Why is Bayesian confirmation theory rarely practiced?

Bayesian confirmation theory is a leading theory to decide the confirmation/refutation of a hypothesis based on probability calculus. While it may be much discussed in philosophy of science, is it actually practiced in terms of hypothesis testing by scientists? Since the assignment of some of the probabilities in the theory is open to debate and the risk of making the wrong decision is unknown, many scientists do not use the theory in hypothesis testing. Instead, they use alternative statistical tests that can measure the risk or the reliability in decision making, circumventing some of the theoretical problems in practice. Therefore, the theory is not very popular in hypothesis testing among scientists at present. However, there are some proponents of Bayesian hypothesis testing, and software packages are made available to accelerate utilization by scientists. Time will tell whether Bayesian confirmation theory can become both a leading theory and a widely practiced method. In addition, this theory can be used to model the (degree of) belief of scientists when testing hypotheses

Insights in how computer science can be a science

Recently, information retrieval is shown to be a science by mapping information retrieval scientific study to scientific study abstracted from physics. The exercise was rather tedious and lengthy. Instead of dealing with the nitty gritty, this paper looks at the insights into how computer science can be made into a science by using that methodology. That is by mapping computer science scientific study to the scientific study abstracted from physics. To show the mapping between computer science and physics, we need to define what is engineering science which computer science belongs to. Some principles and assumptions of engineering science theory are presented. To show computer science is a science, we presented two approaches. Approach 1 considers computer science as simulation of human behaviour similar to the goal of artificial intelligence. Approach 2 is closely related to the actual (scientific) activities in computer science, and this approach considers computer science based on the theory of computation. Finally, we answer some of the common outstanding issues about computer science to convince our reader that computer science is a science

How to handle risky experiments producing uncertain phenomenon like cold fusion?

Some experiments are risky in that they cannot repeatedly produce certain phenomenon at will for study because the scientific knowledge of the process generating the uncertain phenomenon is poorly understood or may directly contradict with existing scientific knowledge. These experiments may have great impact not just to the scientific community but to mankind in general. Banning them from study may incur societies a great opportunity cost but accepting them runs the risk that scientists are doing junk science. How to make an informed decision to accept/reject such study scientifically for the mainstream scientific community is of great importance to mankind. Here, we propose a statistical methodology to handle the situation. Specifically, we consider the likelihood of not observing the phenomenon after n trails so that it is statistically significant to have nil result. Consequently, we reject the hypothesis that there is some probability that we observe the phenomenon

Comparison between instrumental variable and mediation-based methods for reconstructing causal gene networks in yeast

Under embargo until: 2021-12-17Causal gene networks model the flow of information within a cell. Reconstructing causal networks from omics data is challenging because correlation does not imply causation. When genomics and transcriptomics data from a segregating population are combined, genomic variants can be used to orient the direction of causality between gene expression traits. Instrumental variable methods use a local expression quantitative trait locus (eQTL) as a randomized instrument for a gene's expression level, and assign target genes based on distal eQTL associations. Mediation-based methods additionally require that distal eQTL associations are mediated by the source gene. A detailed comparison between these methods has not yet been conducted, due to the lack of a standardized implementation of different methods, the limited sample size of most multi-omics datasets, and the absence of ground-truth networks for most organisms. Here we used Findr, a software package providing uniform implementations of instrumental variable, mediation, and coexpression-based methods, a recent dataset of 1012 segregants from a cross between two budding yeast strains, and the YEASTRACT database of known transcriptional interactions to compare causal gene network inference methods. We found that causal inference methods result in a significant overlap with the ground-truth, whereas coexpression did not perform better than random. A subsampling analysis revealed that the performance of mediation saturates at large sample sizes, due to a loss of sensitivity when residual correlations become significant. Instrumental variable methods on the other hand contain false positive predictions, due to genomic linkage between eQTL instruments. Instrumental variable and mediation-based methods also have complementary roles for identifying causal genes underlying transcriptional hotspots. Instrumental variable methods correctly predicted STB5 targets for a hotspot centred on the transcription factor STB5, whereas mediation failed due to Stb5p auto-regulating its own expression. Mediation suggests a new candidate gene, DNM1, for a hotspot on Chr XII, whereas instrumental variable methods could not distinguish between multiple genes located within the hotspot. In conclusion, causal inference from genomics and transcriptomics data is a powerful approach for reconstructing causal gene networks, which could be further improved by the development of methods to control for residual correlations in mediation analyses, and for genomic linkage and pleiotropic effects from transcriptional hotspots in instrumental variable analyses.acceptedVersio