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Gabriele Malagoli

gabriele.malagoli@mila.quebec
Visiteur de recherche indépendant - Helmholtz Munich
Superviseur⋅e principal⋅e
Guy Wolf

Publications

Geometry-aware graph attention networks to explain single-cell chromatin states and gene expression with SEAGALL
Gabriele Malagoli
Patrick Hanel
Anna Danese
Guy Wolf
Maria Colomé-Tatché
High-throughput single-cell sequencing is widely used to study cell identity. We present SEAGALL (Single-cell Explainable Geometry-Aware Gra… (voir plus)ph Attention Learning pipeLine), a deep learning method to quantify the impact of molecular features on cellular phenotype, based on geometry-regularised autoencoders (GRAE) and explainable graph attention networks (X-GAT). The GRAE embeds the data into a latent space to build a reliable cell-cell graph. The GAT is trained to learn the annotations and XAI is used to explain the predictions, unravelling the features driving cell identity. SEAGALL extracts specific and stable signatures from multiple omics experiments, going beyond differential marker genes.
2026-04-22
Genome Biology (publié)
doi.org
Geometry aware graph attention networks to explain single-cell chromatin state and gene expression
Gabriele Malagoli
Patrick Hanel
Anna Danese
Guy Wolf
Maria Colomé-Tatché
High-throughput measurements that profile the transcriptome or the epigenome of single-cells are becoming a common way to study cell identit… (voir plus)y. These data are high dimensional, sparse and non linear. Here we present SEAGALL (Single-cell Explainable Geometry-Aware Graph Attention Learning pipeLine), a hypothesis free method to extract biologically relevant features from single-cell experiments based on geometry regularised autoencoders (GRAE) and explainable graph attention networks (GAT). We use a GRAE to embed the data into a latent space preserving the data geometry and we construct a cell-to-cell graph computing distances in the GRAE bottleneck. Exploiting the attention mechanism to dynamically learn the relevant edges, we use GATs to classify the cells and we explain the predictions of the model with XAI methods to unravel the features which are driving cell identity beyond marker genes. We apply our method to data sets from scRNA-seq, scATAC-seq and scChIP-seq experiments. SEAGALL can extract cell type specific and stable signatures which not only differ from the ones found in classical linear approaches but are less biassed by coverage and high expression.
2025-05-31
bioRxiv (prépublication)
doi.org