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Peppert, F.

Publications and source records attributed to Peppert, F..

2 recordsLinked to original sources

Chimeric U-Net - Modifying the standard U-Net towards Explainability

Healthcare guided by semantic segmentation has the potential to improve our quality of life through early and accurate disease detection. Convolutional Neural Networks, especially the U-Net-based architectures, are currently the state-of-the-art learningbased segmentation methods and have given unprecedented performances. However, their decision-making processes are still an active field of research. In order to reliably utilize such methods in healthcare, explainability of how the segmentation was performed is mandated. To date, explainability is studied and applied heavily in classification tasks. In this work, we propose the Chimeric U-Net, a U-Net architecture with an invertible decoder unit, that inherently brings explainability into semantic segmentation tasks. We find that having the restriction of an invertible decoder does not hinder the performance of the segmentation task. However, the invertible decoder helps to disentangle the class information in the latent space embedding and to construct meaningful saliency maps. Furthermore, we found that with a simple k-Nearest-Neighbours classifier, we could predict the Intersection over Union scores of unseen data, demonstrating that the latent space, constructed by the Chimeric U-Net, encodes an interpretable representation of the segmentation quality. Explainability is an emerging field, and in this work, we propose an alternative approach, that is, rather than building tools for explaining a generic architecture, we propose constraints on the architecture which induce explainability. With this approach, we could peer into the architecture to reveal its class correlations and local contextual dependencies, taking an insightful step towards trustworthy and reliable A.I. Code to build and utilize the Chimeric U-Net is made available under: https://github.com/kenrickschulze/Chimeric-UNet---Half-invertible-UNet-in-Pytorch

bioinformatics↗

Inferring Gene Regulatory Networks from Single Cell RNA-seq Temporal Snapshot Data Requires Higher Order Moments

Single cell RNA-sequencing (scRNA-seq) has become ubiquitous in biology. Recently, there has been a push for using scRNA-seq snapshot data to infer the underlying gene regulatory networks (GRNs) steering cellular function. To date, this aspiration remains unrealised due to technical- and computational challenges. In this work, we focus on the latter, which is under-represented in the literature. We took a systemic approach by subdividing the GRN inference into three fundamental components: the data pre-processing, the feature extraction, and the inference. We saw that the regulatory signature is captured in the statistical moments of scRNA-seq data, and requires computationally intensive minimisation solvers to extract. Furthermore, current data pre-processing might not conserve these statistical moments. Though our moment-based approach is a didactic tool for understanding the different compartments of GRN inference, this line of thinking-finding computationally feasible multi-dimensional statistics of data-is imperative for designing GRN inference methods.

systems biology↗