A hybrid knowledge and ensemble classification approach for prediction of venous thromboembolism

Clinical narratives such as progress summaries, lab reports, surgical reports, and other narrative texts contain key biomarkers about a patient's health. Evidence-based preventive medicine needs accurate semantic and sentiment analysis to extract and classify medical features as the input to appropriate machine learning classifiers. However, the traditional approach of using single classifiers is limited by the need for dimensionality reduction techniques, statistical feature correlation, a faster learning rate, and the lack of consideration of the semantic relations among features. Hence, extracting semantic and sentiment-based features from clinical text and combining multiple classifiers to create an ensemble intelligent system overcomes many limitations and provides a more robust prediction outcome. The selection of an appropriate approach and its interparameter dependency becomes key for the success of the ensemble method. This paper proposes a hybrid knowledge and ensemble learning framework for prediction of venous thromboembolism (VTE) diagnosis consisting of the following components: a VTE ontology, semantic extraction and sentiment assessment of risk factor framework, and an ensemble classifier. Therefore, a component-based analysis approach was adopted for evaluation using a data set of 250 clinical narratives where knowledge and ensemble achieved the following results with and without semantic extraction and sentiment assessment of risk factor, respectively: a precision of 81.8% and 62.9%, a recall of 81.8% and 57.6%, an F measure of 81.8% and 53.8%, and a receiving operating characteristic of 80.1% and 58.5% in identifying cases of VTE.     

A new reverse reduce-error ensemble pruning algorithm

Although greedy algorithms possess high efficiency, they often receive suboptimal solutions of the ensemble pruning problem, since their exploration areas are limited in large extent. And another marked defect of almost all the currently existing ensemble pruning algorithms, including greedy ones, consists in: they simply abandon all of the classifiers which fail in the competition of ensemble selection, causing a considerable waste of useful resources and information. Inspired by these observations, an interesting greedy Reverse Reduce-Error (RRE) pruning algorithm incorporated with the operation of subtraction is proposed in this work. The RRE algorithm makes the best of the defeated candidate networks in a way that, the Worst Single Model (WSM) is chosen, and then, its votes are subtracted from the votes made by those selected components within the pruned ensemble. The reason is because, for most cases, the WSM might make mistakes in its estimation for the test samples. And, different from the classical RE, the near-optimal solution is produced based on the pruned error of all the available sequential subensembles. Besides, the backfitting step of RE algorithm is replaced with the selection step of a WSM in RRE. Moreover, the problem of ties might be solved more naturally with RRE. Finally, soft voting approach is employed in the testing to RRE algorithm. The performances of RE and RRE algorithms, and two baseline methods, i.e., the method which selects the Best Single Model (BSM) in the initial ensemble, and the method which retains all member networks of the initial ensemble (ALL), are evaluated on seven benchmark classification tasks under different initial ensemble setups. The results of the empirical investigation show the superiority of RRE over the other three ensemble pruning algorithms.     

Chemical-Shift Perturbations Reflect Bile Acid Binding to Norovirus Coat Protein: Recognition Comes in Different Flavors

Bile acids have been reported as important cofactors promoting human and murine norovirus (NoV) infections in cell culture. The underlying mechanisms are not resolved. Through the use of chemical shift perturbation (CSP) NMR experiments, we identified a low-affinity bile acid binding site of a human GII.4 NoV strain. Long-timescale MD simulations reveal the formation of a ligand-accessible binding pocket of flexible shape, allowing the formation of stable viral coat protein–bile acid complexes in agreement with experimental CSP data. CSP NMR experiments also show that this mode of bile acid binding has a minor influence on the binding of histo-blood group antigens and vice versa. STD NMR experiments probing the binding of bile acids to virus-like particles of seven different strains suggest that low-affinity bile acid binding is a common feature of human NoV and should therefore be important for understanding the role of bile acids as cofactors in NoV infection.     

Improving the prediction of petroleum reservoir characterization with a stacked generalization ensemble model of support vector machines

The ensemble learning paradigm has proved to be relevant to solving most challenging industrial problems. Despite its successful application especially in the Bioinformatics, the petroleum industry has not benefited enough from the promises of this machine learning technology. The petroleum industry, with its persistent quest for high-performance predictive models, is in great need of this new learning methodology. A marginal improvement in the prediction indices of petroleum reservoir properties could have huge positive impact on the success of exploration, drilling and the overall reservoir management portfolio. Support vector machines (SVM) is one of the promising machine learning tools that have performed excellently well in most prediction problems. However, its performance is a function of the prudent choice of its tuning parameters most especially the regularization parameter, C. Reports have shown that this parameter has significant impact on the performance of SVM. Understandably, no specific value has been recommended for it. This paper proposes a stacked generalization ensemble model of SVM that incorporates different expert opinions on the optimal values of this parameter in the prediction of porosity and permeability of petroleum reservoirs using datasets from diverse geological formations. The performance of the proposed SVM ensemble was compared to that of conventional SVM technique, another SVM implemented with the bagging method, and Random Forest technique. The results showed that the proposed ensemble model, in most cases, outperformed the others with the highest correlation coefficient, and the lowest mean and absolute errors. The study indicated that there is a great potential for ensemble learning in petroleum reservoir characterization to improve the accuracy of reservoir properties predictions for more successful explorations and increased production of petroleum resources. The results also confirmed that ensemble models perform better than the conventional SVM implementation.     

基于模式间混淆关系自适应构建层次化分类器

为了解决层次化分类器的设计难点——子分类器的层属关系及其内部组成的确定,本文首先定义了模式间混淆关系,用于描述不同模式在判决域中的相互作用;进而提出了基于混淆矩阵度量模式间混淆关系的方法。设计并实现了多模式混淆关系分析机MPCRAM,将有师指派和无师自组两种常用的模式重组方法有机结合,遵循Fisher准则,自适应地产生层次化分类器结构。大量综合测试证实了该方法有效、实用,可显著提高分类器的识别性能和稳健性。     

Optimal ensemble construction via meta-evolutionary ensembles

In this paper, we propose a meta-evolutionary approach to improve on the performance of individual classifiers. In the proposed system, individual classifiers evolve, competing to correctly classify test points, and are given extra rewards for getting difficult points right. Ensembles consisting of multiple classifiers also compete for member classifiers, and are rewarded based on their predictive performance. In this way we aim to build small-sized optimal ensembles rather than form large-sized ensembles of individually-optimized classifiers. Experimental results on 15 data sets suggest that our algorithms can generate ensembles that are more effective than single classifiers and traditional ensemble methods.     

Employing optimized combinations of one-class classifiers for automated currency validation

Automated currency validation requires a decision to be made regarding the authenticity of a banknote presented to the validation system. This decision often has to be made with little or no information regarding the characteristics of possible counterfeits as is the case for issues of new currency. A method for automated currency validation is presented which segments the whole banknote into different regions, builds individual classifiers on each region and then combines a small subset of the region specific classifiers to provide an overall decision. The segmentation and combination of region specific classifiers to provide optimized false positive and false negative rates is achieved by employing a genetic algorithm. Experiments based on high value notes of Sterling currency were carried out to assess the effectiveness of the proposed solution.     

Uncertainty,belief, and probability1

We introduce a new probabilistic approach to dealing with uncertainty, based on the observation that probability theory does not require that every event be assigned a probability. For a nonmeasurable event (one to which we do not assign a probability), we can talk about only the inner measure and outer measure of the event. In addition to removing the requirement that every event be assigned a probability, our approach circumvents other criticisms of probability-based approaches to uncertainty. For example, the measure of belief in an event turns out to be represented by an interval (defined by the inner and outer measures), rather than by a single number. Further, this approach allows us to assign a belief (inner measure) to an event E without committing to a belief about its negation -E (since the inner measure of an event plus the inner measure of its negation is not necessarily one). Interestingly enough, inner measures induced by probability measures turn out to correspond in a precise sense to Dempster-Shafer belief functions. Hence, in addition to providing promising new conceptual tools for dealing with uncertainty, our approach shows that a key part of the important Dempster-Shafer theory of evidence is firmly rooted in classical probability theory. Cet article présente une nouvelle approche probabiliste en ce qui concerne le traitement de l'incertitude; celle-ci est basée sur l'observation que la théorie des probabilityés n'exige pas qu'une probabilityé soit assignée à chaque événement. Dans le cas d'un événement non mesurable (un événement pour lequel on n'assigne aucune probabilityé), nous ne pouvons discuter que de la mesure intérieure et de la mesure extérieure de l'évenément. En plus d'éliminer la nécessité d'assigner une probabilityéà l'événement, cette nouvelle approche apporte une réponse aux autres critiques des approches à l'incertitude basées sur des probabilityés. Par exemple, la mesure de croyance dans un événement est représentée par un intervalle (défini par la mesure intérieure et extérieure) plutǒt que par un nombre unique. De plus, cette approche nous permet d'assigner une croyance (mesure intérieure) à un événement E sans se compromettre vers une croyance à propos de sa négation -E (puisque la mesure intérieure d'un événement et la mesure intérieure de sa négation ne sont pas nécessairement une seule et unique mesure). II est intéressant de noter que les mesures intérieures qui résultent des mesures de probabilityé correspondent d'une manière précise aux fonctions de croyance de Dempster-Shafer. En plus de constituer un nouvel outil conceptuel prometteur dans le traitement de l'incertitude, cette approche démontre qu'une partie importante de la théorie de l'évidence de Dempster-Shafer est fermement ancrée dans la theorie classique des probabilityés.     

Information-Based Evaluation Criterion for Classifier's Performance

In the past few years many systems for learning decision rules from examples were developed. As different systems allow different types of answers when classifying new instances, it is difficult to appropriately evaluate the systems' classification power in comparison with other classification systems or in comparison with human experts. Classification accuracy is usually used as a measure of classification performance. This measure is, however, known to have several defects. A fair evaluation criterion should exclude the influence of the class probabilities which may enable a completely uninformed classifier to trivially achieve high classification accuracy. In this paper a method for evaluating the information score of a classifier's answers is proposed. It excludes the influence of prior probabilities, deals with various types of imperfect or probabilistic answers and can be used also for comparing the performance in different domains.     

模式识别催化剂生产调优

本文介绍如何将模式识别应用于生产调优,着重讨论了多指标(优化目标)因素的分级,提出了用模糊综合评价度量和依有序聚类最小损失函数准则划类,并相继进行变量与样本筛选、信息压缩、特征提取和模拟仿真获得优区操作条件,实施效果显著。