Related papers: Analyzing scRNA-seq data by CCP-assisted UMAP and …

In many real-world problems, we are dealing with collections of high-dimensional data, such as images, videos, text and web documents, DNA microarray data, and more. Often, high-dimensional data lie close to low-dimensional structures…

Misuses of t-SNE and UMAP in visual analytics have become increasingly common. For example, although t-SNE and UMAP projections often do not faithfully reflect the original distances between clusters, practitioners frequently use them to…

High-throughput sequencing is now regularly used for studies of the transcriptome (RNA-seq), particularly for comparisons among experimental conditions. For the time being, a limited number of biological replicates are typically considered…

Single-cell proteomics (SCP) is transforming our understanding of biological complexity by shifting from bulk proteomics, where signals are averaged over thousands of cells, to the proteome analysis of individual cells. This granular…

We propose a weakly-supervised cell tracking method that can train a convolutional neural network (CNN) by using only the annotation of "cell detection" (i.e., the coordinates of cell positions) without association information, in which…

Spectral computed tomography (CT) is an emerging technology capable of providing high chemical specificity, which is crucial for many applications such as detecting threats in luggage. This type of application requires both fast and…

Graph clustering discovers groups or communities within networks. Deep learning methods such as autoencoders (AE) extract effective clustering and downstream representations but cannot incorporate rich structural information. While Graph…

Deep learning based methods have recently pushed the state-of-the-art on the problem of Single Image Super-Resolution (SISR). In this work, we revisit the more traditional interpolation-based methods, that were popular before, now with the…

Single-cell RNA sequencing (scRNA-seq) technologies have enabled the profiling of gene expression for a collection of cells across time during a dynamic biological process. Given that each time point provides only a static snapshot,…

Efficient processing of large-scale time series data is an intricate problem in machine learning. Conventional sensor signal processing pipelines with hand engineered feature extraction often involve huge computational cost with high…

This work presents and analyzes three convolutional neural network (CNN) models for efficient pixelwise classification of images. When using convolutional neural networks to classify single pixels in patches of a whole image, a lot of…

To apply deep CNNs to mobile terminals and portable devices, many scholars have recently worked on the compressing and accelerating deep convolutional neural networks. Based on this, we propose a novel uniform channel pruning (UCP) method…

Rapidly growing public gene expression databases contain a wealth of data for building an unprecedentedly detailed picture of human biology and disease. This data comes from many diverse measurement platforms that make integrating it all…

Conditional t-SNE (ct-SNE) is a recent extension to t-SNE that allows removal of known cluster information from the embedding, to obtain a visualization revealing structure beyond label information. This is useful, for example, when one…

CLIP-seq methods are valuable techniques to experimentally determine transcriptome-wide binding sites of RNA-binding proteins. Despite the constant improvement of such techniques (e.g. eCLIP), the results are affected by various types of…

Person image generation aims to perform non-rigid deformation on source images, which generally requires unaligned data pairs for training. Recently, self-supervised methods express great prospects in this task by merging the disentangled…

Computer-aided diagnosis plays a salient role in more accessible and accurate cardiopulmonary diseases classification and localization on chest radiography. Millions of people get affected and die due to these diseases without an accurate…

We present a novel coupled two-way clustering approach to gene microarray data analysis. The main idea is to identify subsets of the genes and samples, such that when one of these is used to cluster the other, stable and significant…

Numerous tools have been recently developed to predict disease phenotypes using single-cell RNA sequencing (RNA-seq) data. CloudPred is an end-to-end differentiable learning algorithm coupled with a biologically informed mixture model,…

This work aims to improve the sample efficiency of parallel large-scale ranking and selection (R&S) problems by leveraging correlation information. We modify the commonly used "divide and conquer" framework in parallel computing by adding a…