Katja Hose

Maxime Jakubowski, Dominik Tomaszuk, Katja Hose

This paper examines RDF validation practices and challenges to understand stakeholder applications, their needs, and identify areas for improvement in technologies and methodologies, thereby guiding future research and standardization efforts. A community survey was conducted, targeting a diverse group of RDF validation technology users across academia and industry. The survey collected data on current practices, tool usage, perceived benefits, limitations, and desired enhancements to gain a broad overview of the validation landscape. Our analysis shows that while RDF validation is widely adopted and valued for enhancing data quality, significant challenges remain. In particular, users report a need for better documentation, improved tool support, enhanced performance, and greater language expressiveness to handle complex large-scale validation tasks effectively. This work provides crucial insights into the RDF validation landscape, highlighting current practices and key areas for development. It offers a foundation for researchers, developers, and standardization bodies to address current limitations and advance validation technologies, ultimately improving data quality and usability in knowledge graphs.

Andre Lamurias, Alessandro Tibo, Katja Hose et al.

Microbes have a profound impact on our health and environment, but our understanding of the diversity and function of microbial communities is severely limited. Through DNA sequencing of microbial communities (metagenomics), DNA fragments (reads) of the individual microbes can be obtained, which through assembly graphs can be combined into long contiguous DNA sequences (contigs). Given the complexity of microbial communities, single contig microbial genomes are rarely obtained. Instead, contigs are eventually clustered into bins, with each bin ideally making up a full genome. This process is referred to as metagenomic binning. Current state-of-the-art techniques for metagenomic binning rely only on the local features for the individual contigs. These techniques therefore fail to exploit the similarities between contigs as encoded by the assembly graph, in which the contigs are organized. In this paper, we propose to use Graph Neural Networks (GNNs) to leverage the assembly graph when learning contig representations for metagenomic binning. Our method, VaeG-Bin, combines variational autoencoders for learning latent representations of the individual contigs, with GNNs for refining these representations by taking into account the neighborhood structure of the contigs in the assembly graph. We explore several types of GNNs and demonstrate that VaeG-Bin recovers more high-quality genomes than other state-of-the-art binners on both simulated and real-world datasets.

Mossad Helali, Niki Monjazeb, Shubham Vashisth et al.

In recent years, we have witnessed the growing interest from academia and industry in applying data science technologies to analyze large amounts of data. In this process, a myriad of artifacts (datasets, pipeline scripts, etc.) are created. However, there has been no systematic attempt to holistically collect and exploit all the knowledge and experiences that are implicitly contained in those artifacts. Instead, data scientists recover information and expertise from colleagues or learn via trial and error. Hence, this paper presents a scalable platform, KGLiDS, that employs machine learning and knowledge graph technologies to abstract and capture the semantics of data science artifacts and their connections. Based on this information, KGLiDS enables various downstream applications, such as data discovery and pipeline automation. Our comprehensive evaluation covers use cases in data discovery, data cleaning, transformation, and AutoML. It shows that KGLiDS is significantly faster with a lower memory footprint than the state-of-the-art systems while achieving comparable or better accuracy.

Emil Riis Hansen, Thomas Dyhre Nielsen, Thomas Mulvad et al.

Predicting patients hospital length of stay (LOS) is essential for improving resource allocation and supporting decision-making in healthcare organizations. This paper proposes a novel approach for predicting LOS by modeling patient information as sequences of events. Specifically, we present a transformer-based model, termed Medic-BERT (M-BERT), for LOS prediction using the unique features describing patients medical event sequences. We performed empirical experiments on a cohort of more than 45k emergency care patients from a large Danish hospital. Experimental results show that M-BERT can achieve high accuracy on a variety of LOS problems and outperforms traditional nonsequence-based machine learning approaches.

Ikhtiyor Nematov, Dimitris Sacharidis, Tomer Sagi et al.

This study explores the impact of class outliers on the effectiveness of example-based explainability methods for black-box machine learning models. We reformulate existing explainability evaluation metrics, such as correctness and relevance, specifically for example-based methods, and introduce a new metric, distinguishability. Using these metrics, we highlight the shortcomings of current example-based explainability methods, including those who attempt to suppress class outliers. We conduct experiments on two datasets, a text classification dataset and an image classification dataset, and evaluate the performance of four state-of-the-art explainability methods. Our findings underscore the need for robust techniques to tackle the challenges posed by class outliers.

Ikhtiyor Nematov, Dimitris Sacharidis, Tomer Sagi et al.

For many use-cases, it is often important to explain the prediction of a black-box model by identifying the most influential training data samples. Existing approaches lack customization for user intent and often provide a homogeneous set of explanation samples, failing to reveal the model's reasoning from different angles. In this paper, we propose AIDE, an approach for providing antithetical (i.e., contrastive), intent-based, diverse explanations for opaque and complex models. AIDE distinguishes three types of explainability intents: interpreting a correct, investigating a wrong, and clarifying an ambiguous prediction. For each intent, AIDE selects an appropriate set of influential training samples that support or oppose the prediction either directly or by contrast. To provide a succinct summary, AIDE uses diversity-aware sampling to avoid redundancy and increase coverage of the training data. We demonstrate the effectiveness of AIDE on image and text classification tasks, in three ways: quantitatively, assessing correctness and continuity; qualitatively, comparing anecdotal evidence from AIDE and other example-based approaches; and via a user study, evaluating multiple aspects of AIDE. The results show that AIDE addresses the limitations of existing methods and exhibits desirable traits for an explainability method.

Johannes Schrott, Maxime Jakubowski, Katja Hose

In recent years, knowledge graphs (KGs) - in particular in the form of labeled property graphs (LPGs) - have become essential components in a broad range of applications. Although the absence of strict schemas for KGs facilitates structural issues that lead to redundancies and subsequently to inconsistencies and anomalies, the problem of KG quality has so far received only little attention. Inspired by normalization using functional dependencies for relational data, a first approach exploiting dependencies within nodes has been proposed. However, real-world KGs also expose functional dependencies involving edges. In this paper, we therefore propose graph-native normalization, which considers dependencies within nodes, edges, and their combination. We define a range of graph-native normal forms and graph object functional dependencies and propose algorithms for transforming graphs accordingly. We evaluate our contributions using a broad range of synthetic and native graph datasets.

Milos Jovanovik, Marija Vecovska, Maxime Jakubowski et al.

Developing and testing modern RDF-based applications often requires access to RDF datasets with certain characteristics. Unfortunately, it is very difficult to publicly find domain-specific knowledge graphs that conform to a particular set of characteristics. Hence, in this paper we propose RDFGraphGen, an open-source RDF graph generator that uses characteristics provided in the form of SHACL (Shapes Constraint Language) shapes to generate synthetic RDF graphs. RDFGraphGen is domain-agnostic, with configurable graph structure, value constraints, and distributions. It also comes with a number of predefined values for popular schema.org classes and properties, for more realistic graphs. Our results show that RDFGraphGen is scalable and can generate small, medium, and large RDF graphs in any domain.

Anders H. Brams, Anders L. Jakobsen, Theis E. Jendal et al.

Knowledge Graphs (KGs) have been integrated in several models of recommendation to augment the informational value of an item by means of its related entities in the graph. Yet, existing datasets only provide explicit ratings on items and no information is provided about user opinions of other (non-recommendable) entities. To overcome this limitation, we introduce a new dataset, called the MindReader, providing explicit user ratings both for items and for KG entities. In this first version, the MindReader dataset provides more than 102 thousands explicit ratings collected from 1,174 real users on both items and entities from a KG in the movie domain. This dataset has been collected through an online interview application that we also release open source. As a demonstration of the importance of this new dataset, we present a comparative study of the effect of the inclusion of ratings on non-item KG entities in a variety of state-of-the-art recommendation models. In particular, we show that most models, whether designed specifically for graph data or not, see improvements in recommendation quality when trained on explicit non-item ratings. Moreover, for some models, we show that non-item ratings can effectively replace item ratings without loss of recommendation quality. This finding, thanks also to an observed greater familiarity of users towards common KG entities than towards long-tail items, motivates the use of KG entities for both warm and cold-start recommendations.

Antheas Kapenekakis, Bent Thomsen, Katja Hose et al.

To generate synthetic datasets, e.g., in domains such as healthcare, the literature proposes approaches of two main types: Probabilistic Graphical Models (PGMs) and Deep Learning models, such as LLMs. While PGMs produce synthetic data that can be used for advanced analytics, they do not support complex schemas and datasets. LLMs on the other hand, support complex schemas but produce skewed dataset distributions, which are less useful for advanced analytics. In this paper, we therefore present Amalgam, a hybrid LLM-PGM data synthesis algorithm supporting both advanced analytics, realism, and tangible privacy properties. We show that Amalgam synthesizes data with an average 91 % $χ^2 P$ value and scores 3.8/5 for realism using our proposed metric, where state-of-the-art is 3.3 and real data is 4.7.

Ernests Lavrinovics, Russa Biswas, Johannes Bjerva et al.

Large Language Models (LLMs) have revolutionized Natural Language Processing (NLP) based applications including automated text generation, question answering, chatbots, and others. However, they face a significant challenge: hallucinations, where models produce plausible-sounding but factually incorrect responses. This undermines trust and limits the applicability of LLMs in different domains. Knowledge Graphs (KGs), on the other hand, provide a structured collection of interconnected facts represented as entities (nodes) and their relationships (edges). In recent research, KGs have been leveraged to provide context that can fill gaps in an LLM understanding of certain topics offering a promising approach to mitigate hallucinations in LLMs, enhancing their reliability and accuracy while benefiting from their wide applicability. Nonetheless, it is still a very active area of research with various unresolved open problems. In this paper, we discuss these open challenges covering state-of-the-art datasets and benchmarks as well as methods for knowledge integration and evaluating hallucinations. In our discussion, we consider the current use of KGs in LLM systems and identify future directions within each of these challenges.

Ernests Lavrinovics, Russa Biswas, Katja Hose et al.

Large Language Models (LLMs) have inherent limitations of faithfulness and factuality, commonly referred to as hallucinations. Several benchmarks have been developed that provide a test bed for factuality evaluation within the context of English-centric datasets, while relying on supplementary informative context like web links or text passages but ignoring the available structured factual resources. To this end, Knowledge Graphs (KGs) have been identified as a useful aid for hallucination mitigation, as they provide a structured way to represent the facts about entities and their relations with minimal linguistic overhead. We bridge the lack of KG paths and multilinguality for factual language modeling within the existing hallucination evaluation benchmarks and propose a KG-based multilingual, multihop benchmark called MultiHal framed for generative text evaluation. As part of our data collection pipeline, we mined 140k KG-paths from open-domain KGs, from which we pruned noisy KG-paths, curating a high-quality subset of 25.9k. Our baseline evaluation shows an absolute scale improvement by approximately 0.12 to 0.36 points for the semantic similarity score, 0.16 to 0.36 for NLI entailment and 0.29 to 0.42 for hallucination detection in KG-RAG over vanilla QA across multiple languages and multiple models, demonstrating the potential of KG integration. We anticipate MultiHal will foster future research towards several graph-based hallucination mitigation and fact-checking tasks.

Ansgar Scherp, Gerd Groener, Petr Škoda et al.

Ever since the vision was formulated, the Semantic Web has inspired many generations of innovations. Semantic technologies have been used to share vast amounts of information on the Web, enhance them with semantics to give them meaning, and enable inference and reasoning on them. Throughout the years, semantic technologies, and in particular knowledge graphs, have been used in search engines, data integration, enterprise settings, and machine learning. In this paper, we recap the classical concepts and foundations of the Semantic Web as well as modern and recent concepts and applications, building upon these foundations. The classical topics we cover include knowledge representation, creating and validating knowledge on the Web, reasoning and linking, and distributed querying. We enhance this classical view of the so-called ``Semantic Web Layer Cake'' with an update of recent concepts. These include provenance, security and trust, as well as a discussion of practical impacts from industry-led contributions. We also provide an overiew of shallow and deep machine learning methods for knowledge graphs and discuss the relation of language models and knowledge graphs. We conclude with an outlook on the future directions of the Semantic Web.

Ikhtiyor Nematov, Tarik Kalai, Elizaveta Kuzmenko et al.

While attribution methods, such as Shapley values, are widely used to explain the importance of features or training data in traditional machine learning, their application to Large Language Models (LLMs), particularly within Retrieval-Augmented Generation (RAG) systems, is nascent and challenging. The primary obstacle is the substantial computational cost, where each utility function evaluation involves an expensive LLM call, resulting in direct monetary and time expenses. This paper investigates the feasibility and effectiveness of adapting Shapley-based attribution to identify influential retrieved documents in RAG. We compare Shapley with more computationally tractable approximations and some existing attribution methods for LLM. Our work aims to: (1) systematically apply established attribution principles to the RAG document-level setting; (2) quantify how well SHAP approximations can mirror exact attributions while minimizing costly LLM interactions; and (3) evaluate their practical explainability in identifying critical documents, especially under complex inter-document relationships such as redundancy, complementarity, and synergy. This study seeks to bridge the gap between powerful attribution techniques and the practical constraints of LLM-based RAG systems, offering insights into achieving reliable and affordable RAG explainability.

Piero A. Bonatti, John Domingue, Anna Lisa Gentile et al.

Computer-Using Agents (CUA) enable users to automate increasingly-complex tasks using graphical interfaces such as browsers. As many potential tasks require personal data, we propose Computer-Using Personal Agents (CUPAs) that have access to an external repository of the user's personal data. Compared with CUAs, CUPAs offer users better control of their personal data, the potential to automate more tasks involving personal data, better interoperability with external sources of data, and better capabilities to coordinate with other CUPAs in order to solve collaborative tasks involving the personal data of multiple users.

Essam Mansour, Kavitha Srinivas, Katja Hose

Similar to Open Data initiatives, data science as a community has launched initiatives for sharing not only data but entire pipelines, derivatives, artifacts, etc. (Open Data Science). However, the few efforts that exist focus on the technical part on how to facilitate sharing, conversion, etc. This vision paper goes a step further and proposes KEK, an open federated data science platform that does not only allow for sharing data science pipelines and their (meta)data but also provides methods for efficient search and, in the ideal case, even allows for combining and defining pipelines across platforms in a federated manner. In doing so, KEK addresses the so far neglected challenge of actually finding artifacts that are semantically related and that can be combined to achieve a certain goal.