Graphs have emerged as an important foundation for a variety of applications, including capturing and reasoning over factual knowledge, semantic data integration, social networks, and providing factual knowledge for machine learning algorithms. To formalise certain properties of the data and to ensure data quality, there is a need to describe the schema of such graphs. Because of the breadth of applications and availability of different data models, such as RDF and property graphs, both the Semantic Web and the database community have independently developed graph schema languages: SHACL, ShEx, and PG-Schema. Each language has its unique approach to defining constraints and validating graph data, leaving potential users in the dark about their commonalities and differences. In this paper, we provide formal, concise definitions of the core components of each of these schema languages. We employ a uniform framework to facilitate a comprehensive comparison between the languages and identify a common set of functionalities, shedding light on both overlapping and distinctive features of the three languages.
Causal inference across multiple data sources offers a promising avenue to enhance the generalizability and replicability of scientific findings. However, data integration methods for time-to-event outcomes, common in biomedical research, are underdeveloped. Existing approaches focus on binary or continuous outcomes but fail to address the unique challenges of survival analysis, such as censoring and the integration of discrete and continuous time. To bridge this gap, we propose two novel methods for estimating target site-specific causal effects in multi-source settings. First, we develop a semiparametric efficient estimator for settings where individual-level data can be shared across sites. Second, we introduce a federated learning framework designed for privacy-constrained environments, which dynamically reweights source-specific contributions to account for discrepancies with the target population. Both methods leverage flexible, nonparametric machine learning models to improve robustness and efficiency. We illustrate the utility of our approaches through simulation studies and an application to multi-site randomized trials of monoclonal neutralizing antibodies for HIV-1 prevention, conducted among cisgender men and transgender persons in the United States, Brazil, Peru, and Switzerland, as well as among women in sub-Saharan Africa. Our findings underscore the potential of these methods to enable efficient, privacy-preserving causal inference for time-to-event outcomes under distribution shift.
The rapid advancement of high-throughput sequencing and other assay technologies has resulted in the generation of large and complex multi-omics datasets, offering unprecedented opportunities for advancing precision medicine strategies. However, multi-omics data integration presents significant challenges due to the high dimensionality, heterogeneity, experimental gaps, and frequency of missing values across data types. Computational methods have been developed to address these issues, employing statistical and machine learning approaches to uncover complex biological patterns and provide deeper insights into our understanding of disease mechanisms. Here, we comprehensively review state-of-the-art multi-omics data integration methods with a focus on deep generative models, particularly variational autoencoders (VAEs) that have been widely used for data imputation and augmentation, joint embedding creation, and batch effect correction. We explore the technical aspects of loss functions and regularisation techniques including adversarial training, disentanglement and contrastive learning. Moreover, we discuss recent advancements in foundation models and the integration of emerging data modalities, while describing the current limitations and outlining future directions for enhancing multi-modal methodologies in biomedical research.
Traditional remote spirometry lacks the precision required for effective pulmonary monitoring. We present a novel, non-invasive approach using multimodal predictive models that integrate RGB or thermal video data with patient metadata. Our method leverages energy-efficient Spiking Neural Networks (SNNs) for the regression of Peak Expiratory Flow (PEF) and classification of Forced Expiratory Volume (FEV1) and Forced Vital Capacity (FVC), using lightweight CNNs to overcome SNN limitations in regression tasks. Multimodal data integration is improved with a Multi-Head Attention Layer, and we employ K-Fold validation and ensemble learning to boost robustness. Using thermal data, our SNN models achieve 92% accuracy on a breathing-cycle basis and 99.5% patient-wise. PEF regression models attain Relative RMSEs of 0.11 (thermal) and 0.26 (RGB), with an MAE of 4.52% for FEV1/FVC predictions, establishing state-of-the-art performance. Code and dataset can be found on https://github.com/ahmed-sharshar/RespiroDynamics.git
Data integration is an important step in any data science pipeline where the objective is to unify the information available in different datasets for comprehensive analysis. Full Disjunction, which is an associative extension of the outer join operator, has been shown to be an effective operator for integrating datasets. It fully preserves and combines the available information. Existing Full Disjunction algorithms only consider the equi-join scenario where only tuples having the same value on joining columns are integrated. This, however, does not realistically represent an open data scenario, where datasets come from diverse sources with inconsistent values (e.g., synonyms, abbreviations, etc.) and with limited metadata. So, joining just on equal values severely limits the ability of Full Disjunction to fully combine datasets. Thus, in this work, we propose an extension of Full Disjunction to also account for "fuzzy" matches among tuples. We present a novel data-driven approach to enable the joining of approximate or fuzzy matches within Full Disjunction. Experimentally, we show that fuzzy Full Disjunction does not add significant time overhead over a state-of-the-art Full Disjunction implementation and also that it enhances the integration effectiveness.
Large-N nationally representative surveys, which have profoundly shaped American politics scholarship, represent related but distinct domains -a key condition for transfer learning applications. These surveys are related through their shared demographic, party identification, and ideological variables, yet differ in that individual surveys often lack specific policy preference questions that researchers require. Our study introduces a novel application of transfer learning (TL) to address these gaps, marking the first systematic use of TL paradigms in the context of survey data. Specifically, models pre-trained on the Cooperative Election Study (CES) dataset are fine-tuned for use in the American National Election Studies (ANES) dataset to predict policy questions based on demographic variables. Even with a naive architecture, our transfer learning approach achieves approximately 92 percentage accuracy in predicting missing variables across surveys, demonstrating the robust potential of this method. Beyond this specific application, our paper argues that transfer learning is a promising framework for maximizing the utility of existing survey data. We contend that artificial intelligence, particularly transfer learning, opens new frontiers in social science methodology by enabling systematic knowledge transfer between well-administered surveys that share common variables but differ in their outcomes of interest.
Knowledge graphs have proven successful in integrating heterogeneous data across various domains. However, there remains a noticeable dearth of research on their seamless integration among heterogeneous recommender systems, despite knowledge graph-based recommender systems garnering extensive research attention. This study aims to fill this gap by proposing RecKG, a standardized knowledge graph for recommender systems. RecKG ensures the consistent representation of entities across different datasets, accommodating diverse attribute types for effective data integration. Through a meticulous examination of various recommender system datasets, we select attributes for RecKG, ensuring standardized formatting through consistent naming conventions. By these characteristics, RecKG can seamlessly integrate heterogeneous data sources, enabling the discovery of additional semantic information within the integrated knowledge graph. We apply RecKG to standardize real-world datasets, subsequently developing an application for RecKG using a graph database. Finally, we validate RecKG's achievement in interoperability through a qualitative evaluation between RecKG and other studies.
Text classification is a fundamental task in natural language processing, pivotal to various applications such as query optimization, data integration, and schema matching. While neural network-based models, such as CNN and BERT, have demonstrated remarkable performance in text classification, their effectiveness heavily relies on abundant labeled training data. This dependency makes these models less effective in dynamic few-shot text classification, where labeled data is scarce, and target labels frequently evolve based on application needs. Recently, large language models (LLMs) have shown promise due to their extensive pretraining and contextual understanding. Current approaches provide LLMs with text inputs, candidate labels, and additional side information (e.g., descriptions) to predict text labels. However, their effectiveness is hindered by the increased input size and the noise introduced through side information processing. To address these limitations, we propose a graph-based online retrieval-augmented generation framework, namely GORAG, for dynamic few-shot text classification. GORAG constructs and maintains an adaptive information graph by extracting side information across all target texts, rather than treating each input independently. It employs a weighted edge mechanism to prioritize the importance and reliability of extracted information and dynamically retrieves relevant context using a minimum-cost spanning tree tailored for each text input. Empirical evaluations demonstrate that GORAG outperforms existing approaches by providing more comprehensive and accurate contextual information.
Image segmentation is a vital task for providing human assistance and enhancing autonomy in our daily lives. In particular, RGB-D segmentation-leveraging both visual and depth cues-has attracted increasing attention as it promises richer scene understanding than RGB-only methods. However, most existing efforts have primarily focused on semantic segmentation and thus leave a critical gap. There is a relative scarcity of instance-level RGB-D segmentation datasets, which restricts current methods to broad category distinctions rather than fully capturing the fine-grained details required for recognizing individual objects. To bridge this gap, we introduce three RGB-D instance segmentation benchmarks, distinguished at the instance level. These datasets are versatile, supporting a wide range of applications from indoor navigation to robotic manipulation. In addition, we present an extensive evaluation of various baseline models on these benchmarks. This comprehensive analysis identifies both their strengths and shortcomings, guiding future work toward more robust, generalizable solutions. Finally, we propose a simple yet effective method for RGB-D data integration. Extensive evaluations affirm the effectiveness of our approach, offering a robust framework for advancing toward more nuanced scene understanding.
Cybersickness remains a significant barrier to the widespread adoption of immersive virtual reality (VR) experiences, as it can greatly disrupt user engagement and comfort. Research has shown that cybersickness can significantly be reflected in head and eye tracking data, along with other physiological data (e.g., TMP, EDA, and BMP). Despite the application of deep learning techniques such as CNNs and LSTMs, these models often struggle to capture the complex interactions between multiple data modalities and lack the capacity for real-time inference, limiting their practical application. Addressing this gap, we propose a lightweight model that leverages a transformer-based encoder with sparse self-attention to process bio-signal features and a PP-TSN network for video feature extraction. These features are then integrated via a cross-modal fusion module, creating a video-aware bio-signal representation that supports cybersickness prediction based on both visual and bio-signal inputs. Our model, trained with a lightweight framework, was validated on a public dataset containing eye and head tracking data, physiological data, and VR video, and demonstrated state-of-the-art performance in cybersickness prediction, achieving a high accuracy of 93.13\% using only VR video inputs. These findings suggest that our approach not only enables effective, real-time cybersickness prediction but also addresses the longstanding issue of modality interaction in VR environments. This advancement provides a foundation for future research on multimodal data integration in VR, potentially leading to more personalized, comfortable and widely accessible VR experiences.
Leading large language models (LLMs) are trained on public data. However, most of the world's data is dark data that is not publicly accessible, mainly in the form of private organizational or enterprise data. We show that the performance of methods based on LLMs seriously degrades when tested on real-world enterprise datasets. Current benchmarks, based on public data, overestimate the performance of LLMs. We release a new benchmark dataset, the GOBY Benchmark, to advance discovery in enterprise data integration. Based on our experience with this enterprise benchmark, we propose techniques to uplift the performance of LLMs on enterprise data, including (1) hierarchical annotation, (2) runtime class-learning, and (3) ontology synthesis. We show that, once these techniques are deployed, the performance on enterprise data becomes on par with that of public data. The Goby benchmark can be obtained at https://goby-benchmark.github.io/.
Accelerating model convergence in resource-constrained environments is essential for fast and efficient neural network training. This work presents learn2mix, a new training strategy that adaptively adjusts class proportions within batches, focusing on classes with higher error rates. Unlike classical training methods that use static class proportions, learn2mix continually adapts class proportions during training, leading to faster convergence. Empirical evaluations on benchmark datasets show that neural networks trained with learn2mix converge faster than those trained with classical approaches, achieving improved results for classification, regression, and reconstruction tasks under limited training resources and with imbalanced classes. Our empirical findings are supported by theoretical analysis.
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 that include provenance, security and trust, as well as a discussion of practical impacts from industry-led contributions. We conclude with an outlook on the future directions of the Semantic Web.
The traditional interpretation of Intravascular Ultrasound (IVUS) images during Percutaneous Coronary Intervention (PCI) is time-intensive and inconsistent, relying heavily on physician expertise. Regulatory restrictions and privacy concerns further hinder data integration across hospital systems, complicating collaborative analysis. To address these challenges, a parallel 2D U-Net model with a multi-stage segmentation architecture has been developed, utilizing federated learning to enable secure data analysis across institutions while preserving privacy. The model segments plaques by identifying and subtracting the External Elastic Membrane (EEM) and lumen areas, with preprocessing converting Cartesian to polar coordinates for improved computational efficiency. Achieving a Dice Similarity Coefficient (DSC) of 0.706, the model effectively identifies plaques and detects circular boundaries in real-time. Collaborative efforts with domain experts enhance plaque burden interpretation through precise quantitative measurements. Future advancements may involve integrating advanced federated learning techniques and expanding datasets to further improve performance and applicability. This adaptable technology holds promise for environments handling sensitive, distributed data, offering potential to optimize outcomes in medical imaging and intervention.
The integration of multi-omic data is pivotal for understanding complex diseases, but its high dimensionality and noise present significant challenges. Graph Neural Networks (GNNs) offer a robust framework for analyzing large-scale signaling pathways and protein-protein interaction networks, yet they face limitations in expressivity when capturing intricate biological relationships. To address this, we propose Graph Sequence Language Model (GraphSeqLM), a framework that enhances GNNs with biological sequence embeddings generated by Large Language Models (LLMs). These embeddings encode structural and biological properties of DNA, RNA, and proteins, augmenting GNNs with enriched features for analyzing sample-specific multi-omic data. By integrating topological, sequence-derived, and biological information, GraphSeqLM demonstrates superior predictive accuracy and outperforms existing methods, paving the way for more effective multi-omic data integration in precision medicine.
Managing clinical trial information is currently a significant challenge for the medical industry, as traditional methods are both time-consuming and costly. This paper proposes a simple yet effective methodology to extract and integrate clinical trial data in a cost-effective and time-efficient manner. Allowing the medical industry to stay up-to-date with medical developments. Comparing time, cost, and quality of the ontologies created by humans, GPT3.5, GPT4, and Llama3 (8b & 70b). Findings suggest that large language models (LLM) are a viable option to automate this process both from a cost and time perspective. This study underscores significant implications for medical research where real-time data integration from clinical trials could become the norm.
The digital transformation of production requires new methods of data integration and storage, as well as decision making and support systems that work vertically and horizontally throughout the development, production, and use cycle. In this paper, we propose Data-to-Knowledge (and Knowledge-to-Data) pipelines for production as a universal concept building on a network of Digital Shadows (a concept augmenting Digital Twins). We show a proof of concept that builds on and bridges existing infrastructure to 1) capture and semantically annotates trajectory data from multiple similar but independent robots in different organisations and use cases in a data lakehouse and 2) an independent process that dynamically queries matching data for training an inverse dynamic foundation model for robotic control. The article discusses the challenges and benefits of this approach and how Data-to-Knowledge pipelines contribute efficiency gains and industrial scalability in a World Wide Lab as a research outlook.
Resting-state fMRI captures spontaneous neural activity characterized by complex spatiotemporal dynamics. Various metrics, such as local and global brain connectivity and low-frequency amplitude fluctuations, quantify distinct aspects of these dynamics. However, these measures are typically analyzed independently, overlooking their interrelations and potentially limiting analytical sensitivity. Here, we introduce the Fusion Searchlight (FuSL) framework, which integrates complementary information from multiple resting-state fMRI metrics. We demonstrate that combining these metrics enhances the accuracy of pharmacological treatment prediction from rs-fMRI data, enabling the identification of additional brain regions affected by sedation with alprazolam. Furthermore, we leverage explainable AI to delineate the differential contributions of each metric, which additionally improves spatial specificity of the searchlight analysis. Moreover, this framework can be adapted to combine information across imaging modalities or experimental conditions, providing a versatile and interpretable tool for data fusion in neuroimaging.
For the early identification, diagnosis, and treatment of mental health illnesses, the integration of deep learning (DL) and machine learning (ML) has started playing a significant role. By evaluating complex data from imaging, genetics, and behavioral assessments, these technologies have the potential to significantly improve clinical outcomes. However, they also present unique challenges related to data integration and ethical issues. This survey reviews the development of ML and DL methods for the early diagnosis and treatment of mental health issues. It examines a range of applications, with a particular emphasis on behavioral assessments, genetic and biomarker analysis, and medical imaging for diagnosing diseases like depression, bipolar disorder, and schizophrenia. Predictive modeling for illness progression is further discussed, focusing on the role of risk prediction models and longitudinal studies. Key findings highlight how ML and DL can improve diagnostic accuracy and treatment outcomes while addressing methodological inconsistencies, data integration challenges, and ethical concerns. The study emphasizes the importance of building real-time monitoring systems for individualized treatment, enhancing data fusion techniques, and fostering interdisciplinary collaboration. Future research should focus on overcoming these obstacles to ensure the valuable and ethical application of ML and DL in mental health services.
We investigate the problem of selecting features for datasets that can be naturally partitioned into subgroups (e.g., according to socio-demographic groups and age), each with its own dominant set of features. Within this subgroup-oriented framework, we address the challenge of systematic missing data, a scenario in which some feature values are missing for all tuples of a subgroup, due to flawed data integration, regulatory constraints, or privacy concerns. Feature selection is governed by finding mutual Information, a popular quantification of correlation, between features and a target variable. Our goal is to identify top-K feature subsets of some fixed size with the highest joint mutual information with a target variable. In the presence of systematic missing data, the closed form of mutual information could not simply be applied. We argue that in such a setting, leveraging relationships between available feature mutual information within a subgroup or across subgroups can assist inferring missing mutual information values. We propose a generalizable model based on heterogeneous graph neural network to identify interdependencies between feature-subgroup-target variable connections by modeling it as a multiplex graph, and employing information propagation between its nodes. We address two distinct scalability challenges related to training and propose principled solutions to tackle them. Through an extensive empirical evaluation, we demonstrate the efficacy of the proposed solutions both qualitatively and running time wise.