@article{(Open Science Index):https://publications.waset.org/pdf/10012114,
	  title     = {Towards End-To-End Disease Prediction from Raw Metagenomic Data},
	  author    = {Maxence Queyrel and  Edi Prifti and  Alexandre Templier and  Jean-Daniel Zucker},
	  country	= {},
	  institution	= {},
	  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.},
	    journal   = {International Journal of Biomedical and Biological Engineering},
	  volume    = {15},
	  number    = {6},
	  year      = {2021},
	  pages     = {234 - 246},
	  ee        = {https://publications.waset.org/pdf/10012114},
	  url   	= {https://publications.waset.org/vol/174},
	  bibsource = {https://publications.waset.org/},
	  issn  	= {eISSN: 1307-6892},
	  publisher = {World Academy of Science, Engineering and Technology},
	  index 	= {Open Science Index 174, 2021},
	}