Ontologies
Towards a Gateway for Knowledge Graph Schemas Collection, Analysis, and Embedding
Fumagalli, Mattia, Boffo, Marco, Shi, Daqian, Bagchi, Mayukh, Giunchiglia, Fausto
One of the significant barriers to the training of statistical models on knowledge graphs is the difficulty that scientists have in finding the best input data to address their prediction goal. In addition to this, a key challenge is to determine how to manipulate these relational data, which are often in the form of particular triples (i.e., subject, predicate, object), to enable the learning process. Currently, many high-quality catalogs of knowledge graphs, are available. However, their primary goal is the re-usability of these resources, and their interconnection, in the context of the Semantic Web. This paper describes the LiveSchema initiative, namely, a first version of a gateway that has the main scope of leveraging the gold mine of data collected by many existing catalogs collecting relational data like ontologies and knowledge graphs. At the current state, LiveSchema contains - 1000 datasets from 4 main sources and offers some key facilities, which allow to: i) evolving LiveSchema, by aggregating other source catalogs and repositories as input sources; ii) querying all the collected resources; iii) transforming each given dataset into formal concept analysis matrices that enable analysis and visualization services; iv) generating models and tensors from each given dataset.
Knowledge Augmented Machine Learning with Applications in Autonomous Driving: A Survey
Wörmann, Julian, Bogdoll, Daniel, Brunner, Christian, Bührle, Etienne, Chen, Han, Chuo, Evaristus Fuh, Cvejoski, Kostadin, van Elst, Ludger, Gottschall, Philip, Griesche, Stefan, Hellert, Christian, Hesels, Christian, Houben, Sebastian, Joseph, Tim, Keil, Niklas, Kelsch, Johann, Keser, Mert, Königshof, Hendrik, Kraft, Erwin, Kreuser, Leonie, Krone, Kevin, Latka, Tobias, Mattern, Denny, Matthes, Stefan, Motzkus, Franz, Munir, Mohsin, Nekolla, Moritz, Paschke, Adrian, von Pilchau, Stefan Pilar, Pintz, Maximilian Alexander, Qiu, Tianming, Qureishi, Faraz, Rizvi, Syed Tahseen Raza, Reichardt, Jörg, von Rueden, Laura, Sagel, Alexander, Sasdelli, Diogo, Scholl, Tobias, Schunk, Gerhard, Schwalbe, Gesina, Shen, Hao, Shoeb, Youssef, Stapelbroek, Hendrik, Stehr, Vera, Srinivas, Gurucharan, Tran, Anh Tuan, Vivekanandan, Abhishek, Wang, Ya, Wasserrab, Florian, Werner, Tino, Wirth, Christian, Zwicklbauer, Stefan
The availability of representative datasets is an essential prerequisite for many successful artificial intelligence and machine learning models. However, in real life applications these models often encounter scenarios that are inadequately represented in the data used for training. There are various reasons for the absence of sufficient data, ranging from time and cost constraints to ethical considerations. As a consequence, the reliable usage of these models, especially in safety-critical applications, is still a tremendous challenge. Leveraging additional, already existing sources of knowledge is key to overcome the limitations of purely data-driven approaches. Knowledge augmented machine learning approaches offer the possibility of compensating for deficiencies, errors, or ambiguities in the data, thus increasing the generalization capability of the applied models. Even more, predictions that conform with knowledge are crucial for making trustworthy and safe decisions even in underrepresented scenarios. This work provides an overview of existing techniques and methods in the literature that combine data-driven models with existing knowledge. The identified approaches are structured according to the categories knowledge integration, extraction and conformity. In particular, we address the application of the presented methods in the field of autonomous driving.
Ontological Reasoning over Shy and Warded Datalog$+/-$ for Streaming-based Architectures (technical report)
Baldazzi, Teodoro, Bellomarini, Luigi, Favorito, Marco, Sallinger, Emanuel
Recent years witnessed a rising interest towards Datalog-based ontological reasoning systems, both in academia and industry. These systems adopt languages, often shared under the collective name of Datalog$+/-$, that extend Datalog with the essential feature of existential quantification, while introducing syntactic limitations to sustain reasoning decidability and achieve a good trade-off between expressive power and computational complexity. From an implementation perspective, modern reasoners borrow the vast experience of the database community in developing streaming-based data processing systems, such as volcano-iterator architectures, that sustain a limited memory footprint and good scalability. In this paper, we focus on two extremely promising, expressive, and tractable languages, namely, Shy and Warded Datalog$+/-$. We leverage their theoretical underpinnings to introduce novel reasoning techniques, technically, "chase variants", that are particularly fit for efficient reasoning in streaming-based architectures. We then implement them in Vadalog, our reference streaming-based engine, to efficiently solve ontological reasoning tasks over real-world settings.
Using Causal Threads to Explain Changes in a Dynamic System
We explore developing rich semantic models of systems. Specifically, we consider structured causal explanations about state changes in those systems. Essentially, we are developing process-based dynamic knowledge graphs. As an example, we construct a model of the causal threads for geological changes proposed by the Snowball Earth theory. Further, we describe an early prototype of a graphical interface to present the explanations. Unlike statistical approaches to summarization and explanation such as Large Language Models (LLMs), our approach of direct representation can be inspected and verified directly.
From Large Language Models to Knowledge Graphs for Biomarker Discovery in Cancer
Karim, Md. Rezaul, Comet, Lina Molinas, Shajalal, Md, Beyan, Oya Deniz, Rebholz-Schuhmann, Dietrich, Decker, Stefan
Domain experts often rely on most recent knowledge for apprehending and disseminating specific biological processes that help them design strategies for developing prevention and therapeutic decision-making in various disease scenarios. A challenging scenarios for artificial intelligence (AI) is using biomedical data (e.g., texts, imaging, omics, and clinical) to provide diagnosis and treatment recommendations for cancerous conditions.~Data and knowledge about biomedical entities like cancer, drugs, genes, proteins, and their mechanism is spread across structured (knowledge bases (KBs)) and unstructured (e.g., scientific articles) sources. A large-scale knowledge graph (KG) can be constructed by integrating and extracting facts about semantically interrelated entities and relations. Such a KG not only allows exploration and question answering (QA) but also enables domain experts to deduce new knowledge. However, exploring and querying large-scale KGs is tedious for non-domain users due to their lack of understanding of the data assets and semantic technologies. In this paper, we develop a domain KG to leverage cancer-specific biomarker discovery and interactive QA. For this, we constructed a domain ontology called OncoNet Ontology (ONO), which enables semantic reasoning for validating gene-disease (different types of cancer) relations. The KG is further enriched by harmonizing the ONO, metadata, controlled vocabularies, and biomedical concepts from scientific articles by employing BioBERT- and SciBERT-based information extractors. Further, since the biomedical domain is evolving, where new findings often replace old ones, without having access to up-to-date scientific findings, there is a high chance an AI system exhibits concept drift while providing diagnosis and treatment. Therefore, we fine-tune the KG using large language models (LLMs) based on more recent articles and KBs.
Bridging Data-Driven and Knowledge-Driven Approaches for Safety-Critical Scenario Generation in Automated Vehicle Validation
Hao, Kunkun, Liu, Lu, Cui, Wen, Zhang, Jianxing, Yan, Songyang, Pan, Yuxi, Yang, Zijiang
Automated driving vehicles~(ADV) promise to enhance driving efficiency and safety, yet they face intricate challenges in safety-critical scenarios. As a result, validating ADV within generated safety-critical scenarios is essential for both development and performance evaluations. This paper investigates the complexities of employing two major scenario-generation solutions: data-driven and knowledge-driven methods. Data-driven methods derive scenarios from recorded datasets, efficiently generating scenarios by altering the existing behavior or trajectories of traffic participants but often falling short in considering ADV perception; knowledge-driven methods provide effective coverage through expert-designed rules, but they may lead to inefficiency in generating safety-critical scenarios within that coverage. To overcome these challenges, we introduce BridgeGen, a safety-critical scenario generation framework, designed to bridge the benefits of both methodologies. Specifically, by utilizing ontology-based techniques, BridgeGen models the five scenario layers in the operational design domain (ODD) from knowledge-driven methods, ensuring broad coverage, and incorporating data-driven strategies to efficiently generate safety-critical scenarios. An optimized scenario generation toolkit is developed within BridgeGen. This expedites the crafting of safety-critical scenarios through a combination of traditional optimization and reinforcement learning schemes. Extensive experiments conducted using Carla simulator demonstrate the effectiveness of BridgeGen in generating diverse safety-critical scenarios.
Exploring the Consistency, Quality and Challenges in Manual and Automated Coding of Free-text Diagnoses from Hospital Outpatient Letters
Del-Pinto, Warren, Demetriou, George, Jani, Meghna, Patel, Rikesh, Gray, Leanne, Bulcock, Alex, Peek, Niels, Kanter, Andrew S., Dixon, William G, Nenadic, Goran
Coding of unstructured clinical free-text to produce interoperable structured data is essential to improve direct care, support clinical communication and to enable clinical research.However, manual clinical coding is difficult and time consuming, which motivates the development and use of natural language processing for automated coding. This work evaluates the quality and consistency of both manual and automated clinical coding of diagnoses from hospital outpatient letters. Using 100 randomly selected letters, two human clinicians performed coding of diagnosis lists to SNOMED CT. Automated coding was also performed using IMO's Concept Tagger. A gold standard was constructed by a panel of clinicians from a subset of the annotated diagnoses. This was used to evaluate the quality and consistency of both manual and automated coding via (1) a distance-based metric, treating SNOMED CT as a graph, and (2) a qualitative metric agreed upon by the panel of clinicians. Correlation between the two metrics was also evaluated. Comparing human and computer-generated codes to the gold standard, the results indicate that humans slightly out-performed automated coding, while both performed notably better when there was only a single diagnosis contained in the free-text description. Automated coding was considered acceptable by the panel of clinicians in approximately 90% of cases.
Validating ChatGPT Facts through RDF Knowledge Graphs and Sentence Similarity
Mountantonakis, Michalis, Tzitzikas, Yannis
Since ChatGPT offers detailed responses without justifications, and erroneous facts even for popular persons, events and places, in this paper we present a novel pipeline that retrieves the response of ChatGPT in RDF and tries to validate the ChatGPT facts using one or more RDF Knowledge Graphs (KGs). To this end we leverage DBpedia and LODsyndesis (an aggregated Knowledge Graph that contains 2 billion triples from 400 RDF KGs of many domains) and short sentence embeddings, and introduce an algorithm that returns the more relevant triple(s) accompanied by their provenance and a confidence score. This enables the validation of ChatGPT responses and their enrichment with justifications and provenance. To evaluate this service (such services in general), we create an evaluation benchmark that includes 2,000 ChatGPT facts; specifically 1,000 facts for famous Greek Persons, 500 facts for popular Greek Places, and 500 facts for Events related to Greece. The facts were manually labelled (approximately 73% of ChatGPT facts were correct and 27% of facts were erroneous). The results are promising; indicatively for the whole benchmark, we managed to verify the 85.3% of the correct facts of ChatGPT and to find the correct answer for the 58% of the erroneous ChatGPT facts.
Leveraging Activation Maximization and Generative Adversarial Training to Recognize and Explain Patterns in Natural Areas in Satellite Imagery
Emam, Ahmed, Stomberg, Timo T., Roscher, Ribana
Natural protected areas are vital for biodiversity, climate change mitigation, and supporting ecological processes. Despite their significance, comprehensive mapping is hindered by a lack of understanding of their characteristics and a missing land cover class definition. This paper aims to advance the explanation of the designating patterns forming protected and wild areas. To this end, we propose a novel framework that uses activation maximization and a generative adversarial model. With this, we aim to generate satellite images that, in combination with domain knowledge, are capable of offering complete and valid explanations for the spatial and spectral patterns that define the natural authenticity of these regions. Our proposed framework produces more precise attribution maps pinpointing the designating patterns forming the natural authenticity of protected areas. Our approach fosters our understanding of the ecological integrity of the protected natural areas and may contribute to future monitoring and preservation efforts.
Knowledge Graph Representations to enhance Intensive Care Time-Series Predictions
Jain, Samyak, Burger, Manuel, Rätsch, Gunnar, Kuznetsova, Rita
Intensive Care Units (ICU) require comprehensive patient data integration for enhanced clinical outcome predictions, crucial for assessing patient conditions. Recent deep learning advances have utilized patient time series data, and fusion models have incorporated unstructured clinical reports, improving predictive performance. However, integrating established medical knowledge into these models has not yet been explored. The medical domain's data, rich in structural relationships, can be harnessed through knowledge graphs derived from clinical ontologies like the Unified Medical Language System (UMLS) for better predictions. Our proposed methodology integrates this knowledge with ICU data, improving clinical decision modeling. It combines graph representations with vital signs and clinical reports, enhancing performance, especially when data is missing. Additionally, our model includes an interpretability component to understand how knowledge graph nodes affect predictions.