Technology
Feature selection in omics prediction problems using cat scores and false nondiscovery rate control
Ahdesmäki, Miika, Strimmer, Korbinian
We revisit the problem of feature selection in linear discriminant analysis (LDA), that is, when features are correlated. First, we introduce a pooled centroids formulation of the multiclass LDA predictor function, in which the relative weights of Mahalanobis-transformed predictors are given by correlation-adjusted $t$-scores (cat scores). Second, for feature selection we propose thresholding cat scores by controlling false nondiscovery rates (FNDR). Third, training of the classifier is based on James--Stein shrinkage estimates of correlations and variances, where regularization parameters are chosen analytically without resampling. Overall, this results in an effective and computationally inexpensive framework for high-dimensional prediction with natural feature selection. The proposed shrinkage discriminant procedures are implemented in the R package ``sda'' available from the R repository CRAN.
BART: Bayesian additive regression trees
Chipman, Hugh A., George, Edward I., McCulloch, Robert E.
We develop a Bayesian "sum-of-trees" model where each tree is constrained by a regularization prior to be a weak learner, and fitting and inference are accomplished via an iterative Bayesian backfitting MCMC algorithm that generates samples from a posterior. Effectively, BART is a nonparametric Bayesian regression approach which uses dimensionally adaptive random basis elements. Motivated by ensemble methods in general, and boosting algorithms in particular, BART is defined by a statistical model: a prior and a likelihood. This approach enables full posterior inference including point and interval estimates of the unknown regression function as well as the marginal effects of potential predictors. By keeping track of predictor inclusion frequencies, BART can also be used for model-free variable selection. BART's many features are illustrated with a bake-off against competing methods on 42 different data sets, with a simulation experiment and on a drug discovery classification problem.
Mixed-Membership Stochastic Block-Models for Transactional Networks
Transactional network data can be thought of as a list of one-to-many communications(e.g., email) between nodes in a social network. Most social network models convert this type of data into binary relations between pairs of nodes. We develop a latent mixed membership model capable of modeling richer forms of transactional network data, including relations between more than two nodes. The model can cluster nodes and predict transactions. The block-model nature of the model implies that groups can be characterized in very general ways. This flexible notion of group structure enables discovery of rich structure in transactional networks. Estimation and inference are accomplished via a variational EM algorithm. Simulations indicate that the learning algorithm can recover the correct generative model. Interesting structure is discovered in the Enron email dataset and another dataset extracted from the Reddit website. Analysis of the Reddit data is facilitated by a novel performance measure for comparing two soft clusterings. The new model is superior at discovering mixed membership in groups and in predicting transactions.
A bagging SVM to learn from positive and unlabeled examples
Mordelet, Fantine, Vert, Jean-Philippe
In many applications, such as information retrieval or gene ranking, one is given a finite set of data of interest sharing a particular property, and wishes to find other data sharing the same property. In information retrieval, for example, the finite set can be a user query, or a set of documents known to belong to a specific category, and the goal is to scan a large database of documents to identify new documents related to the query or belonging to the same category. In gene ranking, the query is a finite list of genes known to have a given function or to be associated to a given disease, and the goal is to identify new genes sharing the same property (Aerts et al., 2006). In fact this setting is ubiquitous in many applications where identifying a data of interest is difficult or expensive, e.g., because human intervention is necessary or expensive experiments are needed, while unlabeled data can be easily collected. In such cases there is a clear opportunity to alleviate the burden and cost of interesting data identification with the help of machine learning techniques. More formally, let us assign a binary label to each possible data: positive ( 1) for data of interest, negative ( 1) for other data. Unlabeled data are data for which we do not know whether 1 they are interesting or not. Denoting X the set of data, we assume that the "query" is a finite set of data P {x
Trek separation for Gaussian graphical models
Sullivant, Seth, Talaska, Kelli, Draisma, Jan
Gaussian graphical models are semi-algebraic subsets of the cone of positive definite covariance matrices. Submatrices with low rank correspond to generalizations of conditional independence constraints on collections of random variables. We give a precise graph-theoretic characterization of when submatrices of the covariance matrix have small rank for a general class of mixed graphs that includes directed acyclic and undirected graphs as special cases. Our new trek separation criterion generalizes the familiar $d$-separation criterion. Proofs are based on the trek rule, the resulting matrix factorizations and classical theorems of algebraic combinatorics on the expansions of determinants of path polynomials.
Artificial Brain Based on Credible Neural Circuits in a Human Brain
Neurons are individually translated into simple gates to plan a brain based on human psychology and intelligence. State machines, assumed previously learned in subconscious associative memory are shown to enable equation solving and rudimentary thinking using nanoprocessing within short term memory.
Steepest Ascent Hill Climbing For A Mathematical Problem
Abraham, Siby, Kiss, Imre, Sanyal, Sugata, Sanglikar, Mukund
The paper proposes artificial intelligence technique called hill climbing to find numerical solutions of Diophantine Equations. Such equations are important as they have many applications in fields like public key cryptography, integer factorization, algebraic curves, projective curves and data dependency in super computers. Importantly, it has been proved that there is no general method to find solutions of such equations. This paper is an attempt to find numerical solutions of Diophantine equations using steepest ascent version of Hill Climbing. The method, which uses tree representation to depict possible solutions of Diophantine equations, adopts a novel methodology to generate successors. The heuristic function used help to make the process of finding solution as a minimization process. The work illustrates the effectiveness of the proposed methodology using a class of Diophantine equations given by a1. x1 p1 + a2. x2 p2 + ...... + an . xn pn = N where ai and N are integers. The experimental results validate that the procedure proposed is successful in finding solutions of Diophantine Equations with sufficiently large powers and large number of variables.
An Embarrassingly Simple Speed-Up of Belief Propagation with Robust Potentials
Coughlan, James M., Shen, Huiying
We present an exact method of greatly speeding up belief propagation (BP) for a wide variety of potential functions in pairwise MRFs and other graphical models. Specifically, our technique applies whenever the pairwise potentials have been {\em truncated} to a constant value for most pairs of states, as is commonly done in MRF models with robust potentials (such as stereo) that impose an upper bound on the penalty assigned to discontinuities; for each of the $M$ possible states in one node, only a smaller number $m$ of compatible states in a neighboring node are assigned milder penalties. The computational complexity of our method is $O(mM)$, compared with $O(M^2)$ for standard BP, and we emphasize that the method is {\em exact}, in contrast with related techniques such as pruning; moreover, the method is very simple and easy to implement. Unlike some previous work on speeding up BP, our method applies both to sum-product and max-product BP, which makes it useful in any applications where marginal probabilities are required, such as maximum likelihood estimation. We demonstrate the technique on a stereo MRF example, confirming that the technique speeds up BP without altering the solution.
A Comprehensive Survey of Data Mining-based Fraud Detection Research
Phua, Clifton, Lee, Vincent, Smith, Kate, Gayler, Ross
This survey paper categorises, compares, and summarises from almost all published technical and review articles in automated fraud detection within the last 10 years. It defines the professional fraudster, formalises the main types and subtypes of known fraud, and presents the nature of data evidence collected within affected industries. Within the business context of mining the data to achieve higher cost savings, this research presents methods and techniques together with their problems. Compared to all related reviews on fraud detection, this survey covers much more technical articles and is the only one, to the best of our knowledge, which proposes alternative data and solutions from related domains.
Active Tuples-based Scheme for Bounding Posterior Beliefs
Bidyuk, B., Dechter, R., Rollon, E.
The paper presents a scheme for computing lower and upper bounds on the posterior marginals in Bayesian networks with discrete variables. Its power lies in its ability to use any available scheme that bounds the probability of evidence or posterior marginals and enhance its performance in an anytime manner. The scheme uses the cutset conditioning principle to tighten existing bounding schemes and to facilitate anytime behavior, utilizing a fixed number of cutset tuples. The accuracy of the bounds improves as the number of used cutset tuples increases and so does the computation time. We demonstrate empirically the value of our scheme for bounding posterior marginals and probability of evidence using a variant of the bound propagation algorithm as a plug-in scheme.