Posts about reproducible paper (old posts, page 1)

Lack of Reproducibility in Addiction Medicine

Background and aims: Credible research emphasizes transparency, openness, and reproducibility. These characteristics are fundamental to promoting and maintaining research integrity. This aim of this study was to evaluate the current state of transparency and reproducibility in the field of addiction science. Design: Cross-sectional design Measurements: This study used the National Library of Medicine catalog to search for all journals using the subject terms tag: Substance-Related Disorders [ST]. Journals were then searched via PubMed in the timeframe of January 1, 2014 to December 31, 2018 and 300 publications were randomly selected. A pilot-tested Google form containing reproducibility/transparency characteristics was used for data extraction by two investigators who performed this process in a duplicate and blinded fashion. Findings: Slightly more than half of the publications were open access (152/293, 50.7%). Few publications had pre-registration (7/244, 2.87%), material availability (2/237, 1.23%), protocol availability (3/244 ,0.80%), data availability (28/244, 11.48%), and analysis script availability (2/244, 0.82%). Most publications provided a conflict of interest statement (221/293, 75.42%) and funding sources (268/293, 91.47%). One replication study was reported (1/244, 0.04%). Few publications were cited (64/238, 26.89%) and 0 were excluded from meta-analyses and/or systematic reviews. Conclusion: Our study found that current practices that promote transparency and reproducibility are lacking, and thus, there is much room for improvement. First, investigators should preregister studies prior to commencement. Researchers should also make the materials, data, analysis script publicly available. To foster reproducibility, individuals should remain transparent about funding sources for the project and financial conflicts of interest. Research stakeholders should work together toward improved solutions on these matters. With these protections in place, the field of addiction medicine can lead in dissemination of information necessary to treat patients.

On the Index of Repeatability: Estimation and Sample Size Requirements

Background: Repeatability is a statement on the magnitude of measurement error. When biomarkers are used for disease diagnoses, they should be measured accurately. Objectives: We derive an index of repeatability based on the ratio of two variance components. Estimation of the index is derived from the one-way Analysis of Variance table based on the one-way random effects model. We estimate the large sample variance of the estimator and assess its adequacy using bootstrap methods. An important requirement for valid estimation of repeatability is the availability of multiple observations on each subject taken by the same rater and under the same conditions. Methods: We use the delta method to derive the large sample variance of the estimate of repeatability index. The question related to the number of required repeats per subjects is answered by two methods. In first methods we estimate the number of repeats that minimizes the variance of the estimated repeatability index, and the second determine the number of repeats needed under cost-constraints. Results and Novel Contribution: The situation when the measurements do not follow Gaussian distribution will be dealt with. It is shown that the required sample size is quite sensitive to the relative cost. We illustrate the methodologies on the Serum Alanine-aminotransferase (ALT) available from hospital registry data for samples of males and females. Repeatability is higher among females in comparison to males.

Reproducible research into human semiochemical cues and pheromones: learning from psychology’s renaissance

As with other mammals, smell in the form of semiochemicals is likely to influence the behaviour of humans, as olfactory cues to emotions, health, and mate choice. A subset of semiochemicals, pheromones, chemical signals within a species, have been identified in many mammal species. As mammals, we may have pheromones too. Sadly, the story of molecules claimed to be ‘putative human pheromones’ is a classic example of bad science carried out by good scientists. Much of human semiochemicals research including work on ‘human pheromones’ and olfactory cues comes within the field of psychology. Thus, the research is highly likely to be affected by the ‘reproducibility crisis’ in psychology and other life sciences. Psychology researchers have responded with proposals to enable better, more reliable science, with an emphasis on enhancing reproducibility. A key change is the adoption of study pre-registration which will also reduce publication bias. Human semiochemicals research would benefit from adopting these proposals.

I Saw You in the Crowd: Credibility, Reproducibility and Meta-Utility

Crowdsourcing enables novel forms of research and knowledge production. It uses cyberspace to collect diverse research participants, coordinate projects and keep costs low. Recently social scientists began crowdsourcing their peers to engage in mass research targeting a specific topic. This enables meta-analysis of many analysts’ results obtained from a single crowdsourced research project, leading to exponential gains in credibility and scientific utility. Initial applications demonstrate positive returns for both original and replication research using various research instruments, and secondary or experimental data. It can provide more reliable Bayesian priors for selecting models and is an untapped mode of theory production that greatly benefit social science. Finally, in addition to the credibility and reproducibility gains, crowdsourcing embodies many core values of the Open Science Movement because it promotes community and equality among scientists.

A reproducible survey on word embeddings and ontology-based methods for word similarity: Linear combinations outperform the state of the art

Human similarity and relatedness judgements between concepts underlie most of cognitive capabilities, such as categorisation, memory, decision-making and reasoning. For this reason, the proposal of methods for the estimation of the degree of similarity and relatedness between words and concepts has been a very active line of research in the fields of artificial intelligence, information retrieval and natural language processing among others. Main approaches proposed in the literature can be categorised in two large families as follows: (1) Ontology-based semantic similarity Measures (OM) and (2) distributional measures whose most recent and successful methods are based on Word Embedding (WE) models. However, the lack of a deep analysis of both families of methods slows down the advance of this line of research and its applications. This work introduces the largest, reproducible and detailed experimental survey of OM measures and WE models reported in the literature which is based on the evaluation of both families of methods on a same software platform, with the aim of elucidating what is the state of the problem. We show that WE models which combine distributional and ontology-based information get the best results, and in addition, we show for the first time that a simple average of two best performing WE models with other ontology-based measures or WE models is able to improve the state of the art by a large margin. In addition, we provide a very detailed reproducibility protocol together with a collection of software tools and datasets as supplementary material to allow the exact replication of our results.

Meta-analysis for families of experiments in software engineering: a systematic review and reproducibility and validity assessment

To identify families of experiments that used meta-analysis, to investigate their methods for effect size construction and aggregation, and to assess the reproducibility and validity of their results. We performed a systematic review (SR) of papers reporting families of experiments in high quality software engineering journals, that attempted to apply meta-analysis. We attempted to reproduce the reported meta-analysis results using the descriptive statistics and also investigated the validity of the meta-analysis process. Out of 13 identified primary studies, we reproduced only five. Seven studies could not be reproduced. One study which was correctly analyzed could not be reproduced due to rounding errors. When we were unable to reproduce results, we provide revised meta-analysis results. To support reproducibility of analyses presented in our paper, it is complemented by the reproducer R package. Meta-analysis is not well understood by software engineering researchers. To support novice researchers, we present recommendations for reporting and meta-analyzing families of experiments and a detailed example of how to analyze a family of 4-group crossover experiments.