The use of machine learning (ML) in high-stakes societal decisions has encouraged the consideration of fairness throughout the ML lifecycle. Although data integration is one of the primary steps to generate high quality training data, most of the fairness literature ignores this stage. In this work, we consider fairness in the integration component of data management, aiming to identify features that improve prediction without adding any bias to the dataset. We work under the causal interventional fairness paradigm. Without requiring the underlying structural causal model a priori, we propose an approach to identify a sub-collection of features that ensure the fairness of the dataset by performing conditional independence tests between different subsets of features. We use group testing to improve the complexity of the approach. We theoretically prove the correctness of the proposed algorithm to identify features that ensure interventional fairness and show that sub-linear conditional independence tests are sufficient to identify these variables. A detailed empirical evaluation is performed on real-world datasets to demonstrate the efficacy and efficiency of our technique.
During the last decade, various approaches have been put forward to integrate business processes with different types of data. Each of such approaches reflects specific demands in the whole process-data integration spectrum. One particular important point is the capability of these approaches to flexibly accommodate processes with multiple cases that need to co-evolve. In this work, we introduce and study an extension of coloured Petri nets, called catalog-nets, providing two key features to capture this type of processes. On the one hand, net transitions are equipped with guards that simultaneously inspect the content of tokens and query facts stored in a read-only, persistent database. On the other hand, such transitions can inject data into tokens by extracting relevant values from the database or by generating genuinely fresh ones. We systematically encode catalog-nets into one of the reference frameworks for the (parameterised) verification of data and processes. We show that fresh-value injection is a particularly complex feature to handle, and discuss strategies to tame it. Finally, we discuss how catalog nets relate to well-known formalisms in this area.
While the biomedical community has published several "open data" sources in the last decade, most researchers still endure severe logistical and technical challenges to discover, query, and integrate heterogeneous data and knowledge from multiple sources. To tackle these challenges, the community has experimented with Semantic Web and linked data technologies to create the Life Sciences Linked Open Data (LSLOD) cloud. In this paper, we extract schemas from more than 80 publicly available biomedical linked data graphs into an LSLOD schema graph and conduct an empirical meta-analysis to evaluate the extent of semantic heterogeneity across the LSLOD cloud. We observe that several LSLOD sources exist as stand-alone data sources that are not inter-linked with other sources, use unpublished schemas with minimal reuse or mappings, and have elements that are not useful for data integration from a biomedical perspective. We envision that the LSLOD schema graph and the findings from this research will aid researchers who wish to query and integrate data and knowledge from multiple biomedical sources simultaneously on the Web.
Network management, whether for malfunction analysis, failure prediction, performance monitoring and improvement, generally involves large amounts of data from different sources. To effectively integrate and manage these sources, automatically finding semantic matches among their schemas or ontologies is crucial. Existing approaches on database matching mainly fall into two categories. One focuses on the schema-level matching based on schema properties such as field names, data types, constraints and schema structures. Network management databases contain massive tables (e.g., network products, incidents, security alert and logs) from different departments and groups with nonuniform field names and schema characteristics. It is not reliable to match them by those schema properties. The other category is based on the instance-level matching using general string similarity techniques, which are not applicable for the matching of large network management databases. In this paper, we develop a matching technique for large NEtwork MAnagement databases (NEMA) deploying instance-level matching for effective data integration and connection. We design matching metrics and scores for both numerical and non-numerical fields and propose algorithms for matching these fields. The effectiveness and efficiency of NEMA are evaluated by conducting experiments based on ground truth field pairs in large network management databases. Our measurement on large databases with 1,458 fields, each of which contains over 10 million records, reveals that the accuracies of NEMA are up to 95%. It achieves 2%-10% higher accuracy and 5x-14x speedup over baseline methods.
Data integration and sharing maximally enhance the potential for novel and meaningful discoveries. However, it is a non-trivial task as integrating data from multiple sources can put sensitive information of study participants at risk. To address the privacy concern, we present a distributed Bayesian learning approach via Preconditioned Stochastic Gradient Langevin Dynamics with RMSprop, which combines differential privacy and homomorphic encryption in a harmonious manner while protecting private information. We applied the proposed secure and privacy-preserving distributed Bayesian learning approach to logistic regression and survival analysis on distributed data, and demonstrated its feasibility in terms of prediction accuracy and time complexity, compared to the centralized approach.
Selectivity estimation aims at estimating the number of database objects that satisfy a selection criterion. Answering this problem accurately and efficiently is essential to many applications, such as density estimation, outlier detection, query optimization, and data integration. The estimation problem is especially challenging for large-scale high-dimensional data due to the curse of dimensionality, the large variance of selectivity across different queries, and the need to make the estimator consistent (i.e., the selectivity is non-decreasing in the threshold). We propose a new deep learning-based model that learns a query-dependent piecewise linear function as selectivity estimator, which is flexible to fit the selectivity curve of any distance function and query object, while guaranteeing that the output is non-decreasing in the threshold. To improve the accuracy for large datasets, we propose to partition the dataset into multiple disjoint subsets and build a local model on each of them. We perform experiments on real datasets and show that the proposed model consistently outperforms state-of-the-art models in accuracy in an efficient way and is useful for real applications.
Recent advances in biological research have seen the emergence of high-throughput technologies with numerous applications that allow the study of biological mechanisms at an unprecedented depth and scale. A large amount of genomic data is now distributed through consortia like The Cancer Genome Atlas (TCGA), where specific types of biological information on specific type of tissue or cell are available. In cancer research, the challenge is now to perform integrative analyses of high-dimensional multi-omic data with the goal to better understand genomic processes that correlate with cancer outcomes, e.g. elucidate gene networks that discriminate a specific cancer subgroups (cancer sub-typing) or discovering gene networks that overlap across different cancer types (pan-cancer studies). In this paper, we propose a novel mixed graphical model approach to analyze multi-omic data of different types (continuous, discrete and count) and perform model selection by extending the Birth-Death MCMC (BDMCMC) algorithm initially proposed by \citet{stephens2000bayesian} and later developed by \cite{mohammadi2015bayesian}. We compare the performance of our method to the LASSO method and the standard BDMCMC method using simulations and find that our method is superior in terms of both computational efficiency and the accuracy of the model selection results. Finally, an application to the TCGA breast cancer data shows that integrating genomic information at different levels (mutation and expression data) leads to better subtyping of breast cancers.
By combining various cancer cell line (CCL) drug screening panels, the size of the data has grown significantly to begin understanding how advances in deep learning can advance drug response predictions. In this paper we train >35,000 neural network models, sweeping over common featurization techniques. We found the RNA-seq to be highly redundant and informative even with subsets larger than 128 features. We found the inclusion of single nucleotide polymorphisms (SNPs) coded as count matrices improved model performance significantly, and no substantial difference in model performance with respect to molecular featurization between the common open source MOrdred descriptors and Dragon7 descriptors. Alongside this analysis, we outline data integration between CCL screening datasets and present evidence that new metrics and imbalanced data techniques, as well as advances in data standardization, need to be developed.
The recent advances in single-cell technologies have enabled us to profile genomic features at unprecedented resolution and datasets from multiple domains are available, including datasets that profile different types of genomic features and datasets that profile the same type of genomic features across different species. These datasets typically have different powers in identifying the unknown cell types through clustering, and data integration can potentially lead to a better performance of clustering algorithms. In this work, we formulate the problem in an unsupervised transfer learning framework, which utilizes knowledge learned from auxiliary dataset to improve the clustering performance of target dataset. The degree of shared information among the target and auxiliary datasets can vary, and their distributions can also be different. To address these challenges, we propose an elastic coupled co-clustering based transfer learning algorithm, by elastically propagating clustering knowledge obtained from the auxiliary dataset to the target dataset. Implementation on single-cell genomic datasets shows that our algorithm greatly improves clustering performance over the traditional learning algorithms. The source code and data sets are available at https://github.com/cuhklinlab/elasticC3.
The European Materials and Modelling Ontology (EMMO) has recently been advanced in the computational molecular engineering and multiscale modelling communities as a top-level ontology, aiming to support semantic interoperability and data integration solutions, e.g., for research data infrastructures. The present work explores how top-level ontologies that are based on the same paradigm - the same set of fundamental postulates - as the EMMO can be applied to models of physical systems and their use in computational engineering practice. This paradigm, which combines mereology (in its extension as mereotopology) and semiotics (following Peirce's approach), is here referred to as mereosemiotics. Multiple conceivable ways of implementing mereosemiotics are compared, and the design space consisting of the possible types of top-level ontologies following this paradigm is characterized.
Nowadays, the agricultural data can be generated through various sources, such as: Internet of Thing (IoT), sensors, satellites, weather stations, robots, farm equipment, agricultural laboratories, farmers, government agencies and agribusinesses. The analysis of this big data enables farmers, companies and agronomists to extract high business and scientific knowledge, improving their operational processes and product quality. However, before analysing this data, different data sources need to be normalised, homogenised and integrated into a unified data representation. In this paper, we propose an agricultural data integration method using a constellation schema which is designed to be flexible enough to incorporate other datasets and big data models. We also apply some methods to extract knowledge with the view to improve crop yield; these include finding suitable quantities of soil properties, herbicides and insecticides for both increasing crop yield and protecting the environment.
In recent years, precision agriculture is becoming very popular. The introduction of modern information and communication technologies for collecting and processing Agricultural data revolutionise the agriculture practises. This has started a while ago (early 20th century) and it is driven by the low cost of collecting data about everything; from information on fields such as seed, soil, fertiliser, pest, to weather data, drones and satellites images. Specially, the agricultural data mining today is considered as Big Data application in terms of volume, variety, velocity and veracity. Hence it leads to challenges in processing vast amounts of complex and diverse information to extract useful knowledge for the farmer, agronomist, and other businesses. It is a key foundation to establishing a crop intelligence platform, which will enable efficient resource management and high quality agronomy decision making and recommendations. In this paper, we designed and implemented a continental level agricultural data warehouse (ADW). ADW is characterised by its (1) flexible schema; (2) data integration from real agricultural multi datasets; (3) data science and business intelligent support; (4) high performance; (5) high storage; (6) security; (7) governance and monitoring; (8) consistency, availability and partition tolerant; (9) cloud compatibility. We also evaluate the performance of ADW and present some complex queries to extract and return necessary knowledge about crop management.
All productive branches of society need an estimate to be able to control their expenses well. In the energy business, electric utilities use this information to control the power flow in the grid. For better energy production estimation of photovoltaic systems, it is necessary to join multiples geospatial and meteorological variables. This work proposes the creation of a satellite data integration platform, with production estimation models, base stations measurement and actual production capacity. This work presents statistical, probabilistic and artificial intelligence models that generate spatial and temporal production estimates that could improve production gains as well as facilitate the monitoring and supervision of new enterprises are presented.
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 development in machine learning and in particular deep learning has opened the way to more general and more efficient solutions to data integration problems. In this work, we propose a general approach to modeling and integrating entities from structured data, such as relational databases, as well as unstructured sources, such as free text from news articles. Our approach is designed to explicitly model and leverage relations between entities, thereby using all available information and preserving as much context as possible. This is achieved by combining siamese and graph neural networks to propagate information between connected entities and support high scalability. We evaluate our method on the task of integrating data about business entities, and we demonstrate that it outperforms standard rule-based systems, as well as other deep learning approaches that do not use graph-based representations.
Recent observations with varied schedules and types (moving average, snapshot, or regularly spaced) can help to improve streamflow forecasts, but it is challenging to integrate them effectively. Based on a long short-term memory (LSTM) streamflow model, we tested multiple versions of a flexible procedure we call data integration (DI) to leverage recent discharge measurements to improve forecasts. DI accepts lagged inputs either directly or through a convolutional neural network (CNN) unit. DI ubiquitously elevated streamflow forecast performance to unseen levels, reaching a record continental-scale median Nash-Sutcliffe Efficiency coefficient value of 0.86. Integrating moving-average discharge, discharge from the last few days, or even average discharge from the previous calendar month could all improve daily forecasts. Directly using lagged observations as inputs was comparable in performance to using the CNN unit. Importantly, we obtained valuable insights regarding hydrologic processes impacting LSTM and DI performance. Before applying DI, the base LSTM model worked well in mountainous or snow-dominated regions, but less well in regions with low discharge volumes (due to either low precipitation or high precipitation-energy synchronicity) and large inter-annual storage variability. DI was most beneficial in regions with high flow autocorrelation: it greatly reduced baseflow bias in groundwater-dominated western basins and also improved peak prediction for basins with dynamical surface water storage, such as the Prairie Potholes or Great Lakes regions. However, even DI cannot elevate high-aridity basins with one-day flash peaks. Despite this limitation, there is much promise for a deep-learning-based forecast paradigm due to its performance, automation, efficiency, and flexibility.
Background: Adverse Childhood Experiences (ACEs), a set of negative events and processes that a person might encounter during childhood and adolescence, have been proven to be linked to increased risks of a multitude of negative health outcomes and conditions when children reach adulthood and beyond. Objective: To better understand the relationship between ACEs and their relevant risk factors with associated health outcomes and to eventually design and implement preventive interventions, access to an integrated coherent dataset is needed. Therefore, we implemented a formal ontology as a resource to allow the mental health community to facilitate data integration and knowledge modeling and to improve ACEs surveillance and research. Methods: We use advanced knowledge representation and Semantic Web tools and techniques to implement the ontology. The current implementation of the ontology is expressed in the description logic ALCRIQ(D), a sublogic of Web Ontology Language (OWL 2). Results: The ACEs Ontology has been implemented and made available to the mental health community and the public via the BioPortal repository. Moreover, multiple use-case scenarios have been introduced to showcase and evaluate the usability of the ontology in action. The ontology was created to be used by major actors in the ACEs community with different applications, from the diagnosis of individuals and predicting potential negative outcomes that they might encounter to the prevention of ACEs in a population and designing interventions and policies. Conclusions: The ACEs Ontology provides a uniform and reusable semantic network and an integrated knowledge structure for mental health practitioners and researchers to improve ACEs surveillance and evaluation.
Machine learning applications in materials science are often hampered by shortage of experimental data. Integration with legacy data from past experiments is a viable way to solve the problem, but complex calibration is often necessary to use the data obtained under different conditions. In this paper, we present a novel calibration-free strategy to enhance the performance of Bayesian optimization with preference learning. The entire learning process is solely based on pairwise comparison of quantities (i.e., higher or lower) in the same dataset, and experimental design can be done without comparing quantities in different datasets. We demonstrate that Bayesian optimization is significantly enhanced via addition of legacy data for organic molecules and inorganic solid-state materials.
In clinical research, the lack of events of interest often necessitates imbalanced learning. One approach to resolve this obstacle is data integration or sharing, but due to privacy concerns neither is practical. Therefore, there is an increasing demand for a platform on which an analysis can be performed in a federated environment while maintaining privacy. However, it is quite challenging to develop a federated learning algorithm that can address both privacy-preserving and class imbalanced issues. In this study, we introduce a federated generative model learning platform for generating samples in a data-distributed environment while preserving privacy. We specifically propose approximate Bayesian computation-based Gaussian Mixture Model called 'Federated ABC-GMM', which can oversample data in a minor class by estimating the posterior distribution of model parameters across institutions in a privacy-preserving manner. PhysioNet2012, a dataset for prediction of mortality of patients in an Intensive Care Unit (ICU), was used to verify the performance of the proposed method. Experimental results show that our method boosts classification performance in terms of F1 score up to nearly an ideal situation. It is believed that the proposed method can be a novel alternative to solving class imbalance problems.
Recently, there has been significant interest in linear regression in the situation where predictors and responses are not observed in matching pairs corresponding to the same statistical unit as a consequence of separate data collection and uncertainty in data integration. Mismatched pairs can considerably impact the model fit and disrupt the estimation of regression parameters. In this paper, we present a method to adjust for such mismatches under ``partial shuffling" in which a sufficiently large fraction of (predictors, response)-pairs are observed in their correct correspondence. The proposed approach is based on a pseudo-likelihood in which each term takes the form of a two-component mixture density. Expectation-Maximization schemes are proposed for optimization, which (i) scale favorably in the number of samples, and (ii) achieve excellent statistical performance relative to an oracle that has access to the correct pairings as certified by simulations and case studies. In particular, the proposed approach can tolerate considerably larger fraction of mismatches than existing approaches, and enables estimation of the noise level as well as the fraction of mismatches. Inference for the resulting estimator (standard errors, confidence intervals) can be based on established theory for composite likelihood estimation. Along the way, we also propose a statistical test for the presence of mismatches and establish its consistency under suitable conditions.
An ontology makes a special vocabulary which describes the domain of interest and the meaning of the term on that vocabulary. Based on the precision of the specification, the concept of the ontology contains several data and conceptual models. The notion of ontology has emerged into wide ranges of applications including database integration, peer-to-peer systems, e-commerce, semantic web, etc. It can be considered as a practical tool for conceptualizing things which are expressed in computer format. This paper is devoted to ontology matching as a mean or information integration. Several matching solutions have been presented from various areas such as databases, information systems and artificial intelligence. All of them take advantages of different attributes of ontology like, structures, data instances, semantics and labels and its other valuable properties. The solutions have some common techniques and cope with similar problems, but use different methods for combining and exploiting their results. Information integration is among the first classes of applications at which matching was considered as a probable solution. Information integration contains many fields including, data integration, schema integration, catalogue integration and semantic integration. We cover these notions in term of ontology in our proposed paper.