A large-scale study on research code quality and execution

Heterogeneity in effect size estimates

A typical empirical study involves choosing a sample, a research design, and an analysis path. Variation in such choices across studies leads to heterogeneity in results that introduce an additional layer of uncertainty, limiting the generalizability of published scientific findings. We provide a framework for studying heterogeneity in the social sciences and divide heterogeneity into population, design, and analytical heterogeneity. Our framework suggests that after accounting for heterogeneity, the probability that the tested hypothesis is true for the average population, design, and analysis path can be much lower than implied by nominal error rates of statistically significant individual studies. We estimate each type's heterogeneity from 70 multilab replication studies, 11 prospective meta-analyses of studies employing different experimental designs, and 5 multianalyst studies. In our data, population heterogeneity tends to be relatively small, whereas design and analytical heterogeneity are large. Our results should, however, be interpreted cautiously due to the limited number of studies and the large uncertainty in the heterogeneity estimates. We discuss several ways to parse and account for heterogeneity in the context of different methodologies.

The changing landscape of text mining: a review of approaches for ecology and evolution

In ecology and evolutionary biology, the synthesis and modelling of data from published literature are commonly used to generate insights and test theories across systems. However, the tasks of searching, screening, and extracting data from literature are often arduous. Researchers may manually process hundreds to thousands of articles for systematic reviews, meta-analyses, and compiling synthetic datasets. As relevant articles expand to tens or hundreds of thousands, computer-based approaches can increase the efficiency, transparency and reproducibility of literature-based research. Methods available for text mining are rapidly changing owing to developments in machine learning-based language models. We review the growing landscape of approaches, mapping them onto three broad paradigms (frequency-based approaches, traditional Natural Language Processing and deep learning-based language models). This serves as an entry point to learn foundational and cutting-edge concepts, vocabularies, and methods to foster integration of these tools into ecological and evolutionary research. We cover approaches for modelling ecological texts, generating training data, developing custom models and interacting with large language models and discuss challenges and possible solutions to implementing these methods in ecology and evolution.

Reproducible Research Practices in Magnetic Resonance Neuroimaging: A Review Informed by Advanced Language Models

MRI has progressed significantly with the introduction of advanced computational methods and novel imaging techniques, but their wider adoption hinges on their reproducibility. This concise review synthesizes reproducible research insights from recent MRI articles to examine the current state of reproducibility in neuroimaging, highlighting key trends and challenges. It also provides a custom generative pretrained transformer (GPT) model, designed specifically for aiding in an automated analysis and synthesis of information pertaining to the reproducibility insights associated with the articles at the core of this review.

Analytical code sharing practices in biomedical research

Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared. We conducted a comprehensive analysis of 453 manuscripts published between 2016-2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten articles organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability. Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses. In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research. By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.

How much can ChatGPT really help computational biologists in programming?

ChatGPT, a recently developed product by openAI, is successfully leaving its mark as a multi-purpose natural language based chatbot. In this paper, we are more interested in analyzing its potential in the field of computational biology. A major share of work done by computational biologists these days involve coding up bioinformatics algorithms, analyzing data, creating pipelining scripts and even machine learning modeling and feature extraction. This paper focuses on the potential influence (both positive and negative) of ChatGPT in the mentioned aspects with illustrative examples from different perspectives. Compared to other fields of computer science, computational biology has (1) less coding resources, (2) more sensitivity and bias issues (deals with medical data), and (3) more necessity of coding assistance (people from diverse background come to this field). Keeping such issues in mind, we cover use cases such as code writing, reviewing, debugging, converting, refactoring, and pipelining using ChatGPT from the perspective of computational biologists in this paper.

Computational reproducibility of Jupyter notebooks from biomedical publications

BACKGROUND

Jupyter notebooks facilitate the bundling of executable code with its documentation and output in one interactive environment, and they represent a popular mechanism to document and share computational workflows, including for research publications. The reproducibility of computational aspects of research is a key component of scientific reproducibility but has not yet been assessed at scale for Jupyter notebooks associated with biomedical publications.

APPROACH

We address computational reproducibility at 2 levels: (i) using fully automated workflows, we analyzed the computational reproducibility of Jupyter notebooks associated with publications indexed in the biomedical literature repository PubMed Central. We identified such notebooks by mining the article's full text, trying to locate them on GitHub, and attempting to rerun them in an environment as close to the original as possible. We documented reproduction success and exceptions and explored relationships between notebook reproducibility and variables related to the notebooks or publications. (ii) This study represents a reproducibility attempt in and of itself, using essentially the same methodology twice on PubMed Central over the course of 2 years, during which the corpus of Jupyter notebooks from articles indexed in PubMed Central has grown in a highly dynamic fashion.

RESULTS

Out of 27,271 Jupyter notebooks from 2,660 GitHub repositories associated with 3,467 publications, 22,578 notebooks were written in Python, including 15,817 that had their dependencies declared in standard requirement files and that we attempted to rerun automatically. For 10,388 of these, all declared dependencies could be installed successfully, and we reran them to assess reproducibility. Of these, 1,203 notebooks ran through without any errors, including 879 that produced results identical to those reported in the original notebook and 324 for which our results differed from the originally reported ones. Running the other notebooks resulted in exceptions.

CONCLUSIONS

We zoom in on common problems and practices, highlight trends, and discuss potential improvements to Jupyter-related workflows associated with biomedical publications.

Replicability of simulation studies for the investigation of statistical methods: the RepliSims project

Results of simulation studies evaluating the performance of statistical methods can have a major impact on the way empirical research is implemented. However, so far there is limited evidence of the replicability of simulation studies. Eight highly cited statistical simulation studies were selected, and their replicability was assessed by teams of replicators with formal training in quantitative methodology. The teams used information in the original publications to write simulation code with the aim of replicating the results. The primary outcome was to determine the feasibility of replicability based on reported information in the original publications and supplementary materials. Replicasility varied greatly: some original studies provided detailed information leading to almost perfect replication of results, whereas other studies did not provide enough information to implement any of the reported simulations. Factors facilitating replication included availability of code, detailed reporting or visualization of data-generating procedures and methods, and replicator expertise. Replicability of statistical simulation studies was mainly impeded by lack of information and sustainability of information sources. We encourage researchers publishing simulation studies to transparently report all relevant implementation details either in the research paper itself or in easily accessible supplementary material and to make their simulation code publicly available using permanent links.

The five pillars of computational reproducibility: bioinformatics and beyond

Computational reproducibility is a simple premise in theory, but is difficult to achieve in practice. Building upon past efforts and proposals to maximize reproducibility and rigor in bioinformatics, we present a framework called the five pillars of reproducible computational research. These include (1) literate programming, (2) code version control and sharing, (3) compute environment control, (4) persistent data sharing and (5) documentation. These practices will ensure that computational research work can be reproduced quickly and easily, long into the future. This guide is designed for bioinformatics data analysts and bioinformaticians in training, but should be relevant to other domains of study.

Researcher degrees of freedom in statistical software contribute to unreliable results: A comparison of nonparametric analyses conducted in SPSS, SAS, Stata, and R

Researcher degrees of freedom can affect the results of hypothesis tests and consequently, the conclusions drawn from the data. Previous research has documented variability in accuracy, speed, and documentation of output across various statistical software packages. In the current investigation, we conducted Pearson's chi-square test of independence, Spearman's rank-ordered correlation, Kruskal-Wallis one-way analysis of variance, Wilcoxon Mann-Whitney U rank-sum tests, and Wilcoxon signed-rank tests, along with estimates of skewness and kurtosis, on large, medium, and small samples of real and simulated data in SPSS, SAS, Stata, and R and compared the results with those obtained through hand calculation using the raw computational formulas. Multiple inconsistencies were found in the results produced between statistical packages due to algorithmic variation, computational error, and statistical output. The most notable inconsistencies were due to algorithmic variations in the computation of Pearson's chi-square test conducted on 2 × 2 tables, where differences in p-values reported by different software packages ranged from .005 to .162, largely as a function of sample size. We discuss how such inconsistencies may influence the conclusions drawn from the results of statistical analyses depending on the statistical software used, and we urge researchers to analyze their data across multiple packages to check for inconsistencies and report details regarding the statistical procedure used for data analysis.

mmodel: A workflow framework to accelerate the development of experimental simulations

Simulation has become an essential component of designing and developing scientific experiments. The conventional procedural approach to coding simulations of complex experiments is often error-prone, hard to interpret, and inflexible, making it hard to incorporate changes such as algorithm updates, experimental protocol modifications, and looping over experimental parameters. We present mmodel, a Python framework designed to accelerate the writing of experimental simulation packages. mmodel uses a graph-theory approach to represent the experiment steps and can rewrite its own code to implement modifications, such as adding a loop to vary simulation parameters systematically. The framework aims to avoid duplication of effort, increase code readability and testability, and decrease development time.

rang: Reconstructing reproducible R computational environments

A complete declarative description of the computational environment is usually missing when researchers share their materials. Without such description, software obsolescence and missing system components can jeopardize computational reproducibility in the future, even when data and computer code are available. The R package rang is a complete solution for generating the declarative description for other researchers to automatically reconstruct the computational environment at a specific time point. The reconstruction process, based on Docker, has been tested for R code as old as 2001. The declarative description generated by rang satisfies the definition of a reproducible research compendium and can be shared as such. In this contribution, we show how rang can be used to make otherwise unexecutable code, spanning fields such as computational social science and bioinformatics, executable again. We also provide instructions on how to use rang to construct reproducible and shareable research compendia of current research. The package is currently available from CRAN (https://cran.r-project.org/web/packages/rang/index.html) and GitHub (https://github.com/chainsawriot/rang).

What's in a Badge? A Computational Reproducibility Investigation of the Open Data Badge Policy in One Issue of Psychological Science

In April 2019, Psychological Science published its first issue in which all Research Articles received the Open Data badge. We used that issue to investigate the effectiveness of this badge, focusing on the adherence to its aim at Psychological Science: sharing both data and code to ensure reproducibility of results. Twelve researchers of varying experience levels attempted to reproduce the results of the empirical articles in the target issue (at least three researchers per article). We found that all 14 articles provided at least some data and six provided analysis code, but only one article was rated to be exactly reproducible, and three were rated as essentially reproducible with minor deviations. We suggest that researchers should be encouraged to adhere to the higher standard in force at Psychological Science. Moreover, a check of reproducibility during peer review may be preferable to the disclosure method of awarding badges.

Identifying algorithm in program code based on structural features using CNN classification model

In software, an algorithm is a well-organized sequence of actions that provides the optimal way to complete a task. Algorithmic thinking is also essential to break-down a problem and conceptualize solutions in some steps. The proper selection of an algorithm is pivotal to improve computational performance and software productivity as well as to programming learning. That is, determining a suitable algorithm from a given code is widely relevant in software engineering and programming education. However, both humans and machines find it difficult to identify algorithms from code without any meta-information. This study aims to propose a program code classification model that uses a convolutional neural network (CNN) to classify codes based on the algorithm. First, program codes are transformed into a sequence of structural features (SFs). Second, SFs are transformed into a one-hot binary matrix using several procedures. Third, different structures and hyperparameters of the CNN model are fine-tuned to identify the best model for the code classification task. To do so, 61,614 real-world program codes of different types of algorithms collected from an online judge system are used to train, validate, and evaluate the model. Finally, the experimental results show that the proposed model can identify algorithms and classify program codes with a high percentage of accuracy. The average precision, recall, and F-measure scores of the best CNN model are 95.65%, 95.85%, and 95.70%, respectively, indicating that it outperforms other baseline models.

Nine best practices for research software registries and repositories

Scientific software registries and repositories improve software findability and research transparency, provide information for software citations, and foster preservation of computational methods in a wide range of disciplines. Registries and repositories play a critical role by supporting research reproducibility and replicability, but developing them takes effort and few guidelines are available to help prospective creators of these resources. To address this need, the FORCE11 Software Citation Implementation Working Group convened a Task Force to distill the experiences of the managers of existing resources in setting expectations for all stakeholders. In this article, we describe the resultant best practices which include defining the scope, policies, and rules that govern individual registries and repositories, along with the background, examples, and collaborative work that went into their development. We believe that establishing specific policies such as those presented here will help other scientific software registries and repositories better serve their users and their disciplines.