7,194 research outputs found
Noise and Uncertainty in String-Duplication Systems
Duplication mutations play a critical role in the
generation of biological sequences. Simultaneously, they
have a deleterious effect on data stored using in-vivo DNA data storage. While duplications have been studied both as a sequence-generation mechanism and in the context of error correction, for simplicity these studies have not taken into account the presence of other types of mutations. In this work, we consider the capacity of duplication mutations in the presence of point-mutation
noise, and so quantify the generation power of these mutations. We show that if the number of point mutations is vanishingly small compared to the number of duplication mutations of a constant length, the generation capacity of these mutations is zero. However, if the number of point mutations increases to a constant fraction of the number of duplications, then the capacity is nonzero. Lower and upper bounds for this capacity are also presented. Another problem that we study is concerned with the
mismatch between code design and channel in data storage in the DNA of living organisms with respect to duplication mutations. In this context, we consider the uncertainty of such a mismatched coding scheme measured as the maximum number of input codewords that can lead to the same output
Reconstruction Codes for DNA Sequences with Uniform Tandem-Duplication Errors
DNA as a data storage medium has several advantages, including far greater
data density compared to electronic media. We propose that schemes for data
storage in the DNA of living organisms may benefit from studying the
reconstruction problem, which is applicable whenever multiple reads of noisy
data are available. This strategy is uniquely suited to the medium, which
inherently replicates stored data in multiple distinct ways, caused by
mutations. We consider noise introduced solely by uniform tandem-duplication,
and utilize the relation to constant-weight integer codes in the Manhattan
metric. By bounding the intersection of the cross-polytope with hyperplanes, we
prove the existence of reconstruction codes with greater capacity than known
error-correcting codes, which we can determine analytically for any set of
parameters.Comment: 11 pages, 2 figures, Latex; version accepted for publicatio
Information Extraction, Data Integration, and Uncertain Data Management: The State of The Art
Information Extraction, data Integration, and uncertain data management are different areas of research that got vast focus in the last two decades. Many researches tackled those areas of research individually. However, information extraction systems should have integrated with data integration methods to make use of the extracted information. Handling uncertainty in extraction and integration process is an important issue to enhance the quality of the data in such integrated systems. This article presents the state of the art of the mentioned areas of research and shows the common grounds and how to integrate information extraction and data integration under uncertainty management cover
A unified framework for de-duplication and population size estimation (with Discussion)
Data de-duplication is the process of finding records in one or more datasets belonging to the same entity. In this paper we tackle the de-duplication process via a latent entity model, where the observed data are perturbed versions of a set of key variables drawn from a finite population of different entities. The main novelty of our approach is to consider the population size as an unknown model parameter. As a result, one salient feature of the proposed method is the capability of the model to account for the de-duplication uncertainty in the population size estimation. As by-products of our approach we illustrate the relationships between de-duplication problems and capture-recapture models and we obtain a more adequate prior distribution on the linkage structure. Moreover we propose a novel simulation algorithm for the posterior distribution of the matching configuration based on the marginalization of the key variables at the population level. We apply our approach to two synthetic data sets comprising German names. In addition we illustrate a real data application matching records from two lists reporting victims killed in the recent Syrian conflict
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
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