ABLE: Attention based learning for enzyme classification

Classifying proteins into their respective enzyme class is an interesting question for researchers for a variety of reasons. The open source Protein Data Bank (PDB) contains more than 1,60,000 structures, with more being added everyday. This paper proposes an attention-based bidirectional-LSTM model (ABLE) trained on over sampled data generated by SMOTE to analyse and classify a protein into one of the six enzyme classes or a negative class using only the primary structure of the protein described as a string by the FASTA sequence as an input. We achieve the highest F1-score of 0.834 using our proposed model on a dataset of proteins from the PDB. We baseline our model against eighteen other machine learning and deep learning networks, including CNN, LSTM, Bi-LSTM, GRU, and the state-of-the-art DeepEC model. We conduct experiments with two different oversampling techniques, SMOTE and ADASYN. To corroborate the obtained results, we perform extensive experimentation and statistical testing.     

Recurrent and convolutional neural networks for deep terrain classification by autonomous robots

The future challenge for field robots is to increase the level of autonomy towards long distance (>1 km) and duration (>1h) applications. One of the key technologies is the ability to accurately estimate the properties of the traversed terrain to optimize onboard control strategies and energy efficient path-planning, ensuring safety and avoiding possible immobilization conditions that would lead to mission failure. Two main hypotheses are put forward in this research. The first hypothesis is that terrain can be effectively detected by relying exclusively on the measurement of quantities that pertain to the robot-ground interaction, i.e., on proprioceptive signals. Therefore, no visual or depth information is required. Then, artificial deep neural networks can provide an accurate and robust solution to the classification problem of different terrain types. Under these hypotheses, sensory signals are classified as time series directly by a Recurrent Neural Network or by a Convolutional Neural Network in the form of higher-level features or spectrograms resulting from additional processing. In both cases, results obtained from real experiments show comparable or better performance when contrasted with standard Support Vector Machine with the additional advantage of not requiring an a priori definition of the feature space.     

基于级联卷积神经网络的前列腺磁共振图像分类

针对深度学习训练成本高，以及基于磁共振图像的前列腺癌临床诊断需要大量医学常识且极为耗时的问题，本文提出了一种基于级联卷积神经网络（Convolutional Neural Network，CNN）和磁共振图像的前列腺癌（Prostate Cancer，PCa）自动分类诊断方法，该网络以Faster-RCNN作为前网络，对前列腺区域进行提取分割，用于排除前列腺附近组织器官的干扰；以基于ResNet改进的网络结构CNN40_bottleneck作为后网络，用于对前列腺区域病变进行分类.后网络由瓶颈结构串联组成，其中使用批量标准化（Batch Normalization，BN）、全局平均池化（Global Average Pooling，GAP）进行优化.实验结果证明，本文方法对前列腺癌诊断结果较好，而且缩减了训练时间和参数量，有效降低了训练成本.     

Hierarchical Model-Based Clustering for Large Datasets

In recent years, hierarchical model-based clustering has provided promising results in a variety of applications. However, its use with large datasets has been hindered by a time and memory complexity that are at least quadratic in the number of observations. To overcome this difficulty, this article proposes to start the hierarchical agglomeration from an efficient classification of the data in many classes rather than from the usual set of singleton clusters. This initial partition is derived from a subgraph of the minimum spanning tree associated with the data. To this end, we develop graphical tools that assess the presence of clusters in the data and uncover observations difficult to classify. We use this approach to analyze two large, real datasets: a multiband MRI image of the human brain and data on global precipitation climatology. We use the real datasets to discuss ways of integrating the spatial information in the clustering analysis. We focus on two-stage methods, in which a second stage of processing using established methods is applied to the output from the algorithm presented in this article, viewed as a first stage.     

Linguistic cost-sensitive learning of genetic fuzzy classifiers for imprecise data

Cost-sensitive classification is based on a set of weights defining the expected cost of misclassifying an object. In this paper, a Genetic Fuzzy Classifier, which is able to extract fuzzy rules from interval or fuzzy valued data, is extended to this type of classification. This extension consists in enclosing the estimation of the expected misclassification risk of a classifier, when assessed on low quality data, in an interval or a fuzzy number. A cooperative-competitive genetic algorithm searches for the knowledge base whose fitness is primal with respect to a precedence relation between the values of this interval or fuzzy valued risk. In addition to this, the numerical estimation of this risk depends on the entrywise product of cost and confusion matrices. These have been, in turn, generalized to vague data. The flexible assignment of values to the cost function is also tackled, owing to the fact that the use of linguistic terms in the definition of the misclassification cost is allowed.     

An improved ensemble learning machine for biological activity prediction of tyrosine kinase inhibitors

Boosting is one of the most important strategies in ensemble learning because of its ability to improve the stability and performance of weak learners. It is nonparametric, multivariate, fast and interpretable but is not robust against outliers. To enhance its prediction accuracy as well as immunize it against outliers, a modified version of a boosting algorithm (AdaBoost R2) was developed and called AdaBoost R3. In the sampling step, extremum samples were added to the boosting set. In the robustness step, a modified Huber loss function was applied to overcome the outlier problem. In the output step, a deterministic threshold was used to guarantee that bad predictions do not participate in the final output. The performance of the modified algorithm was investigated with two anticancer data sets of tyrosine kinase inhibitors, and the mechanism of inhibition was studied using the relative weighted variable importance procedure. Investigating the effect of base learner's strength reveals that boosting is only successful using the classification and regression tree method (a weak to moderate learner) and does not have a significant effect using the radial basis functions partial least square method (a strong base learners). Copyright © 2015 John Wiley & Sons, Ltd.     

Artificial Neural Networks in water analysis: Theory and applications

Artificial Neural Networks (ANNs) have seen an explosion of interest over the last two decades and have been successfully applied in all fields of chemistry and particularly in analytical chemistry. Inspired from biological systems and originated from the perceptron, i.e. a program unit that learns concepts, ANNs are capable of gradual learning over time and modelling extremely complex functions. In addition to the traditional multivariate chemometric techniques, ANNs are often applied for prediction, clustering, classification, modelling of a property, process control, procedural optimisation and/or regression of the obtained data. This paper aims at presenting the most common network architectures such as Multi-layer Perceptrons (MLPs), Radial Basis Function (RBF) and Kohonen's self-organisations maps (SOM). Moreover, back-propagation (BP), the most widespread algorithm used today and its modifications, such as quick-propagation (QP) and Delta-bar-Delta, are also discussed. All architectures correlate input variables to output variables through non-linear, weighted, parameterised functions, called neurons. In addition, various training algorithms have been developed in order to minimise the prediction error made by the network. The applications of ANNs in water analysis and water quality assessment are also reviewed. Most of the ANNs works are focused on modelling and parameters prediction. In the case of water quality assessment, extended predictive models are constructed and optimised, while variables correlation and significance is usually estimated in the framework of the predictive or classifier models. On the contrary, ANNs models are not frequently used for clustering/classification purposes, although they seem to be an effective tool. ANNs proved to be a powerful, yet often complementary, tool for water quality assessment, prediction and classification.     

新一代运载火箭时序仿真系统信号完整性分析

新一代运载火箭时序仿真系统具有数字电路速度快、集成度高的特点,系统要求发出多路高精度时序、时串信号以满足新一代运载火箭地面测试设备的检查与校准需求,因此信号完整性问题在系统设计中不容忽视。针对仿真系统的典型模块(USB 3.0 Super-speed差分线、FPGA外设数据走线、时钟走线)进行建模分析仿真得出PCB硬件电路设计参数,给出时序仿真系统设计信号完整性问题的抑制和解决方法,优化了板级信号质量,改善系统可靠性、工作连续性和输出精度,可有效提高新一代运载火箭测试效率和测试可靠性。     

基于图像处理的闸机口跳闸事件检测算法

文中提出了一种基于图像处理的闸机口跳闸事件检测方法。首先,利用模板匹配的方法进行预处理,得到闸门图像匹配率;其次,根据跳闸事件的连贯性特点,提取一段连续时间序列的匹配率作为分类特征;最后,采取基于最小错误率的贝叶斯分类方法对这段时间序列特征向量进行分类。实验表明,该算法可以有效的检测出闸机口的跳闸事件,具有实时性好、不需要额外的传感器、成本低的优点,具有较好的工程应用前景。