, they often preclude direct interpretation. While downstream tasks make use of these compressed representations, meaningful interpretation usually requires visualization using dimensionality reduction or specialized machine learning interpretability methods. This paper addresses the challenge of making such embeddings more interpretable and broadly useful, by employing Large Language Models (LLMs) to directly interact with embeddings -- transforming abstract vectors into understandable narratives. By injecting embeddings into LLMs, we enable querying and exploration of complex embedding data. We demonstrate our approach on a variety of diverse tasks, including: enhancing concept activation vectors (CAVs), communicating novel embedded entities, and decoding user preferences in recommender systems. Our work couples the immense information potential of embeddings with the interpretative power of LLMs.

We design a new technique for the distributional semantic modeling with a neural network-based approach to learn distributed term representations (or term embeddings) - term vector space models as a result, inspired by the recent ontology-related approach (using different types of contextual knowledge such as syntactic knowledge, terminological knowledge, semantic knowledge, etc.) to the identification of terms (term extraction) and relations between them (relation extraction) called semantic pre-processing technology - SPT. Our method relies on automatic term extraction from the natural language texts and subsequent formation of the problem-oriented or application-oriented (also deeply annotated) text corpora where the fundamental entity is the term (includes non-compositional and compositional terms). This gives us an opportunity to changeover from distributed word representations (or word embeddings) to distributed term representations (or term embeddings). This transition will allow to generate more accurate semantic maps of different subject domains (also, of relations between input terms - it is useful to explore clusters and oppositions, or to test your hypotheses about them). The semantic map can be represented as a graph using Vec2graph - a Python library for visualizing word embeddings (term embeddings in our case) as dynamic and interactive graphs. The Vec2graph library coupled with term embeddings will not only improve accuracy in solving standard NLP tasks, but also update the conventional concept of automated ontology development. The main practical result of our work is the development kit (set of toolkits represented as web service APIs and web application), which provides all necessary routines for the basic linguistic pre-processing and the semantic pre-processing of the natural language texts in Ukrainian for future training of term vector space models.

Large language models (LLMs) are widely used as general-purpose knowledge sources, but they rely on parametric knowledge, limiting explainability and trustworthiness. In task-oriented dialogue (TOD) systems, this separation is explicit, using an external database structured by an explicit ontology to ensure explainability and controllability. However, building such ontologies requires manual labels or supervised training. We introduce TeQoDO: a Text-to-SQL task-oriented Dialogue Ontology construction method. Here, an LLM autonomously builds a TOD ontology from scratch without supervision using its inherent SQL programming capabilities combined with dialogue theory provided in the prompt. We show that TeQoDO outperforms transfer learning approaches, and its constructed ontology is competitive on a downstream dialogue state tracking task. Ablation studies demonstrate the key role of dialogue theory. TeQoDO also scales to allow construction of much larger ontologies, which we investigate on a Wikipedia and ArXiv dataset. We view this as a step towards broader application of ontologies to increase LLM explainability.

In this paper, we present our approaches for the FinSim-3 Shared Task 2021: Learning Semantic Similarities for the Financial Domain. The aim of this shared task is to correctly classify a list of given terms from the financial domain into the most relevant hypernym (or top-level) concept in an external ontology. For our system submission, we evaluate two methods: a Sentence-RoBERTa (SRoBERTa) embeddings model pre-trained on a custom corpus, and a dual word-sentence embeddings model that builds on the first method by improving the proposed baseline word embeddings construction using the FastText model to boost the classification performance. Our system ranks 2nd overall on both metrics, scoring 0.917 on Average Accuracy and 1.141 on Mean Rank.

Knowledge Graph Embedding (KGE) models are used to learn continuous representations of entities and relations. A key task in the literature is predicting missing links between entities. However, Knowledge Graphs are not just sets of links but also have semantics underlying their structure. Semantics is crucial in several downstream tasks, such as query answering or reasoning. We introduce the subgraph inference task, where a model has to generate likely and semantically valid subgraphs. We propose IntelliGraphs, a set of five new Knowledge Graph datasets. The IntelliGraphs datasets contain subgraphs with semantics expressed in logical rules for evaluating subgraph inference. We also present the dataset generator that produced the synthetic datasets. We designed four novel baseline models, which include three models based on traditional KGEs. We evaluate their expressiveness and show that these models cannot capture the semantics. We believe this benchmark will encourage the development of machine learning models that emphasize semantic understanding.

This work introduces BioLORD, a new pre-training strategy for producing meaningful representations for clinical sentences and biomedical concepts. State-of-the-art methodologies operate by maximizing the similarity in representation of names referring to the same concept, and preventing collapse through contrastive learning. However, because biomedical names are not always self-explanatory, it sometimes results in non-semantic representations. BioLORD overcomes this issue by grounding its concept representations using definitions, as well as short descriptions derived from a multi-relational knowledge graph consisting of biomedical ontologies. Thanks to this grounding, our model produces more semantic concept representations that match more closely the hierarchical structure of ontologies. BioLORD establishes a new state of the art for text similarity on both clinical sentences (MedSTS) and biomedical concepts (MayoSRS).

Ontology Matching (OM) plays an important role in many domains such as bioinformatics and the Semantic Web, and its research is becoming increasingly popular, especially with the application of machine learning (ML) techniques. Although the Ontology Alignment Evaluation Initiative (OAEI) represents an impressive effort for the systematic evaluation of OM systems, it still suffers from several limitations including limited evaluation of subsumption mappings, suboptimal reference mappings, and limited support for the evaluation of ML-based systems. To tackle these limitations, we introduce five new biomedical OM tasks involving ontologies extracted from Mondo and UMLS. Each task includes both equivalence and subsumption matching; the quality of reference mappings is ensured by human curation, ontology pruning, etc.; and a comprehensive evaluation framework is proposed to measure OM performance from various perspectives for both ML-based and non-ML-based OM systems. We report evaluation results for OM systems of different types to demonstrate the usage of these resources, all of which are publicly available as part of the new BioML track at OAEI 2022.

Word embeddings have been shown to be useful across state-of-the-art systems in many natural language processing tasks, ranging from question answering systems to dependency parsing. (Herbelot and Vecchi, 2015) explored word embeddings and their utility for modeling language semantics. In particular, they presented an approach to automatically map a standard distributional semantic space onto a set-theoretic model using partial least squares regression. We show in this paper that a simple baseline achieves a +51% relative improvement compared to their model on one of the two datasets they used, and yields competitive results on the second dataset.

Text embeddings are standard for semantic similarity tasks, yet their evaluation remains an open challenge. Current benchmarks are static, cover only a limited set of languages, are often domain-specific, susceptible to overfitting, and poorly representative of low-resource languages. To address these limitations, we introduce ALEE, a framework that extends Sentence Smith (Li et al., 2025) to the cross-lingual and paragraph level. ALEE uses Abstract Meaning Representations (AMR) to generate English minimal pairs with controlled, fine-grained semantic shifts, which are paired with translations in target languages. This approach enables targeted diagnostics for models in any language with English parallel data. We conduct a large-scale empirical study across a diverse set of embedding models and 275+ languages spanning three parallel datasets. On ALEE, performance varies substantially across languages, text lengths, and linguistic phenomena, exposing persistent gaps in cross-lingual semantic representation that track language prevalence in training resources and subword tokenization. We release ALEE at https://github.com/Andrian0s/any-lang-embed-eval

Biomedical ontology normalization maps free-text expressions to standardized concepts, enabling consistent integration and analysis of biomedical data. This task remains challenging because lexical variation and subtle distinctions among hierarchically related concepts can obscure concept boundaries. We present OntologyAligner, a three-stage framework that combines ontology-aligned retrieval, large language model candidate reranking, and selective hierarchy-guided refinement. We also construct PhenoNormBench, a unified benchmark comprising 13,390 samples from seven Human Phenotype Ontology datasets. OntologyAligner achieved state-of-the-art performance on HPO normalization, with 88.78% Macro Top-1 Accuracy and 86.75% Micro Top-1 Accuracy, exceeding the strongest baseline by 4.85 and 5.07 percentage points, respectively. Ablation analyses showed complementary contributions from all three stages, and sensitivity analyses demonstrated stability across candidate-set sizes and model backbones. Applications to MONDO, MEDIC, and NCBITaxon further established portability to other ontologies. OntologyAligner offers a generalizable framework for accurate mapping of biomedical text to structured ontology concepts. PhenoNormBench and the code are publicly available at https://github.com/zhelishisongjie/OntologyAligner.

This paper introduces a new ontology for Materials Science Laboratory Equipment, termed MSLE. A fundamental issue with materials science laboratory (hereafter lab) equipment in the real world is that scientists work with various types of equipment with multiple specifications. For example, there are many electron microscopes with different parameters in chemical and physical labs. A critical development to unify the description is to build an equipment domain ontology as basic semantic knowledge and to guide the user to work with the equipment appropriately. Here, we propose to develop a consistent ontology for equipment, the MSLE ontology. In the MSLE, two main existing ontologies, the Semantic Sensor Network (SSN) and the Material Vocabulary (MatVoc), have been integrated into the MSLE core to build a coherent ontology. Since various acronyms and terms have been used for equipment, this paper proposes an approach to use a Simple Knowledge Organization System (SKOS) to represent the hierarchical structure of equipment terms. Equipment terms were collected in various languages and abbreviations and coded into the MSLE using the SKOS model. The ontology development was conducted in close collaboration with domain experts and focused on the large-scale devices for materials characterization available in our research group. Competency questions are expected to be addressed through the MSLE ontology. Constraints are modeled in the Shapes Query Language (SHACL); a prototype is shown and validated to show the value of the modeling constraints.

We present NLU++, a novel dataset for natural language understanding (NLU) in task-oriented dialogue (ToD) systems, with the aim to provide a much more challenging evaluation environment for dialogue NLU models, up to date with the current application and industry requirements. NLU++ is divided into two domains (BANKING and HOTELS) and brings several crucial improvements over current commonly used NLU datasets. 1) NLU++ provides fine-grained domain ontologies with a large set of challenging multi-intent sentences, introducing and validating the idea of intent modules that can be combined into complex intents that convey complex user goals, combined with finer-grained and thus more challenging slot sets. 2) The ontology is divided into domain-specific and generic (i.e., domain-universal) intent modules that overlap across domains, promoting cross-domain reusability of annotated examples. 3) The dataset design has been inspired by the problems observed in industrial ToD systems, and 4) it has been collected, filtered and carefully annotated by dialogue NLU experts, yielding high-quality annotated data. Finally, we benchmark a series of current state-of-the-art NLU models on NLU++; the results demonstrate the challenging nature of the dataset, especially in low-data regimes, the validity of `intent modularisation', and call for further research on ToD NLU.

In applications such as personal assistants, large language models (LLMs) must consider the user's personal information and preferences. However, LLMs lack the inherent ability to learn from user interactions. This paper explores capturing personal information from user prompts using ontology and knowledge-graph approaches. We use a subset of the KNOW ontology, which models personal information, to train the language model on these concepts. We then evaluate the success of knowledge capture using a specially constructed dataset. Our code and datasets are publicly available at https://github.com/HaltiaAI/paper-PTODSKC

Machine learning about language can be improved by supplying it with specific knowledge and sources of external information. We present here a new version of the linked open data resource ConceptNet that is particularly well suited to be used with modern NLP techniques such as word embeddings. ConceptNet is a knowledge graph that connects words and phrases of natural language with labeled edges. Its knowledge is collected from many sources that include expert-created resources, crowd-sourcing, and games with a purpose. It is designed to represent the general knowledge involved in understanding language, improving natural language applications by allowing the application to better understand the meanings behind the words people use. When ConceptNet is combined with word embeddings acquired from distributional semantics (such as word2vec), it provides applications with understanding that they would not acquire from distributional semantics alone, nor from narrower resources such as WordNet or DBPedia. We demonstrate this with state-of-the-art results on intrinsic evaluations of word relatedness that translate into improvements on applications of word vectors, including solving SAT-style analogies.

Large Language Models (LLMs) are advancing at a rapid pace, with significant improvements at natural language processing and coding tasks. Yet, their ability to work with formal languages representing data, specifically within the realm of knowledge graph engineering, remains under-investigated. To evaluate the proficiency of various LLMs, we created a set of five tasks that probe their ability to parse, understand, analyze, and create knowledge graphs serialized in Turtle syntax. These tasks, each embodying distinct degrees of complexity and being able to scale with the size of the problem, have been integrated into our automated evaluation system, the LLM-KG-Bench. The evaluation encompassed four commercially available LLMs - GPT-3.5, GPT-4, Claude 1.3, and Claude 2.0, as well as two freely accessible offline models, GPT4All Vicuna and GPT4All Falcon 13B. This analysis offers an in-depth understanding of the strengths and shortcomings of LLMs in relation to their application within RDF knowledge graph engineering workflows utilizing Turtle representation. While our findings show that the latest commercial models outperform their forerunners in terms of proficiency with the Turtle language, they also reveal an apparent weakness. These models fall short when it comes to adhering strictly to the output formatting constraints, a crucial requirement in this context.

Entity linking is a prominent thread of research focused on structured data creation by linking spans of text to an ontology or knowledge source. We revisit the use of structured prediction for entity linking which classifies each individual input token as an entity, and aggregates the token predictions. Our system, called SpEL (Structured prediction for Entity Linking) is a state-of-the-art entity linking system that uses some new ideas to apply structured prediction to the task of entity linking including: two refined fine-tuning steps; a context sensitive prediction aggregation strategy; reduction of the size of the model's output vocabulary, and; we address a common problem in entity-linking systems where there is a training vs. inference tokenization mismatch. Our experiments show that we can outperform the state-of-the-art on the commonly used AIDA benchmark dataset for entity linking to Wikipedia. Our method is also very compute efficient in terms of number of parameters and speed of inference.

Data agents aim to fulfill natural-language instructions over heterogeneous data, including tables, files, and databases. However, data agents face a challenging agent-data gap: heterogeneous data resides outside the agent, while the agent can access it (e.g., column names and file paths) only through generic tools. Existing approaches either let agents directly explore raw data sources or inject manually constructed semantic layers into prompts. However, neither scales well to large heterogeneous data sources nor adapts to different agent behaviors. In this paper, we introduce EvoOntology, a self-evolving ontology layer for data agents. EvoOntology encapsulates the ontology as an MCP server comprising a schema layer, a content layer, and a tool layer, enabling agents to actively query and interact with the ontology at runtime. To this end, we introduce a builder agent for autonomous ontology construction and a self-evolution loop that continuously refines the ontology through attribution-guided typed edits that are accepted only after a backbone-conditional paired evaluation. Experiments on three well-adopted data-agent benchmarks with four LLM backbones demonstrate that EvoOntology consistently outperforms strong baselines and existing semantic-layer approaches, effectively bridging the agent-data gap and enabling more effective interaction with heterogeneous data. Code: https://github.com/ruc-datalab/EvoOntology

Language models and specialized table embedding models have recently demonstrated strong performance on many tasks over tabular data. Researchers and practitioners are keen to leverage these models in many new application contexts; but limited understanding of the strengths and weaknesses of these models, and the table representations they generate, makes the process of finding a suitable model for a given task reliant on trial and error. There is an urgent need to gain a comprehensive understanding of these models to minimize inefficiency and failures in downstream usage. To address this need, we propose Observatory, a formal framework to systematically analyze embedding representations of relational tables. Motivated both by invariants of the relational data model and by statistical considerations regarding data distributions, we define eight primitive properties, and corresponding measures to quantitatively characterize table embeddings for these properties. Based on these properties, we define an extensible framework to evaluate language and table embedding models. We collect and synthesize a suite of datasets and use Observatory to analyze nine such models. Our analysis provides insights into the strengths and weaknesses of learned representations over tables. We find, for example, that some models are sensitive to table structure such as column order, that functional dependencies are rarely reflected in embeddings, and that specialized table embedding models have relatively lower sample fidelity. Such insights help researchers and practitioners better anticipate model behaviors and select appropriate models for their downstream tasks, while guiding researchers in the development of new models.

Word embeddings are an essential instrument in many NLP tasks. Most available resources are trained on general language from Web corpora or Wikipedia dumps. However, word embeddings for domain-specific language are rare, in particular for the social science domain. Therefore, in this work, we describe the creation and evaluation of word embedding models based on 37,604 open-access social science research papers. In the evaluation, we compare domain-specific and general language models for (i) language coverage, (ii) diversity, and (iii) semantic relationships. We found that the created domain-specific model, even with a relatively small vocabulary size, covers a large part of social science concepts, their neighborhoods are diverse in comparison to more general models. Across all relation types, we found a more extensive coverage of semantic relationships.

A key component of deep learning (DL) for natural language processing (NLP) is word embeddings. Word embeddings that effectively capture the meaning and context of the word that they represent can significantly improve the performance of downstream DL models for various NLP tasks. Many existing word embeddings techniques capture the context of words based on word co-occurrence in documents and text; however, they often cannot capture broader domain-specific relationships between concepts that may be crucial for the NLP task at hand. In this paper, we propose a method to integrate external knowledge from medical terminology ontologies into the context captured by word embeddings. Specifically, we use a medical knowledge graph, such as the unified medical language system (UMLS), to find connections between clinical terms in cancer pathology reports. This approach aims to minimize the distance between connected clinical concepts. We evaluate the proposed approach using a Multitask Convolutional Neural Network (MT-CNN) to extract six cancer characteristics -- site, subsite, laterality, behavior, histology, and grade -- from a dataset of ~900K cancer pathology reports. The results show that the MT-CNN model which uses our domain informed embeddings outperforms the same MT-CNN using standard word2vec embeddings across all tasks, with an improvement in the overall micro- and macro-F1 scores by 4.97\%and 22.5\%, respectively.

In this work we will show that language models with less than one billion parameters can be used to translate natural language to SPARQL queries after fine-tuning. Using three different datasets ranging from academic to real world, we identify prerequisites that the training data must fulfill in order for the training to be successful. The goal is to empower users of semantic web technology to use AI assistance with affordable commodity hardware, making them more resilient against external factors.

Schema graphs are an upstream bottleneck of schema-grounded information extraction and knowledge graph construction, yet most extraction systems assume the schema is already available. We introduce SCOPE (Schema Construction and Ontology-induction Pipeline Evaluation), a train-text-only benchmark for corpus-to-schema induction and optional schema fusion from raw text, built from 24 public information extraction sources (15 RE and 9 EE) normalized into evaluation-only gold schema graphs; its core event-extraction target covers event types and within-event argument roles, with inter-event links reported separately. We present SCION (Schema Construction and Induction with Ontology Normalization), an auditable reference pipeline rather than a new extraction architecture; it constructs candidate spaces from train text and restricts naming, merging, filtering, validation, and conservative fusion to candidate-linked evidence under strict JSON contracts. On the SCOPE core suite, SCION-lite attains the highest F1 among released source-schema references, Text2Onto-style, LLM-only, and matched extract-then-aggregate baselines under Literal, Fuzzy, Continuous, and Graph schema-graph metrics, while the compact open-model SCION-RL variant reduces reliance on proprietary LLM schema engineers. These results are reported against normalized typed-edge targets rather than as claims that induced schemas surpass human ontology design; the release includes evidence-linked outputs, parse/fallback logs, candidate retention/merging logs, run manifests, code, and benchmark packages at https://github.com/wandugu/paper_scion.

The core obstacle towards a large-scale deployment of autonomous vehicles currently lies in the long tail of rare events. These are extremely challenging since they do not occur often in the utilized training data for deep neural networks. To tackle this problem, we propose the generation of additional synthetic training data, covering a wide variety of corner case scenarios. As ontologies can represent human expert knowledge while enabling computational processing, we use them to describe scenarios. Our proposed master ontology is capable to model scenarios from all common corner case categories found in the literature. From this one master ontology, arbitrary scenario-describing ontologies can be derived. In an automated fashion, these can be converted into the OpenSCENARIO format and subsequently executed in simulation. This way, also challenging test and evaluation scenarios can be generated.

Conventional representation learning algorithms for knowledge graphs (KG) map each entity to a unique embedding vector. Such a shallow lookup results in a linear growth of memory consumption for storing the embedding matrix and incurs high computational costs when working with real-world KGs. Drawing parallels with subword tokenization commonly used in NLP, we explore the landscape of more parameter-efficient node embedding strategies with possibly sublinear memory requirements. To this end, we propose NodePiece, an anchor-based approach to learn a fixed-size entity vocabulary. In NodePiece, a vocabulary of subword/sub-entity units is constructed from anchor nodes in a graph with known relation types. Given such a fixed-size vocabulary, it is possible to bootstrap an encoding and embedding for any entity, including those unseen during training. Experiments show that NodePiece performs competitively in node classification, link prediction, and relation prediction tasks while retaining less than 10% of explicit nodes in a graph as anchors and often having 10x fewer parameters. To this end, we show that a NodePiece-enabled model outperforms existing shallow models on a large OGB WikiKG 2 graph having 70x fewer parameters.

This paper describes the KnowledgeHub tool, a scientific literature Information Extraction (IE) and Question Answering (QA) pipeline. This is achieved by supporting the ingestion of PDF documents that are converted to text and structured representations. An ontology can then be constructed where a user defines the types of entities and relationships they want to capture. A browser-based annotation tool enables annotating the contents of the PDF documents according to the ontology. Named Entity Recognition (NER) and Relation Classification (RC) models can be trained on the resulting annotations and can be used to annotate the unannotated portion of the documents. A knowledge graph is constructed from these entity and relation triples which can be queried to obtain insights from the data. Furthermore, we integrate a suite of Large Language Models (LLMs) that can be used for QA and summarisation that is grounded in the included documents via a retrieval component. KnowledgeHub is a unique tool that supports annotation, IE and QA, which gives the user full insight into the knowledge discovery pipeline.

The rapid expansion of scientific literature far outpaces the speed of manual curation, creating a fundamental bottleneck in extracting structured knowledge from scientific texts. To address this, we introduce an agentic, ontology-guided framework for knowledge graph (KG) construction. Our framework utilizes specialized agents for document understanding, information extraction, ontology conformance, and entity linking. First, an LLM extracts factual knowledge in the form of triples with explicit textual evidence from research papers. Then the triplets undergo a multistage verification process to ground the triplets in the ontology. By enforcing schema constraints and requiring evidence in the form of text fragments, we ensure the data is both semantically consistent and traceable. In an agreement study over 1,000 extracted triplets, Gemini-2.5-flash achieves Cohen's κ scores of 0.640--0.700 against three human annotators, matching the human--human agreement range of 0.616--0.689. We applied this framework to 2,000 scientific publications and construct a novel, ontology-grounded KG for climate science with 133,990 nodes and 755,308 relations; of the 23,327 triplets that the publications contribute after validation, 98.96\% are judged correct. The pipeline code and KG is publicly available https://github.com/aayushacharya/climatekg.

We present OpenGloss, a synthetic encyclopedic dictionary and semantic knowledge graph for English that integrates lexicographic definitions, encyclopedic context, etymological histories, and semantic relationships in a unified resource. OpenGloss contains 537K senses across 150K lexemes, on par with WordNet 3.1 and Open English WordNet, while providing more than four times as many sense definitions. These lexemes include 9.1M semantic edges, 1M usage examples, 3M collocations, and 60M words of encyclopedic content. Generated through a multi-agent procedural generation pipeline with schema-validated LLM outputs and automated quality assurance, the entire resource was produced in under one week for under $1,000. This demonstrates that structured generation can create comprehensive lexical resources at cost and time scales impractical for manual curation, enabling rapid iteration as foundation models improve. The resource addresses gaps in pedagogical applications by providing integrated content -- definitions, examples, collocations, encyclopedias, etymology -- that supports both vocabulary learning and natural language processing tasks. As a synthetically generated resource, OpenGloss reflects both the capabilities and limitations of current foundation models. The dataset is publicly available on Hugging Face under CC-BY 4.0, enabling researchers and educators to build upon and adapt this resource.

Knowledge graph embedding refers to projecting entities and relations in knowledge graph into continuous vector spaces. State-of-the-art methods, such as TransE, TransH, and TransR build embeddings by treating relation as translation from head entity to tail entity. However, previous models can not deal with reflexive/one-to-many/many-to-one/many-to-many relations properly, or lack of scalability and efficiency. Thus, we propose a novel method, flexible translation, named TransF, to address the above issues. TransF regards relation as translation between head entity vector and tail entity vector with flexible magnitude. To evaluate the proposed model, we conduct link prediction and triple classification on benchmark datasets. Experimental results show that our method remarkably improve the performance compared with several state-of-the-art baselines.

We consider learning representations of entities and relations in KBs using the neural-embedding approach. We show that most existing models, including NTN (Socher et al., 2013) and TransE (Bordes et al., 2013b), can be generalized under a unified learning framework, where entities are low-dimensional vectors learned from a neural network and relations are bilinear and/or linear mapping functions. Under this framework, we compare a variety of embedding models on the link prediction task. We show that a simple bilinear formulation achieves new state-of-the-art results for the task (achieving a top-10 accuracy of 73.2% vs. 54.7% by TransE on Freebase). Furthermore, we introduce a novel approach that utilizes the learned relation embeddings to mine logical rules such as "BornInCity(a,b) and CityInCountry(b,c) => Nationality(a,c)". We find that embeddings learned from the bilinear objective are particularly good at capturing relational semantics and that the composition of relations is characterized by matrix multiplication. More interestingly, we demonstrate that our embedding-based rule extraction approach successfully outperforms a state-of-the-art confidence-based rule mining approach in mining Horn rules that involve compositional reasoning.

Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction towards cognition and human-level intelligence. In this survey, we provide a comprehensive review of knowledge graph covering overall research topics about 1) knowledge graph representation learning, 2) knowledge acquisition and completion, 3) temporal knowledge graph, and 4) knowledge-aware applications, and summarize recent breakthroughs and perspective directions to facilitate future research. We propose a full-view categorization and new taxonomies on these topics. Knowledge graph embedding is organized from four aspects of representation space, scoring function, encoding models, and auxiliary information. For knowledge acquisition, especially knowledge graph completion, embedding methods, path inference, and logical rule reasoning, are reviewed. We further explore several emerging topics, including meta relational learning, commonsense reasoning, and temporal knowledge graphs. To facilitate future research on knowledge graphs, we also provide a curated collection of datasets and open-source libraries on different tasks. In the end, we have a thorough outlook on several promising research directions.

The ability to summarize and organize knowledge into abstract concepts is key to learning and reasoning. Many industrial applications rely on the consistent and systematic use of concepts, especially when dealing with decision-critical knowledge. However, we demonstrate that, when methodically questioned, large language models (LLMs) often display and demonstrate significant inconsistencies in their knowledge. Computationally, the basic aspects of the conceptualization of a given domain can be represented as Is-A hierarchies in a knowledge graph (KG) or ontology, together with a few properties or axioms that enable straightforward reasoning. We show that even simple ontologies can be used to reveal conceptual inconsistencies across several LLMs. We also propose strategies that domain experts can use to evaluate and improve the coverage of key domain concepts in LLMs of various sizes. In particular, we have been able to significantly enhance the performance of LLMs of various sizes with openly available weights using simple knowledge-graph (KG) based prompting strategies.

OpenStreetMap (OSM) is currently the richest publicly available information source on geographic entities (e.g., buildings and roads) worldwide. However, using OSM entities in machine learning models and other applications is challenging due to the large scale of OSM, the extreme heterogeneity of entity annotations, and a lack of a well-defined ontology to describe entity semantics and properties. This paper presents GeoVectors - a unique, comprehensive world-scale linked open corpus of OSM entity embeddings covering the entire OSM dataset and providing latent representations of over 980 million geographic entities in 180 countries. The GeoVectors corpus captures semantic and geographic dimensions of OSM entities and makes these entities directly accessible to machine learning algorithms and semantic applications. We create a semantic description of the GeoVectors corpus, including identity links to the Wikidata and DBpedia knowledge graphs to supply context information. Furthermore, we provide a SPARQL endpoint - a semantic interface that offers direct access to the semantic and latent representations of geographic entities in OSM.

In the large language model (LLM) revolution, embedding is a key component of various systems. For example, it is used to retrieve knowledge or memories for LLMs, to build content moderation filters, etc. As such cases span from English to other natural or programming languages, from retrieval to classification and beyond, it is desirable to build a unified embedding model rather than dedicated ones for each scenario. In this work, we make an initial step towards this goal, demonstrating that multiple languages (both natural and programming) pre-trained transformer decoders can embed universally when finetuned on limited English data. We provide a comprehensive practice with thorough evaluations. On English MTEB, our models achieve competitive performance on different embedding tasks by minimal training data. On other benchmarks, such as multilingual classification and code search, our models (without any supervision) perform comparably to, or even surpass heavily supervised baselines and/or APIs. These results provide evidence of a promising path towards building powerful unified embedders that can be applied across tasks and languages.

Word embeddings are undoubtedly very useful components in many NLP tasks. In this paper, we present word embeddings and other linguistic resources trained on the largest to date digital Greek language corpus. We also present a live web tool for testing the Greek word embeddings, by offering "analogy", "similarity score" and "most similar words" functions. Through our explorer, one could interact with the Greek word vectors.

Creating knowledge bases and ontologies is a time consuming task that relies on a manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrary complex nested knowledge schemas. Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning (ZSL) and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against GPT-3+ to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for all matched elements. We present examples of use of SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease causation graphs. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction (RE) methods, but has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. SPIRES is available as part of the open source OntoGPT package: https://github.com/ monarch-initiative/ontogpt.

Knowledge bases (KBs) and text often contain complementary knowledge: KBs store structured knowledge that can support long range reasoning, while text stores more comprehensive and timely knowledge in an unstructured way. Separately embedding the individual knowledge sources into vector spaces has demonstrated tremendous successes in encoding the respective knowledge, but how to jointly embed and reason with both knowledge sources to fully leverage the complementary information is still largely an open problem. We conduct a large-scale, systematic investigation of aligning KB and text embeddings for joint reasoning. We set up a novel evaluation framework with two evaluation tasks, few-shot link prediction and analogical reasoning, and evaluate an array of KB-text embedding alignment methods. We also demonstrate how such alignment can infuse textual information into KB embeddings for more accurate link prediction on emerging entities and events, using COVID-19 as a case study.

The ever-increasing size of language models curtails their widespread access to the community, thereby galvanizing many companies and startups into offering access to large language models through APIs. One particular API, suitable for dense retrieval, is the semantic embedding API that builds vector representations of a given text. With a growing number of APIs at our disposal, in this paper, our goal is to analyze semantic embedding APIs in realistic retrieval scenarios in order to assist practitioners and researchers in finding suitable services according to their needs. Specifically, we wish to investigate the capabilities of existing APIs on domain generalization and multilingual retrieval. For this purpose, we evaluate the embedding APIs on two standard benchmarks, BEIR, and MIRACL. We find that re-ranking BM25 results using the APIs is a budget-friendly approach and is most effective on English, in contrast to the standard practice, i.e., employing them as first-stage retrievers. For non-English retrieval, re-ranking still improves the results, but a hybrid model with BM25 works best albeit at a higher cost. We hope our work lays the groundwork for thoroughly evaluating APIs that are critical in search and more broadly, in information retrieval.

A person ontology comprising concepts, attributes and relationships of people has a number of applications in data protection, didentification, population of knowledge graphs for business intelligence and fraud prevention. While artificial neural networks have led to improvements in Entity Recognition, Entity Classification, and Relation Extraction, creating an ontology largely remains a manual process, because it requires a fixed set of semantic relations between concepts. In this work, we present a system for automatically populating a person ontology graph from unstructured data using neural models for Entity Classification and Relation Extraction. We introduce a new dataset for these tasks and discuss our results.

Automated insight generation is a common tactic for helping knowledge workers, such as data scientists, to quickly understand the potential value of new and unfamiliar data. Unfortunately, automated insights produced by large-language models can generate code that does not correctly correspond (or align) to the insight. In this paper, we leverage the semantic knowledge of large language models to generate targeted and insightful questions about data and the corresponding code to answer those questions. Then through an empirical study on data from Open-WikiTable, we show that embeddings can be effectively used for filtering out semantically unaligned pairs of question and code. Additionally, we found that generating questions and code together yields more diverse questions.

Most of the major databases on the semantic web have links to Princeton WordNet (PWN) synonym set (synset) identifiers, which differ for each PWN release, and are thus incompatible between versions. On the other hand, both PWN and the more recent Open English Wordnet (OEWN) provide permanent word sense identifiers (the sense keys), which can solve this interoperability problem. We present an algorithm that runs in linear time, to automatically derive a synset mapping between any pair of Wordnet versions that use PWN sense keys. This allows to update old WordNet links, and seamlessly interoperate with newer English Wordnet versions for which no prior mapping exists. By applying the proposed algorithm on the fly, at load time, we combine the Open Multilingual Wordnet (OMW 1.4, which uses old PWN 3.0 identifiers) with OEWN Edition 2021, and obtain almost perfect precision and recall. We compare the results of our approach using respectively synset offsets, versus the Collaborative InterLingual Index (CILI version 1.0) as synset identifiers, and find that the synset offsets perform better than CILI 1.0 in all cases, except a few ties.

With the web getting bigger and assimilating knowledge about different concepts and domains, it is becoming very difficult for simple database driven applications to capture the data for a domain. Thus developers have come out with ontology based systems which can store large amount of information and can apply reasoning and produce timely information. Thus facilitating effective knowledge management. Though this approach has made our lives easier, but at the same time has given rise to another problem. Two different ontologies assimilating same knowledge tend to use different terms for the same concepts. This creates confusion among knowledge engineers and workers, as they do not know which is a better term then the other. Thus we need to merge ontologies working on same domain so that the engineers can develop a better application over it. This paper shows the development of one such matcher which merges the concepts available in two ontologies at two levels; 1) at string level and 2) at semantic level; thus producing better merged ontologies. We have used a graph matching technique which works at the core of the system. We have also evaluated the system and have tested its performance with its predecessor which works only on string matching. Thus current approach produces better results.

Multi-modal Large Language Models (MLLMs) have demonstrated impressive instruction abilities across various open-ended tasks. However, previous methods primarily focus on enhancing multi-modal capabilities. In this work, we introduce a versatile multi-modal large language model, mPLUG-Owl2, which effectively leverages modality collaboration to improve performance in both text and multi-modal tasks. mPLUG-Owl2 utilizes a modularized network design, with the language decoder acting as a universal interface for managing different modalities. Specifically, mPLUG-Owl2 incorporates shared functional modules to facilitate modality collaboration and introduces a modality-adaptive module that preserves modality-specific features. Extensive experiments reveal that mPLUG-Owl2 is capable of generalizing both text tasks and multi-modal tasks and achieving state-of-the-art performances with a single generic model. Notably, mPLUG-Owl2 is the first MLLM model that demonstrates the modality collaboration phenomenon in both pure-text and multi-modal scenarios, setting a pioneering path in the development of future multi-modal foundation models.

Contextual word representations, typically trained on unstructured, unlabeled text, do not contain any explicit grounding to real world entities and are often unable to remember facts about those entities. We propose a general method to embed multiple knowledge bases (KBs) into large scale models, and thereby enhance their representations with structured, human-curated knowledge. For each KB, we first use an integrated entity linker to retrieve relevant entity embeddings, then update contextual word representations via a form of word-to-entity attention. In contrast to previous approaches, the entity linkers and self-supervised language modeling objective are jointly trained end-to-end in a multitask setting that combines a small amount of entity linking supervision with a large amount of raw text. After integrating WordNet and a subset of Wikipedia into BERT, the knowledge enhanced BERT (KnowBert) demonstrates improved perplexity, ability to recall facts as measured in a probing task and downstream performance on relationship extraction, entity typing, and word sense disambiguation. KnowBert's runtime is comparable to BERT's and it scales to large KBs.

By design, word embeddings are unable to model the dynamic nature of words' semantics, i.e., the property of words to correspond to potentially different meanings. To address this limitation, dozens of specialized meaning representation techniques such as sense or contextualized embeddings have been proposed. However, despite the popularity of research on this topic, very few evaluation benchmarks exist that specifically focus on the dynamic semantics of words. In this paper we show that existing models have surpassed the performance ceiling of the standard evaluation dataset for the purpose, i.e., Stanford Contextual Word Similarity, and highlight its shortcomings. To address the lack of a suitable benchmark, we put forward a large-scale Word in Context dataset, called WiC, based on annotations curated by experts, for generic evaluation of context-sensitive representations. WiC is released in https://pilehvar.github.io/wic/.

Failure mode and effects analysis (FMEA) is a critical tool for mitigating potential failures, particular during ramp-up phases of new products. However, its effectiveness is often limited by the missing reasoning capabilities of the FMEA tools, which are usually tabular structured. Meanwhile, large language models (LLMs) offer novel prospects for fine-tuning on custom datasets for reasoning within FMEA contexts. However, LLMs face challenges in tasks that require factual knowledge, a gap that retrieval-augmented generation (RAG) approaches aim to fill. RAG retrieves information from a non-parametric data store and uses a language model to generate responses. Building on this idea, we propose to advance the non-parametric data store with a knowledge graph (KG). By enhancing the RAG framework with a KG, our objective is to leverage analytical and semantic question-answering capabilities on FMEA data. This paper contributes by presenting a new ontology for FMEA observations, an algorithm for creating vector embeddings from the FMEA KG, and a KG enhanced RAG framework. Our approach is validated through a human study and we measure the performance of the context retrieval recall and precision.

The embeddings of entities in a large knowledge base (e.g., Wikipedia) are highly beneficial for solving various natural language tasks that involve real world knowledge. In this paper, we present Wikipedia2Vec, a Python-based open-source tool for learning the embeddings of words and entities from Wikipedia. The proposed tool enables users to learn the embeddings efficiently by issuing a single command with a Wikipedia dump file as an argument. We also introduce a web-based demonstration of our tool that allows users to visualize and explore the learned embeddings. In our experiments, our tool achieved a state-of-the-art result on the KORE entity relatedness dataset, and competitive results on various standard benchmark datasets. Furthermore, our tool has been used as a key component in various recent studies. We publicize the source code, demonstration, and the pretrained embeddings for 12 languages at https://wikipedia2vec.github.io.

Traditional ontologies describe domain structure but cannot generate novel artifacts. Large language models generate fluently but produce outputs lacking structural validity, hallucinating mechanisms without components, goals without end conditions. We introduce Generative Ontology, a framework synthesizing these complementary strengths: ontology provides the grammar; the LLM provides the creativity. Generative Ontology encodes domain knowledge as executable Pydantic schemas constraining LLM generation via DSPy signatures. A multi-agent pipeline assigns specialized roles: a Mechanics Architect designs game systems, a Theme Weaver integrates narrative, a Balance Critic identifies exploits, each carrying a professional "anxiety" that prevents shallow outputs. Retrieval-augmented generation grounds designs in precedents from existing exemplars. We demonstrate the framework through GameGrammar, generating complete tabletop game designs, and present three empirical studies. An ablation study (120 designs, 4 conditions) shows multi-agent specialization produces the largest quality gains (fun d=1.12, depth d=1.59; p<.001), while schema validation eliminates structural errors (d=4.78). A benchmark against 20 published board games reveals structural parity but a bounded creative gap (fun d=1.86): generated designs score 7-8 while published games score 8-9. A test-retest study (50 evaluations) validates the LLM-based evaluator, with 7/9 metrics achieving Good-to-Excellent reliability (ICC 0.836-0.989). The pattern generalizes beyond games. Any domain with expert vocabulary, validity constraints, and accumulated exemplars is a candidate for Generative Ontology.

Pre-trained language representation models (PLMs) cannot well capture factual knowledge from text. In contrast, knowledge embedding (KE) methods can effectively represent the relational facts in knowledge graphs (KGs) with informative entity embeddings, but conventional KE models cannot take full advantage of the abundant textual information. In this paper, we propose a unified model for Knowledge Embedding and Pre-trained LanguagE Representation (KEPLER), which can not only better integrate factual knowledge into PLMs but also produce effective text-enhanced KE with the strong PLMs. In KEPLER, we encode textual entity descriptions with a PLM as their embeddings, and then jointly optimize the KE and language modeling objectives. Experimental results show that KEPLER achieves state-of-the-art performances on various NLP tasks, and also works remarkably well as an inductive KE model on KG link prediction. Furthermore, for pre-training and evaluating KEPLER, we construct Wikidata5M, a large-scale KG dataset with aligned entity descriptions, and benchmark state-of-the-art KE methods on it. It shall serve as a new KE benchmark and facilitate the research on large KG, inductive KE, and KG with text. The source code can be obtained from https://github.com/THU-KEG/KEPLER.

In recent years supervised representation learning has provided state of the art or close to the state of the art results in semantic analysis tasks including ranking and information retrieval. The core idea is to learn how to embed items into a latent space such that they optimize a supervised objective in that latent space. The dimensions of the latent space have no clear semantics, and this reduces the interpretability of the system. For example, in personalization models, it is hard to explain why a particular item is ranked high for a given user profile. We propose a novel model of representation learning called Supervised Explicit Semantic Analysis (SESA) that is trained in a supervised fashion to embed items to a set of dimensions with explicit semantics. The model learns to compare two objects by representing them in this explicit space, where each dimension corresponds to a concept from a knowledge base. This work extends Explicit Semantic Analysis (ESA) with a supervised model for ranking problems. We apply this model to the task of Job-Profile relevance in LinkedIn in which a set of skills defines our explicit dimensions of the space. Every profile and job are encoded to this set of skills their similarity is calculated in this space. We use RNNs to embed text input into this space. In addition to interpretability, our model makes use of the web-scale collaborative skills data that is provided by users for each LinkedIn profile. Our model provides state of the art result while it remains interpretable.

Text representations using neural word embeddings have proven effective in many NLP applications. Recent researches adapt the traditional word embedding models to learn vectors of multiword expressions (concepts/entities). However, these methods are limited to textual knowledge bases (e.g., Wikipedia). In this paper, we propose a novel and simple technique for integrating the knowledge about concepts from two large scale knowledge bases of different structure (Wikipedia and Probase) in order to learn concept representations. We adapt the efficient skip-gram model to seamlessly learn from the knowledge in Wikipedia text and Probase concept graph. We evaluate our concept embedding models on two tasks: (1) analogical reasoning, where we achieve a state-of-the-art performance of 91% on semantic analogies, (2) concept categorization, where we achieve a state-of-the-art performance on two benchmark datasets achieving categorization accuracy of 100% on one and 98% on the other. Additionally, we present a case study to evaluate our model on unsupervised argument type identification for neural semantic parsing. We demonstrate the competitive accuracy of our unsupervised method and its ability to better generalize to out of vocabulary entity mentions compared to the tedious and error prone methods which depend on gazetteers and regular expressions.

Knowledge Bases (KBs) find applications in many knowledge-intensive tasks and, most notably, in information retrieval. Wikidata is one of the largest public general-purpose KBs. Yet, its collaborative nature has led to a convoluted schema and taxonomy. The YAGO 4 KB cleaned up the taxonomy by incorporating the ontology of Schema.org, resulting in a cleaner structure amenable to automated reasoning. However, it also cut away large parts of the Wikidata taxonomy, which is essential for information retrieval. In this paper, we extend YAGO 4 with a large part of the Wikidata taxonomy - while respecting logical constraints and the distinction between classes and instances. This yields YAGO 4.5, a new, logically consistent version of YAGO that adds a rich layer of informative classes. An intrinsic and an extrinsic evaluation show the value of the new resource.

Ontology engineering (OE) in large projects poses a number of challenges arising from the heterogeneous backgrounds of the various stakeholders, domain experts, and their complex interactions with ontology designers. This multi-party interaction often creates systematic ambiguities and biases from the elicitation of ontology requirements, which directly affect the design, evaluation and may jeopardise the target reuse. Meanwhile, current OE methodologies strongly rely on manual activities (e.g., interviews, discussion pages). After collecting evidence on the most crucial OE activities, we introduce OntoChat, a framework for conversational ontology engineering that supports requirement elicitation, analysis, and testing. By interacting with a conversational agent, users can steer the creation of user stories and the extraction of competency questions, while receiving computational support to analyse the overall requirements and test early versions of the resulting ontologies. We evaluate OntoChat by replicating the engineering of the Music Meta Ontology, and collecting preliminary metrics on the effectiveness of each component from users. We release all code at https://github.com/King-s-Knowledge-Graph-Lab/OntoChat.

Semantic Web of Things (SWoT) platforms model physical infrastructure as knowledge graphs typed against domain ontologies, enabling expressive structural and logical queries. However, they lack native mechanisms to express similarity beyond strict ontological equivalence, which represents a critical gap for 3D digital twins in domains such as telecom infrastructure and industrial IoT, where queries must combine ontological constraints with multimodal similarity search over heterogeneous, temporally-evolving scene data. We propose a framework that extends SWoT platforms with a multimodal embedding layer: ontology-typed entities comprising 3D point clouds, temporal attributes, and semantic labels are encoded into latent vector representations stored alongside the knowledge graph, enabling hybrid ontology-vector queries that combine graph-based filtering with similarity search. Implemented on Orange Research's Thing'in platform with the Clock-G temporal graph database, a feasibility evaluation on S3DIS demonstrates that graph filtering effectively restricts the search pool under temporal and relational constraints, and that general-purpose pretrained encoders produce representations sufficient for similarity retrieval and as a preliminary encoding step for downstream predictive tasks.

Previous works on knowledge-to-text generation take as input a few RDF triples or key-value pairs conveying the knowledge of some entities to generate a natural language description. Existing datasets, such as WIKIBIO, WebNLG, and E2E, basically have a good alignment between an input triple/pair set and its output text. However, in practice, the input knowledge could be more than enough, since the output description may only cover the most significant knowledge. In this paper, we introduce a large-scale and challenging dataset to facilitate the study of such a practical scenario in KG-to-text. Our dataset involves retrieving abundant knowledge of various types of main entities from a large knowledge graph (KG), which makes the current graph-to-sequence models severely suffer from the problems of information loss and parameter explosion while generating the descriptions. We address these challenges by proposing a multi-graph structure that is able to represent the original graph information more comprehensively. Furthermore, we also incorporate aggregation methods that learn to extract the rich graph information. Extensive experiments demonstrate the effectiveness of our model architecture.

Entity resolution is a widely studied problem with several proposals to match records across relations. Matching textual content is a widespread task in many applications, such as question answering and search. While recent methods achieve promising results for these two tasks, there is no clear solution for the more general problem of matching textual content and structured data. We introduce a framework that supports this new task in an unsupervised setting for any pair of corpora, being relational tables or text documents. Our method builds a fine-grained graph over the content of the corpora and derives word embeddings to represent the objects to match in a low dimensional space. The learned representation enables effective and efficient matching at different granularity, from relational tuples to text sentences and paragraphs. Our flexible framework can exploit pre-trained resources, but it does not depends on their existence and achieves better quality performance in matching content when the vocabulary is domain specific. We also introduce optimizations in the graph creation process with an "expand and compress" approach that first identifies new valid relationships across elements, to improve matching, and then prunes nodes and edges, to reduce the graph size. Experiments on real use cases and public datasets show that our framework produces embeddings that outperform word embeddings and fine-tuned language models both in results' quality and in execution times.

This paper analyzes the proliferation of cybersecurity ontologies, arguing that this surge cannot be explained solely by technical shortcomings related to quality, but also by a credibility deficit - a lack of trust, endorsement, and adoption by users. This conclusion is based on our first contribution, which is a state-of-the-art review and categorization of cybersecurity ontologies using the Framework for Ontologies Classification framework. To address this gap, we propose a revised framework for assessing credibility, introducing indicators such as institutional support, academic recognition, day-to-day practitioner validation, and industrial adoption. Based on these new credibility indicators, we construct a classification scheme designed to guide the selection of ontologies that are relevant to specific security needs. We then apply this framework to a concrete use case: the Franco-Luxembourgish research project ANCILE, which illustrates how a credibility-aware evaluation can reshape ontology selection for operational contexts.

Current Large Language Models (LLMs) can assist developing program code beside many other things, but can they support working with Knowledge Graphs (KGs) as well? Which LLM is offering the best capabilities in the field of Semantic Web and Knowledge Graph Engineering (KGE)? Is this possible to determine without checking many answers manually? The LLM-KG-Bench framework in Version 3.0 is designed to answer these questions. It consists of an extensible set of tasks for automated evaluation of LLM answers and covers different aspects of working with semantic technologies. In this paper the LLM-KG-Bench framework is presented in Version 3 along with a dataset of prompts, answers and evaluations generated with it and several state-of-the-art LLMs. Significant enhancements have been made to the framework since its initial release, including an updated task API that offers greater flexibility in handling evaluation tasks, revised tasks, and extended support for various open models through the vllm library, among other improvements. A comprehensive dataset has been generated using more than 30 contemporary open and proprietary LLMs, enabling the creation of exemplary model cards that demonstrate the models' capabilities in working with RDF and SPARQL, as well as comparing their performance on Turtle and JSON-LD RDF serialization tasks.

Knowledge graph (KG) embedding has been used to benefit the diagnosis of animal diseases by analyzing electronic medical records (EMRs), such as notes and veterinary records. However, learning representations to capture entities and relations with literal information in KGs is challenging as the KGs show heterogeneous properties and various types of literal information. Meanwhile, the existing methods mostly aim to preserve graph structures surrounding target nodes without considering different types of literals, which could also carry significant information. In this paper, we propose a knowledge graph embedding model for the efficient diagnosis of animal diseases, which could learn various types of literal information and graph structure and fuse them into unified representations, namely LiteralKG. Specifically, we construct a knowledge graph that is built from EMRs along with literal information collected from various animal hospitals. We then fuse different types of entities and node feature information into unified vector representations through gate networks. Finally, we propose a self-supervised learning task to learn graph structure in pretext tasks and then towards various downstream tasks. Experimental results on link prediction tasks demonstrate that our model outperforms the baselines that consist of state-of-the-art models. The source code is available at https://github.com/NSLab-CUK/LiteralKG.

Many mathematical models have been leveraged to design embeddings for representing Knowledge Graph (KG) entities and relations for link prediction and many downstream tasks. These mathematically-inspired models are not only highly scalable for inference in large KGs, but also have many explainable advantages in modeling different relation patterns that can be validated through both formal proofs and empirical results. In this paper, we make a comprehensive overview of the current state of research in KG completion. In particular, we focus on two main branches of KG embedding (KGE) design: 1) distance-based methods and 2) semantic matching-based methods. We discover the connections between recently proposed models and present an underlying trend that might help researchers invent novel and more effective models. Next, we delve into CompoundE and CompoundE3D, which draw inspiration from 2D and 3D affine operations, respectively. They encompass a broad spectrum of techniques including distance-based and semantic-based methods. We will also discuss an emerging approach for KG completion which leverages pre-trained language models (PLMs) and textual descriptions of entities and relations and offer insights into the integration of KGE embedding methods with PLMs for KG completion.

We present a new resource for the NLP community, namely a large (3.5M+ sentence) knowledge base of *generic statements*, e.g., "Trees remove carbon dioxide from the atmosphere", collected from multiple corpora. This is the first large resource to contain *naturally occurring* generic sentences, as opposed to extracted or crowdsourced triples, and thus is rich in high-quality, general, semantically complete statements. All GenericsKB sentences are annotated with their topical term, surrounding context (sentences), and a (learned) confidence. We also release GenericsKB-Best (1M+ sentences), containing the best-quality generics in GenericsKB augmented with selected, synthesized generics from WordNet and ConceptNet. In tests on two existing datasets requiring multihop reasoning (OBQA and QASC), we find using GenericsKB can result in higher scores and better explanations than using a much larger corpus. This demonstrates that GenericsKB can be a useful resource for NLP applications, as well as providing data for linguistic studies of generics and their semantics. GenericsKB is available at https://allenai.org/data/genericskb.

Schemas play a vital role in ensuring data quality and supporting usability in the Semantic Web and natural language processing. Traditionally, their creation demands substantial involvement from knowledge engineers and domain experts. Leveraging the impressive capabilities of large language models (LLMs) in tasks like ontology engineering, we explore schema generation using LLMs. To bridge the resource gap, we introduce two datasets: YAGO Schema and Wikidata EntitySchema, along with novel evaluation metrics. The LLM-based pipelines utilize local and global information from knowledge graphs (KGs) to generate schemas in Shape Expressions (ShEx). Experiments demonstrate LLMs' strong potential in producing high-quality ShEx schemas, paving the way for scalable, automated schema generation for large KGs. Furthermore, our benchmark introduces a new challenge for structured generation, pushing the limits of LLMs on syntactically rich formalisms.

Text embedding has become a foundational technology in natural language processing (NLP) during the deep learning era, driving advancements across a wide array of downstream tasks. While many natural language understanding challenges can now be modeled using generative paradigms and leverage the robust generative and comprehension capabilities of large language models (LLMs), numerous practical applications, such as semantic matching, clustering, and information retrieval, continue to rely on text embeddings for their efficiency and effectiveness. In this survey, we categorize the interplay between LLMs and text embeddings into three overarching themes: (1) LLM-augmented text embedding, enhancing traditional embedding methods with LLMs; (2) LLMs as text embedders, utilizing their innate capabilities for embedding generation; and (3) Text embedding understanding with LLMs, leveraging LLMs to analyze and interpret embeddings. By organizing these efforts based on interaction patterns rather than specific downstream applications, we offer a novel and systematic overview of contributions from various research and application domains in the era of LLMs. Furthermore, we highlight the unresolved challenges that persisted in the pre-LLM era with pre-trained language models (PLMs) and explore the emerging obstacles brought forth by LLMs. Building on this analysis, we outline prospective directions for the evolution of text embedding, addressing both theoretical and practical opportunities in the rapidly advancing landscape of NLP.

Word embeddings are an essential component in a wide range of natural language processing applications. However, distributional semantic models are known to struggle when only a small number of context sentences are available. Several methods have been proposed to obtain higher-quality vectors for these words, leveraging both this context information and sometimes the word forms themselves through a hybrid approach. We show that the current tasks do not suffice to evaluate models that use word-form information, as such models can easily leverage word forms in the training data that are related to word forms in the test data. We introduce 3 new tasks, allowing for a more balanced comparison between models. Furthermore, we show that hyperparameters that have largely been ignored in previous work can consistently improve the performance of both baseline and advanced models, achieving a new state of the art on 4 out of 6 tasks.

Modeling hypernymy, such as poodle is-a dog, is an important generalization aid to many NLP tasks, such as entailment, coreference, relation extraction, and question answering. Supervised learning from labeled hypernym sources, such as WordNet, limits the coverage of these models, which can be addressed by learning hypernyms from unlabeled text. Existing unsupervised methods either do not scale to large vocabularies or yield unacceptably poor accuracy. This paper introduces distributional inclusion vector embedding (DIVE), a simple-to-implement unsupervised method of hypernym discovery via per-word non-negative vector embeddings which preserve the inclusion property of word contexts in a low-dimensional and interpretable space. In experimental evaluations more comprehensive than any previous literature of which we are aware-evaluating on 11 datasets using multiple existing as well as newly proposed scoring functions-we find that our method provides up to double the precision of previous unsupervised embeddings, and the highest average performance, using a much more compact word representation, and yielding many new state-of-the-art results.

In this paper, we explore the capabilities of LLMs in capturing lexical-semantic knowledge from WordNet on the example of the LLaMA-2-7b model and test it on multiple lexical semantic tasks. As the outcome of our experiments, we present TaxoLLaMA, the everything-in-one model, lightweight due to 4-bit quantization and LoRA. It achieves 11 SotA results, 4 top-2 results out of 16 tasks for the Taxonomy Enrichment, Hypernym Discovery, Taxonomy Construction, and Lexical Entailment tasks. Moreover, it demonstrates very strong zero-shot performance on Lexical Entailment and Taxonomy Construction with no fine-tuning. We also explore its hidden multilingual and domain adaptation capabilities with a little tuning or few-shot learning. All datasets, code, and model are available online at https://github.com/VityaVitalich/TaxoLLaMA

Retrieval-Augmented Generation (RAG) systems combine Large Language Models (LLMs) with external knowledge, and their performance depends heavily on how that knowledge is represented. This study investigates how different Knowledge Graph (KG) construction strategies influence RAG performance. We compare a variety of approaches: standard vector-based RAG, GraphRAG, and retrieval over KGs built from ontologies derived either from relational databases or textual corpora. Results show that ontology-guided KGs incorporating chunk information achieve competitive performance with state-of-the-art frameworks, substantially outperforming vector retrieval baselines. Moreover, the findings reveal that ontology-guided KGs built from relational databases perform competitively to ones built with ontologies extracted from text, with the benefit of offering a dual advantage: they require a one-time-only ontology learning process, substantially reducing LLM usage costs; and avoid the complexity of ontology merging inherent to text-based approaches.

Despite the widespread success of self-supervised learning via masked language models (MLM), accurately capturing fine-grained semantic relationships in the biomedical domain remains a challenge. This is of paramount importance for entity-level tasks such as entity linking where the ability to model entity relations (especially synonymy) is pivotal. To address this challenge, we propose SapBERT, a pretraining scheme that self-aligns the representation space of biomedical entities. We design a scalable metric learning framework that can leverage UMLS, a massive collection of biomedical ontologies with 4M+ concepts. In contrast with previous pipeline-based hybrid systems, SapBERT offers an elegant one-model-for-all solution to the problem of medical entity linking (MEL), achieving a new state-of-the-art (SOTA) on six MEL benchmarking datasets. In the scientific domain, we achieve SOTA even without task-specific supervision. With substantial improvement over various domain-specific pretrained MLMs such as BioBERT, SciBERTand and PubMedBERT, our pretraining scheme proves to be both effective and robust.

We present PhiloBERTA, a cross-lingual transformer model that measures semantic relationships between ancient Greek and Latin lexicons. Through analysis of selected term pairs from classical texts, we use contextual embeddings and angular similarity metrics to identify precise semantic alignments. Our results show that etymologically related pairs demonstrate significantly higher similarity scores, particularly for abstract philosophical concepts such as epist\=em\=e (scientia) and dikaiosyn\=e (iustitia). Statistical analysis reveals consistent patterns in these relationships (p = 0.012), with etymologically related pairs showing remarkably stable semantic preservation compared to control pairs. These findings establish a quantitative framework for examining how philosophical concepts moved between Greek and Latin traditions, offering new methods for classical philological research.

Continuous representations of logic formulae allow us to integrate symbolic knowledge into data-driven learning algorithms. If such embeddings are semantically consistent, i.e. if similar specifications are mapped into nearby vectors, they enable continuous learning and optimization directly in the semantic space of formulae. However, to translate the optimal continuous representation into a concrete requirement, such embeddings must be invertible. We tackle this issue by training a Transformer-based decoder-only model to invert semantic embeddings of Signal Temporal Logic (STL) formulae. STL is a powerful formalism that allows us to describe properties of signals varying over time in an expressive yet concise way. By constructing a small vocabulary from STL syntax, we demonstrate that our proposed model is able to generate valid formulae after only 1 epoch and to generalize to the semantics of the logic in about 10 epochs. Additionally, the model is able to decode a given embedding into formulae that are often simpler in terms of length and nesting while remaining semantically close (or equivalent) to gold references. We show the effectiveness of our methodology across various levels of training formulae complexity to assess the impact of training data on the model's ability to effectively capture the semantic information contained in the embeddings and generalize out-of-distribution. Finally, we deploy our model for solving a requirement mining task, i.e. inferring STL specifications that solve a classification task on trajectories, performing the optimization directly in the semantic space.

Knowledge graph is a popular format for representing knowledge, with many applications to semantic search engines, question-answering systems, and recommender systems. Real-world knowledge graphs are usually incomplete, so knowledge graph embedding methods, such as Canonical decomposition/Parallel factorization (CP), DistMult, and ComplEx, have been proposed to address this issue. These methods represent entities and relations as embedding vectors in semantic space and predict the links between them. The embedding vectors themselves contain rich semantic information and can be used in other applications such as data analysis. However, mechanisms in these models and the embedding vectors themselves vary greatly, making it difficult to understand and compare them. Given this lack of understanding, we risk using them ineffectively or incorrectly, particularly for complicated models, such as CP, with two role-based embedding vectors, or the state-of-the-art ComplEx model, with complex-valued embedding vectors. In this paper, we propose a multi-embedding interaction mechanism as a new approach to uniting and generalizing these models. We derive them theoretically via this mechanism and provide empirical analyses and comparisons between them. We also propose a new multi-embedding model based on quaternion algebra and show that it achieves promising results using popular benchmarks. Source code is available on GitHub at https://github.com/tranhungnghiep/AnalyzeKGE.

Embedding-based methods for reasoning in knowledge hypergraphs learn a representation for each entity and relation. Current methods do not capture the procedural rules underlying the relations in the graph. We propose a simple embedding-based model called ReAlE that performs link prediction in knowledge hypergraphs (generalized knowledge graphs) and can represent high-level abstractions in terms of relational algebra operations. We show theoretically that ReAlE is fully expressive and provide proofs and empirical evidence that it can represent a large subset of the primitive relational algebra operations, namely renaming, projection, set union, selection, and set difference. We also verify experimentally that ReAlE outperforms state-of-the-art models in knowledge hypergraph completion, and in representing each of these primitive relational algebra operations. For the latter experiment, we generate a synthetic knowledge hypergraph, for which we design an algorithm based on the Erdos-R'enyi model for generating random graphs.

We present a hybrid methodology for generating large-scale semantic relationship datasets in low-resource languages, demonstrated through a comprehensive Turkish semantic relations corpus. Our approach integrates three phases: (1) FastText embeddings with Agglomerative Clustering to identify semantic clusters, (2) Gemini 2.5-Flash for automated semantic relationship classification, and (3) integration with curated dictionary sources. The resulting dataset comprises 843,000 unique Turkish semantic pairs across three relationship types (synonyms, antonyms, co-hyponyms) representing a 10x scale increase over existing resources at minimal cost ($65). We validate the dataset through two downstream tasks: an embedding model achieving 90% top-1 retrieval accuracy and a classification model attaining 90% F1-macro. Our scalable protocol addresses critical data scarcity in Turkish NLP and demonstrates applicability to other low-resource languages. We publicly release the dataset and models.

The growing power of large language models (LLMs) has revolutionized how people access and utilize information. Notably, the LLMs excel at performing fine-grained data representation, which facilitates precise retrieval of information. They also generate high-quality answers based on external references, enabling the production of useful knowledge. The recent introduction of reasoning models, like OpenAI O1 and DeepSeek R1, marks another leap forward, highlighting LLMs' ability to think progressively before delivering final answers. This breakthrough significantly improves the ability to address complex tasks, e.g., coding and math proofs. Inspired by this progress, we aim to develop similar capabilities for retrieval models, which hold great promise for tackling critical challenges in the field, including multi-task retrieval, zero-shot retrieval, and tasks requiring intensive reasoning of complex relationships. With this motivation, we propose a novel approach called O1 Embedder, which generates useful thoughts for the input query before making retrieval for the target documents. To realize this objective, we conquer two technical difficulties. First, we design a data synthesis workflow, creating training signals for O1 Embedder by generating initial thoughts from an LLM-expert and subsequently refining them using a retrieval committee. Second, we optimize the training process, enabling a pre-trained model to be jointly fine-tuned to generate retrieval thoughts via behavior cloning and perform dense retrieval through contrastive learning. Our approach is evaluated by comprehensive experiments, where substantial improvements are achieved across 12 popular datasets, spanning both in-domain and out-of-domain scenarios. These results highlight O1 Embedder's remarkable accuracy and generalizability, paving the way for the development of next-generation IR foundation models.

One of the main methods for computational interpretation of a text is mapping it into a vector in some embedding space. Such vectors can then be used for a variety of textual processing tasks. Recently, most embedding spaces are a product of training large language models (LLMs). One major drawback of this type of representation is their incomprehensibility to humans. Understanding the embedding space is crucial for several important needs, including the need to debug the embedding method and compare it to alternatives, and the need to detect biases hidden in the model. In this paper, we present a novel method of understanding embeddings by transforming a latent embedding space into a comprehensible conceptual space. We present an algorithm for deriving a conceptual space with dynamic on-demand granularity. We devise a new evaluation method, using either human rater or LLM-based raters, to show that the conceptualized vectors indeed represent the semantics of the original latent ones. We show the use of our method for various tasks, including comparing the semantics of alternative models and tracing the layers of the LLM. The code is available online https://github.com/adiSimhi/Interpreting-Embedding-Spaces-by-Conceptualization.

Digital Twins are digital representations of systems in the Internet of Things (IoT) that are often based on AI models that are trained on data from those systems. Semantic models are used increasingly to link these datasets from different stages of the IoT systems life-cycle together and to automatically configure the AI modelling pipelines. This combination of semantic models with AI pipelines running on external datasets raises unique challenges particular if rolled out at scale. Within this paper we will discuss the unique requirements of applying semantic graphs to automate Digital Twins in different practical use cases. We will introduce the benchmark dataset DTBM that reflects these characteristics and look into the scaling challenges of different knowledge graph technologies. Based on these insights we will propose a reference architecture that is in-use in multiple products in IBM and derive lessons learned for scaling knowledge graphs for configuring AI models for Digital Twins.

The availability of different pre-trained semantic models enabled the quick development of machine learning components for downstream applications. Despite the availability of abundant text data for low resource languages, only a few semantic models are publicly available. Publicly available pre-trained models are usually built as a multilingual version of semantic models that can not fit well for each language due to context variations. In this work, we introduce different semantic models for Amharic. After we experiment with the existing pre-trained semantic models, we trained and fine-tuned nine new different models using a monolingual text corpus. The models are build using word2Vec embeddings, distributional thesaurus (DT), contextual embeddings, and DT embeddings obtained via network embedding algorithms. Moreover, we employ these models for different NLP tasks and investigate their impact. We find that newly trained models perform better than pre-trained multilingual models. Furthermore, models based on contextual embeddings from RoBERTA perform better than the word2Vec models.

Lexical semantics is concerned with both the multiple senses a word can adopt in different contexts, and the semantic relations that exist between meanings of different words. To investigate them, Contextualized Language Models are a valuable tool that provides context-sensitive representations that can be used to investigate lexical meaning. Recent works like XL-LEXEME have leveraged the task of Word-in-Context to fine-tune them to get more semantically accurate representations, but Word-in-Context only compares occurrences of the same lemma, limiting the range of captured information. In this paper, we propose an extension, Concept Differentiation, to include inter-words scenarios. We provide a dataset for this task, derived from SemCor data. Then we fine-tune several representation models on this dataset. We call these models Concept-Aligned Embeddings (CALE). By challenging our models and other models on various lexical semantic tasks, we demonstrate that the proposed models provide efficient multi-purpose representations of lexical meaning that reach best performances in our experiments. We also show that CALE's fine-tuning brings valuable changes to the spatial organization of embeddings.

Large Language Models (LLMs) have recently emerged as a powerful paradigm for Knowledge Graph Completion (KGC), offering strong reasoning and generalization capabilities beyond traditional embedding-based approaches. However, existing LLM-based methods often struggle to fully exploit structured semantic representations, as the continuous embedding space of pretrained KG models is fundamentally misaligned with the discrete token space of LLMs. This discrepancy hinders effective semantic transfer and limits their performance. To address this challenge, we propose ReaLM, a novel and effective framework that bridges the gap between KG embeddings and LLM tokenization through the mechanism of residual vector quantization. ReaLM discretizes pretrained KG embeddings into compact code sequences and integrates them as learnable tokens within the LLM vocabulary, enabling seamless fusion of symbolic and contextual knowledge. Furthermore, we incorporate ontology-guided class constraints to enforce semantic consistency, refining entity predictions based on class-level compatibility. Extensive experiments on two widely used benchmark datasets demonstrate that ReaLM achieves state-of-the-art performance, confirming its effectiveness in aligning structured knowledge with large-scale language models.

The FAIR (Findable, Accessible, Interoperable, and Reusable) data principles [1] promote the interoperability of scientific data by encouraging the use of persistent identifiers, standardized vocabularies, and formal metadata structures. Many resources are created using vocabularies that are FAIR-compliant and well-annotated, yet the collective ecosystem of these resources often fails to interoperate effectively in practice. This continued challenge is mainly due to variation in identifier schemas and data models used in these resources. We have created two tools to bridge the chasm between interoperability in principle and interoperation in practice. Babel solves the problem of multiple identifier schemes by producing a curated set of identifier mappings to create cliques of equivalent identifiers that are exposed through high-performance APIs. ORION solves the problems of multiple data models by ingesting knowledge bases and transforming them into a common, community-managed data model. Here, we describe Babel and ORION and demonstrate their ability to support data interoperation. A library of fully interoperable knowledge bases created through the application of Babel and ORION is available for download and use at https://robokop.renci.org.

We present a new knowledge-base of hasPart relationships, extracted from a large corpus of generic statements. Complementary to other resources available, it is the first which is all three of: accurate (90% precision), salient (covers relationships a person may mention), and has high coverage of common terms (approximated as within a 10 year old's vocabulary), as well as having several times more hasPart entries than in the popular ontologies ConceptNet and WordNet. In addition, it contains information about quantifiers, argument modifiers, and links the entities to appropriate concepts in Wikipedia and WordNet. The knowledge base is available at https://allenai.org/data/haspartkb