ROC ('receiver operator characteristics') analysis is a visual as well as numerical method used for assessing the performance of classification algorithms, such as those used for predicting structures and functions from sequence data. This review summarizes the fundamental concepts of ROC analysis and the interpretation of results using examples of sequence and structure comparison. We overview the available programs and provide evaluation guidelines for genomic/proteomic data, with particular regard to applications to large and heterogeneous databases used in bioinformatics.

Large-margin methods, such as support vector machines (SVMs), have been very successful in classification problems. Recently, maximum margin discriminant analysis (MMDA) was proposed that extends the large-margin idea to feature extraction. It often outperforms traditional methods such as kernel principal component analysis (KPCA) and kernel Fisher discriminant analysis (KFD). However, as in the SVM, its time complexity is cubic in the number of training points m, and is thus computationally inefficient on massive data sets. In this paper, we propose an (1+epsilon)(2)-approximation algorithm for obtaining the MMDA features by extending the core vector machine. The resultant time complexity is only linear in m, while its space complexity is independent of m. Extensive comparisons with the original MMDA, KPCA, and KFD on a number of large data sets show that the proposed feature extractor can improve classification accuracy, and is also faster than these kernel-based methods by over an order of magnitude.

The core vector machine (CVM) is a recent approach for scaling up kernel methods based on the notion of minimum enclosing ball (MEB). Though conceptually simple, an efficient implementation still requires a sophisticated numerical solver. In this paper, we introduce the enclosing ball (EB) problem where the ball's radius is fixed and thus does not have to be minimized. We develop efficient (1 + e)-approximation algorithms that are simple to implement and do not require any numerical solver. For the Gaussian kernel in particular, a suitable choice of this (fixed) radius is easy to determine, and the center obtained from the (1 + e)-approximation of this EB problem is close to the center of the corresponding MEB. Experimental results show that the proposed algorithm has accuracies comparable to the other large-scale SVM implementations, but can handle very large data sets and is even faster than the CVM in general.

Maximum margin discriminant analysis (MMDA) was proposed that uses the margin idea for feature extraction. It often outperforms traditional methods like kernel principal component analysis (KPCA) and kernel Fisher discriminant analysis (KFD). However, as in other kernel methods, its time complexity is cubic in the number of training points m, and is thus computationally inefficient on massive data sets. In this paper, we propose an (1 + ε) 2-approximation algorithm for obtaining the MMDA features by extending the core vector machines. The resultant time complexity is only linear in m, while its space complexity is independent of m. Extensive comparisons with the original MMDA, KPCA, and KFD on a number of large data sets show that the proposed feature extractor can improve classification accuracy, and is also faster than these kernel-based methods by more than an order of magnitude.

MOTIVATION: Likelihood ratio approximants (LRA) have been widely used for model comparison in statistics. The present study was undertaken in order to explore their utility as a scoring (ranking) function in the classification of protein sequences. RESULTS: We used a simple LRA-based on the maximal similarity (or minimal distance) scores of the two top ranking sequence classes. The scoring methods (Smith-Waterman, BLAST, local alignment kernel and compression based distances) were compared on datasets designed to test sequence similarities between proteins distantly related in terms of structure or evolution. It was found that LRA-based scoring can significantly outperform simple scoring methods.

MOTIVATION: In this paper, we propose using the Kalman filter (KF) as a pre-processing step in microarray-based molecular diagnosis. Incorporating the expression covariance between genes is important in such classification problems, since this represents the functional relationships that govern tissue state. Failing to fulfil such requirements may result in biologically implausible class prediction models. Here, we show that employing the KF to remove noise (while retaining meaningful covariance and thus being able to estimate the underlying biological state from microarray measurements) yields linearly separable data suitable for most classification algorithms. RESULTS: We demonstrate the utility and performance of the KF as a robust disease-state estimator on publicly available binary and multi-class microarray datasets in combination with the most widely used classification methods to date. Moreover, using popular graphical representation schemes we show that our filtered datasets also have an improved visualization capability.

MOTIVATION: Distance measures built on the notion of text compression have been used for the comparison and classification of entire genomes and mitochondrial genomes. The present study was undertaken in order to explore their utility in the classification of protein sequences. RESULTS: We constructed compression-based distance measures (CBMs) using the Lempel-Zlv and the PPMZ compression algorithms and compared their performance with that of the Smith-Waterman algorithm and BLAST, using nearest neighbour or support vector machine classification schemes. The datasets included a subset of the SCOP protein structure database to test distant protein similarities, a 3-phosphoglycerate-kinase sequences selected from archaean, bacterial and eukaryotic species as well as low and high-complexity sequence segments of the human proteome, CBMs values show a dependence on the length and the complexity of the sequences compared. In classification tasks CBMs performed especially well on distantly related proteins where the performance of a combined measure, constructed from a CBM and a BLAST score, approached or even slightly exceeded that of the Smith-Waterman algorithm and two hidden Markov model-based algorithms.

This paper proposes a pitch estimation algorithm that is based on optimal harmonic model fitting. The algorithm operates directly on the time-domain signal and has a relatively simple mathematical background. To increase its efficiency and accuracy, the algorithm is applied in combination with an autocorrelation-based initialization phase. For testing purposes we compare its performance on pitch-annotated corpora with several conventional time-domain pitch estimation algorithms, and also with a recently proposed one. The results show that even the autocorrelation-based first phase significantly outperforms the traditional methods, and also slightly the recently proposed yin algorithm. After applying the second phase – the harmonic approximation step – the amount of errors can be further reduced by about 20 % relative to the error obtained in the first phase. 1.

The Projection Pursuit Learner is a multi-class classifier that resembles a two-layer neutral network in which the sigmoid activation functions of the hidden neurons have been replaced by an interpolating polynomial. This modification increases the flexibility of the model but also makes it more inclined to get stuck in a local minimum during gradient-based training. This problem can be alleviated to a certain extent by replacing the random initialization the projection directions by means of feature space transformation methods such as independent component analysis (IDA), principal component analysis (PCA), linear discriminant analysis (LDA) and springy discriminant analysis (SDA). We find that with this refinement the number of processing units can be reduced by 10 - 40%.