Bioinformatics approaches applied to the discovery of antifungal peptides

Antifungal peptides (AFPs) comprise a group of substances with a broad spectrum of activities and complex action mechanisms. They develop in nature via an evolutionary process resulting from the interactions between hosts and pathogens. The AFP database is experimentally verified and curated from research articles, patents, and public databases. In this review, we compile information about the primary databases and bioinformatics tools that have been used in the discovery of AFPs during the last 15 years. We focus on the classification and prediction of AFPs using different physicochemical properties, such as polarity, hydrophobicity, hydrophilicity, mass, acidic, basic, and isoelectric indices, and other structural properties. Another method for discovering AFPs is the implementation of a peptidomic approach and bioinformatics filtering, which gave rise to a new family of peptides that exhibit a broad spectrum of antimicrobial activity against Candida albicans with low hemolytic effects. The application of machine intelligence in the sphere of biological sciences has led to the development of automated tools. The progress made in this area has also paved the way for producing new drugs more quickly and effectively. However, we also identified that further advancements are still needed to complete the AFP libraries

Optimized parameter search for large datasets of the regularization parameter and feature selection for ridge regression

In this paper we propose mathematical optimizations to select the optimal regularization parameter for ridge regression using cross-validation. The resulting algorithm is suited for large datasets and the computational cost does not depend on the size of the training set. We extend this algorithm to forward or backward feature selection in which the optimal regularization parameter is selected for each possible feature set. These feature selection algorithms yield solutions with a sparse weight matrix using a quadratic cost on the norm of the weights. A naive approach to optimizing the ridge regression parameter has a computational complexity of the order with the number of applied regularization parameters, the number of folds in the validation set, the number of input features and the number of data samples in the training set. Our implementation has a computational complexity of the order . This computational cost is smaller than that of regression without regularization for large datasets and is independent of the number of applied regularization parameters and the size of the training set. Combined with a feature selection algorithm the algorithm is of complexity and for forward and backward feature selection respectively, with the number of selected features and the number of removed features. This is an order faster than and for the naive implementation, with for large datasets. To show the performance and reduction in computational cost, we apply this technique to train recurrent neural networks using the reservoir computing approach, windowed ridge regression, least-squares support vector machines (LS-SVMs) in primal space using the fixed-size LS-SVM approximation and extreme learning machines

Time Series Adaptive Online Prediction Method Combined with Modified LS-SVR and AGO

Fault or health condition prediction of the complex systems has attracted more attention in recent years. The complex systems often show complex dynamic behavior and uncertainty, which makes it difficult to establish a precise physical model. Therefore, the time series of complex system is used to implement prediction in practice. Aiming at time series online prediction, we propose a new method to improve the prediction accuracy in this paper, which is based on the grey system theory and incremental learning algorithm. In this method, the accumulated generating operation (AGO) with the raw time series is taken to improve the data quality and regularity firstly; then the prediction is conducted by a modified LS-SVR model, which simplifies the calculation process with incremental learning; finally, the inverse accumulated generating operation (IAGO) is performed to get the prediction results. The results of the prediction experiments indicate preliminarily that the proposed scheme is an effective prediction approach for its good prediction precision and less computing time. The method will be useful in actual application

Theory and Algorithms for Hypothesis Transfer Learning

The design and analysis of machine learning algorithms typically considers the problem of learning on a single task, and the nature of learning in such scenario is well explored. On the other hand, very often tasks faced by machine learning systems arrive sequentially, and therefore it is reasonable to ask whether a better approach can be taken than retraining such systems from scratch given newly available data. Indeed, by drawing analogy from human learning, a novel skill could be acquired more easily whenever the learner shares a relevant past experience. In response to this observation, the machine learning community has drawn its attention towards a form of learning known as transfer learning - learning a novel task by leveraging upon auxiliary information extracted from previous tasks. Tangible progress has been made in both theory and practice of transfer learning; however, many questions are still to be addressed. In this thesis we will focus on an efficient type of transfer learning, known as the Hypothesis Transfer Learning (HTL), where auxiliary information is retained in a form of previously induced hypotheses. This is in contrast to the large body of work where one transfers from the data associated with previously encountered tasks. In particular, we theoretically investigate conditions when HTL guarantees improved generalization on a novel task subject to the relevant auxiliary (source) hypotheses. We investigate HTL theoretically by considering three scenarios: HTL through regularized least squares with biased regularization, through convex empirical risk minimization, and through stochastic optimization, which also touches the theory of non-convex transfer learning problems. In addition, we demonstrate the benefits of HTL empirically, by proposing two algorithms tailored for real-life situations with application to visual learning problems - learning a new class in a multi-class classification setting by transferring from known classes, and an efficient greedy HTL algorithm for learning with large number of source hypotheses. From theoretical point of view this thesis consistently identifies the key quantitative characteristics of relatedness between novel and previous tasks, and explicitates them in generalization bounds. These findings corroborate many previous works in the transfer learning literature and provide a theoretical basis for design and analysis of new HTL algorithms

Efficient tuning in supervised machine learning

The tuning of learning algorithm parameters has become more and more important during the last years. With the fast growth of computational power and available memory databases have grown dramatically. This is very challenging for the tuning of parameters arising in machine learning, since the training can become very time-consuming for large datasets. For this reason efficient tuning methods are required, which are able to improve the predictions of the learning algorithms. In this thesis we incorporate model-assisted optimization techniques, for performing efficient optimization on noisy datasets with very limited budgets. Under this umbrella we also combine learning algorithms with methods for feature construction and selection. We propose to integrate a variety of elements into the learning process. E.g., can tuning be helpful in learning tasks like time series regression using state-of-the-art machine learning algorithms? Are statistical methods capable to reduce noise e ffects? Can surrogate models like Kriging learn a reasonable mapping of the parameter landscape to the quality measures, or are they deteriorated by disturbing factors? Summarizing all these parts, we analyze if superior learning algorithms can be created, with a special focus on efficient runtimes. Besides the advantages of systematic tuning approaches, we also highlight possible obstacles and issues of tuning. Di fferent tuning methods are compared and the impact of their features are exposed. It is a goal of this work to give users insights into applying state-of-the-art learning algorithms profitably in practiceBundesministerium f ür Bildung und Forschung (Germany), Cologne University of Applied Sciences (Germany), Kind-Steinm uller-Stiftung (Gummersbach, Germany)Algorithms and the Foundations of Software technolog