Search results for: Maxence Queyrel

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: deep learning, disease prediction, end-to-end machine learning, metagenomics, multiple instance learning, precision medicine

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Authors: Sylvain Caillol, Maxence Fache, Bernard Boutevin

Abstract:

Recent years have witnessed an increasing demand on renewable resource-derived polymers owing to increasing environmental concern and restricted availability of petrochemical resources. Thus, a great deal of attention was paid to renewable resources-derived polymers and to thermosetting materials especially, since they are crosslinked polymers and thus cannot be recycled. Also, most of thermosetting materials contain aromatic monomers, able to confer high mechanical and thermal properties to the network. Therefore, the access to biobased, non-harmful, and available aromatic monomers is one of the main challenges of the years to come. Starting from phenols available in large volumes from renewable resources, our team designed platforms of chemicals usable for the synthesis of various polymers. One of these phenols, vanillin, which is readily available from lignin, was more specifically studied. Various aromatic building blocks bearing polymerizable functions were synthesized: epoxy, amine, acid, carbonate, alcohol etc. These vanillin-based monomers can potentially lead to numerous polymers. The example of epoxy thermosets was taken, as there is also the problematic of bisphenol A substitution for these polymers. Materials were prepared from the biobased epoxy monomers obtained from vanillin. Their thermo-mechanical properties were investigated and the effect of the monomer structure was discussed. The properties of the materials prepared were found to be comparable to the current industrial reference, indicating a potential replacement of petrosourced, bisphenol A-based epoxy thermosets by biosourced, vanillin-based ones. The tunability of the final properties was achieved through the choice of monomer and through a well-controlled oligomerization reaction of these monomers. This follows the same strategy than the one currently used in industry, which supports the potential of these vanillin-derived epoxy thermosets as substitutes of their petro-based counterparts.

Keywords: lignin, vanillin, epoxy, amine, carbonate

Procedia PDF Downloads 198