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PubMed2005

Improved access to sequential motifs: a note on the architectural bias of recurrent networks.

For many biological sequence problems the available data occupies only sparse regions of the problem space. To use machine learning effectively for the analysis of sparse data we must employ architectures with an appropriate bias. By experimentation we show that the bias of recurrent neural networks--recently analyzed by Tino et al. and Hammer and Tino--offers superior access to motifs (sequential patterns) compared to the, in bioinformatics, standardly used feedforward neural networks.

Computational Biology↗
PubMed2005

Survey of clustering algorithms.

Data analysis plays an indispensable role for understanding various phenomena. Cluster analysis, primitive exploration with little or no prior knowledge, consists of research developed across a wide variety of communities. The diversity, on one hand, equips us with many tools. On the other hand, the profusion of options causes confusion. We survey clustering algorithms for data sets appearing in statistics, computer science, and machine learning, and illustrate their applications in some benchmark data sets, the traveling salesman problem, and bioinformatics, a new field attracting intensive efforts. Several tightly related topics, proximity measure, and cluster validation, are also discussed.

Algorithms↗
PubMed2005

Spatial-temporal modeling of malware propagation in networks.

Network security is an important task of network management. One threat to network security is malware (malicious software) propagation. One type of malware is called topological scanning that spreads based on topology information. The focus of this work is on modeling the spread of topological malwares, which is important for understanding their potential damages, and for developing countermeasures to protect the network infrastructure. Our model is motivated by probabilistic graphs, which have been widely investigated in machine learning. We first use a graphical representation to abstract the propagation of malwares that employ different scanning methods. We then use a spatial-temporal random process to describe the statistical dependence of malware propagation in arbitrary topologies. As the spatial dependence is particularly difficult to characterize, the problem becomes how to use simple (i.e., biased) models to approximate the spatially dependent process. In particular, we propose the independent model and the Markov model as simple approximations. We conduct both theoretical analysis and extensive simulations on large networks using both real measurements and synthesized topologies to test the performance of the proposed models. Our results show that the independent model can capture temporal dependence and detailed topology information and, thus, outperforms the previous models, whereas the Markov model incorporates a certain spatial dependence and, thus, achieves a greater accuracy in characterizing both transient and equilibrium behaviors of malware propagation.

Algorithms↗
PubMed2006

Links between PPCA and subspace methods for complete Gaussian density estimation.

High-dimensional density estimation is a fundamental problem in pattern recognition and machine learning areas. In this letter, we show that, for complete high-dimensional Gaussian density estimation, two widely used methods, probabilistic principal component analysis and a typical subspace method using eigenspace decomposition, actually give the same results. Additionally, we present a unified view from the aspect of robust estimation of the covariance matrix.

Algorithms↗
PubMed2006

OR/AND neurons and the development of interpretable logic models.

In this paper, we are concerned with the concept of fuzzy logic networks and logic-based data analysis realized within this framework. The networks under discussion are homogeneous architectures comprising of OR/AND neurons originally introduced by Hirota and Pedrycz. Being treated here as generic processing units, OR/AND neurons are neurofuzzy constructs that exhibit well-defined logic characteristics and are endowed with a high level of parametric flexibility and come with significant interpretation abilities. The composite logic nature of the logic neurons becomes instrumental in covering a broad spectrum of logic dependencies whose character spread in-between between those being captured by plain and and or logic descriptors (connectives). From the functional standpoint, the developed network realizes a logic approximation of multidimensional mappings between unit hypercubes, that is transformations from [0, 1]n to [0, 1]m. The way in which the structure of the network has been formed is highly modular and becomes reflective of a general concept of decomposition of logic expressions and Boolean functions (as being commonly encountered in two-valued logic). In essence, given a collection of input variables, selected is their subset and transformed into new composite variable, which in turn is used in the consecutive module of the network. These intermediate synthetic variables are the result of the successive problem (mapping) decomposition. The development of the network is realized through genetic optimization. This helps address important issues of structural optimization (where we are concerned with a selection of a subset of variables and their allocation within the network) and reaching a global minimum when carrying out an extensive parametric optimization (adjustments of the connections of the neurons). The paper offers a comprehensive and user-interactive design procedure including a simple pruning mechanism whose intention is to enhance the interpretability of the network while reducing its size. The experimental studies comprise of three parts. First, we demonstrate the performance of the network on Boolean data (that leads to some useful comparative observations considering a wealth of optimization tools available in two-valued logic and digital systems). Second, we discuss synthetic multivalued data that helps focus on the approximation abilities of the network. Finally, show the generation of logic expressions describing selected data sets coming from the machine learning repository.

Algorithms↗
PubMed2006

The BCI competition. III: Validating alternative approaches to actual BCI problems.

A brain-computer interface (BCI) is a system that allows its users to control external devices with brain activity. Although the proof-of-concept was given decades ago, the reliable translation of user intent into device control commands is still a major challenge. Success requires the effective interaction of two adaptive controllers: the user's brain, which produces brain activity that encodes intent, and the BCI system, which translates that activity into device control commands. In order to facilitate this interaction, many laboratories are exploring a variety of signal analysis techniques to improve the adaptation of the BCI system to the user. In the literature, many machine learning and pattern classification algorithms have been reported to give impressive results when applied to BCI data in offline analyses. However, it is more difficult to evaluate their relative value for actual online use. BCI data competitions have been organized to provide objective formal evaluations of alternative methods. Prompted by the great interest in the first two BCI Competitions, we organized the third BCI Competition to address several of the most difficult and important analysis problems in BCI research. The paper describes the data sets that were provided to the competitors and gives an overview of the results.

Algorithms↗
PubMed2005

Structural semantic interconnections: a knowledge-based approach to word sense disambiguation.

Word Sense Disambiguation (WSD) is traditionally considered an Al-hard problem. A break-through in this field would have a significant impact on many relevant Web-based applications, such as Web information retrieval, improved access to Web services, information extraction, etc. Early approaches to WSD, based on knowledge representation techniques, have been replaced in the past few years by more robust machine learning and statistical techniques. The results of recent comparative evaluations of WSD systems, however, show that these methods have inherent limitations. On the other hand, the increasing availability of large-scale, rich lexical knowledge resources seems to provide new challenges to knowledge-based approaches. In this paper, we present a method, called structural semantic interconnections (SSI), which creates structural specifications of the possible senses for each word in a context and selects the best hypothesis according to a grammar G, describing relations between sense specifications. Sense specifications are created from several available lexical resources that we integrated in part manually, in part with the help of automatic procedures. The SSI algorithm has been applied to different semantic disambiguation problems, like automatic ontology population, disambiguation of sentences in generic texts, disambiguation of words in glossary definitions. Evaluation experiments have been performed on specific knowledge domains (e.g., tourism, computer networks, enterprise interoperability), as well as on standard disambiguation test sets.

Algorithms↗
PubMed2006

Nearest neighbors by neighborhood counting.

Finding nearest neighbors is a general idea that underlies many artificial intelligence tasks, including machine learning, data mining, natural language understanding, and information retrieval. This idea is explicitly used in the k-nearest neighbors algorithm (kNN), a popular classification method. In this paper, this idea is adopted in the development of a general methodology, neighborhood counting, for devising similarity functions. We turn our focus from neighbors to neighborhoods, a region in the data space covering the data point in question. To measure the similarity between two data points, we consider all neighborhoods that cover both data points. We propose to use the number of such neighborhoods as a measure of similarity. Neighborhood can be defined for different types of data in different ways. Here, we consider one definition of neighborhood for multivariate data and derive a formula for such similarity, called neighborhood counting measure or NCM. NCM was tested experimentally in the framework of kNN. Experiments show that NCM is generally comparable to VDM and its variants, the state-of-the-art distance functions for multivariate data, and, at the same time, is consistently better for relatively large k values. Additionally, NCM consistently outperforms HEOM (a mixture of Euclidean and Hamming distances), the "standard" and most widely used distance function for multivariate data. NCM has a computational complexity in the same order as the standard Euclidean distance function and NCM is task independent and works for numerical and categorical data in a conceptually uniform way. The neighborhood counting methodology is proven sound for multivariate data experimentally. We hope it will work for other types of data.

Algorithms↗
PubMed1998

A perspective on the control of FES-supported standing.

This special section is about the control of electrical stimulators to restore standing functions to paraplegics. It addresses several important topics regarding the interactions of the intact central nervous systems (CNS) with the artificial control system. The topics are as follows: how paraplegics use their arms to help themselves stand up with functional electrical stimulation (FES); the user-driven artificial control of FES-supported standing up; a controller which is promising for the control of sitting down; the application of reinforcement machine learning for the controllers of standing up; arms-free standing with voluntary upper body balancing and artificially controlled ankle stiffness; and cognitive feedback in balancing. This Commentary introduces the papers in this section and relates them to earlier research.

Electric Stimulation Therapy↗
PubMed2004

Refinement of generated fuzzy production rules by using a fuzzy neural network.

Fuzzy production rules (FPRs) have been used for years to capture and represent fuzzy, vague, imprecise and uncertain domain knowledge in many fuzzy systems. There have been a lot of researches on how to generate or obtain FPRs. There exist two methods to obtain FPRs. One is by painstakingly, repeatedly and time-consuming interviewing domain experts to extract the domain knowledge. The other is by using some machine learning techniques to generate and extract FPRs from some training samples. These extracted rules, however, are found to be nonoptimal and sometimes redundant. Furthermore, these generated rules suffer from the problem of low accuracy of classifying or recognizing unseen examples. The reasons for having these problems are 1) the FPRs generated are not powerful enough to represent the domain knowledge, 2) the techniques used to generate FPRs are pre-matured, ad-hoc or may not be suitable for the problem, and 3) further refinement of the extracted rules has not been done. In this paper we look into the solutions of the above problems by 1) enhancing the representation power of FPRs by including local and global weights, 2) developing a fuzzy neural network (FNN) with enhanced learning algorithm, and 3) using this FNN to refine the local and global weights of FPRs. By experimenting our method with some existing benchmark examples, the proposed method is found to have high accuracy in classifying unseen samples without increasing the number of the FPRs extracted and the time required to consult with domain experts is greatly reduced.

Journal Article↗
PubMed2004

Intelligent automated control of life support systems using proportional representations.

Effective automatic control of Advanced Life Support Systems (ALSS) is a crucial component of space exploration. An ALSS is a coupled dynamical system which can be extremely sensitive and difficult to predict. As a result, such systems can be difficult to control using deliberative and deterministic methods. We investigate the performance of two machine learning algorithms, a genetic algorithm (GA) and a stochastic hill-climber (SH), on the problem of learning how to control an ALSS, and compare the impact of two different types of problem representations on the performance of both algorithms. We perform experiments on three ALSS optimization problems using five strategies with multiple variations of a proportional representation for a total of 120 experiments. Results indicate that although a proportional representation can effectively boost GA performance, it does not necessarily have the same effect on other algorithms such as SH. Results also support previous conclusions that multivector control strategies are an effective method for control of coupled dynamical systems.

Algorithms↗
PubMed2005

Image transform bootstrapping and its applications to semantic scene classification.

The performance of an exemplar-based scene classification system depends largely on the size and quality of its set of training exemplars, which can be limited in practice. In addition, in nontrivial data sets, variations in scene content as well as distracting regions may exist in many testing images to prohibit good matches with the exemplars. Various boosting schemes have been proposed in machine learning, focusing on the feature space. We introduce the novel concept of image-transform bootstrapping using transforms in the image space to address such issues. In particular, three major schemes are described for exploiting this concept to augment training, testing, and both. We have successfully applied it to three applications of increasing difficulty: sunset detection, outdoor scene classification, and automatic image orientation detection. It is shown that appropriate transforms and meta-classification methods can be selected to boost performance according to the domain of the problem and the features/classifier used.

Algorithms↗
PubMed2005

An experimental bias-variance analysis of SVM ensembles based on resampling techniques.

Recently, bias-variance decomposition of error has been used as a tool to study the behavior of learning algorithms and to develop new ensemble methods well suited to the bias-variance characteristics of base learners. We propose methods and procedures, based on Domingo's unified bias-variance theory, to evaluate and quantitatively measure the bias-variance decomposition of error in ensembles of learning machines. We apply these methods to study and compare the bias-variance characteristics of single support vector machines (SVMs) and ensembles of SVMs based on resampling techniques, and their relationships with the cardinality of the training samples. In particular, we present an experimental bias-variance analysis of bagged and random aggregated ensembles of SVMs in order to verify their theoretical variance reduction properties. The experimental bias-variance analysis quantitatively characterizes the relationships between bagging and random aggregating, and explains the reasons why ensembles built on small subsamples of the data work with large databases. Our analysis also suggests new directions for research to improve on classical bagging.

Algorithms↗
PubMed2006

A novel incremental principal component analysis and its application for face recognition.

Principal component analysis (PCA) has been proven to be an efficient method in pattern recognition and image analysis. Recently, PCA has been extensively employed for face-recognition algorithms, such as eigenface and fisherface. The encouraging results have been reported and discussed in the literature. Many PCA-based face-recognition systems have also been developed in the last decade. However, existing PCA-based face-recognition systems are hard to scale up because of the computational cost and memory-requirement burden. To overcome this limitation, an incremental approach is usually adopted. Incremental PCA (IPCA) methods have been studied for many years in the machine-learning community. The major limitation of existing IPCA methods is that there is no guarantee on the approximation error. In view of this limitation, this paper proposes a new IPCA method based on the idea of a singular value decomposition (SVD) updating algorithm, namely an SVD updating-based IPCA (SVDU-IPCA) algorithm. In the proposed SVDU-IPCA algorithm, we have mathematically proved that the approximation error is bounded. A complexity analysis on the proposed method is also presented. Another characteristic of the proposed SVDU-IPCA algorithm is that it can be easily extended to a kernel version. The proposed method has been evaluated using available public databases, namely FERET, AR, and Yale B, and applied to existing face-recognition algorithms. Experimental results show that the difference of the average recognition accuracy between the proposed incremental method and the batch-mode method is less than 1%. This implies that the proposed SVDU-IPCA method gives a close approximation to the batch-mode PCA method.

Algorithms↗
PubMed2006

A vertical-energy-thresholding procedure for data reduction with multiple complex curves.

Due to the development of sensing and computer technology, measurements of many process variables are available in current manufacturing processes. It is very challenging, however, to process a large amount of information in a limited time in order to make decisions about the health of the processes and products. This paper develops a "preprocessing" procedure for multiple sets of complicated functional data in order to reduce the data size for supporting timely decision analyses. The data type studied has been used for fault detection, root-cause analysis, and quality improvement in such engineering applications as automobile and semiconductor manufacturing and nanomachining processes. The proposed vertical-energy-thresholding (VET) procedure balances the reconstruction error against data-reduction efficiency so that it is effective in capturing key patterns in the multiple data signals. The selected wavelet coefficients are treated as the "reduced-size" data in subsequent analyses for decision making. This enhances the ability of the existing statistical and machine-learning procedures to handle high-dimensional functional data. A few real-life examples demonstrate the effectiveness of our proposed procedure compared to several ad hoc techniques extended from single-curve-based data modeling and denoising procedures.

Algorithms↗
PubMedDate not supplied

An intelligent system approach to higher-dimensional classification of volume data.

In volume data visualization, the classification step is used to determine voxel visibility and is usually carried out through the interactive editing of a transfer function that defines a mapping between voxel value and color/opacity. This approach is limited by the difficulties in working effectively in the transfer function space beyond two dimensions. We present a new approach to the volume classification problem which couples machine learning and a painting metaphor to allow more sophisticated classification in an intuitive manner. The user works in the volume data space by directly painting on sample slices of the volume and the painted voxels are used in an iterative training process. The trained system can then classify the entire volume. Both classification and rendering can be hardware accelerated, providing immediate visual feedback as painting progresses. Such an intelligent system approach enables the user to perform classification in a much higher dimensional space without explicitly specifying the mapping for every dimension used. Furthermore, the trained system for one data set may be reused to classify other data sets with similar characteristics.

Algorithms↗
PubMedDate not supplied

Accurate visible speech synthesis based on concatenating variable length motion capture data.

We present a novel approach to synthesizing accurate visible speech based on searching and concatenating optimal variable-length units in a large corpus of motion capture data. Based on a set of visual prototypes selected on a source face and a corresponding set designated for a target face, we propose a machine learning technique to automatically map the facial motions observed on the source face to the target face. In order to model the long distance coarticulation effects in visible speech, a large-scale corpus that covers the most common syllables in English was collected, annotated and analyzed. For any input text, a search algorithm to locate the optimal sequences of concatenated units for synthesis is desrcribed. A new algorithm to adapt lip motions from a generic 3D face model to a specific 3D face model is also proposed. A complete, end-to-end visible speech animation system is implemented based on the approach. This system is currently used in more than 60 kindergarten through third grade classrooms to teach students to read using a lifelike conversational animated agent. To evaluate the quality of the visible speech produced by the animation system, both subjective evaluation and objective evaluation are conducted. The evaluation results show that the proposed approach is accurate and powerful for visible speech synthesis.

Algorithms↗
PubMedDate not supplied

Interactive exploration of data traffic with Hierarchical Network Maps.

Network communication has become indispensable in business, education, and government. With the pervasive role of the Internet as a means of sharing information across networks, its misuse for destructive purposes, such as spreading malicious code, compromising remote hosts, or damaging data through unauthorized access, has grown immensely in the recent years. The classical way of monitoring the operation of large network systems is by analyzing the system logs for detecting anomalies. In this work, we introduce Hierarchical Network Map, an interactive visualization technique for gaining a deeper insight into network flow behavior by means of user-driven visual exploration. Our approach is meant as an enhancement to conventional analysis methods based on statistics or machine learning. We use multidimensional modeling combined with position and display awareness to view source and target data of the hosts in a hierarchical fashion with the ability to interactively change the level of aggregation or apply filtering. The interdisciplinary approach integrating data warehouse technology, information visualization, and decision support, brings about the benefit of efficiently collecting the input data and aggregating over very large data sets, visualizing the results, and providing interactivity to facilitate analytical reasoning.

Algorithms↗