Identifying statistical dependence in genomic sequences via mutual information estimates

Questions of understanding and quantifying the representation and amount of information in organisms have become a central part of biological research, as they potentially hold the key to fundamental advances. In this paper, we demonstrate the use of information-theoretic tools for the task of identifying segments of biomolecules (DNA or RNA) that are statistically correlated. We develop a precise and reliable methodology, based on the notion of mutual information, for finding and extracting statistical as well as structural dependencies. A simple threshold function is defined, and its use in quantifying the level of significance of dependencies between biological segments is explored. These tools are used in two specific applications. First, for the identification of correlations between different parts of the maize zmSRp32 gene. There, we find significant dependencies between the 5' untranslated region in zmSRp32 and its alternatively spliced exons. This observation may indicate the presence of as-yet unknown alternative splicing mechanisms or structural scaffolds. Second, using data from the FBI's Combined DNA Index System (CODIS), we demonstrate that our approach is particularly well suited for the problem of discovering short tandem repeats, an application of importance in genetic profiling.Comment: Preliminary version. Final version in EURASIP Journal on Bioinformatics and Systems Biology. See http://www.hindawi.com/journals/bsb

An optimization method for dynamics of structures with repetitive component patterns

The occurrence of dynamic problems during the operation of machinery may have devastating effects on a product. Therefore, design optimization of these products becomes essential in order to meet safety criteria. In this research, a hybrid design optimization method is proposed where attention is focused on structures having repeating patterns in their geometries. In the proposed method, the analysis is decomposed but the optimization problem itself is treated as a whole. The model of an entire structure is obtained without modeling all the repetitive components using the merits of the Component Mode Synthesis method. Backpropagation Neural Networks are used for surrogate modeling. The optimization is performed using two techniques: Genetic Algorithms (GAs) and Sequential Quadratic Programming (SQP). GAs are utilized to increase the chance of finding the location of the global optimum and since this optimum may not be exact, SQP is employed afterwards to improve the solution. A theoretical test problem is used to demonstrate the method

Generation of folk song melodies using Bayes transforms

The paper introduces the `Bayes transform', a mathematical procedure for putting data into a hierarchical representation. Applicable to any type of data, the procedure yields interesting results when applied to sequences. In this case, the representation obtained implicitly models the repetition hierarchy of the source. There are then natural applications to music. Derivation of Bayes transforms can be the means of determining the repetition hierarchy of note sequences (melodies) in an empirical and domain-general way. The paper investigates application of this approach to Folk Song, examining the results that can be obtained by treating such transforms as generative models

Query-based Deep Improvisation

In this paper we explore techniques for generating new music using a Variational Autoencoder (VAE) neural network that was trained on a corpus of specific style. Instead of randomly sampling the latent states of the network to produce free improvisation, we generate new music by querying the network with musical input in a style different from the training corpus. This allows us to produce new musical output with longer-term structure that blends aspects of the query to the style of the network. In order to control the level of this blending we add a noisy channel between the VAE encoder and decoder using bit-allocation algorithm from communication rate-distortion theory. Our experiments provide new insight into relations between the representational and structural information of latent states and the query signal, suggesting their possible use for composition purposes