1,720,965 research outputs found
quickSparseM: a library for memory- and time-efficient computation on large, sparse matrices with application to omics data
No full textOmics data have revolutionized molecular biology by introducing large-scale data analysis, pushing the field into the realm of big data and presenting substantial challenges in data storage and analysis. Despite describing distinct aspects of molecular biology, most omics data share common characteristics, such as being representable as large, sparse matrices, and requiring similar computational approaches, mainly involving embarrassing parallel tasks across rows or columns. While R is a popular choice for omics analysis, it encounters performance bottlenecks when handling large datasets due to its reliance on dense data formats and constraints like 32-bit indexing in some structures. Even when sparse representations are utilized, the inherent limitations of R lead to inefficiencies. Additionally, its lack of native support for shared-memory parallelism prevents it from fully utilizing modern parallel computing architectures. Similarly, many other data-intensive fields that rely on R face similar challenges with large, sparse data requiring fast and memory-efficient row-wise and column-wise operations. To address these challenges, we introduce quickSparseM, a time- and memory-efficient library for storing and processing large, sparse matrices, available as an R package. Developed in C++ with OpenMP for parallelism, quickSparseM achieves efficient performance while remaining compatible with existing R-based workflows. The library utilizes the R dgCMatrix format to represent sparse matrices in a compressed, column-oriented format and provide functions to compute basic statistics and operations commonly used in omics analyses. Experiments varying dataset sizes and core counts, as well as two case studies using omics data, demonstrate the library’s efficiency and scalability. The results indicate that quickSparseM outperforms state-of-the-art R packages for sparse matrix computation in terms of time, memory usage, and scalability
Interpolation and K-Nearest Neighbours Combined Imputation for Longitudinal ICU Laboratory Data
No full textImportance of Recalibrating Models for Type 2 Diabetes Onset Prediction: Application of the Diabetes Population Risk Tool on the Health and Retirement Study
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Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Detecting Undiagnosed Diabetes: Proof-of-Concept Based on the Health-Information Exchange System of the Veneto Region (North-East Italy)
No full textDiabetes is a chronic illness characterised by elevated blood glucose levels, driving excess mortality. Its prompt detection and accurate management are critical for delaying complications. Nevertheless, diabetes can remain undiagnosed for years from the onset. The identification of undiagnosed diabetes is a public health priority: in Italy, it is estimated that up to 30% of diabetes cases remain undetected, i.e., that ~1.8 million citizens may be unaware they need medical help. Sometimes, this happens even though these subjects undergo routine or emergency check-ups. Veneto, a region in North-East Italy with 4.9 million residents, implements a regional Health Information Exchange system (rHIE) to collect healthcare data, including laboratory reports, and integrate them with administrative claims. Their combination may be instrumental in finding otherwise undetected cases of diabetes. On the one hand, known diabetic patients should have disease management-generated claims; on the other, laboratory test results can be independently evaluated against diagnostic criteria. In the present work, we examined the anonymised claims and laboratory data, extracted from the rHIE, of 23,376 citizens of the Veneto region. We compared their exemptions, diabetes-related hospitalisation discharge codes, and antidiabetic drugs between 2012 and 2018 to the results of their fasting glucose, glycated haemoglobin, and oral glucose tolerance tests in 2017-2018. We identified 1,407 (6.02%) subjects who, according to administrative claims, appear to be free from diabetes, but met at least one laboratory diagnostic criterion. Such a discrepancy suggests that these people may be undiagnosed diabetic patients. To the best of our knowledge, this is the first proof of concept of an automatic system for the detection of undiagnosed diabetes in Italy. Its full integration in the rHIE and its consequent capillary application could potentially reveal thousands of hidden cases throughout Veneto
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