The RML mapping language declares schema transformations to map heterogeneous data into knowledge graphs. Although the schema transformations provided by RML are sufficient for simple use cases, large real-world ones typically involve diverse data and require complex computations. User-defined functions provide the flexibility to enable the creation and application of knowledge graphs for these use cases and also allow reusing existing software packages for data processing in multiple domains. In this work, we present an implementation for data transformations in Morph-KGC. This implementation has the following benefits: (i) it conforms to RML-FNML, the standard module for data transformations in RML, (ii) it can handle user-defined functions written in Python, a widely used programming language for data processing, (iii) it includes support for YARRRML, a user-friendly syntax of RML to maximize usability. The implementation is currently being used by BASF, a large multinational chemical company, to semantically integrate its industrial data in a maintainable and reproducible manner.
Advances in high-throughput technologies have originated an ever-increasing availability of omics datasets. The integration of multiple heterogeneous data sources is currently an issue for biology and bioinformatics. Multiple kernel learning (MKL) has shown to be a flexible and valid approach to consider the diverse nature of multi-omics inputs, despite being an underused tool in genomic data mining. We provide novel MKL approaches based on different kernel fusion strategies. To learn from the meta-kernel of input kernels, we adapted unsupervised integration algorithms for supervised tasks with support vector machines. We also tested deep learning architectures for kernel fusion and classification. The results show that MKL-based models can outperform more complex, state-of-the-art, supervised multi-omics integrative approaches. Multiple kernel learning offers a natural framework for predictive models in multi-omics data. It proved to provide a fast and reliable solution that can compete with and outperform more complex architectures. Our results offer a direction for bio-data mining research, biomarker discovery and further development of methods for heterogeneous data integration.
Entity matching is a critical challenge in data integration and cleaning, central to tasks like fuzzy joins and deduplication. Traditional approaches have focused on overcoming fuzzy term representations through methods such as edit distance, Jaccard similarity, and more recently, embeddings and deep neural networks, including advancements from large language models (LLMs) like GPT. However, the core challenge in entity matching extends beyond term fuzziness to the ambiguity in defining what constitutes a "match," especially when integrating with external databases. This ambiguity arises due to varying levels of detail and granularity among entities, complicating exact matches. We propose a novel approach that shifts focus from purely identifying semantic similarities to understanding and defining the "relations" between entities as crucial for resolving ambiguities in matching. By predefining a set of relations relevant to the task at hand, our method allows analysts to navigate the spectrum of similarity more effectively, from exact matches to conceptually related entities.
Big earth science data offers the scientific community great opportunities. Many more studies at large-scales, over long-terms and at high resolution can now be conducted using the rich information collected by remote sensing satellites, ground-based sensor networks, and even social media input. However, the hundreds of terabytes of information collected and compiled on an hourly basis by NASA and other government agencies present a significant challenge for atmospheric scientists seeking to improve the understanding of the Earth atmospheric system. These challenges include effective discovery, organization, analysis and visualization of large amounts of data. This paper reports the outcomes of an NSF-funded project that developed a geospatial cyberinfrastructure -- the A2CI (Atmospheric Analysis Cyberinfrastructure) -- to support atmospheric research. We first introduce the service-oriented system framework then describe in detail the implementation of the data discovery module, data management module, data integration module, data analysis and visualization modules following the cloud computing principles-Data-as-a-Service, Software-as-a-Service, Platform-as-a-Service and Infrastructure-as-a-Service. We demonstrate the graphic user interface by performing an analysis between Sea Surface Temperature and the intensity of tropical storms in the North Atlantic and Pacific oceans. We expect this work to contribute to the technical advancement of cyberinfrastructure research as well as to the development of an online, collaborative scientific analysis system for atmospheric science.
The adoption of Artificial Intelligence in Education (AIED) holds the promise of revolutionizing educational practices by offering personalized learning experiences, automating administrative and pedagogical tasks, and reducing the cost of content creation. However, the lack of standardized practices in the development and deployment of AIED solutions has led to fragmented ecosystems, which presents challenges in interoperability, scalability, and ethical governance. This article aims to address the critical need to develop and implement industry standards in AIED, offering a comprehensive analysis of the current landscape, challenges, and strategic approaches to overcome these obstacles. We begin by examining the various applications of AIED in various educational settings and identify key areas lacking in standardization, including system interoperability, ontology mapping, data integration, evaluation, and ethical governance. Then, we propose a multi-tiered framework for establishing robust industry standards for AIED. In addition, we discuss methodologies for the iterative development and deployment of standards, incorporating feedback loops from real-world applications to refine and adapt standards over time. The paper also highlights the role of emerging technologies and pedagogical theories in shaping future standards for AIED. Finally, we outline a strategic roadmap for stakeholders to implement these standards, fostering a cohesive and ethical AIED ecosystem. By establishing comprehensive industry standards, such as those by IEEE Artificial Intelligence Standards Committee (AISC) and International Organization for Standardization (ISO), we can accelerate and scale AIED solutions to improve educational outcomes, ensuring that technological advances align with the principles of inclusivity, fairness, and educational excellence.
Data augmentation is arguably the most important regularization technique commonly used to improve generalization performance of machine learning models. It primarily involves the application of appropriate data transformation operations to create new data samples with desired properties. Despite its effectiveness, the process is often challenging because of the time-consuming trial and error procedures for creating and testing different candidate augmentations and their hyperparameters manually. State-of-the-art approaches are increasingly relying on automated machine learning (AutoML) principles. This work presents a comprehensive survey of AutoML-based data augmentation techniques. We discuss various approaches for accomplishing data augmentation with AutoML, including data manipulation, data integration and data synthesis techniques. The focus of this work is on image data augmentation methods. Nonetheless, we cover other data modalities, especially in cases where the specific data augmentations techniques being discussed are more suitable for these other modalities. For instance, since automated data integration methods are more suitable for tabular data, we cover tabular data in the discussion of data integration methods. The work also presents extensive discussion of techniques for accomplishing each of the major subtasks of the image data augmentation process: search space design, hyperparameter optimization and model evaluation. Finally, we carried out an extensive comparison and analysis of the performance of automated data augmentation techniques and state-of-the-art methods based on classical augmentation approaches. The results show that AutoML methods for data augmentation currently outperform state-of-the-art techniques based on conventional approaches.
Schema matching is a crucial task in data integration, involving the alignment of a source schema with a target schema to establish correspondence between their elements. This task is challenging due to textual and semantic heterogeneity, as well as differences in schema sizes. Although machine-learning-based solutions have been explored in numerous studies, they often suffer from low accuracy, require manual mapping of the schemas for model training, or need access to source schema data which might be unavailable due to privacy concerns. In this paper we present a novel method, named ReMatch, for matching schemas using retrieval-enhanced Large Language Models (LLMs). Our method avoids the need for predefined mapping, any model training, or access to data in the source database. Our experimental results on large real-world schemas demonstrate that ReMatch is an effective matcher. By eliminating the requirement for training data, ReMatch becomes a viable solution for real-world scenarios.
Pretrained deep-learning models are the go-to solution for images or text. However, for tabular data the standard is still to train tree-based models. Indeed, transfer learning on tables hits the challenge of data integration: finding correspondences, correspondences in the entries (entity matching) where different words may denote the same entity, correspondences across columns (schema matching), which may come in different orders, names... We propose a neural architecture that does not need such correspondences. As a result, we can pretrain it on background data that has not been matched. The architecture -- CARTE for Context Aware Representation of Table Entries -- uses a graph representation of tabular (or relational) data to process tables with different columns, string embedding of entries and columns names to model an open vocabulary, and a graph-attentional network to contextualize entries with column names and neighboring entries. An extensive benchmark shows that CARTE facilitates learning, outperforming a solid set of baselines including the best tree-based models. CARTE also enables joint learning across tables with unmatched columns, enhancing a small table with bigger ones. CARTE opens the door to large pretrained models for tabular data.
Regression analysis is a central topic in statistical modeling, aimed at estimating the relationships between a dependent variable, commonly referred to as the response variable, and one or more independent variables, i.e., explanatory variables. Linear regression is by far the most popular method for performing this task in various fields of research, such as data integration and predictive modeling when combining information from multiple sources. Classical methods for solving linear regression problems, such as Ordinary Least Squares (OLS), Ridge, or Lasso regressions, often form the foundation for more advanced machine learning (ML) techniques, which have been successfully applied, though without a formal definition of statistical significance. At most, permutation or analyses based on empirical measures (e.g., residuals or accuracy) have been conducted, leveraging the greater sensitivity of ML estimations for detection. In this paper, we introduce Statistical Agnostic Regression (SAR) for evaluating the statistical significance of ML-based linear regression models. This is achieved by analyzing concentration inequalities of the actual risk (expected loss) and considering the worst-case scenario. To this end, we define a threshold that ensures there is sufficient evidence, with a probability of at least $1-\eta$, to conclude the existence of a linear relationship in the population between the explanatory (feature) and the response (label) variables. Simulations demonstrate the ability of the proposed agnostic (non-parametric) test to provide an analysis of variance similar to the classical multivariate $F$-test for the slope parameter, without relying on the underlying assumptions of classical methods. Moreover, the residuals computed from this method represent a trade-off between those obtained from ML approaches and the classical OLS.
Patient-Centric Knowledge Graphs (PCKGs) represent an important shift in healthcare that focuses on individualized patient care by mapping the patient's health information in a holistic and multi-dimensional way. PCKGs integrate various types of health data to provide healthcare professionals with a comprehensive understanding of a patient's health, enabling more personalized and effective care. This literature review explores the methodologies, challenges, and opportunities associated with PCKGs, focusing on their role in integrating disparate healthcare data and enhancing patient care through a unified health perspective. In addition, this review also discusses the complexities of PCKG development, including ontology design, data integration techniques, knowledge extraction, and structured representation of knowledge. It highlights advanced techniques such as reasoning, semantic search, and inference mechanisms essential in constructing and evaluating PCKGs for actionable healthcare insights. We further explore the practical applications of PCKGs in personalized medicine, emphasizing their significance in improving disease prediction and formulating effective treatment plans. Overall, this review provides a foundational perspective on the current state-of-the-art and best practices of PCKGs, guiding future research and applications in this dynamic field.
Multimodal intelligent transportation systems (M-ITS) encompass a range of transportation services that utilise various modes of transport and incorporate intelligent technologies for enhanced efficiency and user experience. There are several challenges in M-ITS including data integration, Interoperability, scalability, user experience, etc. To address these challenges, such a system requires an adaptive system architecture that enables M-ITS to operate as an integrated ecosystem. In this paper, we provide an adaptive, user-centric, and layered architecture for multimodal transportation systems. The proposed architecture ensures scalability for seamless interactions of various subcomponents, that are often managed by different stakeholders. Concurrently, the data architecture is detailed, covering diverse data sources, advanced analytics, and stringent governance, providing a robust basis for intelligent decision-making. We provide two example use cases of the proposed architecture, showing how the data architecture and the system architecture can be fused and serve multimodal intelligent transport services.
Modern manufacturing value chains require intelligent orchestration of processes across company borders in order to maximize profits while fostering social and environmental sustainability. However, the implementation of integrated, systems-level approaches for data-informed decision-making along value chains is currently hampered by privacy concerns associated with cross-organizational data exchange and integration. We here propose Privacy-Preserving Partial Least Squares (P3LS) regression, a novel federated learning technique that enables cross-organizational data integration and process modeling with privacy guarantees. P3LS involves a singular value decomposition (SVD) based PLS algorithm and employs removable, random masks generated by a trusted authority in order to protect the privacy of the data contributed by each data holder. We demonstrate the capability of P3LS to vertically integrate process data along a hypothetical value chain consisting of three parties and to improve the prediction performance on several process-related key performance indicators. Furthermore, we show the numerical equivalence of P3LS and PLS model components on simulated data and provide a thorough privacy analysis of the former. Moreover, we propose a mechanism for determining the relevance of the contributed data to the problem being addressed, thus creating a basis for quantifying the contribution of participants.
In this paper, we introduce eipy--an open-source Python package for developing effective, multi-modal heterogeneous ensembles for classification. eipy simultaneously provides both a rigorous, and user-friendly framework for comparing and selecting the best-performing multi-modal data integration and predictive modeling methods by systematically evaluating their performance using nested cross-validation. The package is designed to leverage scikit-learn-like estimators as components to build multi-modal predictive models. An up-to-date user guide, including API reference and tutorials, for eipy is maintained at https://eipy.readthedocs.io . The main repository for this project can be found on GitHub at https://github.com/GauravPandeyLab/eipy .
Ensemble modeling has been widely used to solve complex problems as it helps to improve overall performance and generalization. In this paper, we propose a novel TemporalAugmenter approach based on ensemble modeling for augmenting the temporal information capturing for long-term and short-term dependencies in data integration of two variations of recurrent neural networks in two learning streams to obtain the maximum possible temporal extraction. Thus, the proposed model augments the extraction of temporal dependencies. In addition, the proposed approach reduces the preprocessing and prior stages of feature extraction, which reduces the required energy to process the models built upon the proposed TemporalAugmenter approach, contributing towards green AI. Moreover, the proposed model can be simply integrated into various domains including industrial, medical, and human-computer interaction applications. Our proposed approach empirically evaluated the speech emotion recognition, electrocardiogram signal, and signal quality examination tasks as three different signals with varying complexity and different temporal dependency features.
High-throughput omics profiling advancements have greatly enhanced cancer patient stratification. However, incomplete data in multi-omics integration presents a significant challenge, as traditional methods like sample exclusion or imputation often compromise biological diversity and dependencies. Furthermore, the critical task of accurately classifying new patients with partial omics data into existing subtypes is commonly overlooked. To address these issues, we introduce IntegrAO (Integrate Any Omics), an unsupervised framework for integrating incomplete multi-omics data and classifying new samples. IntegrAO first combines partially overlapping patient graphs from diverse omics sources and utilizes graph neural networks to produce unified patient embeddings. Our systematic evaluation across five cancer cohorts involving six omics modalities demonstrates IntegrAO's robustness to missing data and its accuracy in classifying new samples with partial profiles. An acute myeloid leukemia case study further validates its capability to uncover biological and clinical heterogeneity in incomplete datasets. IntegrAO's ability to handle heterogeneous and incomplete data makes it an essential tool for precision oncology, offering a holistic approach to patient characterization.
This article explores the critical role of statistical analysis in precision medicine. It discusses how personalized healthcare is enhanced by statistical methods that interpret complex, multidimensional datasets, focusing on predictive modeling, machine learning algorithms, and data visualization techniques. The paper addresses challenges in data integration and interpretation, particularly with diverse data sources like electronic health records (EHRs) and genomic data. It also delves into ethical considerations such as patient privacy and data security. In addition, the paper highlights the evolution of statistical analysis in medicine, core statistical methodologies in precision medicine, and future directions in the field, emphasizing the integration of artificial intelligence (AI) and machine learning (ML).
Digital twins are becoming increasingly popular across many industries for real-time data streaming, processing, and visualization. They allow stakeholders to monitor, diagnose, and optimize assets. Emerging technologies used for immersive visualization, such as virtual reality, open many new possibilities for intuitive access and monitoring of remote assets through digital twins. This is specifically relevant for floating wind farms, where access is often limited. However, the integration of data from multiple sources and access through different devices including virtual reality headsets can be challenging. In this work, a data integration framework for static and real-time data from various sources on the assets and their environment is presented that allows collecting and processing of data in Python and deploying the data in real-time through Unity on different devices, including virtual reality headsets. The integration of data from terrain, weather, and asset geometry is explained in detail. A real-time data stream from the asset to the clients is implemented and reviewed, and instructions are given on the code required to connect Python scripts to any Unity application across devices. The data integration framework is implemented for a digital twin of a floating wind turbine and an onshore wind farm, and the potential for future research is discussed.
Contrastive learning (CL) has emerged as a promising technique for improving recommender systems, addressing the challenge of data sparsity by using self-supervised signals from raw data. Integration of CL with graph convolutional network (GCN)-based collaborative filterings (CFs) has been explored in recommender systems. However, current CL-based recommendation models heavily rely on low-pass filters and graph augmentations. In this paper, inspired by the reaction-diffusion equation, we propose a novel CL method for recommender systems called the reaction-diffusion graph contrastive learning model (RDGCL). We design our own GCN for CF based on the equations of diffusion, i.e., low-pass filter, and reaction, i.e., high-pass filter. Our proposed CL-based training occurs between reaction and diffusion-based embeddings, so there is no need for graph augmentations. Experimental evaluation on 5 benchmark datasets demonstrates that our proposed method outperforms state-of-the-art CL-based recommendation models. By enhancing recommendation accuracy and diversity, our method brings an advancement in CL for recommender systems.
Environmental hazards like water and air pollution, extreme weather, or chemical exposures can affect human health in a number of ways, and it is a persistent apprehension in communities surrounded by mining operations. The application of modern technologies in the environmental monitoring of these Human-made hazards is critical, because while not immediately health-threatening may turn out detrimental with unwanted negative effects. Enabling technologies needed to realise this concept is multifaceted and most especially involves deploying interconnected Internet of Things (IoT) sensors, existing legacy systems, enterprise networks, multi layered software architecture (middleware), and event processing engines, amongst others. Currently, the integration of several early warning systems has inherent challenges, mostly due to the heterogeneity of components. This paper proposes transversal microservice-based middleware aiming at increasing data integration, interoperability, scalability, high availability, and reusability of adopted systems using a container orchestration framework for a multi-hazard early warning system. Devised within the scope of the ICMHEWS project, the proposed platform aims at improving known challenges.
We propose a novel technique to enhance Knowledge Graph Reasoning by combining Graph Convolution Neural Network (GCN) with the Attention Mechanism. This approach utilizes the Attention Mechanism to examine the relationships between entities and their neighboring nodes, which helps to develop detailed feature vectors for each entity. The GCN uses shared parameters to effectively represent the characteristics of adjacent entities. We first learn the similarity of entities for node representation learning. By integrating the attributes of the entities and their interactions, this method generates extensive implicit feature vectors for each entity, improving performance in tasks including entity classification and link prediction, outperforming traditional neural network models. To conclude, this work provides crucial methodological support for a range of applications, such as search engines, question-answering systems, recommendation systems, and data integration tasks.