A Study of SVM Kernel Functions for Sensitivity Classification Ensembles with POS Sequences

Freedom of Information (FOI) laws legislate that government documents should be opened to the public. However, many government documents contain sensitive information, such as confidential information, that is exempt from release. Therefore, government documents must be sensitivity reviewed prior to release, to identify and close any sensitive information. With the adoption of born-digital documents, such as email, there is a need for automatic sensitivity classification to assist digital sensitivity review. SVM classifiers and Part-of-Speech sequences have separately been shown to be promising for sensitivity classification. However, sequence classification methodologies, and specifically SVM kernel functions, have not been fully investigated for sensitivity classification. Therefore, in this work, we present an evaluation of five SVM kernel functions for sensitivity classification using POS sequences. Moreover, we show that an ensemble classifier that combines POS sequence classification with text classification can significantly improve sensitivity classification effectiveness (+6.09% F2) compared with a text classification baseline, according to McNemar's test of significance

The effect of gamma value on support vector machine performance with different kernels

Currently, the support vector machine (SVM) regarded as one of supervised machine learning algorithm that provides analysis of data for classification and regression. This technique is implemented in many fields such as bioinformatics, face recognition, text and hypertext categorization, generalized predictive control and many other different areas. The performance of SVM is affected by some parameters, which are used in the training phase, and the settings of parameters can have a profound impact on the resulting engine’s implementation. This paper investigated the SVM performance based on value of gamma parameter with used kernels. It studied the impact of gamma value on (SVM) efficiency classifier using different kernels on various datasets descriptions. SVM classifier has been implemented by using Python. The kernel functions that have been investigated are polynomials, radial based function (RBF) and sigmoid. UC irvine machine learning repository is the source of all the used datasets. Generally, the results show uneven effect on the classification accuracy of three kernels on used datasets. The changing of the gamma value taking on consideration the used dataset influences polynomial and sigmoid kernels. While the performance of RBF kernel function is more stable with different values of gamma as its accuracy is slightly changed

Motif kernel generated by genetic programming improves remote homology and fold detection

BACKGROUND: Protein remote homology detection is a central problem in computational biology. Most recent methods train support vector machines to discriminate between related and unrelated sequences and these studies have introduced several types of kernels. One successful approach is to base a kernel on shared occurrences of discrete sequence motifs. Still, many protein sequences fail to be classified correctly for a lack of a suitable set of motifs for these sequences. RESULTS: We introduce the GPkernel, which is a motif kernel based on discrete sequence motifs where the motifs are evolved using genetic programming. All proteins can be grouped according to evolutionary relations and structure, and the method uses this inherent structure to create groups of motifs that discriminate between different families of evolutionary origin. When tested on two SCOP benchmarks, the superfamily and fold recognition problems, the GPkernel gives significantly better results compared to related methods of remote homology detection. CONCLUSION: The GPkernel gives particularly good results on the more difficult fold recognition problem compared to the other methods. This is mainly because the method creates motif sets that describe similarities among subgroups of both the related and unrelated proteins. This rich set of motifs give a better description of the similarities and differences between different folds than do previous motif-based methods

Diversified Ensemble Classifiers for Highly Imbalanced Data Learning and their Application in Bioinformatics

In this dissertation, the problem of learning from highly imbalanced data is studied. Imbalance data learning is of great importance and challenge in many real applications. Dealing with a minority class normally needs new concepts, observations and solutions in order to fully understand the underlying complicated models. We try to systematically review and solve this special learning task in this dissertation.We propose a new ensemble learning framework—Diversified Ensemble Classifiers for Imbal-anced Data Learning (DECIDL), based on the advantages of existing ensemble imbalanced learning strategies. Our framework combines three learning techniques: a) ensemble learning, b) artificial example generation, and c) diversity construction by reversely data re-labeling. As a meta-learner, DECIDL utilizes general supervised learning algorithms as base learners to build an ensemble committee. We create a standard benchmark data pool, which contains 30 highly skewed sets with diverse characteristics from different domains, in order to facilitate future research on imbalance data learning. We use this benchmark pool to evaluate and compare our DECIDL framework with several ensemble learning methods, namely under-bagging, over-bagging, SMOTE-bagging, and AdaBoost. Extensive experiments suggest that our DECIDL framework is comparable with other methods. The data sets, experiments and results provide a valuable knowledge base for future research on imbalance learning. We develop a simple but effective artificial example generation method for data balancing. Two new methods DBEG-ensemble and DECIDL-DBEG are then designed to improve the power of imbalance learning. Experiments show that these two methods are comparable to the state-of-the-art methods, e.g., GSVM-RU and SMOTE-bagging. Furthermore, we investigate learning on imbalanced data from a new angle—active learning. By combining active learning with the DECIDL framework, we show that the newly designed Active-DECIDL method is very effective for imbalance learning, suggesting the DECIDL framework is very robust and flexible.Lastly, we apply the proposed learning methods to a real-world bioinformatics problem—protein methylation prediction. Extensive computational results show that the DECIDL method does perform very well for the imbalanced data mining task. Importantly, the experimental results have confirmed our new contributions on this particular data learning problem

ProInflam: a webserver for the prediction of proinflammatory antigenicity of peptides and proteins

Additional file 2: Table S2. Dipeptide composition distribution between proinflammatory and non proinflammatory data

A NEW METHODOLOGY FOR IDENTIFYING INTERFACE RESIDUES INVOLVED IN BINDING PROTEIN COMPLEXES

Genome-sequencing projects with advanced technologies have rapidly increased the amount of protein sequences, and demands for identifying protein interaction sites are significantly increased due to its impact on understanding cellular process, biochemical events and drug design studies. However, the capacity of current wet laboratory techniques is not enough to handle the exponentially growing protein sequence data; therefore, sequence based predictive methods identifying protein interaction sites have drawn increasing interest. In this article, a new predictive model which can be valuable as a first approach for guiding experimental methods investigating protein-protein interactions and localizing the specific interface residues is proposed. The proposed method extracts a wide range of features from protein sequences. Random forests framework is newly redesigned to effectively utilize these features and the problems of imbalanced data classification commonly encountered in binding site predictions. The method is evaluated with 2,829 interface residues and 24,616 non-interface residues extracted from 99 polypeptide chains in the Protein Data Bank. The experimental results show that the proposed method performs significantly better than two other conventional predictive methods and can reliably predict residues involved in protein interaction sites. As blind tests, the proposed method predicts interaction sites and constructs three protein complexes: the DnaK molecular chaperone system, 1YUW and 1DKG, which provide new insight into the sequence-function relationship. Finally, the robustness of the proposed method is assessed by evaluating the performances obtained from four different ensemble methods

Predicting changes in protein thermostability brought about by single- or multi-site mutations

<p>Abstract</p> <p>Background</p> <p>An important aspect of protein design is the ability to predict changes in protein thermostability arising from single- or multi-site mutations. Protein thermostability is reflected in the change in free energy (ΔΔ<it>G</it>) of thermal denaturation.</p> <p>Results</p> <p>We have developed predictive software, Prethermut, based on machine learning methods, to predict the effect of single- or multi-site mutations on protein thermostability. The input vector of Prethermut is based on known structural changes and empirical measurements of changes in potential energy due to protein mutations. Using a 10-fold cross validation test on the M-dataset, consisting of 3366 mutants proteins from ProTherm, the classification accuracy of random forests and the regression accuracy of random forest regression were slightly better than support vector machines and support vector regression, whereas the overall accuracy of classification and the Pearson correlation coefficient of regression were 79.2% and 0.72, respectively. Prethermut performs better on proteins containing multi-site mutations than those with single mutations.</p> <p>Conclusions</p> <p>The performance of Prethermut indicates that it is a useful tool for predicting changes in protein thermostability brought about by single- or multi-site mutations and will be valuable in the rational design of proteins.</p

The distance-profile representation and its application to detection of distantly related protein families

BACKGROUND: Detecting homology between remotely related protein families is an important problem in computational biology since the biological properties of uncharacterized proteins can often be inferred from those of homologous proteins. Many existing approaches address this problem by measuring the similarity between proteins through sequence or structural alignment. However, these methods do not exploit collective aspects of the protein space and the computed scores are often noisy and frequently fail to recognize distantly related protein families. RESULTS: We describe an algorithm that improves over the state of the art in homology detection by utilizing global information on the proximity of entities in the protein space. Our method relies on a vectorial representation of proteins and protein families and uses structure-specific association measures between proteins and template structures to form a high-dimensional feature vector for each query protein. These vectors are then processed and transformed to sparse feature vectors that are treated as statistical fingerprints of the query proteins. The new representation induces a new metric between proteins measured by the statistical difference between their corresponding probability distributions. CONCLUSION: Using several performance measures we show that the new tool considerably improves the performance in recognizing distant homologies compared to existing approaches such as PSIBLAST and FUGUE

Active Learning Strategies for Technology Assisted Sensitivity Review

Government documents must be reviewed to identify and protect any sensitive information, such as personal information, before the documents can be released to the public. However, in the era of digital government documents, such as e-mail, traditional sensitivity review procedures are no longer practical, for example due to the volume of documents to be reviewed. Therefore, there is a need for new technology assisted review protocols to integrate automatic sensitivity classification into the sensitivity review process. Moreover, to effectively assist sensitivity review, such assistive technologies must incorporate reviewer feedback to enable sensitivity classifiers to quickly learn and adapt to the sensitivities within a collection, when the types of sensitivity are not known a priori. In this work, we present a thorough evaluation of active learning strategies for sensitivity review. Moreover, we present an active learning strategy that integrates reviewer feedback, from sensitive text annotations, to identify features of sensitivity that enable us to learn an effective sensitivity classifier (0.7 Balanced Accuracy) using significantly less reviewer effort, according to the sign test (p &lt; 0.01 ). Moreover, this approach results in a 51% reduction in the number of documents required to be reviewed to achieve the same level of classification accuracy, compared to when the approach is deployed without annotation features

Building well-performing classifier ensembles: model and decision level combination.

There is a continuing drive for better, more robust generalisation performance from classification systems, and prediction systems in general. Ensemble methods, or the combining of multiple classifiers, have become an accepted and successful tool for doing this, though the reasons for success are not always entirely understood. In this thesis, we review the multiple classifier literature and consider the properties an ensemble of classifiers - or collection of subsets - should have in order to be combined successfully. We find that the framework of Stochastic Discrimination provides a well-defined account of these properties, which are shown to be strongly encouraged in a number of the most popular/successful methods in the literature via differing algorithmic devices. This uncovers some interesting and basic links between these methods, and aids understanding of their success and operation in terms of a kernel induced on the training data, with form particularly well suited to classification. One property that is desirable in both the SD framework and in a regression context, the ambiguity decomposition of the error, is de-correlation of individuals. This motivates the introduction of the Negative Correlation Learning method, in which neural networks are trained in parallel in a way designed to encourage de-correlation of the individual networks. The training is controlled by a parameter λ governing the extent to which correlations are penalised. Theoretical analysis of the dynamics of training results in an exact expression for the interval in which we can choose λ while ensuring stability of the training, and a value λ∗ for which the training has some interesting optimality properties. These values depend only on the size N of the ensemble. Decision level combination methods often result in a difficult to interpret model, and NCL is no exception. However in some applications, there is a need for understandable decisions and interpretable models. In response to this, we depart from the standard decision level combination paradigm to introduce a number of model level combination methods. As decision trees are one of the most interpretable model structures used in classification, we chose to combine structure from multiple individual trees to build a single combined model. We show that extremely compact, well performing models can be built in this way. In particular, a generalisation of bottom-up pruning to a multiple-tree context produces good results in this regard. Finally, we develop a classification system for a real-world churn prediction problem, illustrating some of the concepts introduced in the thesis, and a number of more practical considerations which are of importance when developing a prediction system for a specific problem