1329357
Data Reduction in Support Vector Machines by a Kernelized Ionic Interaction Model
A major drawback of support vector machines is their high computational complexity. In this paper, we introduce a novel kernelized ionic interaction (IoI) model for data reduction in support vector machines. We also present a data reduction method based on the kernelized instance based (KIB2) algorithm. We show that the computation time can be significantly reduced without any significant decrease in the prediction accuracy.
14943272
Incremental and Decremental Least Squares Support Vector Machine and Its Application to Drug Design
The least squares support vector machine (LS-SVM) has shown to exhibit excellent classification performance in many applications. In this paper, we propose an incremental and decremental LS-SVM based on updating and downdating the QR decomposition. It can efficiently compute the updated solution when data points are appended or removed. The experiment results illustrated that the proposed incremental algorithm efficiently produces the same solutions as those obtained by LS-SVM which recomputes the solution all over even for small changes in the data. For drug design, the results of each biochemistry laboratory test on a new compound can be iteratively included in the training set. This procedure can further improve precision in order to select the next best predicted organic compound. Instead of retraining entire data points, it is much efficient to update solution by incremental LS-SVM.
11702143
Adaptive nonlinear discriminant analysis by regularized minimum squared errors
Kernelized nonlinear extensions of Fisher's discriminant analysis, discriminant analysis based on generalized singular value decomposition (LDA/GSVD), and discriminant analysis based on the minimum squared error formulation (MSE) have recently been widely utilized for handling undersampled high-dimensional problems and nonlinearly separable data sets. As the data sets are modified from incorporating new data points and deleting obsolete data points, there is a need to develop efficient updating and downdating algorithms for these methods to avoid expensive recomputation of the solution from scratch. In this paper, an efficient algorithm for adaptive linear and nonlinear kernel discriminant analysis based on regularized MSE, called adaptive KDA/RMSE, is proposed. In adaptive KDA/RMSE, updating and downdating of the computationally expensive eigenvalue decomposition (EVD) or singular value decomposition (SVD) is approximated by updating and downdating of the QR decomposition achieving an order of magnitude speed up. This fast algorithm for adaptive kernelized discriminant analysis is designed by utilizing regularization techniques and the relationship between linear and nonlinear discriminant analysis and the MSE. In addition, an efficient algorithm to compute leave-one-out cross validation is also introduced by utilizing downdating of KDA/RMSE.
5469426
Unraveling condition specific gene transcriptional regulatory networks in Saccharomyces cerevisiae
BackgroundGene expression and transcription factor (TF) binding data have been used to reveal gene transcriptional regulatory networks. Existing knowledge of gene regulation can be presented using gene connectivity networks. However, these composite connectivity networks do not specify the range of biological conditions of the activity of each link in the network.ResultsWe present a novel method that utilizes the expression and binding patterns of the neighboring nodes of each link in existing experimentally-based, literature-derived gene transcriptional regulatory networks and extend them in silico using TF-gene binding motifs and a compendium of large expression data from Saccharomyces cerevisiae. Using this method, we predict several hundreds of new transcriptional regulatory TF-gene links, along with experimental conditions in which known and predicted links become active. This approach unravels new links in the yeast gene transcriptional regulatory network by utilizing the known transcriptional regulatory interactions, and is particularly useful for breaking down the composite transcriptional regulatory network to condition specific networks.ConclusionOur methods can facilitate future binding experiments, as they can considerably help focus on the TFs that must be surveyed to understand gene regulation.(Supplemental material and the latest version of the MATLAB implementation of the United Signature Algorithm is available online at [1] or [see Additional files 1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
8166541
Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis
MOTIVATION
Many practical pattern recognition problems require non-negativity constraints. For example, pixels in digital images and chemical concentrations in bioinformatics are non-negative. Sparse non-negative matrix factorizations (NMFs) are useful when the degree of sparseness in the non-negative basis matrix or the non-negative coefficient matrix in an NMF needs to be controlled in approximating high-dimensional data in a lower dimensional space.


RESULTS
In this article, we introduce a novel formulation of sparse NMF and show how the new formulation leads to a convergent sparse NMF algorithm via alternating non-negativity-constrained least squares. We apply our sparse NMF algorithm to cancer-class discovery and gene expression data analysis and offer biological analysis of the results obtained. Our experimental results illustrate that the proposed sparse NMF algorithm often achieves better clustering performance with shorter computing time compared to other existing NMF algorithms.


AVAILABILITY
The software is available as supplementary material.
13287397
An analysis of the performance impact of wrong-path memory references on out-of-order and runahead execution processors
High-performance, out-of-order execution processors spend a significant portion of their execution time on the incorrect program path even though they employ aggressive branch prediction algorithms. Although memory references generated on the wrong path do not change the architectural state of the processor, they affect the arrangement of data in the memory hierarchy. This paper examines the effects of wrong-path memory references on processor performance. It is shown that these references significantly affect the IPC (instructions per cycle) performance of a processor. Not modeling them leads to errors of up to 10 percent (4 percent on average) in IPC estimates for the SPEC CPU2000 integer benchmarks on an out-of-order processor and errors of up to 63 percent on a runahead-execution processor. In general, the error in the IPC increases with increasing memory latency and instruction window size. We find that wrong-path references are usually beneficial for performance because they prefetch data that is used by later correct-path references. L2 cache pollution is found to be the most significant negative effect of wrong-path references. Code examples are shown to provide insights into how wrong-path references affect performance. We also show that it is crucial to model wrong-path references to accurately estimate the performance improvement provided by runahead execution.
36946020
Face Representation Method Using Pixel-to-Vertex Map (PVM) for 3D Model Based Face Recognition
3D model based approach for face recognition has been spotlighted as a robust solution under variant conditions of pose and illumination. Since a generative 3D face model consists of a large number of vertices, a 3D model based face recognition system is generally inefficient in computation time. In this paper, we propose a novel 3D face representation algorithm to reduce the number of vertices and optimize its computation time. Finally, we evaluate the performance of proposed algorithm with the Korean face database collected using a stereo-camera based 3D face capturing device.
8295029
Cache filtering techniques to reduce the negative impact of useless speculative memory references on processor performance
High-performance processors employ aggressive speculation and prefetching techniques to increase performance. Speculative memory references caused by these techniques sometimes bring data into the caches that are not needed by correct execution. This paper proposes the use of the first-level caches as filters that predict the usefulness of speculative memory references. With the proposed technique, speculative memory references bring data only into the first-level caches rather than all levels in the cache hierarchy. The processor monitors the use of the cache blocks in the first-level caches and decides which blocks to keep in the cache hierarchy based on the usefulness of cache blocks. It is shown that a simple implementation of this technique usually outperforms inclusive and exclusive baseline cache hierarchies commonly used by today's processors and results in IPC performance improvements of up to 9.2% on the SPEC2000 integer benchmarks.
11289021
Motivations for hyperlinking in scholarly electronic articles: A qualitative study
33400437
Facial Expression Recognition Using Active Appearance Model
This paper describes a facial expression recognition system based upon Active Appearance Model (AAM), which has been typically used for the face recognition task. Given that AAM has been also used in tracking the moving object, we thought it could be effective in recognizing the facial expressions of humans. Our results show that the performance of the facial expression recognition using AAM is reliably high when it combined with an enhanced Fisher classification model.