Approximate String Matching Techniques Research Articles

Association of Patient-Centered Medical Home designation and quality indicators within HRSA-funded community health center delivery sites

BackgroundPatient-Centered Medical Home (PCMH) adoption is an important strategy to help improve primary care quality within Health Resources and Service Administration (HRSA) community health centers (CHC), but evidence of its effect thus far remains mixed. A limitation of previous evaluations has been the inability to account for the proportion of CHC delivery sites that are designated medical homes.MethodsRetrospective cross-sectional study using HRSA Uniform Data System (UDS) and certification files from the National Committee for Quality Assurance (NCQA) and the Joint Commission (JC). Datasets were linked through geocoding and an approximate string-matching algorithm. Predicted probability scores were regressed onto 11 clinical performance measures using 10% increments in site-level designation using beta logistic regression.ResultsThe geocoding and approximate string-matching algorithm identified 2615 of the 6851 (41.8%) delivery sites included in the analyses as having been designated through the NCQA and/or JC. In total, 74.7% (n = 777) of the 1039 CHCs that met the inclusion criteria for the analysis managed at least one NCQA- and/or JC-designated site. A proportional increase in site-level designation showed a positive association with adherence scores for the majority of all indicators, but primarily among CHCs that designated at least 50% of its delivery sites. Once this threshold was achieved, there was a stepwise percentage point increase in adherence scores, ranging from 1.9 to 11.8% improvement, depending on the measure.ConclusionGeocoding and approximate string-matching techniques offer a more reliable and nuanced approach for monitoring the association between site-level PCMH designation and clinical performance within HRSA’s CHC delivery sites. Our findings suggest that transformation does in fact matter, but that it may not appear until half of the delivery sites become designated. There also appears to be a continued stepwise increase in adherence scores once this threshold is achieved.

Information extraction framework to build legislation network

This paper concerns an Information Extraction process for building a dynamic Legislation Network from legal documents. Unlike supervised learning approaches which require additional calculations, the idea here is to apply Information Extraction methodologies by identifying distinct expressions in legal text and extract quality network information. The study highlights the importance of data accuracy in network analysis and improves approximate string matching techniques for producing reliable network data-sets with more than 98 percent precision and recall. The values, applications, and the complexity of the created dynamic Legislation Network are also discussed and challenged.

The implementation of bit-parallelism for DNA sequence alignment

Dynamic Programming (DP) remain the central algorithm of biological sequence alignment. Matching score computation is the most time-consuming process. Bit-parallelism is one of approximate string matching techniques that transform DP matrix cell unit processing into word unit (groups of cell). Bit-parallelism computate the scores column-wise. Adopting from word processing in computer system work, this technique promise reducing time in score computing process in DP matrix. In this paper, we implement bit-parallelism technique for DNA sequence alignment. Our bit-parallelism implementation have less time for score computational process but still need improvement for there construction process.

On the feasibility of character n-grams pseudo-translation for Cross-Language Information Retrieval tasks

The field of Cross-Language Information Retrieval relates techniques close to both the Machine Translation and Information Retrieval fields, although in a context involving characteristics of its own. The present study looks to widen our knowledge about the effectiveness and applicability to that field of non-classical translation mechanisms that work at character n-gram level. For the purpose of this study, an n-gram based system of this type has been developed. This system requires only a bilingual machine-readable dictionary of n-grams, automatically generated from parallel corpora, which serves to translate queries previously n-grammed in the source language. n-Gramming is then used as an approximate string matching technique to perform monolingual text retrieval on the set of n-grammed documents in the target language.The tests for this work have been performed on CLEF collections for seven European languages, taking English as the target language. After an initial tuning phase in order to analyze the most effective way for its application, the results obtained, close to the upper baseline, not only confirm the consistency across languages of this kind of character n-gram based approaches, but also constitute a further proof of their validity and applicability, these not being tied to a given implementation.

Probabilistic correlation-based similarity measure on text records

Large scale unstructured text records are stored in text attributes in databases and information systems, such as scientific citation records or news highlights. Approximate string matching techniques for full text retrieval, e.g., edit distance and cosine similarity, can be adopted for unstructured text record similarity evaluation. However, these techniques do not show the best performance when applied directly, owing to the difference between unstructured text records and full text. In particular, the information are limited in text records of short length, and various information formats such as abbreviation and data missing greatly affect the record similarity evaluation.In this paper, we propose a novel probabilistic correlation-based similarity measure. Rather than simply conducting the matching of tokens between two records, our similarity evaluation enriches the information of records by considering correlations of tokens. The probabilistic correlation between tokens is defined as the probability of them appearing together in the same records. Then we compute weights of tokens and discover correlations of records based on the probabilistic correlations of tokens. The extensive experimental results demonstrate the effectiveness of our proposed approach.

A java API interface for the search of DTV services in embedded multimedia devices

The majority of DTV sets and set top boxes are embedded systems based on Linux. Utilizing network connectivity, they can provide many different kinds of information coming from the Internet such as news, sport events, weather and social networks through a large number of applications that are available for download. Considering the vast amount of data that is available to users, these platforms include specialized applications for unified search and presentation of this data. These applications currently do not support searching of data coming from DTV broadcast stream. This paper presents a proposal for the integration of data coming from DTV broadcast stream into a search mechanism on embedded systems which support the Java programming language. The proposal includes two parts: the Java API specification that is used to access DTV content from search applications, and the DTV native layer API. The latter is used to connect the native code to the Java API and includes approximate string matching technique for reducing spelling errors in search criterion.

Fast Visual Retrieval Using Accelerated Sequence Matching

We present an approach to represent, match, and index various types of visual data, with the primary goal of enabling effective and computationally efficient searches. In this approach, an image/video is represented by an ordered list of feature descriptors. Similarities between such representations are then measured by the approximate string matching technique. This approach unifies visual appearance and the ordering information in a holistic manner with joint consideration of visual-order consistency between the query and the reference instances, and can be used for automatically identifying local alignments between two pieces of visual data. This capability is essential for tasks such as video copy detection where only small portions of the query and the reference videos are similar. To deal with large volumes of data, we further show that this approach can be significantly accelerated along with a dedicated indexing structure. Extensive experiments on various visual retrieval and classification tasks demonstrate the superior performance of the proposed techniques compared to existing solutions.

Does dictionary based bilingual retrieval work in a non-normalized index?

Many operational IR indexes are non-normalized, i.e. no lemmatization or stemming techniques, etc. have been employed in indexing. This poses a challenge for dictionary-based cross-language retrieval (CLIR), because translations are mostly lemmas. In this study, we face the challenge of dictionary-based CLIR in a non-normalized index. We test two optional approaches: FCG (Frequent Case Generation) and s-gramming. The idea of FCG is to automatically generate the most frequent inflected forms for a given lemma. FCG has been tested in monolingual retrieval and has been shown to be a good method for inflected retrieval, especially for highly inflected languages. S-gramming is an approximate string matching technique (an extension of n-gramming). The language pairs in our tests were English–Finnish, English–Swedish, Swedish–Finnish and Finnish–Swedish. Both our approaches performed quite well, but the results varied depending on the language pair. S-gramming and FCG performed quite equally in all the other language pairs except Finnish–Swedish, where s-gramming outperformed FCG.

Proper nouns in English–Arabic cross language information retrieval

AbstractOut of vocabulary words, mostly proper nouns and technical terms, are one main source of performance degradation in Cross Language Information Retrieval (CLIR) systems. Those are words not found in the dictionary. Bilingual dictionaries in general do not cover most proper nouns, which are usually primary keys in the query. As they are spelling variants of each other in most languages, using an approximate string matching technique against the target database index is the common approach taken to find the target language correspondents of the original query key. N‐gram technique proved to be the most effective among other string matching techniques. The issue arises when the languages dealt with have different alphabets. Transliteration is then applied based on phonetic similarities between the languages involved. In this study, both transliteration and the n‐gram technique are combined to generate possible transliterations in an English–Arabic CLIR system. We refer to this technique as Transliteration N‐Gram (TNG). We further enhance TNG by applying Part Of Speech disambiguation on the set of transliterations so that words with a similar spelling, but a different meaning, are excluded. Experimental results show that TNG gives promising results, and enhanced TNG further improves performance.

Approximate personal name‐matching through finite‐state graphs

AbstractThis article shows how finite‐state methods can be employed in a new and different task: the conflation of personal name variants in standard forms. In bibliographic databases and citation index systems, variant forms create problems of inaccuracy that affect information retrieval, the quality of information from databases, and the citation statistics used for the evaluation of scientists' work. A number of approximate string matching techniques have been developed to validate variant forms, based on similarity and equivalence relations. We classify the personal name variants as nonvalid and valid forms. In establishing an equivalence relation between valid variants and the standard form of its equivalence class, we defend the application of finite‐state transducers. The process of variant identification requires the elaboration of: (a) binary matrices and (b) finite‐state graphs. This procedure was tested on samples of author names from bibliographic records, selected from the Library and Information Science Abstracts and Science Citation Index Expanded databases. The evaluation involved calculating the measures of precision and recall, based on completeness and accuracy. The results demonstrate the usefulness of this approach, although it should be complemented with methods based on similarity relations for the recognition of spelling variants and misspellings.

De novo identification of LTR retrotransposons in eukaryotic genomes

BackgroundLTR retrotransposons are a class of mobile genetic elements containing two similar long terminal repeats (LTRs). Currently, LTR retrotransposons are annotated in eukaryotic genomes mainly through the conventional homology searching approach. Hence, it is limited to annotating known elements.ResultsIn this paper, we report a de novo computational method that can identify new LTR retrotransposons without relying on a library of known elements. Specifically, our method identifies intact LTR retrotransposons by using an approximate string matching technique and protein domain analysis. In addition, it identifies partially deleted or solo LTRs using profile Hidden Markov Models (pHMMs). As a result, this method can de novo identify all types of LTR retrotransposons. We tested this method on the two pairs of eukaryotic genomes, C. elegans vs. C. briggsae and D. melanogaster vs. D. pseudoobscura. LTR retrotransposons in C. elegans and D. melanogaster have been intensively studied using conventional annotation methods. Comparing with previous work, we identified new intact LTR retroelements and new putative families, which may imply that there may still be new retroelements that are left to be discovered even in well-studied organisms. To assess the sensitivity and accuracy of our method, we compared our results with a previously published method, LTR_STRUC, which predominantly identifies full-length LTR retrotransposons. In summary, both methods identified comparable number of intact LTR retroelements. But our method can identify nearly all known elements in C. elegans, while LTR_STRUCT missed about 1/3 of them. Our method also identified more known LTR retroelements than LTR_STRUCT in the D. melanogaster genome. We also identified some LTR retroelements in the other two genomes, C. briggsae and D. pseudoobscura, which have not been completely finished. In contrast, the conventional method failed to identify those elements. Finally, the phylogenetic and chromosomal distributions of the identified elements are discussed.ConclusionWe report a novel method for de novo identification of LTR retrotransposons in eukaryotic genomes with favorable performance over the existing methods.

Using clustering strategies for creating authority files

As more online databases are integrated into digital libraries, the issue of quality control of the data becomes increasingly important, especially as it relates to the effective retrieval of information. Authority work, the need to discover and reconcile variant forms of strings in bibliographic entries, will become more critical in the future. Spelling variants, misspellings, and transliteration differences will all increase the difficulty of retrieving information. We investigate a number of approximate string matching techniques that have traditionally been used to help with this problem. We then introduce the notion of approximate word matching and show how it can be used to improve detection and categorization of variant forms. We demonstrate the utility of these approaches using data from the Astrophysics Data System and show how we can reduce the human effort involved in the creation of authority files.

Using clustering strategies for creating authority files

As more online databases are integrated into digital libraries, the issue of quality control of the data becomes increasingly important, especially as it relates to the effective retrieval of information. Authority work, the need to discover and reconcile variant forms of strings in bibliographic entries, will become more critical in the future. Spelling variants, misspellings, and transliteration differences will all increase the difficulty of retrieving information. We investigate a number of approximate string matching techniques that have traditionally been used to help with this problem. We then introduce the notion of approximate word matching and show how it can be used to improve detection and categorization of variant forms. We demonstrate the utility of these approaches using data from the Astrophysics Data System and show how we can reduce the human effort involved in the creation of authority files.