Quality Assessment of Linked Datasets using Probabilistic Approximation

With the increasing application of Linked Open Data, assessing the quality of datasets by computing quality metrics becomes an issue of crucial importance. For large and evolving datasets, an exact, deterministic computation of the quality metrics is too time consuming or expensive. We employ probabilistic techniques such as Reservoir Sampling, Bloom Filters and Clustering Coefficient estimation for implementing a broad set of data quality metrics in an approximate but sufficiently accurate way. Our implementation is integrated in the comprehensive data quality assessment framework Luzzu. We evaluated its performance and accuracy on Linked Open Datasets of broad relevance.Comment: 15 pages, 2 figures, To appear in ESWC 2015 proceeding

Luzzu - A Framework for Linked Data Quality Assessment

With the increasing adoption and growth of the Linked Open Data cloud [9], with RDFa, Microformats and other ways of embedding data into ordinary Web pages, and with initiatives such as schema.org, the Web is currently being complemented with a Web of Data. Thus, the Web of Data shares many characteristics with the original Web of Documents, which also varies in quality. This heterogeneity makes it challenging to determine the quality of the data published on the Web and to subsequently make this information explicit to data consumers. The main contribution of this article is LUZZU, a quality assessment framework for Linked Open Data. Apart from providing quality metadata and quality problem reports that can be used for data cleaning, LUZZU is extensible: third party metrics can be easily plugged-in the framework. The framework does not rely on SPARQL endpoints, and is thus free of all the problems that come with them, such as query timeouts. Another advantage over SPARQL based qual- ity assessment frameworks is that metrics implemented in LUZZU can have more complex functionality than triple matching. Using the framework, we performed a quality assessment of a number of statistical linked datasets that are available on the LOD cloud. For this evaluation, 25 metrics from ten different dimensions were implemented

Probabilistic performance estimators for computational chemistry methods: the empirical cumulative distribution function of absolute errors

Benchmarking studies in computational chemistry use reference datasets to assess the accuracy of a method through error statistics. The commonly used error statistics, such as the mean signed and mean unsigned errors, do not inform end-users on the expected amplitude of prediction errors attached to these methods. We show that, the distributions of model errors being neither normal nor zero-centered, these error statistics cannot be used to infer prediction error probabilities. To overcome this limitation, we advocate for the use of more informative statistics, based on the empirical cumulative distribution function of unsigned errors, namely (1) the probability for a new calculation to have an absolute error below a chosen threshold, and (2) the maximal amplitude of errors one can expect with a chosen high confidence level. Those statistics are also shown to be well suited for benchmarking and ranking studies. Moreover, the standard error on all benchmarking statistics depends on the size of the reference dataset. Systematic publication of these standard errors would be very helpful to assess the statistical reliability of benchmarking conclusions.Comment: Supplementary material: https://github.com/ppernot/ECDF

Scalable Quality Assessment of Linked Data

In a world where the information economy is booming, poor data quality can lead to adverse consequences, including social and economical problems such as decrease in revenue. Furthermore, data-driven indus- tries are not just relying on their own (proprietary) data silos, but are also continuously aggregating data from different sources. This aggregation could then be re-distributed back to “data lakes”. However, this data (including Linked Data) is not necessarily checked for its quality prior to its use. Large volumes of data are being exchanged in a standard and interoperable format between organisations and published as Linked Data to facilitate their re-use. Some organisations, such as government institutions, take a step further and open their data. The Linked Open Data Cloud is a witness to this. However, similar to data in data lakes, it is challenging to determine the quality of this heterogeneous data, and subsequently to make this information explicit to data consumers. Despite the availability of a number of tools and frameworks to assess Linked Data quality, the current solutions do not aggregate a holistic approach that enables both the assessment of datasets and also provides consumers with quality results that can then be used to find, compare and rank datasets’ fitness for use. In this thesis we investigate methods to assess the quality of (possibly large) linked datasets with the intent that data consumers can then use the assessment results to find datasets that are fit for use, that is; finding the right dataset for the task at hand. Moreover, the benefits of quality assessment are two-fold: (1) data consumers do not need to blindly rely on subjective measures to choose a dataset, but base their choice on multiple factors such as the intrinsic structure of the dataset, therefore fostering trust and reputation between the publishers and consumers on more objective foundations; and (2) data publishers can be encouraged to improve their datasets so that they can be re-used more. Furthermore, our approach scales for large datasets. In this regard, we also look into improving the efficiency of quality metrics using various approximation techniques. However the trade-off is that consumers will not get the exact quality value, but a very close estimate which anyway provides the required guidance towards fitness for use. The central point of this thesis is not on data quality improvement, nonetheless, we still need to understand what data quality means to the consumers who are searching for potential datasets. This thesis looks into the challenges faced to detect quality problems in linked datasets presenting quality results in a standardised machine-readable and interoperable format for which agents can make sense out of to help human consumers identifying the fitness for use dataset. Our proposed approach is more consumer-centric where it looks into (1) making the assessment of quality as easy as possible, that is, allowing stakeholders, possibly non-experts, to identify and easily define quality metrics and to initiate the assessment; and (2) making results (quality metadata and quality reports) easy for stakeholders to understand, or at least interoperable with other systems to facilitate a possible data quality pipeline. Finally, our framework is used to assess the quality of a number of heterogeneous (large) linked datasets, where each assessment returns a quality metadata graph that can be consumed by agents as Linked Data. In turn, these agents can intelligently interpret a dataset’s quality with regard to multiple dimensions and observations, and thus provide further insight to consumers regarding its fitness for use

MetAssign: probabilistic annotation of metabolites from LC–MS data using a Bayesian clustering approach

Motivation: The use of liquid chromatography coupled to mass spectrometry (LC–MS) has enabled the high-throughput profiling of the metabolite composition of biological samples. However, the large amount of data obtained can be difficult to analyse and often requires computational processing to understand which metabolites are present in a sample. This paper looks at the dual problem of annotating peaks in a sample with a metabolite, together with putatively annotating whether a metabolite is present in the sample. The starting point of the approach is a Bayesian clustering of peaks into groups, each corresponding to putative adducts and isotopes of a single metabolite.<p></p> Results: The Bayesian modelling introduced here combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The results inherently contain a quantitative estimate of confidence in the peak annotations and allow an accurate trade off between precision and recall. Extensive validation experiments using authentic chemical standards show that this system is able to produce more accurate putative identifications than other state-of-the-art systems, while at the same time giving a probabilistic measure of confidence in the annotations.<p></p> Availability: The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download at http://mzmatch.sourceforge.net/

Probabilistic performance estimators for computational chemistry methods: Systematic Improvement Probability and Ranking Probability Matrix. I. Theory

The comparison of benchmark error sets is an essential tool for the evaluation of theories in computational chemistry. The standard ranking of methods by their Mean Unsigned Error is unsatisfactory for several reasons linked to the non-normality of the error distributions and the presence of underlying trends. Complementary statistics have recently been proposed to palliate such deficiencies, such as quantiles of the absolute errors distribution or the mean prediction uncertainty. We introduce here a new score, the systematic improvement probability (SIP), based on the direct system-wise comparison of absolute errors. Independently of the chosen scoring rule, the uncertainty of the statistics due to the incompleteness of the benchmark data sets is also generally overlooked. However, this uncertainty is essential to appreciate the robustness of rankings. In the present article, we develop two indicators based on robust statistics to address this problem: P_{inv}, the inversion probability between two values of a statistic, and \mathbf{P}_{r}, the ranking probability matrix. We demonstrate also the essential contribution of the correlations between error sets in these scores comparisons

Measuring Accuracy of Triples in Knowledge Graphs

An increasing amount of large-scale knowledge graphs have been constructed in recent years. Those graphs are often created from text-based extraction, which could be very noisy. So far, cleaning knowledge graphs are often carried out by human experts and thus very inefficient. It is necessary to explore automatic methods for identifying and eliminating erroneous information. In order to achieve this, previous approaches primarily rely on internal information i.e. the knowledge graph itself. In this paper, we introduce an automatic approach, Triples Accuracy Assessment (TAA), for validating RDF triples (source triples) in a knowledge graph by finding consensus of matched triples (among target triples) from other knowledge graphs. TAA uses knowledge graph interlinks to find identical resources and apply different matching methods between the predicates of source triples and target triples. Then based on the matched triples, TAA calculates a confidence score to indicate the correctness of a source triple. In addition, we present an evaluation of our approach using the FactBench dataset for fact validation. Our findings show promising results for distinguishing between correct and wrong triples