Questions tagged [reproducible-research]

Research practice of making full experimental description, entire collected data, and all the data analysis scripts publicly available, so that the published results can be reproduced elsewhere.

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19 views

R - Making legit RandomForest results reproducible with set.seed

I guess that my question is kinda weird but: I'm working on a university project where I have to use a RandomForest model to predict if patients have depressive tendencies. And while I'm getting ...
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20 views

Repeatability and Reproducibility Coefficients of Variation

I sometimes see in papers report Repeatability CVs% and Reproducibility CV%. Sometimes its described as within-group CV% and between-group CV%. But in papers I've seen these calculated multiple ...
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How to determine statistical significance of physics dataset?

I am working on a physics paper, which looks at the dependence of resistivity on physical temperature. I obtained data showing a linear trend of the form $$\rho(T)=\rho_0[1+\alpha(T-T_0)]$$ Based on ...
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Machine learning model giving different probability on different scenarios [closed]

I am working on Iris dataset classification model. I am using SVM model and getting the probability of each class using predict_proba function. I tried the same example on different mediums ...
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21 views

Setting seeds despite repeated training of CNNs?

I would like to compare the classification performance (like accuracy, precision, recall etc.) of different CNN architectures. I'm using Google Colab (GPU support), Tensorflow and Keras. Since it is ...
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23 views

How to compare the performance of different SVMs and CNNs?

I'm a beginner in machine learning und I have a problem to find the best way to compare the performance (accuracy) of different SVMs and CNNs (Jupyter Notebook)? The CNNs I train in Google Colab with ...
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1answer
241 views

How to compare CNN models with non-reproducible results?

I try to compare different CNN models. I use Keras and for training, I use a GPU, Google Colab with Tensorflow backend. Unfortunately I'm not able to create the same initial conditions for the CNNs (...
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51 views

How to plot the EOC of a Non Linear Activati

I was trying to replicate this plot as shown in the paper: https://arxiv.org/abs/1802.09979 The plot: The paper describes the formulation of how to obtain this graph for a non-linear activation ...
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39 views

Does a high negative concordance imply reproducible features

Does a high negative(-1) Lin's concordance correlation coefficient(Lins CCC) imply reproducible features ? I am calculating Lin's CCC of radiomic features between two different CT scan settings , ...
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105 views

Is most published research indeed false?

I have come across (Ioannidis, 2005) which explains several reasons (mainly statistics-related, that's why I post this question here) to justify the claim that most published research is indeed false. ...
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140 views

Reproducible numbers in Keras/TensorFlow

Every time I run a Keras/TensorFlow code gives different results. Can someone suggest how to get reproducible numbers?
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146 views

Why do people use PCA when it has so many issues?

(This is a soft question) Recently I'm learning Principal Component Analysis, and it appears to have a lot of issues: You have to transform the data to roughly the same scale before applying PCA, but ...
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Comparing treatment outcomes

I am a statistics noob, my field is medicine, so I'm hoping someone can help me with this: I came across the following problem: "Researchers found that at the end of a 5-year study, 34% of the ...
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38 views

Replicating a wrong analysis

A study measures the performance of patients and controls in two tasks. In task 1, a t-test reveals no significant differences between patients and controls. In task 2, a t-test reveals significant ...
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46 views

Why replication studies use two-tailed tests?

I have been searching replication studies and I found that all of them use two-tailed tests. For example: Open Science Collaboration. (2015). Estimating the reproducibility of psychological science....
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48 views

Has the reproducibility crisis affected confidence intervals as well?

The reproducibility crisis has given many pause over the value (?) of $p$-values to measure the relevance of statistical findings. Given the interpretation of a $p$-value and some knowledge of ...
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158 views

What is a good machine learning academic research workflow/tools? [closed]

I'm interested in ML research and want to get some insights into how its done in practice. In particular: What kind of data are you dealing with? How are you dealing with hyper-param optimization? ...
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25 views

Use Deep learning or RL to maximize long term hit in caching file?

Suppose I have F video files with different file size and with different popularity. I have a memory cache of fixed size. What I have to do is following: I want to cache n files (n < F) in ...
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Choosing the “Correct” Seed for Reproducible Research/Results

I have created this post to spark a discussion around an idea I had regarding the choice of the seed number used to replicate the results of a statistical model. Here is some background on how I came ...
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Put Together Results from GLM Gamma Models

I have a set of healthcare data in which I used GLM Gamma to model the healthcare spending. Then I am trying to put together the results in a style that is similar to this: http://onlinelibrary.wiley....
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259 views

“report the statistical results of the analysis without the covariate”

This is from Psychological Science 22(11), p.1363: If an analysis includes a covariate, authors must report the statistical results of the analysis without the covariate. Reporting covariate-...
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62 views

When to calculate Cronbach's alpha for a paper?

I am doing my undergraduate thesis, and I wonder if I need to do the Cronbach's alpha from my data set, or if I should use the Cronbach's alpha from the commercial questionnaire I will use for this ...
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1answer
80 views

I have all negatives in (some) of my folds in cross validation. Seeking best way to calculate AUC using R in this scenario?

Problem The title explains my problem. I cannot calculate AUC as things currently stand because some of my data sets have only negatives. I have three possible solutions and I need input from more ...
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Two samples t-test and ANOVA

B) When doing a two way ANOVA After calculating the sum of squares column(between), the sum of squares error(within), and the sum of squares block. 1. Are there any other sum of squares? 2. What is ...
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67 views

Simple questions about reproducibility

Suppose we made $m$ tests in 2 samples from the population. For simplicity, we compared $m$ traits (i.e. bmi, temperature, height, etc) for equality in means between 2 groups of people (i.e. Germans ...
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55 views

How to prove two methods are “similar”?

We are testing two imaging machines. One of the machines has been validated numerous times. However, we built the new machine and we need to prove that it is similar/comparable to the validated ...
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123 views

Calculate Cronbach's alpha for three observers

I have a dataset which contains 100 observations, and I asked three expert to describe each observation by one of the letters {A,B,C}. The following three tables shows a sample of the dataset with the ...
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1answer
44 views

Evidence for data mining (specification search) in published results [duplicate]

Is there an established way to assess the prevalence of data mining (as in specification search, not in the machine learning sense) in academic publications? I vaguely remember hearing something ...
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282 views

Statistical significance, repeatability, and sample size (50 shades of grey)

Reading about the problems with significance I wondered how one would approach an experiment in the right way, considering that in practice the sample size cannot be arbitrarily large. While some ...
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How much do we know about p-hacking “in the wild”?

The phrase p-hacking (also: "data dredging", "snooping" or "fishing") refers to various kinds of statistical malpractice in which results become artificially statistically significant. There are many ...
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116 views

How to calculate Cronbach's alpha

For my dissertation I am observing horse race videos to see if horses are right or left handed. In flat races where the horse comes out of the starting stalls I observe which leg (right or left) they ...
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1answer
640 views

Ethics of publishing covariate matrix

I am planning to submit a paper with a Structural Equation Model applied into a dataset built with measurements from schizophrenic patients. In the spirit of promoting an open research culture I've ...
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1answer
998 views

How can I define a multiple-record ID variable for a Cox model in R?

I'm reproducing and translating data from an old Stata file into R for future expansion and analysis. The original data uses a Cox proportional hazard model with ...
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62 views

Sample size for clinical research

I determined the sample size already (25), but I want to know if it has to be increased because of a minor change. Our study consists of two groups - one will be sedated and the other will not. For ...
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123 views

Data analysis: how to compare 2 variables from each subject across 3 groups of 200 subjects?

New here and not a statistician, am MD doing research. Need advice on best method for data analysis. I have 3 groups of 200 subjects each. We collected 2 data points (A,B) from each subject. Baseline ...
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How to organise an iterative manual rotation of n component pairs?

I am currently building a q.rotate() function for the qmethod R package for Q Methodology. As is desirable for Q, I'd like users to be able to iteratively rotate ...
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32k views

What if high validation accuracy but low test accuracy in research?

I have a specific question about validation in machine learning research. As we know, the machine learning regime asks researchers to train their models on the training data, choose from candidate ...
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1answer
103 views

What inputs, ideas or insight the community can offer on the subject “A simulation study of sample size for multilevel logistic regression.” [closed]

I have been assigned a topic on "A simulation study of sample size for multilevel logistic regression." I have searched the topic but found little reference on it. Could you please offer some ...
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1answer
88 views

Is golden section search considered a fitting (regression analysis)?

I am curious if the Golden section search is a form of fitting (or regression analysis in general)? It does find the extremum, but independent of any functional form (it works without modeling, if I ...
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6k views

Is p-value essentially useless and dangerous to use?

This article "The Odds, Continually Updated" from NY Times happened to catch my attention. To be short, it states that [Bayesian statistics] is proving especially useful in approaching complex ...
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1answer
737 views

Can't reproduce results using foreach and RSNNS

I'm trying to train multiple Multi-Layer-Perceptrons using foreach and mlp(...) from the RSNNS package. As I ran into problems reproducing the results generated by mlp() and foreach in a parallel ...
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Has the reported state-of-the-art performance of using paragraph vectors for sentiment analysis been replicated?

I was impressed by the results in the ICML 2014 paper "Distributed Representations of Sentences and Documents" by Le and Mikolov. The technique they describe, called "paragraph vectors", learns ...
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1answer
75 views

Publications in the social sciences or psychology based on freely available datasets?

There are a lot of datasets freely available across the web (see CV questions here, here, or here). Yet, I want the reverse: I am looking for a list of publications in the social sciences or ...
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5k views

Resources to write a statistical analysis plan

Following ICH-E9 guideline on statistical principles for clinical trials, A statistical analysis plan is a document that contains a more technical and detailed elaboration of the principal ...
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302 views

M statistic and software ProtoArray Prospector

I would like to reproduce the statistical result in this paper: http://www.ncbi.nlm.nih.gov/pubmed/24947363 They said "the M-statistic test in ProtoArray Prospector was applied to the normalized ...
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1answer
136 views

How should be statistics on scientific papers read?

Let's take this research published on Plos ONE Increasing carbohydrate intake was associated with increasing stroke risk (HR = 2.01, 95%CI = 1.04–3.86 highest vs. lowest quintile; p for trend 0....
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1answer
202 views

Standards on presenting graphs and charts in vector format?

In his up-voted answer to Software needed to scrape data from graph, Alexey writes (with respect to the need for data scraping off of raster graphs) "But nowadays the good practice is to publish ...
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1k views

Implications of current debate on statistical significance

In the past few years, various scholars have raised a detrimental problem of scientific hypothesis testing, dubbed "researcher degree of freedom," meaning that scientists have numerous choices to make ...
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2k views

Why does lambda.min value in glmnet tuning cross-validation change, when repeating test?

I'm using glmnet package to build a linear regression with $\alpha$ = 0.5, to find best $\lambda$. xMatrix [44x15000] ($p>>...
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104 views

Licensing of analytical code and data - which license to use, and what issues?

Not sure if this belongs to CrossValidated, Computational Science, or something else entirely. I've got some code and data that's going into a publication, but I'd like to make said code and data ...