Biomedical subjects

Yu-Yen Ou

Publications and source records attributed to Yu-Yen Ou.

2 recordsLinked to original sources

PubMed2006

Protein disorder prediction by condensed PSSM considering propensity for order or disorder.

BACKGROUND: More and more disordered regions have been discovered in protein sequences, and many of them are found to be functionally significant. Previous studies reveal that disordered regions of a protein can be predicted by its primary structure, the amino acid sequence. One observation that has been widely accepted is that ordered regions usually have compositional bias toward hydrophobic amino acids, and disordered regions are toward charged amino acids. Recent studies further show that employing evolutionary information such as position specific scoring matrices (PSSMs) improves the prediction accuracy of protein disorder. As more and more machine learning techniques have been introduced to protein disorder detection, extracting more useful features with biological insights attracts more attention. RESULTS: This paper first studies the effect of a condensed position specific scoring matrix with respect to physicochemical properties (PSSMP) on the prediction accuracy, where the PSSMP is derived by merging several amino acid columns of a PSSM belonging to a certain property into a single column. Next, we decompose each conventional physicochemical property of amino acids into two disjoint groups which have a propensity for order and disorder respectively, and show by experiments that some of the new properties perform better than their parent properties in predicting protein disorder. In order to get an effective and compact feature set on this problem, we propose a hybrid feature selection method that inherits the efficiency of uni-variant analysis and the effectiveness of the stepwise feature selection that explores combinations of multiple features. The experimental results show that the selected feature set improves the performance of a classifier built with Radial Basis Function Networks (RBFN) in comparison with the feature set constructed with PSSMs or PSSMPs that adopt simply the conventional physicochemical properties. CONCLUSION: Distinguishing disordered regions from ordered regions in protein sequences facilitates the exploration of protein structures and functions. Results based on independent testing data reveal that the proposed predicting model DisPSSMP performs the best among several of the existing packages doing similar tasks, without either under-predicting or over-predicting the disordered regions. Furthermore, the selected properties are demonstrated to be useful in finding discriminating patterns for order/disorder classification.

Amino Acid Sequence↗

PubMed2005

Data classification with radial basis function networks based on a novel kernel density estimation algorithm.

This paper presents a novel learning algorithm for efficient construction of the radial basis function (RBF) networks that can deliver the same level of accuracy as the support vector machines (SVMs) in data classification applications. The proposed learning algorithm works by constructing one RBF subnetwork to approximate the probability density function of each class of objects in the training data set. With respect to algorithm design, the main distinction of the proposed learning algorithm is the novel kernel density estimation algorithm that features an average time complexity of O(n log n), where n is the number of samples in the training data set. One important advantage of the proposed learning algorithm, in comparison with the SVM, is that the proposed learning algorithm generally takes far less time to construct a data classifier with an optimized parameter setting. This feature is of significance for many contemporary applications, in particular, for those applications in which new objects are continuously added into an already large database. Another desirable feature of the proposed learning algorithm is that the RBF networks constructed are capable of carrying out data classification with more than two classes of objects in one single run. In other words, unlike with the SVM, there is no need to resort to mechanisms such as one-against-one or one-against-all for handling datasets with more than two classes of objects. The comparison with SVM is of particular interest, because it has been shown in a number of recent studies that SVM generally are able to deliver higher classification accuracy than the other existing data classification algorithms. As the proposed learning algorithm is instance-based, the data reduction issue is also addressed in this paper. One interesting observation in this regard is that, for all three data sets used in data reduction experiments, the number of training samples remaining after a naive data reduction mechanism is applied is quite close to the number of support vectors identified by the SVM software. This paper also compares the performance of the RBF networks constructed with the proposed learning algorithm and those constructed with a conventional cluster-based learning algorithm. The most interesting observation learned is that, with respect to data classification, the distributions of training samples near the boundaries between different classes of objects carry more crucial information than the distributions of samples in the inner parts of the clusters.

Algorithms↗