CIDACS-RL: a novel indexing search and scoring-based record linkage system for huge datasets with high accuracy and scalability

Background: Record linkage is the process of identifying and combining records about the same individual from two or more different datasets. While there are many open source and commercial data linkage tools, the volume and complexity of currently available datasets for linkage pose a huge challenge; hence, designing an efficient linkage tool with reasonable accuracy and scalability is required. Methods: We developed CIDACS-RL (Centre for Data and Knowledge Integration for Health – Record Linkage), a novel iterative deterministic record linkage algorithm based on a combination of indexing search and scoring algorithms (provided by Apache Lucene). We described how the algorithm works and compared its performance with four open source linkage tools (AtyImo, Febrl, FRIL and RecLink) in terms of sensitivity and positive predictive value using gold standard dataset. We also evaluated its accuracy and scalability using a case-study and its scalability and execution time using a simulated cohort in serial (single core) and multi-core (eight core) computation settings. Results: Overall, CIDACS-RL algorithm had a superior performance: positive predictive value (99.93% versus AtyImo 99.30%, RecLink 99.5%, Febrl 98.86%, and FRIL 96.17%) and sensitivity (99.87% versus AtyImo 98.91%, RecLink 73.75%, Febrl 90.58%, and FRIL 74.66%). In the case study, using a ROC curve to choose the most appropriate cut-off value (0.896), the obtained metrics were: sensitivity = 92.5% (95% CI 92.07–92.99), specificity = 93.5% (95% CI 93.08–93.8) and area under the curve (AUC) = 97% (95% CI 96.97–97.35). The multi-core computation was about four times faster (150 seconds) than the serial setting (550 seconds) when using a dataset of 20 million records. Conclusion: CIDACS-RL algorithm is an innovative linkage tool for huge datasets, with higher accuracy, improved scalability, and substantially shorter execution time compared to other existing linkage tools. In addition, CIDACS-RL can be deployed on standard computers without the need for high-speed processors and distributed infrastructures

A Bayesian Approach to Graphical Record Linkage and De-duplication

We propose an unsupervised approach for linking records across arbitrarily many files, while simultaneously detecting duplicate records within files. Our key innovation involves the representation of the pattern of links between records as a bipartite graph, in which records are directly linked to latent true individuals, and only indirectly linked to other records. This flexible representation of the linkage structure naturally allows us to estimate the attributes of the unique observable people in the population, calculate transitive linkage probabilities across records (and represent this visually), and propagate the uncertainty of record linkage into later analyses. Our method makes it particularly easy to integrate record linkage with post-processing procedures such as logistic regression, capture-recapture, etc. Our linkage structure lends itself to an efficient, linear-time, hybrid Markov chain Monte Carlo algorithm, which overcomes many obstacles encountered by previously record linkage approaches, despite the high-dimensional parameter space. We illustrate our method using longitudinal data from the National Long Term Care Survey and with data from the Italian Survey on Household and Wealth, where we assess the accuracy of our method and show it to be better in terms of error rates and empirical scalability than other approaches in the literature.Comment: 39 pages, 8 figures, 8 tables. Longer version of arXiv:1403.0211, In press, Journal of the American Statistical Association: Theory and Methods (2015

Embedding Techniques to Solve Large-scale Entity Resolution

Entity resolution (ER) identifies and links records that belong to the same real-world entities, where an entity refer to any real-world object. It is a primary task in data integration. Accurate and efficient ER substantially impacts various commercial, security, and scientific applications. Often, there are no unique identifiers for entities in datasets/databases that would make the ER task easy. Therefore record matching depends on entity identifying attributes and approximate matching techniques. The issues of efficiently handling large-scale data remain an open research problem with the increasing volumes and velocities in modern data collections. Fast, scalable, real-time and approximate entity matching techniques that provide high-quality results are highly demanding. This thesis proposes solutions to address the challenges of lack of test datasets and the demand for fast indexing algorithms in large-scale ER. The shortage of large-scale, real-world datasets with ground truth is a primary concern in developing and testing new ER algorithms. Usually, for many datasets, there is no information on the ground truth or ‘gold standard’ data that specifies if two records correspond to the same entity or not. Moreover, obtaining test data for ER algorithms that use personal identifying keys (e.g., names, addresses) is difficult due to privacy and confidentiality issues. Towards this challenge, we proposed a numerical simulation model that produces realistic large-scale data to test new methods when suitable public datasets are unavailable. One of the important findings of this work is the approximation of vectors that represent entity identification keys and their relationships, e.g., dissimilarities and errors. Indexing techniques reduce the search space and execution time in the ER process. Based on the ideas of the approximate vectors of entity identification keys, we proposed a fast indexing technique (Em-K indexing) suitable for real-time, approximate entity matching in large-scale ER. Our Em-K indexing method provides a quick and accurate block of candidate matches for a querying record by searching an existing reference database. All our solutions are metric-based. We transform metric or non-metric spaces to a lowerdimensional Euclidean space, known as configuration space, using multidimensional scaling (MDS). This thesis discusses how to modify MDS algorithms to solve various ER problems efficiently. We proposed highly efficient and scalable approximation methods that extend the MDS algorithm for large-scale datasets. We empirically demonstrate the improvements of our proposed approaches on several datasets with various parameter settings. The outcomes show that our methods can generate large-scale testing data, perform fast real-time and approximate entity matching, and effectively scale up the mapping capacity of MDS.Thesis (Ph.D.) -- University of Adelaide, School of Mathematical Sciences, 202

MinoanER: Schema-Agnostic, Non-Iterative, Massively Parallel Resolution of Web Entities

Entity Resolution (ER) aims to identify different descriptions in various Knowledge Bases (KBs) that refer to the same entity. ER is challenged by the Variety, Volume and Veracity of entity descriptions published in the Web of Data. To address them, we propose the MinoanER framework that simultaneously fulfills full automation, support of highly heterogeneous entities, and massive parallelization of the ER process. MinoanER leverages a token-based similarity of entities to define a new metric that derives the similarity of neighboring entities from the most important relations, as they are indicated only by statistics. A composite blocking method is employed to capture different sources of matching evidence from the content, neighbors, or names of entities. The search space of candidate pairs for comparison is compactly abstracted by a novel disjunctive blocking graph and processed by a non-iterative, massively parallel matching algorithm that consists of four generic, schema-agnostic matching rules that are quite robust with respect to their internal configuration. We demonstrate that the effectiveness of MinoanER is comparable to existing ER tools over real KBs exhibiting low Variety, but it outperforms them significantly when matching KBs with high Variety.Comment: Presented at EDBT 2001

Toward Concept-Based Text Understanding and Mining

There is a huge amount of text information in the world, written in natural languages. Most of the text information is hard to access compared with other well-structured information sources such as relational databases. This is because reading and understanding text requires the ability to disambiguate text fragments at several levels, syntactically and semantically, abstracting away details and using background knowledge in a variety of ways. One possible solution to these problems is to implement a framework of concept-based text understanding and mining, that is, a mechanism of analyzing and integrating segregated information, and a framework of organizing, indexing, accessing textual information centered around real-world concepts. A fundamental difficulty toward this goal is caused by the concept ambiguity of natural language. In text, the real-world entities are referred using their names. The variability in writing a given concept, along with the fact that different concepts/enities may have very similar writings, poses a significant challenge to progress in text understanding and mining. Supporting concept-based natural language understanding requires resolving conceptual ambiguity, and in particular, identifying whether different mentions of real world entities, within and across documents, actually represent the same concept. This thesis systematically studies this fundamental problem. We study and propose different machine learning techniques to address different aspects of this problem and show that as more information can be exploited, the learning techniques developed accordingly, can continuously improve the identification accuracy. In addition, we extend our global probabilistic model to address a significant application -- semantic integration between text and databases