The Infona portal uses cookies, i.e. strings of text saved by a browser on the user's device. The portal can access those files and use them to remember the user's data, such as their chosen settings (screen view, interface language, etc.), or their login data. By using the Infona portal the user accepts automatic saving and using this information for portal operation purposes. More information on the subject can be found in the Privacy Policy and Terms of Service. By closing this window the user confirms that they have read the information on cookie usage, and they accept the privacy policy and the way cookies are used by the portal. You can change the cookie settings in your browser.
This paper proposes a novel multi-objective optimisatìon approach to solving both the problem of finding good structural and parametric choices in an ANN and the problem of training a classifier with a heavily skewed data set. The state-of-the-art CMA-PAES-HAGA multi-objective evolutionary algorithm [41] is used to simultaneously optimise the structure, weights, and biases of a population of ANNs...
Shotgun sequencing has facilitated the analysis of complex microbial communities. Recently we have shown how local binary patterns (LBP) from image processing can be used to analyse the sequenced samples. LBP codes represent the data in a sparse high dimensional space. To improve the performance of our pipeline, marginalised stacked autoencoders are used here to learn frequent LBP codes and map the...
The requirements for treatments vary for different diseases. These have to be considered in order to plan ahead the expenditures for the health care system. In this sense, disease surveillance has a significant impact on resource planning. To this end, we study the problem of predicting the number of incidences for a given disease based on the internet search and access log statistics. A number of...
Proteins of importance to human biology can populate significantly different three-dimensional (3d) structures at equilibrium. By doing so, a protein is able to interface with different molecules in the cell and so modulate its function. A structure-by-structure characterization of a protein's transition between two structures is central to elucidate the role of structural dynamics in regulating molecular...
This paper proposes a data-driven longitudinal model that brings together factor graphs and learning methods to demonstrate a significant improvement in predictability in clinical outcomes of patients with major depressive disorder treated with antidepressants. Using data from the Mayo Clinic PGRN-AMPS trial and the STAR∗D trial for validation, this work makes two significant contributions in the...
This paper concerns the diagnosis of schizophrenia using encephalographic signals and introduces a new framework based on image processing technique. Time-frequency approach or spectrogram image processing technique was used to analyze EEG signals. The spectrogram images were formed from EEG signals, then the Gray Level Co-occurrence Matrix (GLCM) texture feature was extracted from the images. This...
The advances in complex statistics and machine learning methods lead to the development of powerful classifiers that can be used to recognize cellular states (such as gene expression profiles) that are associated to a number of gene-scale expressed diseases, for instance, cancer. However, the data-driven models built by means of learning from datasets in a number of cases represent “black boxes” that...
Pulmonary nodules detection play a significant role in the early detection and treatment of lung cancer. False positive reduction is the one of the major parts of pulmonary nodules detection systems. In this study a novel method aimed at recognizing real pulmonary nodule among a large group of candidates was proposed. The method consists of three steps: appropriate receptive field selection, feature...
Bone suppression in lung radiographs is an important task, as it improves the results on other related tasks, such as nodule detection or pathologies classification. In this paper, we propose two architectures that suppress bones in radiographs by treating them as noise. In the proposed methods, we create end-to-end learning frameworks that minimize noise in the images while maintaining sharpness...
Methanogenic archaea probably played a major role in the evolution of earth's atmosphere. Here we report the results of a comparative analysis of metabolic networks of mesophilic archaeon Methanosarcina acetivorans (M. acetivorans) and the thermophilic archaeon Methanopyrus kandleri (M. kandleri). In this study, we used simulated annealing (SA) to obtain different modules of their metabolic networks...
Despite significant effort, there is currently no formal or de facto standard framework or format for constructing, representing, or manipulating general neural networks. In computational neuroscience, there have been some attempts to formalize connectionist notations and generative operations for neural networks, including Connection Set Algebra, but none are truly formal or general. In computational...
The optimisation of classifier performance in pattern recognition and medical prognosis tasks is a complex and poorly miderstood problem. Classifier performance is greatly affected by the choice of artificial neural network architecture and starting weights and biases — yet there exists very little guidance in the literature as to how to choose these parameters. Recently evolutionary artificial neural...
Ensemble methods for clustering take a collection of input partitions, produced for the same data set, and generate an ensemble partition that tries to preserve the information carried in this collective. Acceptance of the resulting partition(s) by decision makers can be a problem, due to the inherent complexity of ensemble techniques, and the associated lack of intuition on how a consensus has been...
Computational methods adopted in the field of Systems Biology require the complete knowledge of reaction kinetic constants to perform simulations of the dynamics and understand the emergent behavior of biochemical systems. However, kinetic parameters of biochemical reactions are often difficult or impossible to measure, thus they are generally inferred from experimental data, in a process known as...
The study of biological systems is growing rapidly, and can be considered as an intrinsic task in biological research, and a prerequisite for diagnosing diseases and drug development. The integration of biological studies with computer technologies led to noticeable developments in biology with the appearance of many powerful modeling and simulation techniques and tools. The help of computers in biology...
In this paper, we present a toolbox for a specific optimization problem that frequently arises in bioinformatics or genomics. In this specific optimisation problem, the state space is a set of words of specified length over a finite alphabet. To each word is associated a score. The overall objective is to find the words which have the lowest possible score. This type of general optimization problem...
Protein structure comparison is one of the most challenging problem in bioinformatics. This problem is modeled as a contact map overlap problem in which the similarity of the two proteins being compared is measured by the amount of overlap between their corresponding protein contact maps. To find a maximum overlap is proved to be an NP-hard problem in this area. Protein contact map is a two dimensional...
Embeddable biomarkers are short strands of DNA that can be incorporated into genetic constructs to enable later identification. They are drawn from error correcting codes on the DNA alphabet relative to the Levenshtein metric. This study uses three types of evolutionary algorithms to improve the best known size of DNA error correcting codes, improving the bound for nine different code parameters....
In many real-world problems, as the protein structure prediction (PSP), a number of conflicting objectives have to be simultaneously optimized. In this paper, the Aggregation Tree (AT) method is applied to arrange the energy function terms used by a protein three-dimensional structure prediction program (called GAPF) that is based on a multiobjective genetic algorithm. The results achieved using the...
Set the date range to filter the displayed results. You can set a starting date, ending date or both. You can enter the dates manually or choose them from the calendar.