I am interested in maximal information coefficient mic as an alternative to pearson correlation when looking at gene coexpression from microarray data. However, in biology, ecology and finance, to name a few, applications involving nonlinear multivariate dependence prevail. An opensource software implementation of these two measures. The maximal information coefficient mic is a good measure of dependence for twovariable relationships which can capture a wide range of associations. For such applications, the correlation coefficient is. Wang is with the school of software engineering, university of science.
The maximal information coefficient mic has been proposed to discover relationships and associations between pairs of variables. Nick romito principal software engineer cribl linkedin. Improved approximation algorithm for maximal information. Since it relies on moments, it assumes statistical linear dependence. Data mining with the maximal information coefficient by ben lorica. Binning has been used for some time as a way of applying mutual information to continuous distributions. Maximal information coefficient mic in practical bioinformatics applications. Detecting novel associations in large data sets science. The tcn models comprised of long shortterm memory networks lstm. 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. Here, we present a measure of dependence for twovariable relationships. The description of the package stipulates that the function mine x,y works only with 2 matrices a and b of the same size. Software engineering research entails investigation and application of software engineering principles to the design, development, maintenance, testing, and evaluation of the software and systems.
The mic is a very useful complement to standard and rank correlation measures. A new algorithm to optimize maximal information coefficient plos. 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. New genetic algorithm with a maximal information coefficient. With support from the national science foundation, researchers from the broad institute and harvard university recently developed a tool that can uncover patterns in large data sets in a way that no other software program can. The minerva package provide a function to perform the maximal information coefficient mic. The information coefficient is a performance measure used for. 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. An opensource software implementation of these two measures providing a complete procedure to test their significance would be extremely useful. You can only do it if the relationship is monotone.
Nick romito principal software engineer at cribl were hiring. Correlation and maximal information coefficient values. What is the difference between the maximal information coefficient and hierarchical agglomerative clustering in identifying functional and non functional dependencies. Proceedings of the 23rd ieee international conference on software analysis, evolution, and reengineering saner 2016, osaka, japan. Temporal convolutionnetworkbased models for modeling. A novel algorithm for the precise calculation of the. The application of maximum information coefficient in the identification of mirna expression differences in valvular heart disease. An empirical study of the maximal and total information. Abstract the maximal information coefficient mic has been proposed to discover relationships and associations between. The impact of feature selection on defect prediction. Software engineering research also include software project management. Employing mic, a graph model is proposed for preventing railway accidents which avoids complex mathematical computation. Maximal information nonparametric exploration software using mic the breakthrough method from reshef brothers described in a recent science paper improves upon pearson correlation coefficient and introduces a new mic criteria to find a wide range of nonlinear association.
Oct 17, 2014 measuring associations is an important scientific task. 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. Defect prediction via feature selection based on maximal information coefficient with hierarchical agglomerative clustering. Finger gesture recognition based on 3daccelerometer and 3d.
It extends current software algorithm into parallel manner and achieves linear speedup without the affecting the correctness and sensitivity. Identifying interesting relationships between pairs of variables in large datasets is increasingly important. A novel measurement method maximal information coefficient mic was proposed to identify a broad class of associations. In other words, as pearsons r gives a measure of the noise surrounding a linear regression, mic should give. The algorithm used to calculate mic applies concepts from information theory and probability to continuous data. In this paper, the maximal information coefficient mic will be used to modify the genetic algorithm ga in order to solve multivariable optimization problems more efficiently and accurately. 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. In the present report, we look at mic maximal information coefficient as a novel processing method to search for a new knowledge in tool data dalabasc, and construct a hierarchical clustering method based on mic as a data mining method comparinga predicting equation derived from the conventional catalog mining method based on a traditional statistics with one based on mic. Improved approximation algorithm for maximal information coefficient. It has an important characteristic of model independence, which is suitable for the studies of unknown models such as gene expression. Despite the potential of this approach, an e cient software.
A novel algorithm for the precise calculation of the maximal. 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. Mar 04, 2014 by contrast, a recently introduced dependence measure called the maximal information coefficient is seen to violate equitability. Called maximal information coefficient or mic, the tool can can tease out multiple, recurring events or sets of data hidden in health information from around the globe, or in the changing bacterial landscape of the gut or even in statistics amassed from a season of competitive sportsand much more. Ive read some very good posts on this website on mic. At the heart of this definition is a naive mutual information estimate computed using a datadependent binning scheme. Equitability analysis of the maximal information coefficient. In this study, a temporal convolution network tcn with two engineering methods principal component analysis pca and maximal information coefficient mic was developed to predict et c using a twoyear dataset from lysimeters for maize under drip irrigation with film mulch. Intuitively, mic is based on the idea that if a relationship exists between two variables, then a grid can be drawn on the scatterplot. A copula statistic for measuring nonlinear multivariate. A practical tool for maximal information coefficient analysis biorxiv. Mathworks is the leading developer of mathematical computing software for engineers and scientists. Regarding the latter, i also had difficulties running the software on r.
Maximal information nonparametric exploration software. View rabindra nath nandis profile on linkedin, the worlds largest professional community. Learn more about digital image processing, correlation, matlab similarity matlab. Measuring associations is an important scientific task. 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. Mic is part of a larger family of maximal informationbased. A practical tool for maximal information coefficient analysis ncbi. The mic modified ga micga learns the problem structure by calculating the mic.
Data mining with the maximal information coefficient verisi. Mic abbreviation stands for maximal information coefficient. 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. 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. A graph model for preventing railway accidents based on the. Equitability analysis of the maximal information coe cient, with comparisons david n. What is the abbreviation for maximal information coefficient. Besides, we work out a faster calculation method, which is based on the features of top 30 maximal information coefficient. The maximal information coefficient mic is a recent method for detecting nonlinear dependencies between variables, devised in 2011. Dec 16, 2011 identifying interesting relationships between pairs of variables in large data sets is increasingly important. Equitability, mutual information, and the maximal information. An opensource software implementation of these two measures providing a comprehensive procedure to test their significance would be. For example, if you chose to minimize the 1norm of the entries of the matrix, youd get a different solution than if you minimized the 2norm. Jun 10, 2019 minepy maximal informationbased nonparametric exploration minepyminepy.
This tool demonstrates that accelerators parallel processing power can be fully mobilized to achieve high. A novel measurement method maximal information coefficient mic was proposed to identify a. Maximal information coefficient matlab answers matlab central. It searches for optimal binning and turns mutual information score into a metric that lies in range 0. Bioinformatics with maximal information coefficient chao wang, member ieee, xi li, dong dai, aili wang and xuehai zhou abstract the maximal information coefficient mic has been proposed to discover relationships and associations between pairs of variables. The impact of feature selection on defect prediction performance. It poses significant challenges for bioinformatics scientists to accelerate the mic calculation, especially in genome sequencing and biological annotations. Equitability analysis of the maximal information coe cient. The maximal information coefficient uses binning as a means to apply mutual information on continuous random variables. 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. A correlation value that measures the relationship between a variables predicted and actual values.
Defect prediction via feature selection based on maximal information coefficient with hierarchical agglomerative clustering, in proc. 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. Mar 16, 2012 how can the maximal information coefficient be. Rapid computation of the maximal information coefficient. However, the data used in these applications are not gold standard but real data. Feature selection methods with code examples analytics. The software sgmic and its manual are freely available at. Maximal information coefficient applied to differentially. In this paper, maximal information coefficient is adopted for examining the effect of features on the gesture classification. 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. Maximal information coefficient matlab answers matlab. 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. Catalog mining using mic maximal information coefficient. Maximal information coefficient just a messedup estimate.
Maximal information coefficient mic is a novel correlation statistic that measures the association strength of linear and nonlinear relationships between paired variables. Aug 21, 2019 in this paper, maximal information coefficient is adopted for examining the effect of features on the gesture classification. The funders had no role in study design, data collection and analysis, decision to publish. A novel statistical maximal information coefficient mic that can detect the nonlinear relationships in large data sets was proposed by reshef et al. The common correlation coefficient r was invented in 1888 by charles darwins halfcousin francis galton 2. Developed the genetic algorithm with a maximal information coefficient based mutation and performed over 100 various tests. The strategic objective of the software engineering research group serg is to pursue research in a software engineering fashioned approach, aimed at bridging the gap between research and development in software engineering field.
Feb 10, 20 maximal information coefficient just a messedup estimate of mutual information. Empirical software engineering researchers are concerned with understanding the relationships between outcomes of interest, e. Finger gesture recognition based on 3daccelerometer and. Supermic is a uniform accelerating cluster based system. 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. Information coefficient ic definition investopedia. Defect prediction based on maximal information coefficient and fast. Proceedings of the 23rd ieee international conference on software analysis, evolution, and reengineering saner. Maximal information coefficient vs hierarchical agglomerative. The maximal information coefficient mic is a measure of twovariable dependence designed specifically for rapid exploration of manydimensional data sets. We conclude that estimating mutual information provides a natural and practical method for equitably quantifying associations in large datasets. Software engineering icse, 2012 34th international conference on, 25 35, 2012. We suggest to use mictools, a comprehensive and effective pipeline for tice and mice analysis.
Rabindra nath nandi principal software engineer bjit. Defect prediction via feature selection based on maximal information coefficient with hierarchical agglomerative clustering z xu, j xuan, j liu, x cui 2016 ieee 23rd international conference on software analysis, evolution, and, 2016. The mic belongs to the maximal information based nonparametric exploration mine class of statistics. I declare that software defect prediction using maximal information coefficient and fast correlationbased filter feature selection, is my own work and that all the sources that i have used or quoted have been indicated and acknowledged by means of complete references.
In light of a recent paper by simon and tibshirani, im recommending the distance correlation instead of the mic. Called maximal information coefficient or mic, the tool can can tease out multiple, recurring events or sets of data. In this study, pearson correlation coefficient pcc 34 and maximal information coefficient mic 36 are used to explore the line and nonline correlation between wind speed and meteorological. 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.
The mic belongs to the maximal informationbased nonparametric exploration mine class of statistics. 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. Maximal information coefficient is a technique developed to address these shortcomings. A new bivariate measure of association, maximal information coefficient mic 1, promises to simultaneously discover if two variables have. Maximal information coefficient mic is a novel statistical method to explore some unknown relationships between two variables. We describe our first attempt in applying mic in the clinical domain for a textual feature evaluation. 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. You still need to define how close to zero is for that vector of values. Maximal information coefficient part ii 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. Represents a technique for large scale biological datasets using mapreduce framework. Reshef harvardmit division of heath sciences and technology.
Dec 16, 2011 identifying interesting relationships between pairs of variables in large datasets is increasingly important. Pdf a practical tool for maximal information coefficient analysis. Maximal information coefficient for feature selection for. Identifies relevant associations amongst a large number of variables. A novel measurement method maximal information coefficient mic was proposed to.
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