Biomedical subjects

Chih-Jen Lin

Publications and source records attributed to Chih-Jen Lin.

10 recordsLinked to original sources

PubMed2006

A study on SMO-type decomposition methods for support vector machines.

Decomposition methods are currently one of the major methods for training support vector machines. They vary mainly according to different working set selections. Existing implementations and analysis usually consider some specific selection rules. This paper studies sequential minimal optimization type decomposition methods under a general and flexible way of choosing the two-element working set. The main results include: 1) a simple asymptotic convergence proof, 2) a general explanation of the shrinking and caching techniques, and 3) the linear convergence of the methods. Extensions to some support vector machine variants are also discussed.

Algorithms↗

PubMed2005

Enhanced resonant raman scattering and electron-phonon coupling from self-assembled secondary ZnO nanoparticles.

Self-assembled secondary ZnO nanoparticles, recognized with the agglomeration of crystalline subcrystals, are successfully synthesized by a simple sol-gel method. TEM images display that one artificial cluster behaves in a single-crystal-like wurtzite structure because subcrystals coagulate as the same crystal orientation. Moreover, from the resonant Raman scattering, the as-grown sample exhibits phonon red shift; meanwhile, the coupling strength between electron and longitudinal optical phonon, determined by the ratio of second- to first-order Raman scattering cross sections, diminishes compared with the samples after postannealing at 350 and 500 degrees C. The size dependence of electron-phonon coupling is principally as a result of the Fröhlich interaction.

Journal Article↗

PubMed2004

Prediction of the bonding states of cysteines using the support vector machines based on multiple feature vectors and cysteine state sequences.

The support vector machine (SVM) method is used to predict the bonding states of cysteines. Besides using local descriptors such as the local sequences, we include global information, such as amino acid compositions and the patterns of the states of cysteines (bonded or nonbonded), or cysteine state sequences, of the proteins. We found that SVM based on local sequences or global amino acid compositions yielded similar prediction accuracies for the data set comprising 4136 cysteine-containing segments extracted from 969 nonhomologous proteins. However, the SVM method based on multiple feature vectors (combining local sequences and global amino acid compositions) significantly improves the prediction accuracy, from 80% to 86%. If coupled with cysteine state sequences, SVM based on multiple feature vectors yields 90% in overall prediction accuracy and a 0.77 Matthews correlation coefficient, around 10% and 22% higher than the corresponding values obtained by SVM based on local sequence information.

Amino Acids↗

PubMed2004

Analysis of switching dynamics with competing support vector machines.

We present a framework for the unsupervised segmentation of switching dynamics using support vector machines. Following the architecture by Pawelzik et al., where annealed competing neural networks were used to segment a nonstationary time series, in this paper, we exploit the use of support vector machines, a well-known learning technique. First, a new formulation of support vector regression is proposed. Second, an expectation-maximization step is suggested to adaptively adjust the annealing parameter. Results indicate that the proposed approach is promising.

Artificial Intelligence↗

PubMed2004

Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions.

Gram-negative bacteria have five major subcellular localization sites: the cytoplasm, the periplasm, the inner membrane, the outer membrane, and the extracellular space. The subcellular location of a protein can provide valuable information about its function. With the rapid increase of sequenced genomic data, the need for an automated and accurate tool to predict subcellular localization becomes increasingly important. We present an approach to predict subcellular localization for Gram-negative bacteria. This method uses the support vector machines trained by multiple feature vectors based on n-peptide compositions. For a standard data set comprising 1443 proteins, the overall prediction accuracy reaches 89%, which, to the best of our knowledge, is the highest prediction rate ever reported. Our prediction is 14% higher than that of the recently developed multimodular PSORT-B. Because of its simplicity, this approach can be easily extended to other organisms and should be a useful tool for the high-throughput and large-scale analysis of proteomic and genomic data.

Artificial Intelligence↗

PubMed2003

Fine-grained protein fold assignment by support vector machines using generalized npeptide coding schemes and jury voting from multiple-parameter sets.

In the coarse-grained fold assignment of major protein classes, such as all-alpha, all-beta, alpha + beta, alpha/beta proteins, one can easily achieve high prediction accuracy from primary amino acid sequences. However, the fine-grained assignment of folds, such as those defined in the Structural Classification of Proteins (SCOP) database, presents a challenge due to the larger amount of folds available. Recent study yielded reasonable prediction accuracy of 56.0% on an independent set of 27 most populated folds. In this communication, we apply the support vector machine (SVM) method, using a combination of protein descriptors based on the properties derived from the composition of n-peptide and jury voting, to the fine-grained fold prediction, and are able to achieve an overall prediction accuracy of 69.6% on the same independent set-significantly higher than the previous results. On 10-fold cross-validation, we obtained a prediction accuracy of 65.3%. Our results show that SVM coupled with suitable global sequence-coding schemes can significantly improve the fine-grained fold prediction. Our approach should be useful in structure prediction and modeling.

Animals↗

PubMed2003

Asymptotic behaviors of support vector machines with Gaussian kernel.

Support vector machines (SVMs) with the gaussian (RBF) kernel have been popular for practical use. Model selection in this class of SVMs involves two hyperparameters: the penalty parameter C and the kernel width sigma. This letter analyzes the behavior of the SVM classifier when these hyperparameters take very small or very large values. Our results help in understanding the hyperparameter space that leads to an efficient heuristic method of searching for hyperparameter values with small generalization errors. The analysis also indicates that if complete model selection using the gaussian kernel has been conducted, there is no need to consider linear SVM.

Models, Theoretical↗

PubMed2003

Radius margin bounds for support vector machines with the RBF kernel.

An important approach for efficient support vector machine (SVM) model selection is to use differentiable bounds of the leave-one-out (loo) error. Past efforts focused on finding tight bounds of loo (e.g., radius margin bounds, span bounds). However, their practical viability is still not very satisfactory. Duan, Keerthi, and Poo (2003) showed that radius margin bound gives good prediction for L2-SVM, one of the cases we look at. In this letter, through analyses about why this bound performs well for L2-SVM, we show that finding a bound whose minima are in a region with small loo values may be more important than its tightness. Based on this principle, we propose modified radius margin bounds for L1-SVM (the other case) where the original bound is applicable only to the hard-margin case. Our modification for L1-SVM achieves comparable performance to L2-SVM. To study whether L1- or L2-SVM should be used, we analyze other properties, such as their differentiability, number of support vectors, and number of free support vectors. In this aspect, L1-SVM possesses the advantage of having fewer support vectors. Their implementations are also different, so we discuss related issues in detail.

Artificial Intelligence↗

PubMed2002

A note on the decomposition methods for support vector regression.

The dual formulation of support vector regression involves two closely related sets of variables. When the decomposition method is used, many existing approaches use pairs of indices from these two sets as the working set. Basically, they select a base set first and then expand it so all indices are pairs. This makes the implementation different from that for support vector classification. In addition, a larger optimization subproblem has to be solved in each iteration. We provide theoretical proofs and conduct experiments to show that using the base set as the working set leads to similar convergence (number of iterations). Therefore, by using a smaller working set while keeping a similar number of iterations, the program can be simpler and more efficient.

Journal Article↗

PubMed2002

Training nu-support vector regression: theory and algorithms.

We discuss the relation between epsilon-support vector regression (epsilon-SVR) and nu-support vector regression (nu-SVR). In particular, we focus on properties that are different from those of C-support vector classification (C-SVC) and nu-support vector classification (nu-SVC). We then discuss some issues that do not occur in the case of classification: the possible range of epsilon and the scaling of target values. A practical decomposition method for nu-SVR is implemented, and computational experiments are conducted. We show some interesting numerical observations specific to regression.

Journal Article↗