The software sgmic and its manual are freely available at. We describe our first attempt in applying mic in the clinical domain for a textual feature evaluation. 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. 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 new bivariate measure of association, maximal information coefficient mic 1, promises to simultaneously discover if two variables have. Jun 10, 2019 minepy maximal informationbased nonparametric exploration minepyminepy. 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. Oct 17, 2014 measuring associations is an important scientific task. Maximal information coefficient applied to differentially. Reshef harvardmit division of heath sciences and technology. Feb 10, 20 maximal information coefficient just a messedup estimate of mutual information. At the heart of this definition is a naive mutual information estimate computed using a datadependent binning scheme. A novel algorithm for the precise calculation of the. Finger gesture recognition based on 3daccelerometer and.
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. Tool enables scientists to uncover patterns in vast data. Identifies relevant associations amongst a large number of variables. Maximal information coefficient vs hierarchical agglomerative. 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. If you are just interested in monotonic relationships between variables i would suggest to use the spearmans rank coefficient. Feature selection methods with code examples analytics. The mic belongs to the maximal information based nonparametric exploration mine class of statistics. Proceedings of the 23rd ieee international conference on software analysis, evolution, and reengineering saner. 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. Software engineering research entails investigation and application of software engineering principles to the design, development, maintenance, testing, and evaluation of the software and systems. Finger gesture recognition based on 3daccelerometer and 3d. Measuring associations is an important scientific task. Improving crosscompany defect prediction with data filtering. Defect prediction via feature selection based on maximal information coefficient with hierarchical agglomerative clustering, in proc. The minerva package provide a function to perform the maximal information coefficient mic.
What is the abbreviation for maximal information coefficient. Maximal information coefficient for feature selection for. The impact of feature selection on defect prediction performance. Wang is with the school of software engineering, university of science. 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. However, the data used in these applications are not gold standard but real data. Regarding the latter, i also had difficulties running the software on r. Improved approximation algorithm for maximal information. Empirical software engineering researchers are concerned with understanding the relationships between outcomes of interest, e. We conclude that estimating mutual information provides a natural and practical method for equitably quantifying associations in large datasets. Maximal information coefficient matlab answers matlab central.
A practical tool for maximal information coefficient analysis ncbi. Information coefficient ic definition investopedia. Equitability analysis of the maximal information coe cient, with comparisons david n. 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. This tool demonstrates that accelerators parallel processing power can be fully mobilized to achieve high. Ive read some very good posts on this website on mic. 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.
Equitability analysis of the maximal information coefficient. Developed the genetic algorithm with a maximal information coefficient based mutation and performed over 100 various tests. Maximal information coefficient is a technique developed to address these shortcomings. The maximal information coefficient uses binning as a means to apply mutual information on continuous random variables. Software engineering icse, 2012 34th international conference on, 25 35, 2012. Maximal information coefficient just a messedup estimate. 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. The maximal information coefficient mic has been proposed to discover relationships and associations between pairs of variables. 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. Maximal information coefficient matlab answers matlab. 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. In this paper, maximal information coefficient is adopted for examining the effect of features on the gesture classification.
A copula statistic for measuring nonlinear multivariate. Dec 16, 2011 identifying interesting relationships between pairs of variables in large datasets is increasingly important. The mic belongs to the maximal informationbased nonparametric exploration mine class of statistics. Maximal information coefficient mic is a novel correlation statistic that measures the association strength of linear and nonlinear relationships between paired variables. An opensource software implementation of these two measures providing a complete procedure to test their significance would be extremely useful. The algorithm used to calculate mic applies concepts from information theory and probability to continuous data. Context likelihood of relatedness with maximal information coefficient for gene regulatory network inference 18th international conference on computer and information technology. 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. Nick romito principal software engineer at cribl were hiring. A correlation value that measures the relationship between a variables predicted and actual values.
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. You still need to define how close to zero is for that vector of values. In light of a recent paper by simon and tibshirani, im recommending the distance correlation instead of the mic. Mar 16, 2012 how can the maximal information coefficient be. The tcn models comprised of long shortterm memory networks lstm. A graph model for preventing railway accidents based on the. 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. The maximal information coefficient mic is a good measure of dependence for twovariable relationships which can capture a wide range of associations.
It poses significant challenges for bioinformatics scientists to accelerate the mic calculation, especially in genome sequencing and biological annotations. Here, we present a measure of dependence for twovariable relationships. Rabindra nath nandi principal software engineer bjit. Improved approximation algorithm for maximal information coefficient. 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 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.
The application of maximum information coefficient in the identification of mirna expression differences in valvular heart disease. Mic is part of a larger family of maximal informationbased. 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. It searches for optimal binning and turns mutual information score into a metric that lies in range 0.
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 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. Supermic is a uniform accelerating cluster based system. Data mining with the maximal information coefficient verisi.
You can only do it if the relationship is monotone. Binning has been used for some time as a way of applying mutual information to continuous distributions. A novel statistical maximal information coefficient mic that can detect the nonlinear relationships in large data sets was proposed by reshef et al. Maximal information nonparametric exploration software. Aug 21, 2019 in this paper, maximal information coefficient is adopted for examining the effect of features on the gesture classification. 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. Called maximal information coefficient or mic, the tool can can tease out multiple, recurring events or sets of data. 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. New genetic algorithm with a maximal information coefficient.
The information coefficient is a performance measure used for. The maximal information coefficient mic captures dependences between paired. Intuitively, mic is based on the idea that if a relationship exists between two variables, then a grid can be drawn on the scatterplot. Mar 04, 2014 by contrast, a recently introduced dependence measure called the maximal information coefficient is seen to violate equitability. In other words, as pearsons r gives a measure of the noise surrounding a linear regression, mic should give.
Maximal information coefficient mic in practical bioinformatics applications. The funders had no role in study design, data collection and analysis, decision to publish. Abstract the maximal information coefficient mic has been proposed to discover relationships and associations between. Defect prediction via feature selection based on maximal information coefficient with hierarchical agglomerative clustering. Besides, we work out a faster calculation method, which is based on the features of top 30 maximal information coefficient. Maximal information coefficient mic is a novel statistical method to explore some unknown relationships between two variables. Catalog mining using mic maximal information coefficient. Detecting novel associations in large data sets science. Pdf a practical tool for maximal information coefficient analysis.
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. Software engineering research also include software project management. Learn more about digital image processing, correlation, matlab similarity matlab. It extends current software algorithm into parallel manner and achieves linear speedup without the affecting the correctness and sensitivity. The mic modified ga micga learns the problem structure by calculating the mic.
The impact of feature selection on defect prediction. Rapid computation of the maximal information coefficient. A novel algorithm for the precise calculation of the maximal. 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. Since it relies on moments, it assumes statistical linear dependence. Data mining with the maximal information coefficient by ben lorica. Represents a technique for large scale biological datasets using mapreduce framework. View rabindra nath nandis profile on linkedin, the worlds largest professional community.
The maximal information coefficient mic is a measure of twovariable dependence designed specifically for rapid exploration of manydimensional data sets. Despite the potential of this approach, an e cient software. A novel measurement method maximal information coefficient mic was proposed to identify a broad class of associations. Proceedings of the 23rd ieee international conference on software analysis, evolution, and reengineering saner 2016, osaka, japan. 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. For such applications, the correlation coefficient is. We suggest to use mictools, a comprehensive and effective pipeline for tice and mice analysis. 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.
It has an important characteristic of model independence, which is suitable for the studies of unknown models such as gene expression. A practical tool for maximal information coefficient analysis biorxiv. What is the difference between the maximal information coefficient and hierarchical agglomerative clustering in identifying functional and non functional dependencies. I am interested in maximal information coefficient mic as an alternative to pearson correlation when looking at gene coexpression from microarray data. A novel measurement method maximal information coefficient mic was proposed to identify a. A novel measurement method maximal information coefficient mic was proposed to. Mic abbreviation stands for maximal information coefficient. The description of the package stipulates that the function mine x,y works only with 2 matrices a and b of the same size. Mathworks is the leading developer of mathematical computing software for engineers and scientists. 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. 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.
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. The mic is a very useful complement to standard and rank correlation measures. An opensource software implementation of these two measures. 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. 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. Temporal convolutionnetworkbased models for modeling. Defect prediction based on maximal information coefficient and fast. Nick romito principal software engineer cribl linkedin. A new algorithm to optimize maximal information coefficient plos. Equitability analysis of the maximal information coe cient. However, in biology, ecology and finance, to name a few, applications involving nonlinear multivariate dependence prevail. Employing mic, a graph model is proposed for preventing railway accidents which avoids complex mathematical computation.
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