Classification of Protein Kinases on the Basis of Both Kinase and Non-Kinase Regions

Background: Protein phosphorylation is a generic way to regulate signal transduction pathways in all kingdoms of life. In many organisms, it is achieved by the large family of Ser/Thr/Tyr protein kinases which are traditionally classified into groups and subfamilies on the basis of the amino acid sequence of their catalytic domains. Many protein kinases are multidomain in nature but the diversity of the accessory domains and their organization are usually not taken into account while classifying kinases into groups or subfamilies. Methodology: Here, we present an approach which considers amino acid sequences of complete gene products, in order to suggest refinements in sets of pre-classified sequences. The strategy is based on alignment-free similarity scores and iterative Area Under the Curve (AUC) computation. Similarity scores are computed by detecting common patterns between two sequences and scoring them using a substitution matrix, with a consistent normalization scheme. This allows us to handle full-length sequences, and implicitly takes into account domain diversity and domain shuffling. We quantitatively validate our approach on a subset of 212 human protein kinases. We then employ it on the complete repertoire of human protein kinases and suggest few qualitative refinements in the subfamily assignment stored in the KinG database, which is based on catalytic domains only. Based on our new measure, we delineate 37 cases of potential hybrid kinases: sequences for which classical classification based entirely on catalytic domains is inconsistent with the full-length similarity scores computed here, which implicitly consider multi-domain nature and regions outside the catalytic kinase domain. We also provide some examples of hybrid kinases of the protozoan parasite Entamoeba histolytica. Conclusions: The implicit consideration of multi-domain architectures is a valuable inclusion to complement other classification schemes. The proposed algorithm may also be employed to classify other families of enzymes with multidomain architecture.

Semi-Supervised Classification Using Sparse Gaussian Process Regression

Gaussian Processes (GPs) are promising Bayesian methods for classification and regression problems. They have also been used for semi-supervised learning tasks. In this paper, we propose a new algorithm for solving semi-supervised binary classification problem using sparse GP regression (GPR) models. It is closely related to semi-supervised learning based on support vector regression (SVR) and maximum margin clustering. The proposed algorithm is simple and easy to implement. It gives a sparse solution directly unlike the SVR based algorithm. Also, the hyperparameters are estimated easily without resorting to expensive cross-validation technique. Use of sparse GPR model helps in making the proposed algorithm scalable. Preliminary results on synthetic and real-world data sets demonstrate the efficacy of the new algorithm.

Validation based sparse Gaussian processes for ordinal regression

This paper proposes a sparse modeling approach to solve ordinal regression problems using Gaussian processes (GP). Designing a sparse GP model is important from training time and inference time viewpoints. We first propose a variant of the Gaussian process ordinal regression (GPOR) approach, leave-one-out GPOR (LOO-GPOR). It performs model selection using the leave-one-out cross-validation (LOO-CV) technique. We then provide an approach to design a sparse model for GPOR. The sparse GPOR model reduces computational time and storage requirements. Further, it provides faster inference. We compare the proposed approaches with the state-of-the-art GPOR approach on some benchmark data sets. Experimental results show that the proposed approaches are competitive.

Achievable rate region of gaussian broadcast channel with finite input alphabet and quantized output

In this paper, we study the achievable rate region of two-user Gaussian broadcast channel (GBC) when the messages to be transmitted to both the users take values from finite signal sets and the received signal is quantized at both the users. We refer to this channel as quantized broadcast channel (QBC). We first observe that the capacity region defined for a GBC does not carry over as such to QBC. Also, we show that the optimal decoding scheme for GBC (i.e., high SNR user doing successive decoding and low SNR user decoding its message alone) is not optimal for QBC. We then propose an achievable rate region for QBC based on two different schemes. We present achievable rate region results for the case of uniform quantization at the receivers. We find that rotation of one of the user's input alphabet with respect to the other user's alphabet marginally enlarges the achievable rate region of QBC when almost equal powers are allotted to both the users.

Tractable nonparametric bayesian inference in poisson processes with Gaussian process intensities

The inhomogeneous Poisson process is a point process that has varying intensity across its domain (usually time or space). For nonparametric Bayesian modeling, the Gaussian process is a useful way to place a prior distribution on this intensity. The combination of a Poisson process and GP is known as a Gaussian Cox process, or doubly-stochastic Poisson process. Likelihood-based inference in these models requires an intractable integral over an infinite-dimensional random function. In this paper we present the first approach to Gaussian Cox processes in which it is possible to perform inference without introducing approximations or finitedimensional proxy distributions. We call our method the Sigmoidal Gaussian Cox Process, which uses a generative model for Poisson data to enable tractable inference via Markov chain Monte Carlo. We compare our methods to competing methods on synthetic data and apply it to several real-world data sets. Copyright 2009.

Tractable nonparametric Bayesian inference in Poisson processes with Gaussian process intensities

The inhomogeneous Poisson process is a point process that has varying intensity across its domain (usually time or space). For nonparametric Bayesian modeling, the Gaussian process is a useful way to place a prior distribution on this intensity. The combination of a Poisson process and GP is known as a Gaussian Cox process, or doubly-stochastic Poisson process. Likelihood-based inference in these models requires an intractable integral over an infinite-dimensional random function. In this paper we present the first approach to Gaussian Cox processes in which it is possible to perform inference without introducing approximations or finite-dimensional proxy distributions. We call our method the Sigmoidal Gaussian Cox Process, which uses a generative model for Poisson data to enable tractable inference via Markov chain Monte Carlo. We compare our methods to competing methods on synthetic data and apply it to several real-world data sets.

FUZZY SOLID SETS FOR MATHEMATICAL MORPHOLOGY AND OPTICAL IMPLEMENTATION

Fuzzy sets in the subject space are transformed to fuzzy solid sets in an increased object space on the basis of the development of the local umbra concept. Further, a counting transform is defined for reconstructing the fuzzy sets from the fuzzy solid sets, and the dilation and erosion operators in mathematical morphology are redefined in the fuzzy solid-set space. The algebraic structures of fuzzy solid sets can lead not only to fuzzy logic but also to arithmetic operations. Thus a fuzzy solid-set image algebra of two image transforms and five set operators is defined that can formulate binary and gray-scale morphological image-processing functions consisting of dilation, erosion, intersection, union, complement, addition, subtraction, and reflection in a unified form. A cellular set-logic array architecture is suggested for executing this image algebra. The optical implementation of the architecture, based on area coding of gray-scale values, is demonstrated. (C) 1995 Optical Society of America

Spectral anomalies of focused hollow Gaussian beams at the geometrical focal plane

On the basis of diffraction integral and the expansion of the hard-aperture function into a finite series of complex Gaussian functions, an approximate expression for spatially fully coherent polychromatic hollow Gaussian beams passing through aperture lens is obtained. Detailed numerical results indicate that remarkable spectral changes always occurs near the points where the field amplitude has zero value. The effects of truncation parameter, Fresnel number and the beam order on spectral shifts and spectral switches are investigated numerically. (C) 2008 Elsevier B.V. All rights reserved.

Far-field intensity distribution and M-2 factor of hollow Gaussian beams

The far-field intensity distribution of hollow Gaussian beams was investigated based on scalar diffraction theory. An analytical expression of the M-2 factor of the beams was derived on the basis of the second-order moments. Moreover, numerical examples to illustrate our analytical results are given. (c) 2005 Optical Society of America.

Gaussian process change point models

We combine Bayesian online change point detection with Gaussian processes to create a nonparametric time series model which can handle change points. The model can be used to locate change points in an online manner; and, unlike other Bayesian online change point detection algorithms, is applicable when temporal correlations in a regime are expected. We show three variations on how to apply Gaussian processes in the change point context, each with their own advantages. We present methods to reduce the computational burden of these models and demonstrate it on several real world data sets. Copyright 2010 by the author(s)/owner(s).

Gaussian mixture modeling with Gaussian process latent variable models

Density modeling is notoriously difficult for high dimensional data. One approach to the problem is to search for a lower dimensional manifold which captures the main characteristics of the data. Recently, the Gaussian Process Latent Variable Model (GPLVM) has successfully been used to find low dimensional manifolds in a variety of complex data. The GPLVM consists of a set of points in a low dimensional latent space, and a stochastic map to the observed space. We show how it can be interpreted as a density model in the observed space. However, the GPLVM is not trained as a density model and therefore yields bad density estimates. We propose a new training strategy and obtain improved generalisation performance and better density estimates in comparative evaluations on several benchmark data sets. © 2010 Springer-Verlag.

Structured precision modelling with Cholesky basis superposition for speech recognition

Structured precision modelling is an important approach to improve the intra-frame correlation modelling of the standard HMM, where Gaussian mixture model with diagonal covariance are used. Previous work has all been focused on direct structured representation of the precision matrices. In this paper, a new framework is proposed, where the structure of the Cholesky square root of the precision matrix is investigated, referred to as Cholesky Basis Superposition (CBS). Each Cholesky matrix associated with a particular Gaussian distribution is represented as a linear combination of a set of Gaussian independent basis upper-triangular matrices. Efficient optimization methods are derived for both combination weights and basis matrices. Experiments on a Chinese dictation task showed that the proposed approach can significantly outperformed the direct structured precision modelling with similar number of parameters as well as full covariance modelling. © 2011 IEEE.

Free energy surface reconstruction from umbrella samples using Gaussian process regression II: Multiple collective variables

We demonstrate how a prior assumption of smoothness can be used to enhance the reconstruction of free energy profiles from multiple umbrella sampling simulations using the Bayesian Gaussian process regression approach. The method we derive allows the concurrent use of histograms and free energy gradients and can easily be extended to include further data. In Part I we review the necessary theory and test the method for one collective variable. We demonstrate improved performance with respect to the weighted histogram analysis method and obtain meaningful error bars without any significant additional computation. In Part II we consider the case of multiple collective variables and compare to a reconstruction using least squares fitting of radial basis functions. We find substantial improvements in the regimes of spatially sparse data or short sampling trajectories. A software implementation is made available on www.libatoms.org.

Calibrating the Gaussian multi-target tracking model

We present novel batch and online (sequential) versions of the expectation-maximisation (EM) algorithm for inferring the static parameters of a multiple target tracking (MTT) model. Online EM is of particular interest as it is a more practical method for long data sets since in batch EM, or a full Bayesian approach, a complete browse of the data is required between successive parameter updates. Online EM is also suited to MTT applications that demand real-time processing of the data. Performance is assessed in numerical examples using simulated data for various scenarios. For batch estimation our method significantly outperforms an existing gradient based maximum likelihood technique, which we show to be significantly biased. © 2014 Springer Science+Business Media New York.

Accurate description of a radially polarized Gaussian beam

An accurate description of a radially polarized fundamental Gaussian beam is presented on the basis of complex-source-point spherical waves (CSPSWs). In contrast to other descriptions based on the perturbative Lax series, the expressions for the electromagnetic field components of this description have explicit and simple mathematical forms. Numerical calculations show that both paraxial and fifth-order corrected beam descriptions have large relative error when the diffraction angle is large, while the accurate description based on the CSPSW approach proposed here can give field expressions which satisfy Maxwell's equations with great accuracy.