Abstract: As an alternative to the frequently used "reference design" for two-channel microarrays, other designs have been proposed. These designs have been shown to be more profitable from a theoretical point of view (more replicates of the conditions of interest for the same number of arrays). However, the interpretation of the measurements is less straightforward and a reconstruction method is needed to convert the observed ratios into the genuine profile of interest (e.g. a time profile). The potential advantages of using these alternative designs thus largely depend on the success of the profile reconstruction. Therefore, we compared to what extent different linear models agree with each other in reconstructing expression ratios and corresponding time profiles from a complex design. On average the correlation between the estimated ratios was high, and all methods agreed with each other in predicting the same profile, especially for genes of which the expression profile showed a large variance across the different time points. Assessing the similarity in profile shape, it appears that, the more similar the underlying principles of the methods (model and input data), the more similar their results. Methods with a dye effect seemed more robust against array failure. The influence of a different normalization was not drastic and independent of the method used. Including a dye effect such as in the methods lmbr_dye, anovaFix and anovaMix compensates for residual dye related inconsistencies in the data and renders the results more robust against array failure. Including random effects requires more parameters to be estimated and is only advised when a design is used with a sufficient number of replicates. Because of this, we believe lmbr_dye, anovaFix and anovaMix are most appropriate for practical use.

Abstract: The degree of similarity of two protein three-dimensional structures is usually measured with the root-mean-square distance between equivalent atom pairs. Such a similarity measure depends on the dimension of the proteins, that is, on the number of equivalent atom pairs. The present communication presents a simple procedure to make the root-mean-square distances between pairs of three-dimensional structures independent of their dimensions. This normalization may be useful in evolutionary and fold classification studies as well as in simple comparisons between different structural models.

Abstract: Motivation: Gene-expression microarrays are currently being applied in a variety of biomedical applications. This article considers the problem of how to merge datasets arising from different gene-expression studies of a common organism and phenotype. Of particular interest is how to merge data from different technological platforms. Results: The article makes two contributions to the problem. The first is a simple cross-study normalization method, which is based on linked gene/sample clustering of the given datasets. The second is the introduction and description of several general validation measures that can be used to assess and compare cross-study normalization methods. The proposed normalization method is applied to three existing breast cancer datasets, and is compared to several competing normalization methods using the proposed validation measures. Availability: The supplementary materials and XPN Matlab code are publicly available at website: https://genome.unc.edu/xpn Contact: shabalin@email.unc.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Abstract: Multi-criteria decision making is used in many areas of human activities. Each alternative in multi-criteria decision making problem can be described by a set of criteria. Criteria can be qualitative and quantitative. They usually have different units of measurement and different optimization direction. The normalization aims at obtaining comparable scales of criteria values. The normalization of criteria values is not always needed, but it may be essential. In the new program LEVI 3.1 the following normalization methods are possible: vector, linear scale, non-linear and new logarithmic techniques. Logarithmic normalization has never been used before. The present research is focused on introducing a new logarithmic method for decision making matrix normalization.

Abstract: A few distinct cortical operations have been postulated over the past few years, suggested by experimental data on nonlinear neural response across different areas in the cortex. Among these, the energy model proposes the summation of quadrature pairs following a squaring nonlinearity in order to explain phase invariance of complex V1 cells. The divisive normalization model assumes a gain-controlling, divisive inhibition to explain sigmoid-like response profiles within a pool of neurons. A gaussian-like operation hypothesizes a bell-shaped response tuned to a specific, optimal pattern of activation of the presynaptic inputs. A max-like operation assumes the selection and transmission of the most active response among a set of neural inputs. We propose that these distinct neural operations can be computed by the same canonical circuitry, involving divisive normalization and polynomial nonlinearities, for different parameter values within the circuit. Hence, this canonical circuit may provide a unifying framework for several circuit models, such as the divisive normalization and the energy models. As a case in point, we consider a feedforward hierarchical model of the ventral pathway of the primate visual cortex, which is built on a combination of the gaussian-like and max-like operations. We show that when the two operations are approximated by the circuit proposed here, the model is capable of generating selective and invariant neural responses and performing object recognition, in good agreement with neurophysiological data.

Abstract: Illumina Infinium whole genome genotyping (WGG) arrays are increasingly being applied in cancer genomics to study gene copy number alterations and allele-specific aberrations such as loss-of-heterozygosity (LOH). Methods developed for normalization of WGG arrays have mostly focused on diploid, normal samples. However, for cancer samples genomic aberrations may confound normalization and data interpretation. Therefore, we examined the effects of the conventionally used normalization method for Illumina Infinium arrays when applied to cancer samples. We demonstrate an asymmetry in the detection of the two alleles for each SNP, which deleteriously influences both allelic proportions and copy number estimates. The asymmetry is caused by a remaining bias between the two dyes used in the Infinium II assay after using the normalization method in Illumina's proprietary software (BeadStudio). We propose a quantile normalization strategy for correction of this dye bias. We tested the normalization strategy using 535 individual hybridizations from 10 data sets from the analysis of cancer genomes and normal blood samples generated on Illumina Infinium II 300 k version 1 and 2, 370 k and 550 k BeadChips. We show that the proposed normalization strategy successfully removes asymmetry in estimates of both allelic proportions and copy numbers. Additionally, the normalization strategy reduces the technical variation for copy number estimates while retaining the response to copy number alterations. The proposed normalization strategy represents a valuable tool that improves the quality of data obtained from Illumina Infinium arrays, in particular when used for LOH and copy number variation studies.

Abstract: In the named entity normalization task, a system identifies a canonical unambiguous referent for names like Bush or Alabama. Resolving synonymy and ambiguity of such names can benefit end-to-end information access tasks. We evaluate two entity normalization methods based on Wikipedia in the context of both passage and document retrieval for question anwering. We find that even a simple normalization method leads to improvements of early precision, both for document and passage retrieval. Moreover, better normalization results in better retrieval performance.

Abstract: In the named entity normalization task, a system identifies a canonical unambiguous referent for names like Bush or Alabama. Resolving synonymy and ambiguity of such names can benefit end-to-end information access tasks. We evaluate two entity normalization methods based on Wikipedia in the context of both passage and document retrieval for question anwering. We find that even a simple normalization method leads to improvements of early precision, both for document and passage retrieval. Moreover, better normalization results in better retrieval performance.

Abstract: It is well known that the effect of illumination is mainly on the large-scale features (low-frequency components) of a face image. In solving the illumination problem for face recognition, most (if not all) existing methods either only use extracted small-scale features while discard large-scale features, or perform normalization on the whole image. In the latter case, small-scale features may be distorted when the large-scale features are modified. In this paper, we argue that large-scale features of face image are important and contain useful information for face recognition as well as visual quality of normalized image. Moreover, this paper suggests that illumination normalization should mainly perform on large-scale features of face image rather than the whole face image. Along this line, a novel framework for face illumination normalization is proposed. In this framework, a single face image is first decomposed into large- and small- scale feature images using logarithmic total variation (LTV) model. After that, illumination normalization is performed on large-scale feature image while small-scale feature image is smoothed. Finally, a normalized face image is generated by combination of the normalized large-scale feature image and smoothed small-scale feature image. CMU PIE and (Extended) YaleB face databases with different illumination variations are used for evaluation and the experimental results show that the proposed method outperforms existing methods.

Abstract: One of the difficulties in mapping biomedical named entities, e.g. genes, proteins, chemicals and diseases, to their concept identifiers stems from the potential variability of the terms. Soft string matching is a possible solution to the problem, but its inherent heavy computational cost discourages its use when the dictionaries are large or when real time processing is required. A less computationally demanding approach is to normalize the terms by using heuristic rules, which enables us to look up a dictionary in a constant time regardless of its size. The development of good heuristic rules, however, requires extensive knowledge of the terminology in question and thus is the bottleneck of the normalization approach. We present a novel framework for discovering a list of normalization rules from a dictionary in a fully automated manner. The rules are discovered in such a way that they minimize the ambiguity and variability of the terms in the dictionary. We evaluated our algorithm using two large dictionaries: a human gene/protein name dictionary built from BioThesaurus and a disease name dictionary built from UMLS. The experimental results showed that automatically discovered rules can perform comparably to carefully crafted heuristic rules in term mapping tasks, and the computational overhead of rule application is small enough that a very fast implementation is possible. This work will help improve the performance of term-concept mapping tasks in biomedical information extraction especially when good normalization heuristics for the target terminology are not fully known.

Abstract: A method for providing normalized physiological monitoring data of an individual with a measure of the quality of the normalization, including providing a reference feature based on a physiological attribute of the individual for which an attribute value can be determined; unobtrusively capturing physiological monitoring data for the individual during a series of capture events and determining the capture conditions present during each capture event; detecting the presence of the reference feature in the series of captured physiological monitoring data and determining associated attribute values for each capture event; normalizing the captured physiological monitoring data from each capture event according to differences in the attribute values associated with each event and previously calculated attribute values; and calculating normalization confidence values for the individual at the series of capture events, based on capture conditions, normalization transforms, or semantic data, wherein the confidence values statistically measure the quality of the normalization.

Abstract: As the background error covariance matrix is a key component of any assimilation system, its modelling is an important step. Usually, this matrix is decomposed into correlations and variance matrices. An interesting method for modelling the correlation matrix of the background error for complex geometry, like ocean grid, consists in computing correlation functions using a diffusion operator. The background error correlation functions can be estimated for example from an ensemble of perturbed forecasts. The diffusion operator is able to represent heterogeneous correlation functions at a reasonable numerical cost. But afirst challenge resides in the determination of the local diffusion tensor corresponding to the local correlation function. Then the second challenge resides in the determination of the normalization to make sure that the matrix modelled through the diffusion operator is a correlation matrix. In this article, we propose to build a background error correlation matrix using a diffusion operator based on a local diffusion tensor. The estimation of this local tensor is performed using an ensemble of perturbed forecasts. A validation within a randomization method illustrates the feasibility and the accuracy of the proposed method. In particular, it is shown that the local geographical variations of diagnosed correlation functions (through an ensemble of perturbed forecast) are well represented. This is first illustrated in an analytical one-dimensional framework. In that context, the diffusion field and the normalization field are deduced from a given correlation length-scale field. The resulting length-scales are shown to correspond to the initial length-scale when the given length-scale field spectrum is red. The approximate normalization, computed from the local length-scale, is close to the true normalization under the same condition of a red spectrum. Then, the method is illustrated in a real context using an ensemble of perturbed forecasts from the MOCAGE-PALM assimilation system. In that case, length-scale and anisotropy diagnosis reveal the complexity of the correlation of stratospheric ozone forecast errors. The local diffusion tensor deduced from these diagnosis are shown be able to represent such an existing heterogeneity and anisotropy. As in the one-dimensional case, the approximate normalization, based on the local diffusion tensor, appears to be a really good approximation of the true normalization.

Abstract: Background: Microarray technology has become very popular for globally evaluating gene expression in biological samples. However, non-linear variation associated with the technology can make data interpretation unreliable. Therefore, methods to correct this kind of technical variation are critical. Here we consider a method to reduce this type of variation applied after three common procedures for processing microarray data: MAS 5.0, RMA, and dChip®. Results: We commonly observe intensity-dependent technical variation between samples in a single microarray experiment. This is most common when MAS 5.0 is used to process probe level data, but we also see this type of technical variation with RMA and dChip ® processed data. Datasets with unbalanced numbers of up and down regulated genes seem to be particularly susceptible to this type of intensity-dependent technical variation. Unbalanced gene regulation is common when studying cancer samples or genetically manipulated animal models and preservation of this biologically relevant information, while removing technical variation has not been well addressed in the literature. We propose a method based on using rank-invariant, endogenous transcripts as reference points for normalization (GRSN). While the use of rank-invariant transcripts has been described previously, we have added to this concept by the creation of a global rank-invariant set of transcripts used to generate a robust average reference that is used to normalize all samples within a dataset. The global rank-invariant set is selected in an iterative manner so as to preserve unbalanced gene expression. Moreover, our method works well as an overlay that can be applied to data already processed with other probe set summary methods. We demonstrate that this additional normalization step at the "probe set level" effectively corrects a specific type of technical variation that often distorts samples in datasets. Conclusion: We have developed a simple post-processing tool to help detect and correct nonlinear technical variation in microarray data and demonstrate how it can reduce technical variation and improve the results of downstream statistical gene selection and pathway identification methods.

Abstract: In this paper, we address the pair-activity classification problem, which explores the relationship between two active objects based on their motion information. Our contributions are three-fold. First, we design a set of features, e.g., causality ratio and feedback ratio based on the Granger Causality Test (GCT), for describing the pair-activities encoded as trajectory pairs. These features along with conventional velocity and position features are essentially of multi-modalities, and may be greatly different in scale and importance. To make full use of them, we then present a novel feature normalization procedure to learn the coefficients for weighting these features by maximizing the discriminating power measured by weighted correlation. Finally, we collected a pair-activity database of five categories, each of which consists of about 170 instances. The extensive experiments on this database validate the effectiveness of the designed features for pair-activity representation, and also demonstrate that the proposed feature normalization procedure greatly boosts the pair-activity classification accuracy.

Abstract: Background It is well known that the normalization step of microarray data makes a difference in the downstream analysis. All normalization methods rely on certain assumptions, so differences in results can be traced to different sensitivities to violation of the assumptions. Illustrating the lack of robustness, in a striking spike-in experiment all existing normalization methods fail because of an imbalance between up- and down-regulated genes. This means it is still important to develop a normalization method that is robust against violation of the standard assumptions

Abstract: Neural networks have shown good results for detecting a certain pattern in a given image. In this paper, faster neural networks for pattern detection are presented. Such processors are designed based on cross correlation in the frequency domain between the input matrix and the input weights of neural networks. This approach is developed to reduce the computation steps required by these faster neural networks for the detection process. The principle of divide and conquer strategy is applied through matrix decomposition. Each matrix is divided into smaller in size submatrices and then each one is tested separately by using a single faster neural processor. Furthermore, faster pattern detection is obtained by using parallel processing techniques to test the resulting submatrices at the same time using the same number of faster neural networks. In contrast to faster neural networks, the speed up ratio is increased with the size of the input matrix when using faster neural networks and matrix decomposition. Moreover, the problem of local submatrix normalization in the frequency domain is solved. The effect of matrix normalization on the speed up ratio of pattern detection is discussed. Simulation results show that local submatrix normalization through weight normalization is faster than submatrix normalization in the spatial domain. The overall speed up ratio of the detection process is increased as the normalization of weights is done off line.

Abstract: A medical device for sensing cardiac events that includes a plurality of light sources capable of emitting light at a plurality of wavelengths, and a detector to detect the emitted light. A processor determines a plurality of light measurements in response to the emitted light detected by the detector, updates, for each of the plurality of wavelengths, a first normalization coefficient and a second normalization coefficient in response to the detected emitted light, and adjusts the determined plurality of light measurements in response to the first normalization coefficient and the second normalization coefficient.

Abstract: Edge-preserving filters such as local M-smoothers or bilateral filtering are usually designed for Gaussian noise. This paper investigates how these filters can be adapted in order to efficiently deal with Poissonian noise. In addition, the issue of photometry invariance is addressed by changing the way filter coefficients are normalized. The proposed normalization is additive, instead of being multiplicative, and leads to a strong connection with anisotropic diffusion. Experiments show that ensuring the photometry invariance leads to comparable denoising performances in terms of the root mean square error computed on the signal.

Abstract: Biological vision systems are adept at combining cues to maximize the reliability of object boundary detection, but given a set of co-localized edge detectors operating on different sensory channels, how should their responses be combined to compute overall edge probability? To approach this question, we collected joint responses of red-green and blue-yellow edge detectors both ON- and OFF-edges using a human-labeled image database as ground truth (D. Martin, C. Fowlkes, D. Tal, & J. Malik, 2001). From a Bayesian perspective, the rule for combining edge cues is linear in the individual cue strengths when the ON-edge and OFF-edge joint distributions are (1) statistically independent and (2) lie in an exponential ratio to each other. Neither condition held in the color edge data we collected, and the function P(ON cues)-dubbed the "combination rule"-was correspondingly complex and nonlinear. To characterize the statistical dependencies between edge cues, we developed a generative model ("saturated common factor," SCF) that provided good fits to the measured ON-edge and OFF-edge joint distributions. We also found that a divisive normalization scheme derived from the SCF model transformed raw edge detector responses into values with simpler distributions that satisfied both preconditions for a linear combination rule. A comparison to another normalization scheme (O. Schwartz & E. Simoncelli, 2001) suggests that apparently minor details of the normalization process can strongly influence its performance. Implications of the SCF normalization scheme for cue combination in biological sensory systems are discussed.

Abstract: We give a new construction of primitive idempotents of the Hecke algebras associated with the symmetric groups. The idempotents are found as evaluated products of certain rational functions thus providing a new version of the fusion procedure for the Hecke algebras. We show that the normalization factors which occur in the procedure are related to the Ocneanu--Markov trace of the idempotents.

Abstract: Genome-wide RNA interference (RNAi) screening allows investigation of the role of individual genes in a process of choice. Most RNAi screens identify a large number of genes with a continuous gradient in the assessed phenotype. Screeners must decide whether to examine genes with the most robust phenotype or the full gradient of genes that cause an effect and how to identify candidate genes. The authors have used RNAi in Drosophila cells to examine viability in a 384-well plate format and compare 2 screens, untreated control and treatment. They compare multiple normalization methods, which take advantage of different features within the data, including quantile normalization, background subtraction, scaling, cellHTS2 (Boutros et al. 2006), and interquartile range measurement. Considering the false-positive potential that arises from RNAi technology, a robust validation method was designed for the purpose of gene selection for future investigations. In a retrospective analysis, the authors describe the use of validation data to evaluate each normalization method. Although no method worked ideally, a combination of 2 methods, background subtraction followed by quantile normalization and cellHTS2, at different thresholds, captures the most dependable and diverse candidate genes. Thresholds are suggested depending on whether a few candidate genes are desired or a more extensive systems-level analysis is sought. The normalization approaches and experimental design to perform validation experiments are likely to apply to those high-throughput screening systems attempting to identify genes for systems-level analysis.

Abstract: It has been shown that the authentication performance of a biometric system is dependent on the models/templates specific to a user. As a result, some users may be more easily recognized or impersonated than others. The various categories of users have been characterized by Doddington et al. (1988). We refer to this unbalanced performance across users as the Doddington's zoo effect. In the context of fusion, we argue that this effect is system-dependent, i.e., a user model that is easily impersonated (a lamb) in one system may be easily recognized in another system (a sheep). While in principle, a fusion system could be trained to cope with the changing animal behavior of users from system to system, the lack of training data makes it impossible. We believe that one major cause of the Doddington's zoo effect is the variation of class conditional scores from one speaker model to another. We propose a two-level fusion framework that effectively realizes a fusion classifier adapted to each user. First, one applies a client-specific (or model-specific) score normalization procedure to each of the system outputs to be combined. Then, one feeds the resulting normalized outputs to a fusion classifier (common to all users) as input to obtain a final combined score. Two existing model-specific score normalization procedures are considered in this framework, i.e., F- and Z-norms. In addition to them, a novel score normalization method called model-specific log-likelihood ratio (MS-LLR) is also proposed. While Z-norm is impostor-centric, i.e., it makes use of only the impostor score statistics, F-norm and the proposed MS-LLR are client-impostor centric, i.e., they consider both the client and impostor score statistics simultaneously. Our findings based on the XM2VTS and the NIST2005 databases show that when client-impostor centric normalization procedures are used to implement the proposed two-level fusion framework, the resulting fusion classifier outperforms the conventional fusion classifier (without applying any user-specific score normalization) in the majority of experiments.

Abstract: The modulation transfer function (MTF) is widely used to describe the spatial resolution of x-ray imaging systems. The MTF is defined to have a zero-frequency value of unity, and it is common practice to ensure this by normalizing a measured MTF curve by the zero-frequency value. However, truncation of the line spread function (LSF) within a finite region of interest (ROI) results in spectral leakage and causes a reduction in the measured MTF zero-frequency value equal to the area of truncated LSF tails. Subsequent normalization by this value may result in inflated MTF values. We show that open-field normalization with the edge method produces accurate MTF values at all nonzero frequencies without need for further normalization by the zero-frequency value, regardless of ROI size. While both normalization techniques are equivalent for a sufficiently large ROI, a 5% inflation in MTF values was observed for a CsI-based flat-panel system when using a 10 cm ROI. Use of open-field normalization avoids potential inflation caused by zero-frequency normalization.

Abstract: This article formalizes normalization by evaluation as implemented in Isabelle. Lambda calculus plus term rewriting is compiled into a functional program with pattern matching. It is proved that the result of a successful evaluation is a) correct, i.e. equivalent to the input, and b) in normal form. An earlier version of this theory is described in a paper by Aehlig et al. [1]. The normal form proof is not in that paper.

Abstract: An approximate solution of the Schrodinger equation with the Hulth$\acute{e}$n potential is obtained in D-dimensions with an exponential approximation of the centrifugal term. Solution to the corresponding hyper-radial equation is given using the conventional Nikiforov-Uvarov method. The normalization constants for the Hulth$\acute{e}$n potential are also computed. The expectation values $ $,$ $, are also obtained using the Feynman-Hellmann theorem.