An opensource software implementation of these two measures. In this paper, we develop a new method, chimic, to calculate the mic values. Maximal information coefficient matlab answers matlab. Mictools is an opensource software that provides i an efficient implementation of total information coefficient tice and maximal information coefficient mic estimators, ii a permutationbased strategy for estimating tice empirical p values, iii several methods for multiple testing correction, iv the mice estimates for each. To address this issue, a new attribute selection method nasm is proposed in this paper. I am interested in maximal information coefficient mic as an alternative to pearson correlation when looking at gene coexpression from microarray data.
The chimic algorithm uses the chisquare test to terminate grid optimization and then removes the restriction of maximal grid size limitation of original approxmaxmi. Denis boigelot, wikimedia commonsa paper published this week in science outlines a new statistic called the maximal information coefficient mic, which is able to equally describe the correlation between paired variables regardless of linear or nonlinear relationship. In other words, as pearsons r gives a measure of the noise surrounding a linear regression, mic should give. Mictools is an opensource software that provides i an efficient implementation of total information coefficient tice and maximal information coefficient mic estimators, ii a permutationbased strategy for estimating tice empirical p values, iii several methods for multiple testing correction, iv the mice. In light of a recent paper by simon and tibshirani, im recommending the distance correlation instead of the mic. The algorithm used to calculate mic applies concepts from information theory and probability to. In other words, as pearsons r gives a measure of the noise surrounding a linear regression, mic should give similar scores to equally noisy relationships. Describes how to use a data analysis tool provided in the real statistics resource pack to perform nonparametric tests in excel. Associations of maximal strength and muscular endurance. We conclude that estimating mutual information provides a natural and practical method for equitably quantifying associations in large datasets. Network analysis was performed using the maximal information coefficient mic scores in mine software reshef et al. What is the difference between the maximal information coefficient and hierarchical agglomerative clustering in identifying functional and non functional dependencies.
Dec 14, 2012 minepy provides a library for the maximal information based nonparametric exploration mic and mine family. An opensource software implementation of these two measures providing a complete procedure to test their significance would be extremely useful. Ive read some very good posts on this website on mic. The information coefficient is a performance measure used for. Equitability analysis of the maximal information coe cient, with comparisons david n. Dec 16, 2011 identifying interesting relationships between pairs of variables in large datasets is increasingly important. The reaction from others in the field upon publication has not been that positive, e. If you could help me to find a specific information about maximal information coefficient mic, and its values and the. The maximal information coefficient mic is a measure of twovariable dependence designed specifically for rapid exploration of manydimensional data sets. Identifies relevant associations amongst a large number of variables.
Mic captures a wide range of associations both functional and not, and for functional relationships provides a score that roughly equals the coefficient of determination. Network analysis reveals functional redundancy and. Since the maximal information coefficient mic was proposed by reshef et al. This turned out to be quite a popular post, and included a lively discussion as to the merits of the work and difficulties in using the. Binning has been used for some time as a way of applying mutual information to continuous distributions. The maximal information coefficient mic intuitively, mic is based on the idea that if a relationship exists between two variables, then a grid can be drawn on the scatterplot of the two variables that partitions the data to encapsulate that relationship. Maximal information coefficient matlab answers matlab central. Moreover, with respect to the nonlinear correlation, one of the mutual information based measures, maximal information coefficient mic was also employed to identify the nonlinear association. Twotailed t test showed that the average of the mic values by sg 0.
Equitability analysis of the maximal information coefficient. Maximal information coefficient applied to differentially. A paper published this week in science outlines a new statistic called the maximal information coefficient mic, which is able to equally describe the correlation between paired variables regardless of linear or nonlinear relationship. The maximal information coefficient statistical modeling. Jan 27, 20 thus an equitable statistic, such as the maximal information coefficient mic, can be useful for analyzing highdimensional data sets. Identifying multivariable relationships based on the. A novel measurement method maximal information coefficient mic was proposed to. Wadsworth advanced books and software, belmont, ca. Maximal information coefficient just a messedup estimate. Wuhan university was founded in 1893, which locates in wuhan, a central city of china. Maximal information coefficient for feature selection for.
However, the data used in these applications are not gold standard but real data. Mic is a part of a larger family of maximal information based nonparametric exploration mine statistics, which can be used to identify and characterize important. Recently, a family of measures based on the concept of mutual information has been proposed, and one of the most popular and debated members of this family, the maximal information coefficient mic, has been shown to have good equitability. In statistics, the pearson correlation coefficient pcc, pronounced. Efficient test for nonlinear dependence of two continuous.
Mutual information based measures of association are particularly promising, in particular after the recent introduction of the tic e and mic e estimators, which combine. A new algorithm to optimize maximal information coefficient plos. Reshef harvardmit division of heath sciences and technology. Proceedings of the 23rd ieee international conference on software analysis, evolution, and reengineering saner 2016, osaka, japan. A practical tool for maximal information coefficient analysis biorxiv. Here, we explore both equitability and the properties of mic, and discuss several aspects of the theory and practice of mic.
Maximal strength was measured using isometric bench press, leg extension and grip strength. A novel algorithm for the precise calculation of the maximal. A practical tool for maximal information coefficient analysis ncbi. The description of the package stipulates that the function mine x,y. Maximal information coefficient, equitability, total information coeffi. Firstly, we compute the maximal information coefficient matrix between the attributes in the method, and then these attributes are clustered by spectral clustering according to the maximal information coefficient matrix. Data mining with the maximal information coefficient by ben lorica. Feb 06, 2020 a practical tool for maximal information coefficient mic analysis minepymictools. A practical tool for maximal information coefficient analysis. It searches for optimal binning and turns mutual information score into a metric that lies in range 0. Despite that, a complete software implementation of these two measures and of a statistical procedure to test the signi cance of each association. A practical tool for maximal information coefficient mic analysis. The minerva package in r provides the value of maximal information coefficient mic of two vectors,two matrices.
Cleaning up the record on the maximal information coefficient and equitability. An opensource software implementation of these two measures providing a comprehensive procedure to test their significance would be extremely useful. The maximal information coefficient mic captures dependences between paired. The maximal information coefficient mic is a new and very promising measure of twovariable dependence designed specifically for rapid exploration of manydimensional data sets. Why is the maximal information coefficient mic important. Since the coefficient is between 0 and 1, i would like to know if the mic allows us to know if the relationship between the two variables are positive or negative. He is a member of cstar centre of software testing, analysis and. Posted on february 10, 20 march 31, 20 by florian markowetz in science theory papers almost never make it into top journals and this is why i have blogged about the paper detecting novel associations in large data sets in science by reshef et al. In the recent research i had to explain few low values appearing from the correlation calculation, so i went for maximal information coefficient mic to see if there is a possibility of having nonlinear relation between the variables which were reporting values close to 0 when calculating correlation. Jifeng xuan is a professor at school of computer science, wuhan university, china. Model selection method based on maximal information. Aug 21, 2019 maximal information coefficient is a technique developed to address these shortcomings. Maximal information coefficient is a technique developed to address these shortcomings.
Detecting novel associations in large data sets science. Bagging nearestneighbor prediction independence test. Measuring associations is an important scientific task. Information coefficient ic definition investopedia. Davide albanese, michele filosi, roberto visintainer, samantha riccadonna, giuseppe jurman and cesare furlanello. A correlation value that measures the relationship between a variables predicted and actual values. A practical tool for maximal information coefficient mic analysis minepymictools. Mic values reported in this paper were computed using the software. Nov 07, 2017 a practical tool for maximal information coefficient analysis. Software defect prediction using maximal information coefficient and fast correlationbased filter feature selection by bongeka mpofu submitted in accordance with the requirements for the degree of doctor of philosophy in the subject computer science at the university of south africa supervisor. Maximal information coefficient for feature selection for clinical document classification our training data includes 2,792 notes which are selected from 821 patients from the brigham and womens hospital bwh database. Mar 23, 2016 maximal information coefficient based feature screening mcone maximal information coefficient mic tests the dependence between two variables and whether they have a linear or other functional relationship. The description of the package stipulates that the function mine x,y works only with 2 matrices a and b of the same size. Improved approximation algorithm for maximal information coefficient.
Defect prediction via feature selection based on maximal information coefficient with hierarchical agglomerative clustering zhou xu 1, jifeng xuan, jin liu1, xiaohui cui2 1state key lab of software engineering, school of computer, wuhan university, wuhan, china 2international school of software, wuhan university, wuhan, china. Maximum entropy method redirects to principle of maximum entropy. Feb 10, 20 maximal information coefficient just a messedup estimate of mutual information. Sequence abundance data for bacteria and fungi were rarefied to 1797 and 1685 sequences per sample, respectively, based on the lowest number of sequences per sample. Correlation and maximal information coefficient values. These show that, for a large collection of test functions with varied sample sizes, noise levels, and noise models, mic roughly equals the coefficient of determination r 2 relative to each respective noiseless function.
In statistics, the maximal information coefficient mic is a measure of the strength of the linear or nonlinear association between two variables x and y. Oct 17, 2014 measuring associations is an important scientific task. Mutual information based measures of association are particularly promising, in particular after the recent introduction of the tic e and mic e estimators, which combine computational. Jun 29, 2018 maximal exercise test refers to a standardized measure used to assess and evaluate the reciprocal proportion of oxygen absorption to carbon dioxide expulsion in the cardiopulmonary system during heavy workout sessions. The minerva package provide a function to perform the maximal information coefficient mic. Dec 16, 2011 identifying interesting relationships between pairs of variables in large data sets is increasingly important. I wanted to let you know that the critique mickey atwal and i wrote regarding equitability and the maximal information coefficient has just been published we discussed this paper last year, under the heading, too many mcs not enough mics, or what principles should govern attempts to summarize bivariate associations in large multivariate datasets. Yesterday, we opensourced the predictive power score pps and published an article on towards data science. Maximal information coefficient mic in practical bioinformatics. In statistics, the maximal information coefficient mic is a measure of the strength of the linear.
The measurement mic is symmetric and normalized into a range 0, 1. More robust correlational measures include the spearman math\rhomath which is a nonparametric correlation measure tha. Improved approximation algorithm for maximal information. Pdf a practical tool for maximal information coefficient analysis. For multiple testing correction, mictools makes available the strategies.
An empirical study of the maximal and total information. Sep 17, 2014 a while back, i wrote a post simply announcing a recent paper that described a new statistic called the maximal information coefficient mic, which is able to describe the correlation between paired variables regardless of linear or nonlinear relationship. Background the ability of finding complex associations in large omics datasets, assessing their significance, and prioritizing them according to their strength can be of great help in the data exploration phase. Equitability analysis of the maximal information coe cient. The maximal information coefficient is primarily a measure of effect size, and gives similar scores for relationships of similar strength regardless of relationship type. Feature selection methods with code examples analytics.
The mine function which returns the mic value,also returns some other parameters value. Mictools is an opensource software that provides i an efficient implementation of total information coefficient tice and maximal information coefficient mic. Mic captures a wide range of associations both functional and not, and for functional relationships provides a score that roughly equals the coefficient of. Maximal information coefficient mic and the total information coefficient tic, lopespaz et al. A novel algorithm for the precise calculation of the. A copula statistic for measuring nonlinear multivariate. Measures of effect size can be used to test for independence using a null hypothesis of zero effect size. The software sgmic and its manual are freely available at. Maximum entropy classifier redirects to logistic regression. Dec 19, 2011 a paper published this week in science outlines a new statistic called the maximal information coefficient mic, which is able to equally describe the correlation between paired variables regardless of linear or nonlinear relationship. The mic belongs to the maximal information based nonparametric exploration mine class of statistics.
The major purpose of canova is to offer a test of independence. Identifying interesting relationships between pairs of variables in large data sets is increasingly important. Maximal information coefficient vs hierarchical agglomerative. The maximal information coefficient mic captures dependences between paired variables, including both functional and nonfunctional relationships.
The city of wuhan has a long history of 3,500 years with a current population of over 10 million people here is his official homepage at wuhan university. By contrast, a recently introduced dependence measure called the maximal information coefficient is seen to violate equitability. Equitability, mutual information, and the maximal information. The chimic algorithm uses the chisquare test to terminate grid optimization and then. Data analysis tools for nonparametric tests real statistics. Pearson r correlation coefficients for various distributions of paired data credit. Mic is part of a larger family of maximal information based nonparametric exploration mine statistics, which can be used not only to identify important relationships in data sets but also. Other commonly used statistical methods to evaluate the correlations of two random variables include distance correlation, hoeffdings independence test, maximal information coefficient.
A while back, i wrote a post simply announcing a recent paper that described a new statistic called the maximal information coefficient mic, which is able to describe the correlation between paired variables regardless of linear or nonlinear relationship. The pps is an alternative to the correlation that finds more patterns in your data because it also finds nonlinear relationships, it can handle categoric columns and it. A new algorithm to optimize maximal information coefficient. Learn more about digital image processing, correlation, matlab similarity matlab. Muscular endurance tests consisted of pushups, situps and. A novel statistical maximal information coefficient mic that can detect the nonlinear relationships in large data sets was proposed by reshef et al. The maximal information coefficient mic is a recent method for detecting nonlinear dependencies between variables, devised in 2011.
Two tailed t test showed that the average of the mic values by sg 0. Maximal information coefficient mic is a novel, nonparametric statistic that has been successfully applied to genomewide association studies and differentially gene and mirna expression analysis. Pdf a practical tool for maximal information coefficient. We suggest to use mictools, a comprehensive and effective pipeline for tice and mice analysis. Here, we present a measure of dependence for twovariable relationships. The maximal information coefficient uses binning as a means to apply mutual information on continuous random variables.
Maximal information nonparametric exploration software. A novel measurement method maximal information coefficient mic was proposed to identify a. Tice is used to perform efficiently a high throughput screening of all the possible pairwise relationships assessing their significance, while mice is used to rank the subset of significant associations on the bases of. What type of correlation should i use for a quadratic.
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