EnDNA-Prot:identification of DNA-binding proteins by applying ensemble learning

DNA-binding proteins are crucial for various cellular processes, such as recognition of specific nucleotide, regulation of transcription, and regulation of gene expression. Developing an effective model for identifying DNA-binding proteins is an urgent research problem. Up to now, many methods have been proposed, but most of them focus on only one classifier and cannot make full use of the large number of negative samples to improve predicting performance. This study proposed a predictor called enDNA-Prot for DNA-binding protein identification by employing the ensemble learning technique. Experiential results showed that enDNA-Prot was comparable with DNA-Prot and outperformed DNAbinder and iDNA-Prot with performance improvement in the range of 3.97-9.52% in ACC and 0.08-0.19 in MCC. Furthermore, when the benchmark dataset was expanded with negative samples, the performance of enDNA-Prot outperformed the three existing methods by 2.83-16.63% in terms of ACC and 0.02-0.16 in terms of MCC. It indicated that enDNA-Prot is an effective method for DNA-binding protein identification and expanding training dataset with negative samples can improve its performance. For the convenience of the vast majority of experimental scientists, we developed a user-friendly web-server for enDNA-Prot which is freely accessible to the public. © 2014 Ruifeng Xu et al.

Induction by a Hilbert hypercube representation

This thesis describes a novel connectionist machine utilizing induction by a Hilbert hypercube representation. This representation offers a number of distinct advantages which are described. We construct a theoretical and practical learning machine which lies in an area of overlap between three disciplines - neural nets, machine learning and knowledge acquisition - hence it is refered to as a "coalesced" machine. To this unifying aspect is added the various advantages of its orthogonal lattice structure as against less structured nets. We discuss the case for such a fundamental and low level empirical learning tool and the assumptions behind the machine are clearly outlined. Our theory of an orthogonal lattice structure the Hilbert hypercube of an n-dimensional space using a complemented distributed lattice as a basis for supervised learning is derived from first principles on clearly laid out scientific principles. The resulting "subhypercube theory" was implemented in a development machine which was then used to test the theoretical predictions again under strict scientific guidelines. The scope, advantages and limitations of this machine were tested in a series of experiments. Novel and seminal properties of the machine include: the "metrical", deterministic and global nature of its search; complete convergence invariably producing minimum polynomial solutions for both disjuncts and conjuncts even with moderate levels of noise present; a learning engine which is mathematically analysable in depth based upon the "complexity range" of the function concerned; a strong bias towards the simplest possible globally (rather than locally) derived "balanced" explanation of the data; the ability to cope with variables in the network; and new ways of reducing the exponential explosion. Performance issues were addressed and comparative studies with other learning machines indicates that our novel approach has definite value and should be further researched.

PDNAsite:identification of DNA-binding site from protein sequence by incorporating spatial and sequence context

Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. In the present study, for each target residue, we applied both the spatial context and the sequence context to construct the feature space. Subsequently, Latent Semantic Analysis (LSA) was applied to remove the redundancies in the feature space. Finally, a predictor (PDNAsite) was developed through the integration of the support vector machines (SVM) classifier and ensemble learning. Results on the PDNA-62 and the PDNA-224 datasets demonstrate that features extracted from spatial context provide more information than those from sequence context and the combination of them gives more performance gain. An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. The comparison between our proposed PDNAsite method and the existing methods indicate that PDNAsite outperforms most of the existing methods and is a useful tool for DNA-binding site identification. A web-server of our predictor (http://hlt.hitsz.edu.cn:8080/PDNAsite/) is made available for free public accessible to the biological research community.

Visual data mining: integrating machine learning with information visualization

Today, the data available to tackle many scientific challenges is vast in quantity and diverse in nature. The exploration of heterogeneous information spaces requires suitable mining algorithms as well as effective visual interfaces. Most existing systems concentrate either on mining algorithms or on visualization techniques. Though visual methods developed in information visualization have been helpful, for improved understanding of a complex large high-dimensional dataset, there is a need for an effective projection of such a dataset onto a lower-dimension (2D or 3D) manifold. This paper introduces a flexible visual data mining framework which combines advanced projection algorithms developed in the machine learning domain and visual techniques developed in the information visualization domain. The framework follows Shneiderman’s mantra to provide an effective user interface. The advantage of such an interface is that the user is directly involved in the data mining process. We integrate principled projection methods, such as Generative Topographic Mapping (GTM) and Hierarchical GTM (HGTM), with powerful visual techniques, such as magnification factors, directional curvatures, parallel coordinates, billboarding, and user interaction facilities, to provide an integrated visual data mining framework. Results on a real life high-dimensional dataset from the chemoinformatics domain are also reported and discussed. Projection results of GTM are analytically compared with the projection results from other traditional projection methods, and it is also shown that the HGTM algorithm provides additional value for large datasets. The computational complexity of these algorithms is discussed to demonstrate their suitability for the visual data mining framework.

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Machine learning for large-scale wearable sensor data in Parkinson disease:concepts, promises, pitfalls, and futures

For the treatment and monitoring of Parkinson's disease (PD) to be scientific, a key requirement is that measurement of disease stages and severity is quantitative, reliable, and repeatable. The last 50 years in PD research have been dominated by qualitative, subjective ratings obtained by human interpretation of the presentation of disease signs and symptoms at clinical visits. More recently, “wearable,” sensor-based, quantitative, objective, and easy-to-use systems for quantifying PD signs for large numbers of participants over extended durations have been developed. This technology has the potential to significantly improve both clinical diagnosis and management in PD and the conduct of clinical studies. However, the large-scale, high-dimensional character of the data captured by these wearable sensors requires sophisticated signal processing and machine-learning algorithms to transform it into scientifically and clinically meaningful information. Such algorithms that “learn” from data have shown remarkable success in making accurate predictions for complex problems in which human skill has been required to date, but they are challenging to evaluate and apply without a basic understanding of the underlying logic on which they are based. This article contains a nontechnical tutorial review of relevant machine-learning algorithms, also describing their limitations and how these can be overcome. It discusses implications of this technology and a practical road map for realizing the full potential of this technology in PD research and practice. © 2016 International Parkinson and Movement Disorder Society.

User-centred ontology learning for knowledge management

Automatic ontology building is a vital issue in many fields where they are currently built manually. This paper presents a user-centred methodology for ontology construction based on the use of Machine Learning and Natural Language Processing. In our approach, the user selects a corpus of texts and sketches a preliminary ontology (or selects an existing one) for a domain with a preliminary vocabulary associated to the elements in the ontology (lexicalisations). Examples of sentences involving such lexicalisation (e.g. ISA relation) in the corpus are automatically retrieved by the system. Retrieved examples are validated by the user and used by an adaptive Information Extraction system to generate patterns that discover other lexicalisations of the same objects in the ontology, possibly identifying new concepts or relations. New instances are added to the existing ontology or used to tune it. This process is repeated until a satisfactory ontology is obtained. The methodology largely automates the ontology construction process and the output is an ontology with an associated trained leaner to be used for further ontology modifications.

The learning dynamics of a universal approximator

The learning properties of a universal approximator, a normalized committee machine with adjustable biases, are studied for on-line back-propagation learning. Within a statistical mechanics framework, numerical studies show that this model has features which do not exist in previously studied two-layer network models without adjustable biases, e.g., attractive suboptimal symmetric phases even for realizable cases and noiseless data.

The exact sample complexity of PAC-learning problems with unit VC dimension

The Vapnik-Chervonenkis (VC) dimension is a combinatorial measure of a certain class of machine learning problems, which may be used to obtain upper and lower bounds on the number of training examples needed to learn to prescribed levels of accuracy. Most of the known bounds apply to the Probably Approximately Correct (PAC) framework, which is the framework within which we work in this paper. For a learning problem with some known VC dimension, much is known about the order of growth of the sample-size requirement of the problem, as a function of the PAC parameters. The exact value of sample-size requirement is however less well-known, and depends heavily on the particular learning algorithm being used. This is a major obstacle to the practical application of the VC dimension. Hence it is important to know exactly how the sample-size requirement depends on VC dimension, and with that in mind, we describe a general algorithm for learning problems having VC dimension 1. Its sample-size requirement is minimal (as a function of the PAC parameters), and turns out to be the same for all non-trivial learning problems having VC dimension 1. While the method used cannot be naively generalised to higher VC dimension, it suggests that optimal algorithm-dependent bounds may improve substantially on current upper bounds.

Globally optimal on-line learning rules for multi-layer neural networks

We present a method for determining the globally optimal on-line learning rule for a soft committee machine under a statistical mechanics framework. This rule maximizes the total reduction in generalization error over the whole learning process. A simple example demonstrates that the locally optimal rule, which maximizes the rate of decrease in generalization error, may perform poorly in comparison.

Noisy fitness evaluation in genetic algorithms and the dynamics of learning

A theoretical model is presented which describes selection in a genetic algorithm (GA) under a stochastic fitness measure and correctly accounts for finite population effects. Although this model describes a number of selection schemes, we only consider Boltzmann selection in detail here as results for this form of selection are particularly transparent when fitness is corrupted by additive Gaussian noise. Finite population effects are shown to be of fundamental importance in this case, as the noise has no effect in the infinite population limit. In the limit of weak selection we show how the effects of any Gaussian noise can be removed by increasing the population size appropriately. The theory is tested on two closely related problems: the one-max problem corrupted by Gaussian noise and generalization in a perceptron with binary weights. The averaged dynamics can be accurately modelled for both problems using a formalism which describes the dynamics of the GA using methods from statistical mechanics. The second problem is a simple example of a learning problem and by considering this problem we show how the accurate characterization of noise in the fitness evaluation may be relevant in machine learning. The training error (negative fitness) is the number of misclassified training examples in a batch and can be considered as a noisy version of the generalization error if an independent batch is used for each evaluation. The noise is due to the finite batch size and in the limit of large problem size and weak selection we show how the effect of this noise can be removed by increasing the population size. This allows the optimal batch size to be determined, which minimizes computation time as well as the total number of training examples required.

The role of biases in on-line learning of two-layer networks

The influence of biases on the learning dynamics of a two-layer neural network, a normalized soft-committee machine, is studied for on-line gradient descent learning. Within a statistical mechanics framework, numerical studies show that the inclusion of adjustable biases dramatically alters the learning dynamics found previously. The symmetric phase which has often been predominant in the original model all but disappears for a non-degenerate bias task. The extended model furthermore exhibits a much richer dynamical behavior, e.g. attractive suboptimal symmetric phases even for realizable cases and noiseless data.

Incorporating curvature information into on-line learning

We analyse the dynamics of a number of second order on-line learning algorithms training multi-layer neural networks, using the methods of statistical mechanics. We first consider on-line Newton's method, which is known to provide optimal asymptotic performance. We determine the asymptotic generalization error decay for a soft committee machine, which is shown to compare favourably with the result for standard gradient descent. Matrix momentum provides a practical approximation to this method by allowing an efficient inversion of the Hessian. We consider an idealized matrix momentum algorithm which requires access to the Hessian and find close correspondence with the dynamics of on-line Newton's method. In practice, the Hessian will not be known on-line and we therefore consider matrix momentum using a single example approximation to the Hessian. In this case good asymptotic performance may still be achieved, but the algorithm is now sensitive to parameter choice because of noise in the Hessian estimate. On-line Newton's method is not appropriate during the transient learning phase, since a suboptimal unstable fixed point of the gradient descent dynamics becomes stable for this algorithm. A principled alternative is to use Amari's natural gradient learning algorithm and we show how this method provides a significant reduction in learning time when compared to gradient descent, while retaining the asymptotic performance of on-line Newton's method.

Globally optimal on-line learning rules

We present a method for determining the globally optimal on-line learning rule for a soft committee machine under a statistical mechanics framework. This work complements previous results on locally optimal rules, where only the rate of change in generalization error was considered. We maximize the total reduction in generalization error over the whole learning process and show how the resulting rule can significantly outperform the locally optimal rule.

Upper and lower bounds on the learning curve for Gaussian processes

In this paper we introduce and illustrate non-trivial upper and lower bounds on the learning curves for one-dimensional Gaussian Processes. The analysis is carried out emphasising the effects induced on the bounds by the smoothness of the random process described by the Modified Bessel and the Squared Exponential covariance functions. We present an explanation of the early, linearly-decreasing behavior of the learning curves and the bounds as well as a study of the asymptotic behavior of the curves. The effects of the noise level and the lengthscale on the tightness of the bounds are also discussed.