Learning mixture models with support vector machines for sequence classification and segmentation

This paper focuses on learning recognition systems able to cope with sequential data for classification and segmentation tasks. It investigates the integration of discriminant power in the learning of generative models, which are usually used for such data. Based on a procedure that transforms a sample data into a generative model, learning is viewed as the selection of efficient component models in a mixture of generative models. This may be done through the learning of a support vector machine. We propose a few kernels for this and report experimental results for classification and segmentation tasks.     

Learning state machine-based string edit kernels

During the past few years, several works have been done to derive string kernels from probability distributions. For instance, the Fisher kernel uses a generative model M (e.g. a hidden Markov model) and compares two strings according to how they are generated by M. On the other hand, the marginalized kernels allow the computation of the joint similarity between two instances by summing conditional probabilities. In this paper, we adapt this approach to edit distance-based conditional distributions and we present a way to learn a new string edit kernel. We show that the practical computation of such a kernel between two strings x and x^′ built from an alphabet Σ requires (i) to learn edit probabilities in the form of the parameters of a stochastic state machine and (ii) to calculate an infinite sum over Σ^* by resorting to the intersection of probabilistic automata as done for rational kernels. We show on a handwritten character recognition task that our new kernel outperforms not only the state of the art string kernels and string edit kernels but also the standard edit distance used by a neighborhood-based classifier.     

Spikernels: predicting arm movements by embedding population spike rate patterns in inner-product spaces

Inner-product operators, often referred to as kernels in statistical learning, define a mapping from some input space into a feature space. The focus of this letter is the construction of biologically motivated kernels for cortical activities. The kernels we derive, termed Spikernels, map spike count sequences into an abstract vector space in which we can perform various prediction tasks. We discuss in detail the derivation of Spikernels and describe an efficient algorithm for computing their value on any two sequences of neural population spike counts. We demonstrate the merits of our modeling approach by comparing the Spikernel to various standard kernels in the task of predicting hand movement velocities from cortical recordings. All of the kernels that we tested in our experiments outperform the standard scalar product used in linear regression, with the Spikernel consistently achieving the best performance.     

String kernels construction and fusion: a survey with bioinformatics application

The kernel method, especially the kernel-fusion method, is widely used in social networks, computer vision, bioinformatics, and other applications. It deals effectively with nonlinear classification problems, which can map linearly inseparable biological sequence data from low to high-dimensional space for more accurate differentiation, enabling the use of kernel methods to predict the structure and function of sequences. Therefore, the kernel method is significant in the solution of bioinformatics problems. Various kernels applied in bioinformatics are explained clearly, which can help readers to select proper kernels to distinguish tasks. Mass biological sequence data occur in practical applications. Research of the use of machine learning methods to obtain knowledge, and how to explore the structure and function of biological methods for theoretical prediction, have always been emphasized in bioinformatics. The kernel method has gradually become an important learning algorithm that is widely used in gene expression and biological sequence prediction. This review focuses on the requirements of classification tasks of biological sequence data. It studies kernel methods and optimization algorithms, including methods of constructing kernel matrices based on the characteristics of biological sequences and kernel fusion methods existing in a multiple kernel learning framework.     

边际核函数在生物序列分类中的应用

在核方法的基础上,介绍了一种自潜变量生成模型构造核函数的新方法;并专门探讨了结合生物序列的自身特点,按照该方法提取了几个边际核函数;随后将它们应用于具体的gyrB(旋转酶B亚单位)氨基酸序列分类实验中,实验结果表明边际核具有良好的识别效果及极佳的推广能力,也肯定了此种核构造方法的先进性.     

Some sets of orthogonal polynomial kernel functions

Kernel methods provide high performance in a variety of machine learning tasks. However, the success of kernel methods is heavily dependent on the selection of the right kernel function and proper setting of its parameters. Several sets of kernel functions based on orthogonal polynomials have been proposed recently. Besides their good performance in the error rate, these kernel functions have only one parameter chosen from a small set of integers, and it facilitates kernel selection greatly. Two sets of orthogonal polynomial kernel functions, namely the triangularly modified Chebyshev kernels and the triangularly modified Legendre kernels, are proposed in this study. Furthermore, we compare the construction methods of some orthogonal polynomial kernels and highlight the similarities and differences among them. Experiments on 32 data sets are performed for better illustration and comparison of these kernel functions in classification and regression scenarios. In general, there is difference among these orthogonal polynomial kernels in terms of accuracy, and most orthogonal polynomial kernels can match the commonly used kernels, such as the polynomial kernel, the Gaussian kernel and the wavelet kernel. Compared with these universal kernels, the orthogonal polynomial kernels each have a unique easily optimized parameter, and they store statistically significantly less support vectors in support vector classification. New presented kernels can obtain better generalization performance both for classification tasks and regression tasks.     

基于混合核函数的SVM及其应用

支持向量机可以很好地应用于函数拟合中,其中核函数的选择尤其重要。由于普通核函数各有其利弊,为了得到学习能力和泛化性能都很强的核函数,文中采用了混合核函数,并将由其构造的支持向量机运用于函数拟合中,且与普通核函数构造的支持向量机的实验结果进行了比较。结果表明其性能明显优于由普通核函数构造的支持向量机。     

基于互信息的选择性集成核极端学习机

针对集成学习中的准确性和差异性平衡问题, 提出一种基于信息论的选择性集成核极端学习机. 采用具有结构简单、训练简便、泛化性能好的核极端学习作为基学习器. 引入相关性准则描述准确性, 冗余性准则描述差异性,将选择性集成问题转化为变量选择问题. 利用基于互信息的最大相关最小冗余准则对生成的核极端学习机进行选择, 从而实现准确性和差异性的平衡. 基于UCI 基准回归和分类数据的仿真结果验证了所提出算法的优越性.

     

A comprehensive review of computer-aided whole-slide image analysis: from datasets to feature extraction,segmentation, classification and detection approaches

With the development of Computer-aided Diagnosis (CAD) and image scanning techniques, Whole-slide Image (WSI) scanners are widely used in the field of pathological diagnosis. Therefore, WSI analysis has become the key to modern digital histopathology. Since 2004, WSI has been used widely in CAD. Since machine vision methods are usually based on semi-automatic or fully automatic computer algorithms, they are highly efficient and labor-saving. The combination of WSI and CAD technologies for segmentation, classification, and detection helps histopathologists to obtain more stable and quantitative results with minimum labor costs and improved diagnosis objectivity. This paper reviews the methods of WSI analysis based on machine learning. Firstly, the development status of WSI and CAD methods are introduced. Secondly, we discuss publicly available WSI datasets and evaluation metrics for segmentation, classification, and detection tasks. Then, the latest development of machine learning techniques in WSI segmentation, classification, and detection are reviewed. Finally, the existing methods are studied, and the application prospects of the methods in this field are forecasted.

     

Machine learning for vessel trajectories using compression,alignments and domain knowledge

In this paper we present a machine learning framework to analyze moving object trajectories from maritime vessels. Within this framework we perform the tasks of clustering, classification and outlier detection with vessel trajectory data. First, we apply a piecewise linear segmentation method to the trajectories to compress them. We adapt an existing technique to better retain stop and move information and show the better performance of our method with experimental results. Second, we use a similarity based approach to perform the clustering, classification and outlier detection tasks using kernel methods. We present experiments that investigate different alignment kernels and the effect of piecewise linear segmentation in the three different tasks. The experimental results show that compression does not negatively impact task performance and greatly reduces computation time for the alignment kernels. Finally, the alignment kernels allow for easy integration of geographical domain knowledge. In experiments we show that this added domain knowledge enhances performance in the clustering and classification tasks.