The unprecedented volume, diversity and richness of aviation data that can be acquired, generated, stored, and managed provides unique capabilities for the aviation-related industries and pertains value that remains to be unlocked with the adoption of the innovative Big Data Analytics technologies. Despite the large efforts and investments on research and innovation, the Big Data technologies introduce a number of challenges to its adopters. Besides the effective storage and access to the underlying big data, efficient data integration and data interoperability should be considered, while at the same time multiple data sources should be effectively combined by performing data exchange and data sharing between the different stakeholders. However, this reveals additional challenges for the crucial preservation of the information security of the collected data, the trusted and secure data exchange and data sharing, as well as the robust data access control. The current paper aims to introduce the ICARUS big data-enabled platform that aims provide a multi-sided platform that offers a novel aviation data and intelligence marketplace accompanied by a trusted and secure analytics workspace. It holistically handles the complete big data lifecycle from the data collection, data curation and data exploration to the data integration and data analysis of data originating from heterogeneous data sources with different velocity, variety and volume in a trusted and secure manner.
Empirically observed time series in physics, biology, or medicine, are commonly generated by some underlying dynamical system (DS) which is the target of scientific interest. There is an increasing interest to harvest machine learning methods to reconstruct this latent DS in a data-driven, unsupervised way. In many areas of science it is common to sample time series observations from many data modalities simultaneously, e.g. electrophysiological and behavioral time series in a typical neuroscience experiment. However, current machine learning tools for reconstructing DSs usually focus on just one data modality. Here we propose a general framework for multi-modal data integration for the purpose of nonlinear DS reconstruction and the analysis of cross-modal relations. This framework is based on dynamically interpretable recurrent neural networks as general approximators of nonlinear DSs, coupled to sets of modality-specific decoder models from the class of generalized linear models. Both an expectation-maximization and a variational inference algorithm for model training are advanced and compared. We show on nonlinear DS benchmarks that our algorithms can efficiently compensate for too noisy or missing information in one data channel by exploiting other channels, and demonstrate on experimental neuroscience data how the algorithm learns to link different data domains to the underlying dynamics.
Time-series modeling has shown great promise in recent studies using the latest deep learning algorithms such as LSTM (Long Short-Term Memory). These studies primarily focused on watershed-scale rainfall-runoff modeling or streamflow forecasting, but the majority of them only considered a single watershed as a unit. Although this simplification is very effective, it does not take into account spatial information, which could result in significant errors in large watersheds. Several studies investigated the use of GNN (Graph Neural Networks) for data integration by decomposing a large watershed into multiple sub-watersheds, but each sub-watershed is still treated as a whole, and the geoinformation contained within the watershed is not fully utilized. In this paper, we propose the GNRRM (Graph Neural Rainfall-Runoff Model), a novel deep learning model that makes full use of spatial information from high-resolution precipitation data, including flow direction and geographic information. When compared to baseline models, GNRRM has less over-fitting and significantly improves model performance. Our findings support the importance of hydrological data in deep learning-based rainfall-runoff modeling, and we encourage researchers to include more domain knowledge in their models.
Named entity disambiguation (NED), which involves mapping textual mentions to structured entities, is particularly challenging in the medical domain due to the presence of rare entities. Existing approaches are limited by the presence of coarse-grained structural resources in biomedical knowledge bases as well as the use of training datasets that provide low coverage over uncommon resources. In this work, we address these issues by proposing a cross-domain data integration method that transfers structural knowledge from a general text knowledge base to the medical domain. We utilize our integration scheme to augment structural resources and generate a large biomedical NED dataset for pretraining. Our pretrained model with injected structural knowledge achieves state-of-the-art performance on two benchmark medical NED datasets: MedMentions and BC5CDR. Furthermore, we improve disambiguation of rare entities by up to 57 accuracy points.
ICLP is the premier international event for presenting research in logic programming. Contributions to ICLP 2021 were sought in all areas of logic programming, including but not limited to: Foundations: Semantics, Formalisms, Nonmonotonic reasoning, Knowledge representation. Languages issues: Concurrency, Objects, Coordination, Mobility, Higher order, Types, Modes, Assertions, Modules, Meta-programming, Logic-based domain-specific languages, Programming techniques. Programming support: Program analysis, Transformation, Validation, Verification, Debugging, Profiling, Testing, Execution visualization. Implementation: Compilation, Virtual machines, Memory management, Parallel and Distributed execution, Constraint handling rules, Tabling, Foreign interfaces, User interfaces. Related Paradigms and Synergies: Inductive and coinductive logic programming, Constraint logic programming, Answer set programming, Interaction with SAT, SMT and CSP solvers, Theorem proving, Argumentation, Probabilistic programming, Machine learning. Applications: Databases, Big data, Data integration and federation, Software engineering, Natural language processing, Web and semantic web, Agents, Artificial intelligence, Computational life sciences, Cyber-security, Robotics, Education.
Schema matching is a core task of any data integration process. Being investigated in the fields of databases, AI, Semantic Web and data mining for many years, the main challenge remains the ability to generate quality matches among data concepts (e.g., database attributes). In this work, we examine a novel angle on the behavior of humans as matchers, studying match creation as a process. We analyze the dynamics of common evaluation measures (precision, recall, and f-measure), with respect to this angle and highlight the need for unbiased matching to support this analysis. Unbiased matching, a newly defined concept that describes the common assumption that human decisions represent reliable assessments of schemata correspondences, is, however, not an inherent property of human matchers. In what follows, we design PoWareMatch that makes use of a deep learning mechanism to calibrate and filter human matching decisions adhering the quality of a match, which are then combined with algorithmic matching to generate better match results. We provide an empirical evidence, established based on an experiment with more than 200 human matchers over common benchmarks, that PoWareMatch predicts well the benefit of extending the match with an additional correspondence and generates high quality matches. In addition, PoWareMatch outperforms state-of-the-art matching algorithms.
Understanding the semantics of tables at scale is crucial for tasks like data integration, preparation, and search. Table understanding methods aim at detecting a table's topic, semantic column types, column relations, or entities. With the rise of deep learning, powerful models have been developed for these tasks with excellent accuracy on benchmarks. However, we observe that there exists a gap between the performance of these models on these benchmarks and their applicability in practice. In this paper, we address the question: what do we need for these models to work in practice? We discuss three challenges of deploying table understanding models and propose a framework to address them. These challenges include 1) difficulty in customizing models to specific domains, 2) lack of training data for typical database tables often found in enterprises, and 3) lack of confidence in the inferences made by models. We present SigmaTyper which implements this framework for the semantic column type detection task. SigmaTyper encapsulates a hybrid model trained on GitTables and integrates a lightweight human-in-the-loop approach to customize the model. Lastly, we highlight avenues for future research that further close the gap towards making table understanding effective in practice.
The occurrence and distributions of wildlife populations and communities are shifting as a result of global changes. To evaluate whether these shifts are negatively impacting biodiversity processes, it is critical to monitor the status, trends, and effects of environmental variables on entire communities. However, modeling the dynamics of multiple species simultaneously can require large amounts of diverse data, and few modeling approaches exist to simultaneously provide species and community level inferences. We present an "integrated community occupancy model" (ICOM) that unites principles of data integration and hierarchical community modeling in a single framework to provide inferences on species-specific and community occurrence dynamics using multiple data sources. We use simulations to compare the ICOM to previously developed hierarchical community occupancy models and single species integrated distribution models. We then apply our model to assess the occurrence and biodiversity dynamics of foliage-gleaning birds in the White Mountain National Forest in the northeastern USA from 2010-2018 using three independent data sources. Simulations reveal that integrating multiple data sources in the ICOM increased precision and accuracy of species and community level inferences compared to single data source models, although benefits of integration were dependent on data source quality (e.g., amount of replication). Compared to single species models, the ICOM yielded more precise species-level estimates. Within our case study, the ICOM had the highest out-of-sample predictive performance compared to single species models and models that used only a subset of the three data sources. The ICOM offers an attractive approach to estimate species and biodiversity dynamics, which is additionally valuable to inform management objectives of both individual species and their broader communities.
The limited representation of minorities and disadvantaged populations in large-scale clinical and genomics research has become a barrier to translating precision medicine research into practice. Due to heterogeneity across populations, risk prediction models are often found to be underperformed in these underrepresented populations, and therefore may further exacerbate known health disparities. In this paper, we propose a two-way data integration strategy that integrates heterogeneous data from diverse populations and from multiple healthcare institutions via a federated transfer learning approach. The proposed method can handle the challenging setting where sample sizes from different populations are highly unbalanced. With only a small number of communications across participating sites, the proposed method can achieve performance comparable to the pooled analysis where individual-level data are directly pooled together. We show that the proposed method improves the estimation and prediction accuracy in underrepresented populations, and reduces the gap of model performance across populations. Our theoretical analysis reveals how estimation accuracy is influenced by communication budgets, privacy restrictions, and heterogeneity across populations. We demonstrate the feasibility and validity of our methods through numerical experiments and a real application to a multi-center study, in which we construct polygenic risk prediction models for Type II diabetes in AA population.
Big Data are rapidly produced from various heterogeneous data sources. They are of different types (text, image, video or audio) and have different levels of reliability and completeness. One of the most interesting architectures that deal with the large amount of emerging data at high velocity is called the lambda architecture. In fact, it combines two different processing layers namely batch and speed layers, each providing specific views of data while ensuring robustness, fast and scalable data processing. However, most papers dealing with the lambda architecture are focusing one single type of data generally produced by a single data source. Besides, the layers of the architecture are implemented independently, or, at best, are combined to perform basic processing without assessing either the data reliability or completeness. Therefore, inspired by the lambda architecture, we propose in this paper a generic multimodal architecture that combines both batch and streaming processing in order to build a complete, global and accurate insight in near-real-time based on the knowledge extracted from multiple heterogeneous Big Data sources. Our architecture uses batch processing to analyze the data structures and contents, build the learning models and calculate the reliability index of the involved sources, while the streaming processing uses the built-in models of the batch layer to immediately process incoming data and rapidly provide results. We validate our architecture in the context of urban traffic management systems in order to detect congestions.
In this paper, we consider existential rules, an expressive formalism well suited to the representation of ontological knowledge and data-to-ontology mappings in the context of ontology-based data integration. The chase is a fundamental tool to do reasoning with existential rules as it computes all the facts entailed by the rules from a database instance. We introduce parallelisable sets of existential rules, for which the chase can be computed in a single breadth-first step from any instance. The question we investigate is the characterization of such rule sets. We show that parallelisable rule sets are exactly those rule sets both bounded for the chase and belonging to a novel class of rules, called pieceful. The pieceful class includes in particular frontier-guarded existential rules and (plain) datalog. We also give another characterization of parallelisable rule sets in terms of rule composition based on rewriting.
Learning meaningful representations of data that can address challenges such as batch effect correction and counterfactual inference is a central problem in many domains including computational biology. Adopting a Conditional VAE framework, we show that marginal independence between the representation and a condition variable plays a key role in both of these challenges. We propose the Contrastive Mixture of Posteriors (CoMP) method that uses a novel misalignment penalty defined in terms of mixtures of the variational posteriors to enforce this independence in latent space. We show that CoMP has attractive theoretical properties compared to previous approaches, and we prove counterfactual identifiability of CoMP under additional assumptions. We demonstrate state-of-the-art performance on a set of challenging tasks including aligning human tumour samples with cancer cell-lines, predicting transcriptome-level perturbation responses, and batch correction on single-cell RNA sequencing data. We also find parallels to fair representation learning and demonstrate that CoMP is competitive on a common task in the field.
Nowadays, the amount of heterogeneous biomedical data is increasing more and more thanks to novel sensing techniques and high-throughput technologies. In reference to biomedical image analysis, the advances in image acquisition modalities and high-throughput imaging experiments are creating new challenges. This huge information ensemble could overwhelm the analytic capabilities needed by physicians in their daily decision-making tasks as well as by biologists investigating complex biochemical systems. In particular, quantitative imaging methods convey scientifically and clinically relevant information in prediction, prognosis or treatment response assessment, by also considering radiomics approaches. Therefore, the computational analysis of medical and biological images plays a key role in radiology and laboratory applications. In this regard, frameworks based on advanced Machine Learning and Computational Intelligence can significantly improve traditional Image Processing and Pattern Recognition approaches. However, conventional Artificial Intelligence techniques must be tailored to address the unique challenges concerning biomedical imaging data. This thesis aims at proposing novel and advanced computer-assisted methods for biomedical image analysis, also as an instrument in the development of Clinical Decision Support Systems, by always keeping in mind the clinical feasibility of the developed solutions. In conclusion, the ultimate goal of these research studies is to gain clinically and biologically useful insights that can guide differential diagnosis and therapies, leading towards biomedical data integration for personalized medicine. As a matter of fact, the proposed computer-assisted bioimage analysis methods can be beneficial for the definition of imaging biomarkers, as well as for quantitative medicine and biology.
Prediction of node and graph labels are prominent network science tasks. Data analyzed in these tasks are sometimes related: entities represented by nodes in a higher-level (higher-scale) network can themselves be modeled as networks at a lower level. We argue that systems involving such entities should be integrated with a "network of networks" (NoN) representation. Then, we ask whether entity label prediction using multi-level NoN data via our proposed approaches is more accurate than using each of single-level node and graph data alone, i.e., than traditional node label prediction on the higher-level network and graph label prediction on the lower-level networks. To obtain data, we develop the first synthetic NoN generator and construct a real biological NoN. We evaluate accuracy of considered approaches when predicting artificial labels from the synthetic NoNs and proteins' functions from the biological NoN. For the synthetic NoNs, our NoN approaches outperform or are as good as node- and network-level ones depending on the NoN properties. For the biological NoN, our NoN approaches outperform the single-level approaches for just under half of the protein functions, and for 30% of the functions, only our NoN approaches make meaningful predictions, while node- and network-level ones achieve random accuracy. So, NoN-based data integration is important.
As metabolomics datasets are becoming larger and more complex, there is an increasing need for model-based data integration and analysis to optimally leverage these data. Dynamical models of metabolism allow for the integration of heterogeneous data and the analysis of dynamical phenotypes. Here, we review recent efforts in using dynamical metabolic models for data integration, focusing on approaches that are not restricted to steady-state measurements or that require flux distributions as inputs. Furthermore, we discuss recent advances and current challenges. We conclude that much progress has been made in various areas, such as the development of scalable simulation tools, and that, although challenges remain, dynamical modeling is a powerful tool for metabolomics data analysis that is not yet living up to its full potential.
We propose a novel approach to the problem of semantic heterogeneity where data are organized into a set of stratified and independent representation layers, namely: conceptual(where a set of unique alinguistic identifiers are connected inside a graph codifying their meaning), language(where sets of synonyms, possibly from multiple languages, annotate concepts), knowledge(in the form of a graph where nodes are entity types and links are properties), and data(in the form of a graph of entities populating the previous knowledge graph). This allows us to state the problem of semantic heterogeneity as a problem of Representation Diversity where the different types of heterogeneity, viz. Conceptual, Language, Knowledge, and Data, are uniformly dealt within each single layer, independently from the others. In this paper we describe the proposed stratified representation of data and the process by which data are first transformed into the target representation, then suitably integrated and then, finally, presented to the user in her preferred format. The proposed framework has been evaluated in various pilot case studies and in a number of industrial data integration problems.
Data integration has been studied extensively for decades and approached from different angles. However, this domain still remains largely rule-driven and lacks universal automation. Recent developments in machine learning and in particular deep learning have opened the way to more general and efficient solutions to data-integration tasks. In this paper, we demonstrate an approach that allows modeling and integrating entities by leveraging their relations and contextual information. This is achieved by combining siamese and graph neural networks to effectively propagate information between connected entities and support high scalability. We evaluated our approach on the task of integrating data about business entities, demonstrating that it outperforms both traditional rule-based systems and other deep learning approaches.
Along with the rapid expansion of information technology and digitalization of health data, there is an increasing concern on maintaining data privacy while garnering the benefits in medical field. Two critical challenges are identified: Firstly, medical data is naturally distributed across multiple local sites, making it difficult to collectively train machine learning models without data leakage. Secondly, in medical applications, data are often collected from different sources and views, resulting in heterogeneity and complexity that requires reconciliation. This paper aims to provide a generic Federated Multi-View Learning (FedMV) framework for multi-view data leakage prevention, which is based on different types of local data availability and enables to accommodate two types of problems: Vertical Federated Multi-View Learning (V-FedMV) and Horizontal Federated Multi-View Learning (H-FedMV). We experimented with real-world keyboard data collected from BiAffect study. The results demonstrated that the proposed FedMV approach can make full use of multi-view data in a privacy-preserving way, and both V-FedMV and H-FedMV methods perform better than their single-view and pairwise counterparts. Besides, the proposed model can be easily adapted to deal with multi-view sequential data in a federated environment, which has been modeled and experimentally studied. To the best of our knowledge, this framework is the first to consider both vertical and horizontal diversification in the multi-view setting, as well as their sequential federated learning.
Deep learning has empowered analysis for single-cell sequencing data in many ways and has generated deep understanding about a range of complex cellular systems. As the booming single-cell sequencing technologies brings the surge of high dimensional data that come from different sources and represent cellular systems with different features, there is an equivalent rise and challenge of integrating single-cell sequence across modalities. Here, we present a novel adversarial approach to integrate single-cell chromatin accessibility and gene expression data in a semi-supervised manner. We demonstrate that our method substantially improves data integration from a simple adversarial domain adaption approach, and it also outperforms two state-of-the-art (SOTA) methods.
Many platforms for benchmarking optimization algorithms offer users the possibility of sharing their experimental data with the purpose of promoting reproducible and reusable research. However, different platforms use different data models and formats, which drastically inhibits identification of relevant data sets, their interpretation, and their interoperability. Consequently, a semantically rich, ontology-based, machine-readable data model is highly desired. We report in this paper on the development of such an ontology, which we name OPTION (OPTImization algorithm benchmarking ONtology). Our ontology provides the vocabulary needed for semantic annotation of the core entities involved in the benchmarking process, such as algorithms, problems, and evaluation measures. It also provides means for automated data integration, improved interoperability, powerful querying capabilities and reasoning, thereby enriching the value of the benchmark data. We demonstrate the utility of OPTION by annotating and querying a corpus of benchmark performance data from the BBOB workshop data - a use case which can be easily extended to cover other benchmarking data collections.