Sparsely-connected autoencoder (SCA) for single cell RNAseq data mining

Abstract Single-cell RNA sequencing (scRNAseq) is an essential tool to investigate cellular heterogeneity. Thus, it would be of great interest being able to disclose biological information belonging to cell subpopulations, which can be defined by clustering analysis of scRNAseq data. In this manuscript, we report a tool that we developed for the functional mining of single cell clusters based on Sparsely-Connected Autoencoder (SCA). This tool allows uncovering hidden features associated with scRNAseq data. We implemented two new metrics, QCC (Quality Control of Cluster) and QCM (Quality Control of Model), which allow quantifying the ability of SCA to reconstruct valuable cell clusters and to evaluate the quality of the neural network achievements, respectively. Our data indicate that SCA encoded space, derived by different experimentally validated data (TF targets, miRNA targets, Kinase targets, and cancer-related immune signatures), can be used to grasp single cell cluster-specific functional features. In our implementation, SCA efficacy comes from its ability to reconstruct only specific clusters, thus indicating only those clusters where the SCA encoding space is a key element for cells aggregation. SCA analysis is implemented as module in rCASC framework and it is supported by a GUI to simplify it usage for biologists and medical personnel

Deep Neural Ensemble for Retinal Vessel Segmentation in Fundus Images towards Achieving Label-free Angiography

Automated segmentation of retinal blood vessels in label-free fundus images entails a pivotal role in computed aided diagnosis of ophthalmic pathologies, viz., diabetic retinopathy, hypertensive disorders and cardiovascular diseases. The challenge remains active in medical image analysis research due to varied distribution of blood vessels, which manifest variations in their dimensions of physical appearance against a noisy background. In this paper we formulate the segmentation challenge as a classification task. Specifically, we employ unsupervised hierarchical feature learning using ensemble of two level of sparsely trained denoised stacked autoencoder. First level training with bootstrap samples ensures decoupling and second level ensemble formed by different network architectures ensures architectural revision. We show that ensemble training of auto-encoders fosters diversity in learning dictionary of visual kernels for vessel segmentation. SoftMax classifier is used for fine tuning each member auto-encoder and multiple strategies are explored for 2-level fusion of ensemble members. On DRIVE dataset, we achieve maximum average accuracy of 95.33\% with an impressively low standard deviation of 0.003 and Kappa agreement coefficient of 0.708 . Comparison with other major algorithms substantiates the high efficacy of our model.Comment: Accepted as a conference paper at IEEE EMBC, 201

Learning the Structure of Auto-Encoding Recommenders

Autoencoder recommenders have recently shown state-of-the-art performance in the recommendation task due to their ability to model non-linear item relationships effectively. However, existing autoencoder recommenders use fully-connected neural network layers and do not employ structure learning. This can lead to inefficient training, especially when the data is sparse as commonly found in collaborative filtering. The aforementioned results in lower generalization ability and reduced performance. In this paper, we introduce structure learning for autoencoder recommenders by taking advantage of the inherent item groups present in the collaborative filtering domain. Due to the nature of items in general, we know that certain items are more related to each other than to other items. Based on this, we propose a method that first learns groups of related items and then uses this information to determine the connectivity structure of an auto-encoding neural network. This results in a network that is sparsely connected. This sparse structure can be viewed as a prior that guides the network training. Empirically we demonstrate that the proposed structure learning enables the autoencoder to converge to a local optimum with a much smaller spectral norm and generalization error bound than the fully-connected network. The resultant sparse network considerably outperforms the state-of-the-art methods like \textsc{Mult-vae/Mult-dae} on multiple benchmarked datasets even when the same number of parameters and flops are used. It also has a better cold-start performance.Comment: Proceedings of The Web Conference 202