Posts about reproducible paper (old posts, page 21)

Vive la Petite Différence! Exploiting Small Differences for Gender Attribution of Short Texts

This article describes a series of experiments on gender attribution of Polish texts. The research was conducted on the publicly available corpus called "He Said She Said", consisting of a large number of short texts from the Polish version of Common Crawl. As opposed to other experiments on gender attribution, this research takes on a task of classifying relatively short texts, authored by many different people. For the sake of this work, the original "He Said She Said" corpus was filtered in order to eliminate noise and apparent errors in the training data. In the next step, various machine learning algorithms were developed in order to achieve better classification accuracy. Interestingly, the results of the experiments presented in this paper are fully reproducible, as all the source codes were deposited in the open platform allows for defining machine learning tasks to be tackled by multiple researchers and provides the researchers with easy access to each other’s results.

The Reproducibility and Relative Validity of a Mexican Diet Quality Index (ICDMx) for the Assessment of the Habitual Diet of Adults

The study of diet quality in a population provides information for the development of programs to improve nutritional status through better directed actions. The aim of this study was to assess the reproducibility and relative validity of a Mexican Diet Quality Index (ICDMx) for the assessment of the habitual diet of adults.

Assessing the reproducibility of exome copy number variations predictions

Reproducibility is receiving increased attention across many domains of science and genomics is no exception. Efforts to identify copy number variations (CNVs) from exome sequence (ES) data have been increasing. Many algorithms have been published to discover CNVs from exomes and a major challenge is the reproducibility in other datasets. Here we test exome CNV calling reproducibility under three conditions: data generated by different sequencing centers; varying sample sizes; and varying capture methodology.

Standardized Mixed-Meal Tolerance and Arginine Stimulation Tests Provide Reproducible and Complementary Measures ofb-cell Function: Results From the Foundation for the National Institutes of Health Biomarkers Consortium Investigative Series

Standardized, reproducible, and feasible quantification ofb-cell function (BCF) is necessary for the evaluation of interventions to improve insulin secretion and important for comparison across studies. We therefore characterized the re-sponses to, and reproducibility of, standardized methods of in vivo BCF across different glucose tolerance states. Reproducibility for the AST was very good, with ICC values >0.8 across all variables and populations.

Where next for the reproducibility agenda in computational biology?

The concept of reproducibility is a foundation of the scientific method. With the arrival of fast and powerful computers over the last few decades, there has been an explosion of results based on complex computational analyses and simulations. The reproducibility of these results has been addressed mainly in terms of exact replicability or numerical equivalence, ignoring the wider issue of the reproducibility of conclusions through equivalent, extended or alternative methods.

samExploreR: Exploring reproducibility and robustness of RNA-seq results based on SAM files

Data from RNA-seq experiments provide us with many new possibilities to gain insights into biological and disease mechanisms of cellular functioning. However, the reproducibility and robustness of RNA-seq data analysis results is often unclear. This is in part attributed to the two counter acting goals of (a) a cost efficient and (b) an optimal experimental design leading to a compromise, e.g., in the sequencing depth of experiments.