Building Gene Expression Profile Classifiers with a Simple and Efficient Rejection Option in R

Background: The collection of gene expression profiles from DNA microarrays and their analysis with pattern recognition algorithms is a powerful technology applied to several biological problems. Common pattern recognition systems classify samples assigning them to a set of known classes. However, in a clinical diagnostics setup, novel and unknown classes (new pathologies) may appear and one must be able to reject those samples that do not fit the trained model. The problem of implementing a rejection option in a multi-class classifier has not been widely addressed in the statistical literature. Gene expression profiles represent a critical case study since they suffer from the curse of dimensionality problem that negatively reflects on the reliability of both traditional rejection models and also more recent approaches such as one-class classifiers. Results: This paper presents a set of empirical decision rules that can be used to implement a rejection option in a set of multi-class classifiers widely used for the analysis of gene expression profiles. In particular, we focus on the classifiers implemented in the R Language and Environment for Statistical Computing (R for short in the remaining of this paper). The main contribution of the proposed rules is their simplicity, which enables an easy integration with available data analysis environments. Since in the definition of a rejection model tuning of the involved parameters is often a complex and delicate task, in this paper we exploit an evolutionary strategy to automate this process. This allows the final user to maximize the rejection accuracy with minimum manual intervention. Conclusions: This paper shows how the use of simple decision rules can be used to help the use of complex machine learning algorithms in real experimental setups. The proposed approach is almost completely automated and therefore a good candidate for being integrated in data analysis flows in labs where the machine learning expertise required to tune traditional classifiers might not be availabl

Technology assessment of advanced automation for space missions

Six general classes of technology requirements derived during the mission definition phase of the study were identified as having maximum importance and urgency, including autonomous world model based information systems, learning and hypothesis formation, natural language and other man-machine communication, space manufacturing, teleoperators and robot systems, and computer science and technology

Probabilistic Inference from Arbitrary Uncertainty using Mixtures of Factorized Generalized Gaussians

This paper presents a general and efficient framework for probabilistic inference and learning from arbitrary uncertain information. It exploits the calculation properties of finite mixture models, conjugate families and factorization. Both the joint probability density of the variables and the likelihood function of the (objective or subjective) observation are approximated by a special mixture model, in such a way that any desired conditional distribution can be directly obtained without numerical integration. We have developed an extended version of the expectation maximization (EM) algorithm to estimate the parameters of mixture models from uncertain training examples (indirect observations). As a consequence, any piece of exact or uncertain information about both input and output values is consistently handled in the inference and learning stages. This ability, extremely useful in certain situations, is not found in most alternative methods. The proposed framework is formally justified from standard probabilistic principles and illustrative examples are provided in the fields of nonparametric pattern classification, nonlinear regression and pattern completion. Finally, experiments on a real application and comparative results over standard databases provide empirical evidence of the utility of the method in a wide range of applications

CLASSIFICATION OF FEATURE SELECTION BASED ON ARTIFICIAL NEURAL NETWORK

Pattern recognition (PR) is the central in a variety of engineering applications. For this reason, it is indeed vital to develop efficient pattern recognition systems that facilitate decision making automatically and reliably. In this study, the implementation of PR system based on computational intelligence approach namely artificial neural network (ANN) is performed subsequent to selection of the best feature vectors. A framework to determine the best eigenvectors which we named as ‘eigenpostures’ of four main human postures specifically, standing, squatting/sitting, bending and lying based on the rules of thumb of Principal Component Analysis (PCA) has been developed. Accordingly, all three rules of PCA namely the KG-rule, Cumulative Variance and the Scree test suggest retaining only 35 main principal component or ‘eigenpostures’. Next, these ‘eigenpostures’ are statistically analyzed via Analysis of Variance (ANOVA) prior to classification. Thus, the most relevant component of the selected eigenpostures can be determined. Both categories of ‘eigenpostures’ prior to ANOVA as well as after ANOVA served as inputs to the ANN classifier to verify the effectiveness of feature selection based on statistical analysis. Results attained confirmed that the statistical analysis has enabled us to perform effectively the selection of eigenpostures for classification of four types of human postures

Linear and Order Statistics Combiners for Pattern Classification

Several researchers have experimentally shown that substantial improvements can be obtained in difficult pattern recognition problems by combining or integrating the outputs of multiple classifiers. This chapter provides an analytical framework to quantify the improvements in classification results due to combining. The results apply to both linear combiners and order statistics combiners. We first show that to a first order approximation, the error rate obtained over and above the Bayes error rate, is directly proportional to the variance of the actual decision boundaries around the Bayes optimum boundary. Combining classifiers in output space reduces this variance, and hence reduces the "added" error. If N unbiased classifiers are combined by simple averaging, the added error rate can be reduced by a factor of N if the individual errors in approximating the decision boundaries are uncorrelated. Expressions are then derived for linear combiners which are biased or correlated, and the effect of output correlations on ensemble performance is quantified. For order statistics based non-linear combiners, we derive expressions that indicate how much the median, the maximum and in general the ith order statistic can improve classifier performance. The analysis presented here facilitates the understanding of the relationships among error rates, classifier boundary distributions, and combining in output space. Experimental results on several public domain data sets are provided to illustrate the benefits of combining and to support the analytical results.Comment: 31 page

Classifiers With a Reject Option for Early Time-Series Classification

Early classification of time-series data in a dynamic environment is a challenging problem of great importance in signal processing. This paper proposes a classifier architecture with a reject option capable of online decision making without the need to wait for the entire time series signal to be present. The main idea is to classify an odor/gas signal with an acceptable accuracy as early as possible. Instead of using posterior probability of a classifier, the proposed method uses the "agreement" of an ensemble to decide whether to accept or reject the candidate label. The introduced algorithm is applied to the bio-chemistry problem of odor classification to build a novel Electronic-Nose called Forefront-Nose. Experimental results on wind tunnel test-bed facility confirms the robustness of the forefront-nose compared to the standard classifiers from both earliness and recognition perspectives

Cursive script recognition using wildcards and multiple experts

Variability in handwriting styles suggests that many letter recognition engines cannot correctly identify some hand-written letters of poor quality at reasonable computational cost. Methods that are capable of searching the resulting sparse graph of letter candidates are therefore required. The method presented here employs ‘wildcards’ to represent missing letter candidates. Multiple experts are used to represent different aspects of handwriting. Each expert evaluates closeness of match and indicates its confidence. Explanation experts determine the degree to which the word alternative under consideration explains extraneous letter candidates. Schemata for normalisation and combination of scores are investigated and their performance compared. Hill climbing yields near-optimal combination weights that outperform comparable methods on identical dynamic handwriting data