Learning extended tree augmented naive structures

This work proposes an extended version of the well-known tree-augmented naive Bayes (TAN) classifier where the structure learning step is performed without requiring features to be connected to the class. Based on a modification of Edmonds' algorithm, our structure learning procedure explores a superset of the structures that are considered by TAN, yet achieves global optimality of the learning score function in a very efficient way (quadratic in the number of features, the same complexity as learning TANs). We enhance our procedure with a new score function that only takes into account arcs that are relevant to predict the class, as well as an optimization over the equivalent sample size during learning. These ideas may be useful for structure learning of Bayesian networks in general. A range of experiments shows that we obtain models with better prediction accuracy than naive Bayes and TAN, and comparable to the accuracy of the state-of-the-art classifier averaged one-dependence estimator (AODE). We release our implementation of ETAN so that it can be easily installed and run within Weka.     

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.     

Single-Molecule Sensing of Acidic Catecholamine Metabolites Using a Programmable Nanopore

Acidic catecholamine metabolites, which could serve as diagnostic markers for many diseases, demonstrate an importance of accurate sensing. However, they share a highly similar chemical structure, which is a challenge in the design of sensing strategies. A nanopore may be engineered to sense these metabolites in a single molecule manner. To achieve this, a recently developed programmable nano-reactor for stochastic sensing (PNRSS) technique adapted with a phenylboronic acid (PBA) adaptor was applied. Three acidic catecholamine metabolites, including 3,4-dihydroxyphenylacetic acid (DOPAC), 3,4-dihydroxymandelic acid (DHMA) and 3-methoxy-4-hydroxymandetic acid (VMA) were investigated by PNRSS. Specifically, DHMA, which contains an α-hydroxycarboxylate moiety and an adjacent cis-hydroxyl groups on its benzene ring, reports two binding modes simultaneously resolvable by PNRSS. Assisted with the high resolution of PNRSS, direct regulation of these two binding modes by pH can also be observed. A custom machine learning algorithm was also developed to achieve automatic event classification.     

Optimal time delays in a class of reaction-diffusion equations

ABSTRACT

A class of semilinear parabolic reaction diffusion equations with multiple time delays is considered. These time delays and corresponding weights are to be optimized such that the associated solution of the delay equation is the best approximation of a desired state function. The differentiability of the mapping is proved that associates the solution of the delay equation to the vector of weights and delays. Based on an adjoint calculus, first-order necessary optimality conditions are derived. Numerical test examples show the applicability of the concept of optimizing time delays.     

关于极限理论的学习经验

分析极限理论在数学分析学习中的重要性，介绍学习极限理论的三点经验与体会，即充分理解基本内容；加强基本功训练；试着多问自己一些问题，学会举出各种各样的例子。     

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.     

Induction of decision trees using genetic programming for modelling ecotoxicity data: adaptive discretization of real-valued endpoints

Recent literature has demonstrated the applicability of genetic programming to induction of decision trees for modelling toxicity endpoints. Compared with other decision tree induction techniques that are based upon recursive partitioning employing greedy searches to choose the best splitting attribute and value at each node that will necessarily miss regions of the search space, the genetic programming based approach can overcome the problem. However, the method still requires the discretization of the often continuous-valued toxicity endpoints prior to the tree induction. A novel extension of this method, YAdapt, is introduced in this work which models the original continuous endpoint by adaptively finding suitable ranges to describe the endpoints during the tree induction process, removing the need for discretization prior to tree induction and allowing the ordinal nature of the endpoint to be taken into account in the models built.     

基于改进极根学习机的回转窑煅烧带温度预测方法

针对传统算法预测回转窑煅烧带温度存在精度低、速度慢的问题,提出了基于改进极限学习机(ELM)的回转窑煅烧带温度预测方法。对ELM输入权值矩阵定义了变换系数,采用黄金分割法在给定区间内搜寻变换系数的最佳值,改进了ELM网络参数的确定方式,弥补了随机确定输入权值并且不作调整的缺陷,在保证ELM训练速度的前提下提高预测精度、减小模型随机性。实验结果表明,改进的ELM预测精度高、训练速度快、模型性能优,可满足工况恶劣的回转窑的生产需要。     

基于MetropolisQ学习的蜂窝网络在线信道分配

针对现有的蜂窝网络的在线动态分配模型具有的信道需求量大、呼叫动态变化时阻塞率高和收敛速度慢的缺点,设计了一种基于MetropoisQ学习的蜂窝网络的在线信道分配方法。首先,在考虑同信道限制、邻居信道限制和同小区限制的基础上,设计了在线信道分配的数学模型,然后在Q-Learning算法基础上的设计了一种基于资格迹的Q(λ)算法实现信道的在线分配,为了进一步提高收敛速度,采用Metropois规则对算法中动作的选择方式进行改进,实现探索和利用的平衡。为了验证文中方法,采用Matlab工具上进行实验,仿真实验结果表明文中方法能实现蜂窝通信网络的在线信道分配,且与其它方法比较,具有较少的信道需求量、较低的阻塞率和收敛速度,较其它方法具有较大优越性。