On the Complex Network Structure of Musical Pieces: Analysis of Some Use Cases from Different Music Genres

This paper focuses on the modeling of musical melodies as networks. Notes of a melody can be treated as nodes of a network. Connections are created whenever notes are played in sequence. We analyze some main tracks coming from different music genres, with melodies played using different musical instruments. We find out that the considered networks are, in general, scale free networks and exhibit the small world property. We measure the main metrics and assess whether these networks can be considered as formed by sub-communities. Outcomes confirm that peculiar features of the tracks can be extracted from this analysis methodology. This approach can have an impact in several multimedia applications such as music didactics, multimedia entertainment, and digital music generation.Comment: accepted to Multimedia Tools and Applications, Springe

AlignNemo: A Local Network Alignment Method to Integrate Homology and Topology

Local network alignment is an important component of the analysis of protein-protein interaction networks that may lead to the identification of evolutionary related complexes. We present AlignNemo, a new algorithm that, given the networks of two organisms, uncovers subnetworks of proteins that relate in biological function and topology of interactions. The discovered conserved subnetworks have a general topology and need not to correspond to specific interaction patterns, so that they more closely fit the models of functional complexes proposed in the literature. The algorithm is able to handle sparse interaction data with an expansion process that at each step explores the local topology of the networks beyond the proteins directly interacting with the current solution. To assess the performance of AlignNemo, we ran a series of benchmarks using statistical measures as well as biological knowledge. Based on reference datasets of protein complexes, AlignNemo shows better performance than other methods in terms of both precision and recall. We show our solutions to be biologically sound using the concept of semantic similarity applied to Gene Ontology vocabularies. The binaries of AlignNemo and supplementary details about the algorithms and the experiments are available at: sourceforge.net/p/alignnemo

A Novel Framework for the Comparative Analysis of Biological Networks

Genome sequencing projects provide nearly complete lists of the individual components present in an organism, but reveal little about how they work together. Follow-up initiatives have deciphered thousands of dynamic and context-dependent interrelationships between gene products that need to be analyzed with novel bioinformatics approaches able to capture their complex emerging properties. Here, we present a novel framework for the alignment and comparative analysis of biological networks of arbitrary topology. Our strategy includes the prediction of likely conserved interactions, based on evolutionary distances, to counter the high number of missing interactions in the current interactome networks, and a fast assessment of the statistical significance of individual alignment solutions, which vastly increases its performance with respect to existing tools. Finally, we illustrate the biological significance of the results through the identification of novel complex components and potential cases of cross-talk between pathways and alternative signaling routes

Integrative Network Biology: Graph Prototyping for Co-Expression Cancer Networks

Network-based analysis has been proven useful in biologically-oriented areas, e.g., to explore the dynamics and complexity of biological networks. Investigating a set of networks allows deriving general knowledge about the underlying topological and functional properties. The integrative analysis of networks typically combines networks from different studies that investigate the same or similar research questions. In order to perform an integrative analysis it is often necessary to compare the properties of matching edges across the data set. This identification of common edges is often burdensome and computational intensive. Here, we present an approach that is different from inferring a new network based on common features. Instead, we select one network as a graph prototype, which then represents a set of comparable network objects, as it has the least average distance to all other networks in the same set. We demonstrate the usefulness of the graph prototyping approach on a set of prostate cancer networks and a set of corresponding benign networks. We further show that the distances within the cancer group and the benign group are statistically different depending on the utilized distance measure

Segmentation of Biological Volume Datasets Using a Level-Set Framework

This paper presents a framework for extracting surface models from a broad variety of volume datasets. These datasets are produced from standard 3D imaging devices, and are all noisy samplings of complex biological structures with boundaries that have low and often varying contrasts. The level set segmentation method, which is well documented in the literature, creates a new volume from the input data by solving an initial-value partial differential equation (PDE) with user-defined feature-extracting terms. However, level set deformations alone are not sufficient, they must be combined with powerful initialization techniques in order to produce successful segmentations. Our level set segmentation approach consists of defining a set of suitable pre-processing techniques for initialization and selecting/tuning different feature-extracting terms in the level set algorithm. This collection of techniques forms a toolkit that can be applied, under the guidance of a user, to segment a variety of volumetric data.