Peptide classification using optimal and information theoretic syntactic modeling

We consider the problem of classifying peptides using the information residing in their syntactic representations. This problem, which has been studied for more than a decade, has typically been investigated using distance-based metrics that involve the edit operations required in the peptide comparisons. In this paper, we shall demonstrate that the Optimal and Information Theoretic (OIT) model of Oommen and Kashyap [22] applicable for syntactic pattern recognition can be used to tackle peptide classification problem. We advocate that one can model the differences between compared strings as a mutation model consisting of random substitutions, insertions and deletions obeying the OIT model. Thus, in this paper, we show that the probability measure obtained from the OIT model can be perceived as a sequence similarity metric, using which a support vector machine (SVM)-based peptide classifier can be devised. The classifier, which we have built has been tested for eight different substitution matrices and for two different data sets, namely, the HIV-1 Protease cleavage sites and the T-cell epitopes. The results show that the OIT model performs significantly better than the one which uses a Needleman-Wunsch sequence alignment score, it is less sensitive to the substitution matrix than the other methods compared, and that when combined with a SVM, is among the best peptide classification methods availabl

Fast insect damage detection in wheat kernels using transmittance images

We used transmittance images and different learning algorithms to classify insect damaged and un-damaged wheat kernels. Using the histogram of the pixels of the wheat images as the feature, and the linear model as the learning algorithm, we achieved a False Positive Rate (1-specificity) of 0.12 at the True Positive Rate (sensitivity) of 0.8 and an Area Under the ROC Curve (AUC) of 0.90 ± 0.02. Combining the linear model and a Radial Basis Function Network in a committee resulted in a FP Rate of 0.09 at the TP Rate of 0.8 and an AUC of 0.93 ± 0.03

Preface

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Identification of insect damaged wheat kernels using transmittance images

We used transmittance images and different learning algorithms to classify insect damaged and un-damaged wheat kernels. Using the histogram of the pixels of the wheat images as the feature, and the linear model as the learning algorithm, we achieved a False Positive Rate (1-specificity) of 0.2 at the True Positive Rate (sensitivity) of 0.8 and an Area Under the ROC Curve (AUC) of 0.86. Combining the linear model and a Radial Basis Function Network in a committee resulted in a FP Rate of 0.1 at the TP Rate of 0.8 and an AUC of 0.92. © 2004 IEEE

Improving music genre classification using automatically induced harmony rules

We present a new genre classification framework using both low-level signal-based features and high-level harmony features. A state-of-the-art statistical genre classifier based on timbral features is extended using a first-order random forest containing for each genre rules derived from harmony or chord sequences. This random forest has been automatically induced, using the first-order logic induction algorithm TILDE, from a dataset, in which for each chord the degree and chord category are identified, and covering classical, jazz and pop genre classes. The audio descriptor-based genre classifier contains 206 features, covering spectral, temporal, energy, and pitch characteristics of the audio signal. The fusion of the harmony-based classifier with the extracted feature vectors is tested on three-genre subsets of the GTZAN and ISMIR04 datasets, which contain 300 and 448 recordings, respectively. Machine learning classifiers were tested using 5 × 5-fold cross-validation and feature selection. Results indicate that the proposed harmony-based rules combined with the timbral descriptor-based genre classification system lead to improved genre classification rates

Peptide classification using optimal and information theoretic syntactic modeling

We consider the problem of classifying peptides using the information residing in their syntactic representations. This problem, which has been studied for more than a decade, has typically been investigated using distance-based metrics that involve the edit operations required in the peptide comparisons. In this paper, we shall demonstrate that the Optimal and Information Theoretic (OIT) model of Oommen and Kashyap [22] applicable for syntactic pattern recognition can be used to tackle peptide classification problem. We advocate that one can model the differences between compared strings as a mutation model consisting of random substitutions, insertions and deletions obeying the OIT model. Thus, in this paper, we show that the probability measure obtained from the OIT model can be perceived as a sequence similarity metric, using which a support vector machine (SVM)-based peptide classifier can be devised. The classifier, which we have built has been tested for eight different substitution matrices and for two different data sets, namely, the HIV-1 Protease cleavage sites and the T-cell epitopes. The results show that the OIT model performs significantly better than the one which uses a Needleman-Wunsch sequence alignment score, it is less sensitive to the substitution matrix than the other methods compared, and that when combined with a SVM, is among the best peptide classification methods available

On utilizing optimal and information theoretic syntactic modeling for peptide classification

Syntactic methods in pattern recognition have been used extensively in bioinformatics, and in particular, in the analysis of gene and protein expressions, and in the recognition and classification of bio-sequences. These methods are almost universally distance-based. This paper concerns the use of an Optimal and Information Theoretic (OIT) probabilistic model [11] to achieve peptide classification using the information residing in their syntactic representations. The latter has traditionally been achieved using the edit distances required in the respective peptide comparisons. We advocate that one can model the differences between compared strings as a mutation model consisting of random Substitutions, Insertions and Deletions (SID) obeying the OIT model. Thus, in this paper, we show that the probability measure obtained from the OIT model can be perceived as a sequence similarity metric, using which a Support Vector Machine (SVM)-based peptide classifier, referred to as OIT-SVM, can be devised. The classifier, which we have built has been tested for eight different "substitution" matrices and for two different data sets, namely, the HIV-1 Protease Cleavage sites and the T-cell Epitopes. The results show that the OIT model performs significantly better than the one which uses a Needleman-Wunsch sequence alignment score, and the peptide classification methods that previously experimented with the same two datasets