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Maria-Esther Vidal

Publications and source records attributed to Maria-Esther Vidal.

At least 19 recordsLinked to original sources

BLINKG: A Benchmark for LLM-Integrated Knowledge Graph Generation

Generating Knowledge Graphs (KGs) remains one of the most time-consuming and labor-intensive tasks for knowledge engineers, as they need to identify semantic equivalences between input data sources and ontology terms. While declarative solutions (e.g., RML, SPARQL-Anything) have helped to generalize this process, aligning input schema elements with ontology terms still involves intricate transformations and requires considerable manual effort. With the advent of Large Language Models (LLMs), there is growing interest in leveraging their capabilities to assist KG engineers. Although some studies have explored using LLMs to automate KG construction, there is still no standardized framework for assessing how effectively they establish correspondences between data schemes and ontology concepts. Therefore, in this paper, we propose BLINKG, a benchmark designed to evaluate the mapping capabilities of LLMs in constructing KGs from heterogeneous data sources. The benchmark includes a set of scenarios with increasing complexity, based on real-world use cases. We conduct an extensive experimental evaluation of several stateof-the-art LLMs using BLINK and observe that they already offer promising solutions. However, their performance remains limited in complex scenarios. Thanks to this benchmark, we can already assess the current capabilities of LLMs for KG construction. Additionally, we define a set of requirements for achieving (semi)automated (LLM-driven) KG construction, opening new research lines in this area.

cs.AI

Semantic Web: Past, Present, and Future (with Machine Learning on Knowledge Graphs and Language Models on Knowledge Graphs)

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.

cs.AI

Articulation Work and Tinkering for Fairness in Machine Learning

The field of fair AI aims to counter biased algorithms through computational modelling. However, it faces increasing criticism for perpetuating the use of overly technical and reductionist methods. As a result, novel approaches appear in the field to address more socially-oriented and interdisciplinary (SOI) perspectives on fair AI. In this paper, we take this dynamic as the starting point to study the tension between computer science (CS) and SOI research. By drawing on STS and CSCW theory, we position fair AI research as a matter of 'organizational alignment': what makes research 'doable' is the successful alignment of three levels of work organization (the social world, the laboratory, and the experiment). Based on qualitative interviews with CS researchers, we analyze the tasks, resources, and actors required for doable research in the case of fair AI. We find that CS researchers engage with SOI research to some extent, but organizational conditions, articulation work, and ambiguities of the social world constrain the doability of SOI research for them. Based on our findings, we identify and discuss problems for aligning CS and SOI as fair AI continues to evolve.

cs.CY

iASiS: Towards Heterogeneous Big Data Analysis for Personalized Medicine

The vision of IASIS project is to turn the wave of big biomedical data heading our way into actionable knowledge for decision makers. This is achieved by integrating data from disparate sources, including genomics, electronic health records and bibliography, and applying advanced analytics methods to discover useful patterns. The goal is to turn large amounts of available data into actionable information to authorities for planning public health activities and policies. The integration and analysis of these heterogeneous sources of information will enable the best decisions to be made, allowing for diagnosis and treatment to be personalised to each individual. The project offers a common representation schema for the heterogeneous data sources. The iASiS infrastructure is able to convert clinical notes into usable data, combine them with genomic data, related bibliography, image data and more, and create a global knowledge base. This facilitates the use of intelligent methods in order to discover useful patterns across different resources. Using semantic integration of data gives the opportunity to generate information that is rich, auditable and reliable. This information can be used to provide better care, reduce errors and create more confidence in sharing data, thus providing more insights and opportunities. Data resources for two different disease categories are explored within the iASiS use cases, dementia and lung cancer.

cs.AI

Leveraging Ontologies to Document Bias in Data

Machine Learning (ML) systems are capable of reproducing and often amplifying undesired biases. This puts emphasis on the importance of operating under practices that enable the study and understanding of the intrinsic characteristics of ML pipelines, prompting the emergence of documentation frameworks with the idea that ``any remedy for bias starts with awareness of its existence''. However, a resource that can formally describe these pipelines in terms of biases detected is still amiss. To fill this gap, we present the Doc-BiasO ontology, a resource that aims to create an integrated vocabulary of biases defined in the \textit{fair-ML} literature and their measures, as well as to incorporate relevant terminology and the relationships between them. Overseeing ontology engineering best practices, we re-use existing vocabulary on machine learning and AI, to foster knowledge sharing and interoperability between the actors concerned with its research, development, regulation, among others. Overall, our main objective is to contribute towards clarifying existing terminology on bias research as it rapidly expands to all areas of AI and to improve the interpretation of bias in data and downstream impact.

cs.AI

Traditional Machine Learning Models and Bidirectional Encoder Representations From Transformer (BERT)-Based Automatic Classification of Tweets About Eating Disorders: Algorithm Development and Validation Study

Background: Eating disorders are increasingly prevalent, and social networks offer valuable information. Objective: Our goal was to identify efficient machine learning models for categorizing tweets related to eating disorders. Methods: Over three months, we collected tweets about eating disorders. A 2,000-tweet subset was labeled for: (1) being written by individuals with eating disorders, (2) promoting eating disorders, (3) informativeness, and (4) scientific content. Both traditional machine learning and deep learning models were employed for classification, assessing accuracy, F1 score, and computational time. Results: From 1,058,957 collected tweets, transformer-based bidirectional encoder representations achieved the highest F1 scores (71.1%-86.4%) across all four categories. Conclusions: Transformer-based models outperform traditional techniques in classifying eating disorder-related tweets, though they require more computational resources.

cs.CL

Empowering machine learning models with contextual knowledge for enhancing the detection of eating disorders in social media posts

Social networks are vital for information sharing, especially in the health sector for discussing diseases and treatments. These platforms, however, often feature posts as brief texts, posing challenges for Artificial Intelligence (AI) in understanding context. We introduce a novel hybrid approach combining community-maintained knowledge graphs (like Wikidata) with deep learning to enhance the categorization of social media posts. This method uses advanced entity recognizers and linkers (like Falcon 2.0) to connect short post entities to knowledge graphs. Knowledge graph embeddings (KGEs) and contextualized word embeddings (like BERT) are then employed to create rich, context-based representations of these posts. Our focus is on the health domain, particularly in identifying posts related to eating disorders (e.g., anorexia, bulimia) to aid healthcare providers in early diagnosis. We tested our approach on a dataset of 2,000 tweets about eating disorders, finding that merging word embeddings with knowledge graph information enhances the predictive models' reliability. This methodology aims to assist health experts in spotting patterns indicative of mental disorders, thereby improving early detection and accurate diagnosis for personalized medicine.

cs.LG

Trust, Accountability, and Autonomy in Knowledge Graph-based AI for Self-determination

Knowledge Graphs (KGs) have emerged as fundamental platforms for powering intelligent decision-making and a wide range of Artificial Intelligence (AI) services across major corporations such as Google, Walmart, and AirBnb. KGs complement Machine Learning (ML) algorithms by providing data context and semantics, thereby enabling further inference and question-answering capabilities. The integration of KGs with neuronal learning (e.g., Large Language Models (LLMs)) is currently a topic of active research, commonly named neuro-symbolic AI. Despite the numerous benefits that can be accomplished with KG-based AI, its growing ubiquity within online services may result in the loss of self-determination for citizens as a fundamental societal issue. The more we rely on these technologies, which are often centralised, the less citizens will be able to determine their own destinies. To counter this threat, AI regulation, such as the European Union (EU) AI Act, is being proposed in certain regions. The regulation sets what technologists need to do, leading to questions concerning: How can the output of AI systems be trusted? What is needed to ensure that the data fuelling and the inner workings of these artefacts are transparent? How can AI be made accountable for its decision-making? This paper conceptualises the foundational topics and research pillars to support KG-based AI for self-determination. Drawing upon this conceptual framework, challenges and opportunities for citizen self-determination are illustrated and analysed in a real-world scenario. As a result, we propose a research agenda aimed at accomplishing the recommended objectives.

cs.AI

Scaling Up Knowledge Graph Creation to Large and Heterogeneous Data Sources

RDF knowledge graphs (KG) are powerful data structures to represent factual statements created from heterogeneous data sources. KG creation is laborious and demands data management techniques to be executed efficiently. This paper tackles the problem of the automatic generation of KG creation processes declaratively specified; it proposes techniques for planning and transforming heterogeneous data into RDF triples following mapping assertions specified in the RDF Mapping Language (RML). Given a set of mapping assertions, the planner provides an optimized execution plan by partitioning and scheduling the execution of the assertions. First, the planner assesses an optimized number of partitions considering the number of data sources, type of mapping assertions, and the associations between different assertions. After providing a list of partitions and assertions that belong to each partition, the planner determines their execution order. A greedy algorithm is implemented to generate the partitions' bushy tree execution plan. Bushy tree plans are translated into operating system commands that guide the execution of the partitions of the mapping assertions in the order indicated by the bushy tree. The proposed optimization approach is evaluated over state-of-the-art RML-compliant engines, and existing benchmarks of data sources and RML triples maps. Our experimental results suggest that the performance of the studied engines can be considerably improved, particularly in a complex setting with numerous triples maps and large data sources. As a result, engines that time out in complex cases are enabled to produce at least a portion of the KG applying the planner.

cs.AI

Dragoman: Efficiently Evaluating Declarative Mapping Languages over Frameworks for Knowledge Graph Creation

In recent years, there have been valuable efforts and contributions to make the process of RDF knowledge graph creation traceable and transparent; extending and applying declarative mapping languages is an example. One challenging step is the traceability of procedures that aim to overcome interoperability issues, a.k.a. data-level integration. In most pipelines, data integration is performed by ad-hoc programs, preventing traceability and reusability. However, formal frameworks provided by function-based declarative mapping languages such as FunUL and RML+FnO empower expressiveness. Data-level integration can be defined as functions and integrated as part of the mappings performing schema-level integration. However, combining functions with the mappings introduces a new source of complexity that can considerably impact the required number of resources and execution time. We tackle the problem of efficiently executing mappings with functions and formalize the transformation of them into function-free mappings. These transformations are the basis of an optimization process that aims to perform an eager evaluation of function-based mapping rules. These techniques are implemented in a framework named Dragoman. We demonstrate the correctness of the transformations while ensuring that the function-free data integration processes are equivalent to the original one. The effectiveness of Dragoman is empirically evaluated in 230 testbeds composed of various types of functions integrated with mapping rules of different complexity. The outcomes suggest that evaluating function-free mapping rules reduces execution time in complex knowledge graph creation pipelines composed of large data sources and multiple types of mapping rules. The savings can be up to 75%, suggesting that eagerly executing functions in mapping rules enable making these pipelines applicable and scalable in real-world settings.

cs.DB

Knowledge4COVID-19: A Semantic-based Approach for Constructing a COVID-19 related Knowledge Graph from Various Sources and Analysing Treatments' Toxicities

In this paper, we present Knowledge4COVID-19, a framework that aims to showcase the power of integrating disparate sources of knowledge to discover adverse drug effects caused by drug-drug interactions among COVID-19 treatments and pre-existing condition drugs. Initially, we focus on constructing the Knowledge4COVID-19 knowledge graph (KG) from the declarative definition of mapping rules using the RDF Mapping Language. Since valuable information about drug treatments, drug-drug interactions, and side effects is present in textual descriptions in scientific databases (e.g., DrugBank) or in scientific literature (e.g., the CORD-19, the Covid-19 Open Research Dataset), the Knowledge4COVID-19 framework implements Natural Language Processing. The Knowledge4COVID-19 framework extracts relevant entities and predicates that enable the fine-grained description of COVID-19 treatments and the potential adverse events that may occur when these treatments are combined with treatments of common comorbidities, e.g., hypertension, diabetes, or asthma. Moreover, on top of the KG, several techniques for the discovery and prediction of interactions and potential adverse effects of drugs have been developed with the aim of suggesting more accurate treatments for treating the virus. We provide services to traverse the KG and visualize the effects that a group of drugs may have on a treatment outcome. Knowledge4COVID-19 was part of the Pan-European hackathon#EUvsVirus in April 2020 and is publicly available as a resource through a GitHub repository (https://github.com/SDM-TIB/Knowledge4COVID-19) and a DOI (https://zenodo.org/record/4701817#.YH336-8zbol).

cs.DB

Efficient Semantic Summary Graphs for Querying Large Knowledge Graphs

Knowledge Graphs (KGs) integrate heterogeneous data, but one challenge is the development of efficient tools for allowing end users to extract useful insights from these sources of knowledge. In such a context, reducing the size of a Resource Description Framework (RDF) graph while preserving all information can speed up query engines by limiting data shuffle, especially in a distributed setting. This paper presents two algorithms for RDF graph summarization: Grouping Based Summarization (GBS) and Query Based Summarization (QBS). The latter is an optimized and lossless approach for the former method. We empirically study the effectiveness of the proposed lossless RDF graph summarization to retrieve complete data, by rewriting an RDF Query Language called SPARQL query with fewer triple patterns using a semantic similarity. We conduct our experimental study in instances of four datasets with different sizes. Compared with the state-of-the-art query engine Sparklify executed over the original RDF graphs as a baseline, QBS query execution time is reduced by up to 80% and the summarized RDF graph is decreased by up to 99%.

cs.DB

EABlock: A Declarative Entity Alignment Block for Knowledge Graph Creation Pipelines

Despite encoding enormous amount of rich and valuable data, existing data sources are mostly created independently, being a significant challenge to their integration. Mapping languages, e.g., RML and R2RML, facilitate declarative specification of the process of applying meta-data and integrating data into a knowledge graph. Mapping rules can also include knowledge extraction functions in addition to expressing correspondences among data sources and a unified schema. Combining mapping rules and functions represents a powerful formalism to specify pipelines for integrating data into a knowledge graph transparently. Surprisingly, these formalisms are not fully adapted, and many knowledge graphs are created by executing ad-hoc programs to pre-process and integrate data. In this paper, we present EABlock, an approach integrating Entity Alignment (EA) as part of RML mapping rules. EABlock includes a block of functions performing entity recognition from textual attributes and link the recognized entities to the corresponding resources in Wikidata, DBpedia, and domain specific thesaurus, e.g., UMLS. EABlock provides agnostic and efficient techniques to evaluate the functions and transfer the mappings to facilitate its application in any RML-compliant engine. We have empirically evaluated EABlock performance, and results indicate that EABlock speeds up knowledge graph creation pipelines that require entity recognition and linking in state-of-the-art RML-compliant engines. EABlock is also publicly available as a tool through a GitHub repository(https://github.com/SDM-TIB/EABlock) and a DOI(https://doi.org/10.5281/zenodo.5779773).

cs.AI

Analyzing a Knowledge Graph of Industry4.0 Standards

In this article, we tackle the problem of standard interoperability across different standardization frameworks, and devise a knowledge-driven approach that allows for the description of standards and standardization frameworks into an Industry 4.0 knowledge graph (I40KG). The STO ontology represents properties of standards and standardization frameworks, as well as relationships among them. The I40KG integrates more than 200 standards and four standardization frameworks. To populate the I40KG, the landscape of standards has been analyzed from a semantic perspective and the resulting I40KG represents knowledge expressed in more than 200 industrial related documents including technical reports, research articles, and white papers. Additionally, the I40KG has been linked to existing knowledge graphs and an automated reasoning has been implemented to reveal implicit relations between standards as well as mappings across standardization frameworks. We analyze both the number of discovered relations between standards and the accuracy of these relations. Observed results indicate that both reasoning and linking processes enable for increasing the connectivity in the knowledge graph by up to 80%, whilst up to 96% of the relations can be validated. These outcomes suggest that integrating standards and standardization frameworks into the I40KG enables the resolution of semantic interoperability conflicts, empowering the communication in smart factories.

cs.DL

Knowledge-driven Data Ecosystems Towards Data Transparency

A Data Ecosystem offers a keystone-player or alliance-driven infrastructure that enables the interaction of different stakeholders and the resolution of interoperability issues among shared data. However, despite years of research in data governance and management, trustability is still affected by the absence of transparent and traceable data-driven pipelines. In this work, we focus on requirements and challenges that data ecosystems face when ensuring data transparency. Requirements are derived from the data and organizational management, as well as from broader legal and ethical considerations. We propose a novel knowledge-driven data ecosystem architecture, providing the pillars for satisfying the analyzed requirements. We illustrate the potential of our proposal in a real-world scenario. Lastly, we discuss and rate the potential of the proposed architecture in the fulfillment of these requirements.

cs.DB

Enhancing Virtual Ontology Based Access over Tabular Data with Morph-CSV

Ontology-Based Data Access (OBDA) has traditionally focused on providing a unified view of heterogeneous datasets, either by materializing integrated data into RDF or by performing on-the fly querying via SPARQL query translation. In the specific case of tabular datasets represented as several CSV or Excel files, query translation approaches have been applied by considering each source as a single table that can be loaded into a relational database management system (RDBMS). Nevertheless, constraints over these tables are not represented; thus, neither consistency among attributes nor indexes over tables are enforced. As a consequence, efficiency of the SPARQL-to-SQL translation process may be affected, as well as the completeness of the answers produced during the evaluation of the generated SQL query. Our work is focused on applying implicit constraints on the OBDA query translation process over tabular data. We propose Morph-CSV, a framework for querying tabular data that exploits information from typical OBDA inputs (e.g., mappings, queries) to enforce constraints that can be used together with any SPARQL-to-SQL OBDA engine. Morph-CSV relies on both a constraint component and a set of constraint operators. For a given set of constraints, the operators are applied to each type of constraint with the aim of enhancing query completeness and performance. We evaluate Morph-CSV in several domains: e-commerce with the BSBM benchmark; transportation with a benchmark using the GTFS dataset from the Madrid subway; and biology with a use case extracted from the Bio2RDF project. We compare and report the performance of two SPARQL-to-SQL OBDA engines, without and with the incorporation of MorphCSV. The observed results suggest that Morph-CSV is able to speed up the total query execution time by up to two orders of magnitude, while it is able to produce all the query answers.

cs.DB

Trav-SHACL: Efficiently Validating Networks of SHACL Constraints

Knowledge graphs have emerged as expressive data structures for Web data. Knowledge graph potential and the demand for ecosystems to facilitate their creation, curation, and understanding, is testified in diverse domains, e.g., biomedicine. The Shapes Constraint Language (SHACL) is the W3C recommendation language for integrity constraints over RDF knowledge graphs. Enabling quality assements of knowledge graphs, SHACL is rapidly gaining attention in real-world scenarios. SHACL models integrity constraints as a network of shapes, where a shape contains the constraints to be fullfiled by the same entities. The validation of a SHACL shape schema can face the issue of tractability during validation. To facilitate full adoption, efficient computational methods are required. We present Trav-SHACL, a SHACL engine capable of planning the traversal and execution of a shape schema in a way that invalid entities are detected early and needless validations are minimized. Trav-SHACL reorders the shapes in a shape schema for efficient validation and rewrites target and constraint queries for the fast detection of invalid entities. Trav-SHACL is empirically evaluated on 27 testbeds executed against knowledge graphs of up to 34M triples. Our experimental results suggest that Trav-SHACL exhibits high performance gradually and reduces validation time by a factor of up to 28.93 compared to the state of the art.

cs.DB

Compact Representations for Efficient Storage of Semantic Sensor Data

Nowadays, there is a rapid increase in the number of sensor data generated by a wide variety of sensors and devices. Data semantics facilitate information exchange, adaptability, and interoperability among several sensors and devices. Sensor data and their meaning can be described using ontologies, e.g., the Semantic Sensor Network (SSN) Ontology. Notwithstanding, semantically enriched, the size of semantic sensor data is substantially larger than raw sensor data. Moreover, some measurement values can be observed by sensors several times, and a huge number of repeated facts about sensor data can be produced. We propose a compact or factorized representation of semantic sensor data, where repeated measurement values are described only once. Furthermore, these compact representations are able to enhance the storage and processing of semantic sensor data. To scale up to large datasets, factorization based, tabular representations are exploited to store and manage factorized semantic sensor data using Big Data technologies. We empirically study the effectiveness of a semantic sensor's proposed compact representations and their impact on query processing. Additionally, we evaluate the effects of storing the proposed representations on diverse RDF implementations. Results suggest that the proposed compact representations empower the storage and query processing of sensor data over diverse RDF implementations, and up to two orders of magnitude can reduce query execution time.

cs.DB