Institut de Mathématiques de Marseille, UMR 7373




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13 mai 2019: 3 événements

Séminaire

  • Séminaire Mathématiques et Algorithmique pour la Biologie des Systèmes (MABioS)

    Lundi 13 mai 11:00-12:00 - Quentin FERRÉ - TAGC & LIS, Aix-Marseille Université

    Correlating TRBS ChIP-seq peaks from multiple datasets in ReMap using deep convolutional autoencoders

    Résumé : Cis-regulatory elements (CREs) are genomic regions regulating gene expression by binding proteins called Transcriptional Regulators (TRs). TR binding is mostly studied experimentally, via ChIP-Seq, but these experiments have false positives, and there is no method to discern them. However, TRs are known to be co-occurent, and many replica datasets exist. As such, we use common TR and/or datasets combinations to identify “atypical” peaks. We use the ReMap database to learn such correlations.
    CREs are represented as 3D tensors of peak presence (namely ‘position’, ‘TR’, and ‘dataset’). We use an autoencoder to perform a lossy compression of each, to keep common patterns and discard rare elements (atypical peaks). The regions are viewed by the model through convolutional filters to focus on the correlations. Each peak gets an anomaly score corresponding to the autoencoder reconstruction error.
    We use artificial data to confirm the model’s ability to discover correlation groups of TR/datasets and label lonely/anomalous peaks. Application to ReMap is in progress, currently on a curated subset of data. To our knowledge, our research shows the first use of a large-scale meta-analysis to corroborate different ChIP-Seq datasets, using deep learning to integrate them in complex combinations and eliminate atypical peaks.

    Lieu : Salle de réunion du 3ème étage (300-302) - Institut de Mathématiques de Marseille (UMR 7373)
    Site Sud - Bâtiment TPR2
    Campus de Luminy, Case 907
    13288 MARSEILLE Cedex 9

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En savoir plus : Séminaire Mathématiques et Algorithmique pour la Biologie des Systèmes (MABioS)

  • Séminaire Géométrie, Dynamique et Topologie (GDT)

    Lundi 13 mai 14:00-15:00 - Christophe PITTET - I2M, Aix-Marseille Université

    Bounded cohomology and flat bundles

    Résumé : Applying Hironaka resolution of singularities, Gromov proved in 1982 that all characteristic classes of algebraic groups defined over the reals are bounded. We propose a more down-to-earth approach of this result. With the help of the stable commutator norm, we characterize Lie groups with all characteristic classes bounded. This is joined work with Chatterji, Cornulier, Mislin.

    JPEG - 14.8 ko
    Christophe PITTET

    Lieu : CMI, salle de séminaire R164 (1er étage) - I2M - Château-Gombert
    39 rue Frédéric Joliot-Curie
    13453 MARSEILLE cedex 13

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    En savoir plus : Séminaire Géométrie, Dynamique et Topologie (GDT)

  • Séminaire Statistique

    Lundi 13 mai 14:00-15:00 -

    Séminaire reporté !!!

    Lieu : FRUMAM 1er étage - Aix-Marseille Université - Site St Charles
    3, place Victor Hugo - case 39
    13331 MARSEILLE Cedex 03

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    En savoir plus : Séminaire Statistique