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Authors: Maxence Queyrel, Edi Prifti, Alexandre Templier, Jean-Daniel Zucker

Abstract:

Analysis of the human microbiome using metagenomic sequencing data has demonstrated high ability in discriminating various human diseases. Raw metagenomic sequencing data require multiple complex and computationally heavy bioinformatics steps prior to data analysis. Such data contain millions of short sequences read from the fragmented DNA sequences and stored as fastq files. Conventional processing pipelines consist in multiple steps including quality control, filtering, alignment of sequences against genomic catalogs (genes, species, taxonomic levels, functional pathways, etc.). These pipelines are complex to use, time consuming and rely on a large number of parameters that often provide variability and impact the estimation of the microbiome elements. Training Deep Neural Networks directly from raw sequencing data is a promising approach to bypass some of the challenges associated with mainstream bioinformatics pipelines. Most of these methods use the concept of word and sentence embeddings that create a meaningful and numerical representation of DNA sequences, while extracting features and reducing the dimensionality of the data. In this paper we present an end-to-end approach that classifies patients into disease groups directly from raw metagenomic reads: metagenome2vec. This approach is composed of four steps (i) generating a vocabulary of k-mers and learning their numerical embeddings; (ii) learning DNA sequence (read) embeddings; (iii) identifying the genome from which the sequence is most likely to come and (iv) training a multiple instance learning classifier which predicts the phenotype based on the vector representation of the raw data. An attention mechanism is applied in the network so that the model can be interpreted, assigning a weight to the influence of the prediction for each genome. Using two public real-life data-sets as well a simulated one, we demonstrated that this original approach reaches high performance, comparable with the state-of-the-art methods applied directly on processed data though mainstream bioinformatics workflows. These results are encouraging for this proof of concept work. We believe that with further dedication, the DNN models have the potential to surpass mainstream bioinformatics workflows in disease classification tasks.

Keywords: Metagenomics, phenotype prediction, deep learning, embeddings, multiple instance learning.

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Authors: Justyna Humięcka-Jakubowska

Abstract:

Background in music analysis: Traditionally, when we think about a composer’s sketches, the chances are that we are thinking in terms of the working out of detail, rather than the evolution of an overall concept. Since music is a “time art,” it follows that questions of a form cannot be entirely detached from considerations of time. One could say that composers tend to regard time either as a place gradually and partially intuitively filled, or they can look for a specific strategy to occupy it. It seems that the one thing that sheds light on Stockhausen’s compositional thinking is his frequent use of “form schemas,” that is often a single-page representation of the entire structure of a piece. Background in music technology: Sonic Visualiser is a program used to study a musical recording. It is an open source application for viewing, analyzing, and annotating music audio files. It contains a number of visualisation tools, which are designed with useful default parameters for musical analysis. Additionally, the Vamp plugin format of SV supports to provide analysis such as for example structural segmentation. Aims: The aim of paper is to show how SV may be used to obtain a better understanding of the specific musical work, and how the compositional strategy does impact on musical structures and musical surfaces. It is known that “traditional” music analytic methods don’t allow indicating interrelationships between musical surface (which is perceived) and underlying musical/acoustical structure. Main Contribution: Stockhausen had dealt with the most diverse musical problems by the most varied methods. A characteristic which he had never ceased to be placed at the center of his thought and works, it was the quest for a new balance founded upon an acute connection between speculation and intuition. In the case with Mikrophonie I (1964) for tam-tam and 6 players Stockhausen makes a distinction between the “connection scheme,” which indicates the ground rules underlying all versions, and the form scheme, which is associated with a particular version. The preface to the published score includes both the connection scheme, and a single instance of a “form scheme,” which is what one can hear on the CD recording. In the current study, the insight into the compositional strategy chosen by Stockhausen was been compared with auditory image, that is, with the perceived musical surface. Stockhausen’s musical work is analyzed both in terms of melodic/voice and timbre evolution. Implications: The current study shows how musical structures have determined of musical surface. The general assumption is this, that while listening to music we can extract basic kinds of musical information from musical surfaces. It is shown that interactive strategies of musical structure analysis can offer a very fruitful way of looking directly into certain structural features of music.

Keywords: Automated analysis, composer's strategy, Mikrophonie I, musical surface, Stockhausen.

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