Daily Papers

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.

The synergy between symbolic knowledge, often represented by Knowledge Graphs (KGs), and the generative capabilities of neural networks is central to advancing neurosymbolic AI. A primary bottleneck in realizing this potential is the difficulty of automating KG construction, which faces challenges related to output reliability, consistency, and verifiability. These issues can manifest as structural inconsistencies within the generated graphs, such as the formation of disconnected isolated islands of data or the inaccurate conflation of abstract classes with specific instances. To address these challenges, we propose HyDRA, a Hybrid-Driven Reasoning Architecture designed for verifiable KG automation. Given a domain or an initial set of documents, HyDRA first constructs an ontology via a panel of collaborative neurosymbolic agents. These agents collaboratively agree on a set of competency questions (CQs) that define the scope and requirements the ontology must be able to answer. Given these CQs, we build an ontology graph that subsequently guides the automated extraction of triplets for KG generation from arbitrary documents. Inspired by design-by-contracts (DbC) principles, our method leverages verifiable contracts as the primary control mechanism to steer the generative process of Large Language Models (LLMs). To verify the output of our approach, we extend beyond standard benchmarks and propose an evaluation framework that assesses the functional correctness of the resulting KG by leveraging symbolic verifications as described by the neurosymbolic AI framework, SymbolicAI. This work contributes a hybrid-driven architecture for improving the reliability of automated KG construction and the exploration of evaluation methods for measuring the functional integrity of its output. The code is publicly available.

In recent years, graph representation learning has undergone a paradigm shift, driven by the emergence and proliferation of graph neural networks (GNNs) and their heterogeneous counterparts. Heterogeneous GNNs have shown remarkable success in extracting low-dimensional embeddings from complex graphs that encompass diverse entity types and relationships. While meta-path-based techniques have long been recognized for their ability to capture semantic affinities among nodes, their dependence on manual specification poses a significant limitation. In contrast, matrix-focused methods accelerate processing by utilizing structural cues but often overlook contextual richness. In this paper, we challenge the current paradigm by introducing ontology as a fundamental semantic primitive within complex graphs. Our goal is to integrate the strengths of both matrix-centric and meta-path-based approaches into a unified framework. We propose perturbation Ontology-based Graph Attention Networks (POGAT), a novel methodology that combines ontology subgraphs with an advanced self-supervised learning paradigm to achieve a deep contextual understanding. The core innovation of POGAT lies in our enhanced homogeneous perturbing scheme designed to generate rigorous negative samples, encouraging the model to explore minimal contextual features more thoroughly. Through extensive empirical evaluations, we demonstrate that POGAT significantly outperforms state-of-the-art baselines, achieving a groundbreaking improvement of up to 10.78\% in F1-score for the critical task of link prediction and 12.01\% in Micro-F1 for the critical task of node classification.

Knowledge Graph-to-Text (G2T) generation involves verbalizing structured knowledge graphs into natural language text. Recent advancements in Pretrained Language Models (PLMs) have improved G2T performance, but their effectiveness depends on datasets with precise graph-text alignment. However, the scarcity of high-quality, general-domain G2T generation datasets restricts progress in the general-domain G2T generation research. To address this issue, we introduce Wikipedia Ontology-Free Graph-text dataset (WikiOFGraph), a new large-scale G2T dataset generated using a novel method that leverages Large Language Model (LLM) and Data-QuestEval. Our new dataset, which contains 5.85M general-domain graph-text pairs, offers high graph-text consistency without relying on external ontologies. Experimental results demonstrate that PLM fine-tuned on WikiOFGraph outperforms those trained on other datasets across various evaluation metrics. Our method proves to be a scalable and effective solution for generating high-quality G2T data, significantly advancing the field of G2T generation.

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.

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.

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.

Knowledge graphs (KGs) provide structured, verifiable grounding for large language models (LLMs), but current LLM-based systems commonly use KGs as auxiliary structures for text retrieval, leaving their intrinsic quality underexplored. In this work, we propose Wikontic, a multi-stage pipeline that constructs KGs from open-domain text by extracting candidate triplets with qualifiers, enforcing Wikidata-based type and relation constraints, and normalizing entities to reduce duplication. The resulting KGs are compact, ontology-consistent, and well-connected; on MuSiQue, the correct answer entity appears in 96% of generated triplets. On HotpotQA, our triplets-only setup achieves 76.0 F1, and on MuSiQue 59.8 F1, matching or surpassing several retrieval-augmented generation baselines that still require textual context. In addition, Wikontic attains state-of-the-art information-retention performance on the MINE-1 benchmark (86%), outperforming prior KG construction methods. Wikontic is also efficient at build time: KG construction uses less than 1,000 output tokens, about 3times fewer than AriGraph and <1/20 of GraphRAG. The proposed pipeline enhances the quality of the generated KG and offers a scalable solution for leveraging structured knowledge in LLMs.

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

Recommender systems (RS) are currently being studied to mitigate limitations during cold-start conditions by leveraging modality information or introducing Agent concepts based on the exceptional reasoning capabilities of Large Language Models (LLMs). Meanwhile, food and beverage recommender systems have traditionally used knowledge graph and ontology concepts due to the domain's unique data attributes and relationship characteristics. On this background, we propose MARC, a multimodal and multi-task cocktail recommender system based on Agentic Retrieval-Augmented Generation (RAG) utilizing graph database under cold-start conditions. The proposed system generates high-quality, contextually appropriate answers through two core processes: a task recognition router and a reflection process. The graph database was constructed by processing cocktail data from Kaggle, and its effectiveness was evaluated using 200 manually crafted questions. The evaluation used both LLM-as-a-judge and human evaluation to demonstrate that answers generated via the graph database outperformed those from a simple vector database in terms of quality. The code is available at https://github.com/diddbwls/cocktail_rec_agentrag

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.

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.

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.

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet clinical uptake requires regulator-ready interpretability. We present the first technical survey of interpretable graph based models for multimodal biomedical data, covering 26 studies published between Jan 2019 and Sep 2024. Most target disease classification, notably cancer and rely on static graphs from simple similarity measures, while graph-native explainers are rare; post-hoc methods adapted from non-graph domains such as gradient saliency, and SHAP predominate. We group existing approaches into four interpretability families, outline trends such as graph-in-graph hierarchies, knowledge-graph edges, and dynamic topology learning, and perform a practical benchmark. Using an Alzheimer disease cohort, we compare Sensitivity Analysis, Gradient Saliency, SHAP and Graph Masking. SHAP and Sensitivity Analysis recover the broadest set of known AD pathways and Gene-Ontology terms, whereas Gradient Saliency and Graph Masking surface complementary metabolic and transport signatures. Permutation tests show all four beat random gene sets, but with distinct trade-offs: SHAP and Graph Masking offer deeper biology at higher compute cost, while Gradient Saliency and Sensitivity Analysis are quicker though coarser. We also provide a step-by-step flowchart covering graph construction, explainer choice and resource budgeting to help researchers balance transparency and performance. This review synthesises the state of interpretable graph learning for multimodal medicine, benchmarks leading techniques, and charts future directions, from advanced XAI tools to under-studied diseases, serving as a concise reference for method developers and translational scientists.

In this work we study various Retrieval Augmented Regeneration (RAG) approaches to gain an understanding of the strengths and weaknesses of each approach in a question-answering analysis. To gain this understanding we use a case-study subset of the Global Database of Events, Language, and Tone (GDELT) dataset as well as a corpus of raw text scraped from the online news articles. To retrieve information from the text corpus we implement a traditional vector store RAG as well as state-of-the-art large language model (LLM) based approaches for automatically constructing KGs and retrieving the relevant subgraphs. In addition to these corpus approaches, we develop a novel ontology-based framework for constructing knowledge graphs (KGs) from GDELT directly which leverages the underlying schema of GDELT to create structured representations of global events. For retrieving relevant information from the ontology-based KGs we implement both direct graph queries and state-of-the-art graph retrieval approaches. We compare the performance of each method in a question-answering task. We find that while our ontology-based KGs are valuable for question-answering, automated extraction of the relevant subgraphs is challenging. Conversely, LLM-generated KGs, while capturing event summaries, often lack consistency and interpretability. Our findings suggest benefits of a synergistic approach between ontology and LLM-based KG construction, with proposed avenues toward that end.

Knowledge graphs (KGs) generated by large language models (LLMs) are becoming increasingly valuable for Retrieval-Augmented Generation (RAG) applications that require knowledge-intensive reasoning. However, existing KG extraction methods predominantly rely on prompt-based approaches, which are inefficient for processing large-scale corpora. These approaches often suffer from information loss, particularly with long documents, due to the lack of specialized design for KG construction. Additionally, there is a gap in evaluation datasets and methodologies for ontology-free KG construction. To overcome these limitations, we propose SynthKG, a multi-step, document-level ontology-free KG synthesis workflow based on LLMs. By fine-tuning a smaller LLM on the synthesized document-KG pairs, we streamline the multi-step process into a single-step KG generation approach called Distill-SynthKG, substantially reducing the number of LLM inference calls. Furthermore, we re-purpose existing question-answering datasets to establish KG evaluation datasets and introduce new evaluation metrics. Using KGs produced by Distill-SynthKG, we also design a novel graph-based retrieval framework for RAG. Experimental results demonstrate that Distill-SynthKG not only surpasses all baseline models in KG quality -- including models up to eight times larger -- but also consistently excels in retrieval and question-answering tasks. Our proposed graph retrieval framework also outperforms all KG-retrieval methods across multiple benchmark datasets. We release the SynthKG dataset and Distill-SynthKG model publicly to support further research and development.

LLMs usually exhibit limitations in their ability to incorporate new knowledge, the generation of hallucinations, and the transparency of their decision-making process. In this paper, we explore how to prompt LLMs with knowledge graphs (KG), working as a remedy to engage LLMs with up-to-date knowledge and elicit the reasoning pathways from LLMs. Specifically, we build a prompting pipeline that endows LLMs with the capability of comprehending KG inputs and inferring with a combined implicit knowledge and the retrieved external knowledge. In addition, we investigate eliciting the mind map on which LLMs perform the reasoning and generate the answers. It is identified that the produced mind map exhibits the reasoning pathways of LLMs grounded on the ontology of knowledge, hence bringing the prospects of probing and gauging LLM inference in production. The experiments on three question & answering datasets also show that MindMap prompting leads to a striking empirical gain. For instance, prompting a GPT-3.5 with MindMap yields an overwhelming performance over GPT-4 consistently. We also demonstrate that with structured facts retrieved from KG, MindMap can outperform a series of prompting-with-document-retrieval methods, benefiting from more accurate, concise, and comprehensive knowledge from KGs. To reproduce our results and extend the framework further, we make our codebase available at https://github.com/wyl.willing/MindMap.

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

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

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.

Biomedical knowledge graphs (BioMedKGs) are essential infrastructures for biomedical and healthcare big data and artificial intelligence (AI), facilitating natural language processing, model development, and data exchange. For decades, these knowledge graphs have been developed via expert curation; however, this method can no longer keep up with today's AI development, and a transition to algorithmically generated BioMedKGs is necessary. In this work, we introduce the Biomedical Informatics Ontology System (BIOS), the first large-scale publicly available BioMedKG generated completely by machine learning algorithms. BIOS currently contains 4.1 million concepts, 7.4 million terms in two languages, and 7.3 million relation triplets. We present the methodology for developing BIOS, including the curation of raw biomedical terms, computational identification of synonymous terms and aggregation of these terms to create concept nodes, semantic type classification of the concepts, relation identification, and biomedical machine translation. We provide statistics on the current BIOS content and perform preliminary assessments of term quality, synonym grouping, and relation extraction. The results suggest that machine learning-based BioMedKG development is a viable alternative to traditional expert curation.

Ontologies and knowledge graphs (KGs) are general-purpose computable representations of some domain, such as human anatomy, and are frequently a crucial part of modern information systems. Most of these structures change over time, incorporating new knowledge or information that was previously missing. Managing these changes is a challenge, both in terms of communicating changes to users, and providing mechanisms to make it easier for multiple stakeholders to contribute. To fill that need, we have created KGCL, the Knowledge Graph Change Language, a standard data model for describing changes to KGs and ontologies at a high level, and an accompanying human-readable controlled natural language. This language serves two purposes: a curator can use it to request desired changes, and it can also be used to describe changes that have already happened, corresponding to the concepts of "apply patch" and "diff" commonly used for managing changes in text documents and computer programs. Another key feature of KGCL is that descriptions are at a high enough level to be useful and understood by a variety of stakeholders--for example, ontology edits can be specified by commands like "add synonym 'arm' to 'forelimb'" or "move 'Parkinson disease' under 'neurodegenerative disease'". We have also built a suite of tools for managing ontology changes. These include an automated agent that integrates with and monitors GitHub ontology repositories and applies any requested changes, and a new component in the BioPortal ontology resource that allows users to make change requests directly from within the BioPortal user interface. Overall, the KGCL data model, its controlled natural language, and associated tooling allow for easier management and processing of changes associated with the development of ontologies and KGs.

Besides entity-centric knowledge, usually organized as Knowledge Graph (KG), events are also an essential kind of knowledge in the world, which trigger the spring up of event-centric knowledge representation form like Event KG (EKG). It plays an increasingly important role in many downstream applications, such as search, question-answering, recommendation, financial quantitative investments, and text generation. This paper provides a comprehensive survey of EKG from history, ontology, instance, and application views. Specifically, to characterize EKG thoroughly, we focus on its history, definition, schema induction, acquisition, related representative graphs/systems, and applications. The development processes and trends are studied therein. We further summarize prospective directions to facilitate future research on EKG.

Zero-shot Learning (ZSL), which aims to predict for those classes that have never appeared in the training data, has arisen hot research interests. The key of implementing ZSL is to leverage the prior knowledge of classes which builds the semantic relationship between classes and enables the transfer of the learned models (e.g., features) from training classes (i.e., seen classes) to unseen classes. However, the priors adopted by the existing methods are relatively limited with incomplete semantics. In this paper, we explore richer and more competitive prior knowledge to model the inter-class relationship for ZSL via ontology-based knowledge representation and semantic embedding. Meanwhile, to address the data imbalance between seen classes and unseen classes, we developed a generative ZSL framework with Generative Adversarial Networks (GANs). Our main findings include: (i) an ontology-enhanced ZSL framework that can be applied to different domains, such as image classification (IMGC) and knowledge graph completion (KGC); (ii) a comprehensive evaluation with multiple zero-shot datasets from different domains, where our method often achieves better performance than the state-of-the-art models. In particular, on four representative ZSL baselines of IMGC, the ontology-based class semantics outperform the previous priors e.g., the word embeddings of classes by an average of 12.4 accuracy points in the standard ZSL across two example datasets (see Figure 4).

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.

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.

Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified communities and connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. The graph has an inherently scale-free nature, is highly connected, and can be used for graph reasoning by taking advantage of transitive and isomorphic properties that reveal unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. We compute deep node embeddings for combinatorial node similarity ranking for use in a path sampling strategy links dissimilar concepts that have previously not been related. One comparison revealed structural parallels between biological materials and Beethoven's 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed a hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky's 'Composition VII' painting. The resulting material integrates an innovative set of concepts that include a balance of chaos/order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.

Enterprise applications of Large Language Models (LLMs) hold promise for question answering on enterprise SQL databases. However, the extent to which LLMs can accurately respond to enterprise questions in such databases remains unclear, given the absence of suitable Text-to-SQL benchmarks tailored to enterprise settings. Additionally, the potential of Knowledge Graphs (KGs) to enhance LLM-based question answering by providing business context is not well understood. This study aims to evaluate the accuracy of LLM-powered question answering systems in the context of enterprise questions and SQL databases, while also exploring the role of knowledge graphs in improving accuracy. To achieve this, we introduce a benchmark comprising an enterprise SQL schema in the insurance domain, a range of enterprise queries encompassing reporting to metrics, and a contextual layer incorporating an ontology and mappings that define a knowledge graph. Our primary finding reveals that question answering using GPT-4, with zero-shot prompts directly on SQL databases, achieves an accuracy of 16%. Notably, this accuracy increases to 54% when questions are posed over a Knowledge Graph representation of the enterprise SQL database. Therefore, investing in Knowledge Graph provides higher accuracy for LLM powered question answering systems.

In this paper, we present a new theoretical approach for enabling domain knowledge acquisition by intelligent systems. We introduce a hybrid model that starts with minimal input knowledge in the form of an upper ontology of concepts, stores and reasons over this knowledge through a knowledge graph database and learns new information through a Logic Neural Network. We study the behavior of this architecture when handling new data and show that the final system is capable of enriching its current knowledge as well as extending it to new domains.

There is increasing evidence that question-answering (QA) systems with Large Language Models (LLMs), which employ a knowledge graph/semantic representation of an enterprise SQL database (i.e. Text-to-SPARQL), achieve higher accuracy compared to systems that answer questions directly on SQL databases (i.e. Text-to-SQL). Our previous benchmark research showed that by using a knowledge graph, the accuracy improved from 16% to 54%. The question remains: how can we further improve the accuracy and reduce the error rate? Building on the observations of our previous research where the inaccurate LLM-generated SPARQL queries followed incorrect paths, we present an approach that consists of 1) Ontology-based Query Check (OBQC): detects errors by leveraging the ontology of the knowledge graph to check if the LLM-generated SPARQL query matches the semantic of ontology and 2) LLM Repair: use the error explanations with an LLM to repair the SPARQL query. Using the chat with the data benchmark, our primary finding is that our approach increases the overall accuracy to 72% including an additional 8% of "I don't know" unknown results. Thus, the overall error rate is 20%. These results provide further evidence that investing knowledge graphs, namely the ontology, provides higher accuracy for LLM powered question answering systems.

Despite the progress in automatic detection of radiologic findings from chest X-ray (CXR) images in recent years, a quantitative evaluation of the explainability of these models is hampered by the lack of locally labeled datasets for different findings. With the exception of a few expert-labeled small-scale datasets for specific findings, such as pneumonia and pneumothorax, most of the CXR deep learning models to date are trained on global "weak" labels extracted from text reports, or trained via a joint image and unstructured text learning strategy. Inspired by the Visual Genome effort in the computer vision community, we constructed the first Chest ImaGenome dataset with a scene graph data structure to describe 242,072 images. Local annotations are automatically produced using a joint rule-based natural language processing (NLP) and atlas-based bounding box detection pipeline. Through a radiologist constructed CXR ontology, the annotations for each CXR are connected as an anatomy-centered scene graph, useful for image-level reasoning and multimodal fusion applications. Overall, we provide: i) 1,256 combinations of relation annotations between 29 CXR anatomical locations (objects with bounding box coordinates) and their attributes, structured as a scene graph per image, ii) over 670,000 localized comparison relations (for improved, worsened, or no change) between the anatomical locations across sequential exams, as well as ii) a manually annotated gold standard scene graph dataset from 500 unique patients.

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.