Since the first conference held in Marseille in 1982, ICLP has been the premier international event for presenting research in logic programming. Contributions are sought in all areas of logic programming, including but not restricted to: Foundations: Semantics, Formalisms, Nonmonotonic reasoning, Knowledge representation. Languages: Concurrency, Objects, Coordination, Mobility, Higher Order, Types, Modes, Assertions, Modules, Meta-programming, Logic-based domain-specific languages, Programming Techniques. Declarative programming: Declarative program development, Analysis, Type and mode inference, Partial evaluation, Abstract interpretation, Transformation, Validation, Verification, Debugging, Profiling, Testing, Execution visualization Implementation: Virtual machines, Compilation, Memory management, Parallel/distributed execution, Constraint handling rules, Tabling, Foreign interfaces, User interfaces. Related Paradigms and Synergies: Inductive and Co-inductive Logic Programming, Constraint Logic Programming, Answer Set Programming, Interaction with SAT, SMT and CSP solvers, Logic programming techniques for type inference and theorem proving, Argumentation, Probabilistic Logic Programming, Relations to object-oriented and Functional programming. Applications: Databases, Big Data, Data integration and federation, Software engineering, Natural language processing, Web and Semantic Web, Agents, Artificial intelligence, Computational life sciences, Education, Cybersecurity, and Robotics.
Deep learning based techniques have been recently used with promising results for data integration problems. Some methods directly use pre-trained embeddings that were trained on a large corpus such as Wikipedia. However, they may not always be an appropriate choice for enterprise datasets with custom vocabulary. Other methods adapt techniques from natural language processing to obtain embeddings for the enterprise's relational data. However, this approach blindly treats a tuple as a sentence, thus losing a large amount of contextual information present in the tuple. We propose algorithms for obtaining local embeddings that are effective for data integration tasks on relational databases. We make four major contributions. First, we describe a compact graph-based representation that allows the specification of a rich set of relationships inherent in the relational world. Second, we propose how to derive sentences from such a graph that effectively "describe" the similarity across elements (tokens, attributes, rows) in the two datasets. The embeddings are learned based on such sentences. Third, we propose effective optimization to improve the quality of the learned embeddings and the performance of integration tasks. Finally, we propose a diverse collection of criteria to evaluate relational embeddings and perform an extensive set of experiments validating them against multiple baseline methods. Our experiments show that our framework, EmbDI, produces meaningful results for data integration tasks such as schema matching and entity resolution both in supervised and unsupervised settings.
Entity linking and resolution is a fundamental database problem with applications in data integration, data cleansing, information retrieval, knowledge fusion, and knowledge-base population. It is the task of accurately identifying multiple, differing, and possibly contradicting representations of the same real-world entity in data. In this work, we propose an entity linking and resolution system capable of linking entities across different databases and mentioned-entities extracted from text data. Our entity linking/resolution solution, called Certus, uses a graph model to represent the profiles of entities. The graph model is versatile, thus, it is capable of handling multiple values for an attribute or a relationship, as well as the provenance descriptions of the values. Provenance descriptions of a value provide the settings of the value, such as validity periods, sources, security requirements, etc. This paper presents the architecture for the entity linking system, the logical, physical, and indexing models used in the system, and the general linking process. Furthermore, we demonstrate the performance of update operations of the physical storage models when the system is implemented in two state-of-the-art database management systems, HBase and Postgres.
Record linkage is an essential part of nearly all real-world systems that consume structured and unstructured data coming from different sources. Typically no common key is available for connecting records. Massive data cleaning and data integration processes often have to be completed before any data analytics and further processing can be performed. Although record linkage is frequently regarded as a somewhat tedious but necessary step, it reveals valuable insights into the data at hand. These insights guide further analytic approaches to the data and support data visualization. In this work we focus on company entity matching, where company name, location and industry are taken into account. Our contribution is an end-to-end, highly scalable, enterprise-grade system that uses rule-based linkage algorithms extended with a machine learning approach to account for short company names. Linkage time is greatly reduced by efficient decomposition of the search space using MinHash. High linkage accuracy is achieved by the proposed thorough scoring process of the matching candidates. Based on real-world ground truth datasets, we show that our approach reaches a recall of 91% compared to 73% for baseline approaches. These results are achieved while scaling linearly with the number of nodes used in the system.
High-quality data is key to interpretable and trustworthy data analytics and the basis for meaningful data-driven decisions. In practical scenarios, data quality is typically associated with data preprocessing, profiling, and cleansing for subsequent tasks like data integration or data analytics. However, from a scientific perspective, a lot of research has been published about the measurement (i.e., the detection) of data quality issues and different generally applicable data quality dimensions and metrics have been discussed. In this work, we close the gap between research into data quality measurement and practical implementations by investigating the functional scope of current data quality tools. With a systematic search, we identified 667 software tools dedicated to "data quality", from which we evaluated 13 tools with respect to three functionality areas: (1) data profiling, (2) data quality measurement in terms of metrics, and (3) continuous data quality monitoring. We selected the evaluated tools with regard to pre-defined exclusion criteria to ensure that they are domain-independent, provide the investigated functions, and are evaluable freely or as trial. This survey aims at a comprehensive overview on state-of-the-art data quality tools and reveals potential for their functional enhancement. Additionally, the results allow a critical discussion on concepts, which are widely accepted in research, but hardly implemented in any tool observed, for example, generally applicable data quality metrics.
Data integration systems allow users to access data sitting in multiple sources by means of queries over a global schema, related to the sources via mappings. Data sources often contain sensitive information, and thus an analysis is needed to verify that a schema satisfies a privacy policy, given as a set of queries whose answers should not be accessible to users. Such an analysis should take into account not only knowledge that an attacker may have about the mappings, but also what they may know about the semantics of the sources. In this paper, we show that source constraints can have a dramatic impact on disclosure analysis. We study the problem of determining whether a given data integration system discloses a source query to an attacker in the presence of constraints, providing both lower and upper bounds on source-aware disclosure analysis.
In recent years, precision agriculture that uses modern information and communication technologies is becoming very popular. Raw and semi-processed agricultural data are usually collected through various sources, such as: Internet of Thing (IoT), sensors, satellites, weather stations, robots, farm equipment, farmers and agribusinesses, etc. Besides, agricultural datasets are very large, complex, unstructured, heterogeneous, non-standardized, and inconsistent. Hence, the agricultural data mining is considered as Big Data application in terms of volume, variety, velocity and veracity. It is a key foundation to establishing a crop intelligence platform, which will enable resource efficient agronomy decision making and recommendations. In this paper, we designed and implemented a continental level agricultural data warehouse by combining Hive, MongoDB and Cassandra. Our data warehouse capabilities: (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) replication and recovery; (9) consistency, availability and partition tolerant; (10) distributed and cloud deployment. We also evaluate the performance of our data warehouse.
Data integration methods that analyze multiple sources of data simultaneously can often provide more holistic insights than can separate inquiries of each data source. Motivated by the advantages of data integration in the era of "big data", we investigate feature selection for high-dimensional multi-view data with mixed data types (e.g. continuous, binary, count-valued). This heterogeneity of multi-view data poses numerous challenges for existing feature selection methods. However, after critically examining these issues through empirical and theoretically-guided lenses, we develop a practical solution, the Block Randomized Adaptive Iterative Lasso (B-RAIL), which combines the strengths of the randomized Lasso, adaptive weighting schemes, and stability selection. B-RAIL serves as a versatile data integration method for sparse regression and graph selection, and we demonstrate the effectiveness of B-RAIL through extensive simulations and a case study to infer the ovarian cancer gene regulatory network. In this case study, B-RAIL successfully identifies well-known biomarkers associated with ovarian cancer and hints at novel candidates for future ovarian cancer research.
This work tackles the problem of fuzzy joining of strings that naturally tokenize into meaningful substrings, e.g., full names. Tokenized-string joins have several established applications in the context of data integration and cleaning. This work is primarily motivated by fraud detection, where attackers slightly modify tokenized strings, e.g., names on accounts, to create numerous identities that she can use to defraud service providers, e.g., Google, and LinkedIn. To detect such attacks, all the accounts are pair-wise compared, and the resulting similar accounts are considered suspicious and are further investigated. Comparing the tokenized-string features of a large number of accounts requires an intuitive tokenized-string distance that can detect subtle edits introduced by an adversary, and a very scalable algorithm. This is not achievable by existing distance measure that are unintuitive, hard to tune, and whose join algorithms are serial and hence unscalable. We define a novel intuitive distance measure between tokenized strings, Normalized Setwise Levenshtein Distance (NSLD). To the best of our knowledge, NSLD is the first metric proposed for comparing tokenized strings. We propose a scalable distributed framework, Tokenized-String Joiner (TSJ), that adopts existing scalable string-join algorithms as building blocks to perform NSLD-joins. We carefully engineer optimizations and approximations that dramatically improve the efficiency of TSJ. The effectiveness of the TSJ framework is evident from the evaluation conducted on tens of millions of tokenized-string names from Google accounts. The superiority of the tokenized-string-specific TSJ framework over the general-purpose metric-spaces joining algorithms has been established.
Entity resolution (ER) is one of the fundamental problems in data integration, where machine learning (ML) based classifiers often provide the state-of-the-art results. Considerable human effort goes into feature engineering and training data creation. In this paper, we investigate a new problem: Given a dataset D_T for ER with limited or no training data, is it possible to train a good ML classifier on D_T by reusing and adapting the training data of dataset D_S from same or related domain? Our major contributions include (1) a distributed representation based approach to encode each tuple from diverse datasets into a standard feature space; (2) identification of common scenarios where the reuse of training data can be beneficial; and (3) five algorithms for handling each of the aforementioned scenarios. We have performed comprehensive experiments on 12 datasets from 5 different domains (publications, movies, songs, restaurants, and books). Our experiments show that our algorithms provide significant benefits such as providing superior performance for a fixed training data size.
New technologies have enabled the investigation of biology and human health at an unprecedented scale and in multiple dimensions. These dimensions include a myriad of properties describing genome, epigenome, transcriptome, microbiome, phenotype, and lifestyle. No single data type, however, can capture the complexity of all the factors relevant to understanding a phenomenon such as a disease. Integrative methods that combine data from multiple technologies have thus emerged as critical statistical and computational approaches. The key challenge in developing such approaches is the identification of effective models to provide a comprehensive and relevant systems view. An ideal method can answer a biological or medical question, identifying important features and predicting outcomes, by harnessing heterogeneous data across several dimensions of biological variation. In this Review, we describe the principles of data integration and discuss current methods and available implementations. We provide examples of successful data integration in biology and medicine. Finally, we discuss current challenges in biomedical integrative methods and our perspective on the future development of the field.
The explosion of available data along with the need to integrate and utilize that data has led to a pressing interest in data integration techniques. In terms of Semantic Web technologies, Ontology Alignment is a key step in the process of integrating heterogeneous knowledge bases. In this paper, we present the Edge Confidence technique, a modification and improvement over the popular Similarity Flooding technique for Ontology Alignment.
Many database resources, such as Reactome, collect manually annotated reactions, interactions, and pathways from peer-reviewed publications. The interactors (e.g., a protein), interactions, and pathways in these data resources are often represented as instances in using BioPAX, a standard pathway data exchange format. However, these interactions are better represented as classes (or universals) since they always occur given appropriate conditions. This study aims to represent various human interaction pathways and networks as classes via a formal ontology aligned with the Basic Formal Ontology (BFO). Towards this goal, the Human Interaction Network Ontology (HINO) was generated by extending the BFO-aligned Interaction Network Ontology (INO). All human pathways and associated processes and interactors listed in Reactome and represented in BioPAX were first converted to ontology classes by aligning them under INO. Related terms and associated relations and hierarchies from external ontologies (e.g., CHEBI and GO) were also retrieved and imported into HINO. HINO ontology terms were resolved in the linked ontology data server Ontobee. The RDF triples stored in the RDF triple store are queryable through a SPARQL program. Such an ontology system supports advanced pathway data integration and applications.
The modelling, analysis, and visualisation of dynamic geospatial phenomena has been identified as a key developmental challenge for next-generation Geographic Information Systems (GIS). In this context, the envisaged paradigmatic extensions to contemporary foundational GIS technology raises fundamental questions concerning the ontological, formal representational, and (analytical) computational methods that would underlie their spatial information theoretic underpinnings. We present the conceptual overview and architecture for the development of high-level semantic and qualitative analytical capabilities for dynamic geospatial domains. Building on formal methods in the areas of commonsense reasoning, qualitative reasoning, spatial and temporal representation and reasoning, reasoning about actions and change, and computational models of narrative, we identify concrete theoretical and practical challenges that accrue in the context of formal reasoning about `space, events, actions, and change'. With this as a basis, and within the backdrop of an illustrated scenario involving the spatio-temporal dynamics of urban narratives, we address specific problems and solutions techniques chiefly involving `qualitative abstraction', `data integration and spatial consistency', and `practical geospatial abduction'. From a broad topical viewpoint, we propose that next-generation dynamic GIS technology demands a transdisciplinary scientific perspective that brings together Geography, Artificial Intelligence, and Cognitive Science. Keywords: artificial intelligence; cognitive systems; human-computer interaction; geographic information systems; spatio-temporal dynamics; computational models of narrative; geospatial analysis; geospatial modelling; ontology; qualitative spatial modelling and reasoning; spatial assistance systems
This paper explores combinatorial optimization for problems of max-weight graph matching on multi-partite graphs, which arise in integrating multiple data sources. Entity resolution-the data integration problem of performing noisy joins on structured data-typically proceeds by first hashing each record into zero or more blocks, scoring pairs of records that are co-blocked for similarity, and then matching pairs of sufficient similarity. In the most common case of matching two sources, it is often desirable for the final matching to be one-to-one (a record may be matched with at most one other); members of the database and statistical record linkage communities accomplish such matchings in the final stage by weighted bipartite graph matching on similarity scores. Such matchings are intuitively appealing: they leverage a natural global property of many real-world entity stores-that of being nearly deduped-and are known to provide significant improvements to precision and recall. Unfortunately unlike the bipartite case, exact max-weight matching on multi-partite graphs is known to be NP-hard. Our two-fold algorithmic contributions approximate multi-partite max-weight matching: our first algorithm borrows optimization techniques common to Bayesian probabilistic inference; our second is a greedy approximation algorithm. In addition to a theoretical guarantee on the latter, we present comparisons on a real-world ER problem from Bing significantly larger than typically found in the literature, publication data, and on a series of synthetic problems. Our results quantify significant improvements due to exploiting multiple sources, which are made possible by global one-to-one constraints linking otherwise independent matching sub-problems. We also discover that our algorithms are complementary: one being much more robust under noise, and the other being simple to implement and very fast to run.
Many aspects of macroevolutionary theory and our understanding of biotic responses to global environmental change derive from literature-based compilations of palaeontological data. Existing manually assembled databases are, however, incomplete and difficult to assess and enhance. Here, we develop and validate the quality of a machine reading system, PaleoDeepDive, that automatically locates and extracts data from heterogeneous text, tables, and figures in publications. PaleoDeepDive performs comparably to humans in complex data extraction and inference tasks and generates congruent synthetic macroevolutionary results. Unlike traditional databases, PaleoDeepDive produces a probabilistic database that systematically improves as information is added. We also show that the system can readily accommodate sophisticated data types, such as morphological data in biological illustrations and associated textual descriptions. Our machine reading approach to scientific data integration and synthesis brings within reach many questions that are currently underdetermined and does so in ways that may stimulate entirely new modes of inquiry.
Nonnegative matrix factorization (NMF) methods have proved to be powerful across a wide range of real-world clustering applications. Integrating multiple types of measurements for the same objects/subjects allows us to gain a deeper understanding of the data and refine the clustering. We have developed a novel Graph-reguarized multiview NMF-based method for data integration called EquiNMF. The parameters for our method are set in a completely automated data-specific unsupervised fashion, a highly desirable property in real-world applications. We performed extensive and comprehensive experiments on multiview imaging data. We show that EquiNMF consistently outperforms other single-view NMF methods used on concatenated data and multi-view NMF methods with different types of regularizations.
Manufacturing Operations Management (MOM) systems are complex in the sense that they integrate data from heterogeneous systems inside the automation pyramid. The need for context-aware analytics arises from the dynamics of these systems that influence data generation and hamper comparability of analytics, especially predictive models (e.g. predictive maintenance), where concept drift affects application of these models in the future. Recently, an increasing amount of research has been directed towards data integration using semantic context models. Manual construction of such context models is an elaborate and error-prone task. Therefore, we pose the challenge to apply combinations of knowledge extraction techniques in the domain of analytics in MOM, which comprises the scope of data integration within Product Life-cycle Management (PLM), Enterprise Resource Planning (ERP), and Manufacturing Execution Systems (MES). We describe motivations, technological challenges and show benefits of context-aware analytics, which leverage from and regard the interconnectedness of semantic context data. Our example scenario shows the need for distribution and effective change tracking of context information.
For most problems in science and engineering we can obtain data sets that describe the observed system from various perspectives and record the behavior of its individual components. Heterogeneous data sets can be collectively mined by data fusion. Fusion can focus on a specific target relation and exploit directly associated data together with contextual data and data about system's constraints. In the paper we describe a data fusion approach with penalized matrix tri-factorization (DFMF) that simultaneously factorizes data matrices to reveal hidden associations. The approach can directly consider any data that can be expressed in a matrix, including those from feature-based representations, ontologies, associations and networks. We demonstrate the utility of DFMF for gene function prediction task with eleven different data sources and for prediction of pharmacologic actions by fusing six data sources. Our data fusion algorithm compares favorably to alternative data integration approaches and achieves higher accuracy than can be obtained from any single data source alone.
Matrix completion has attracted significant recent attention in many fields including statistics, applied mathematics and electrical engineering. Current literature on matrix completion focuses primarily on independent sampling models under which the individual observed entries are sampled independently. Motivated by applications in genomic data integration, we propose a new framework of structured matrix completion (SMC) to treat structured missingness by design. Specifically, our proposed method aims at efficient matrix recovery when a subset of the rows and columns of an approximately low-rank matrix are observed. We provide theoretical justification for the proposed SMC method and derive lower bound for the estimation errors, which together establish the optimal rate of recovery over certain classes of approximately low-rank matrices. Simulation studies show that the method performs well in finite sample under a variety of configurations. The method is applied to integrate several ovarian cancer genomic studies with different extent of genomic measurements, which enables us to construct more accurate prediction rules for ovarian cancer survival.