eLife

SqueakPose Studio: An end-to-end platform for pose estimation and real-time edge-AI deployment

This important work introduces an integrated open-source platform for behavioral acquisition and pose estimation that substantially improves the accessibility and speed of real-time animal tracking ...
InfoQ

Embedding Atlas: Apple’s Open-Source Tool for Exploring Large-Scale Embeddings Locally

Unlock the full InfoQ experience by logging in! Stay updated with your favorite authors and topics, engage with content, and download exclusive resources. Spencer Judge discusses the architectural ...
IEEE

CBMAP: Clustering-Based Manifold Approximation and Projection for Dimensionality Reduction

Abstract: Dimensionality reduction methods are employed to decrease data dimensionality, either to enhance machine learning performance or to facilitate data visualization in two or three-dimensional ...
GitHub

UMAP Implementation on Single-Cell RNA Sequencing Data

This is a simplified implementation of UMAP (Uniform Manifold Approximation and Projection), programmed from scratch and applied to GEO scRNA-seq data. A project assignment for BINF6250 (Algorithmic ...
GitHub

Mugen-UMAP: UMAP visualization and clustering of mutated genes in single-cell DNA sequencing data.

This Python program provides a comprehensive pipeline for processing ANNOVAR files, converting them into AnnData format, and generating UMAP visualizations along with various summary reports based on ...
Nature

Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters

Two-dimensional (2D) embedding methods are crucial for single-cell data visualization. Popular methods such as t-distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation ...
PNAS

Computational inference of eIF4F complex function and structure in human cancers

To understand the importance of eIF4F components, we employed computational methods on large public datasets to investigate the impact of positive selection on eIF4F dysregulation in cancer. By ...
Frontiers

Retinal astrocyte morphology predicts integration of vascular and neuronal architecture

Astrocytes are important regulators of blood flow and play a key role in the response to injury and disease in the central nervous system (CNS). Despite having an understanding that structural changes ...
C&EN

Spatiochemical Characterization of the Pancreas Using Mass Spectrometry Imaging and Topological Data Analysis

STADIUS Center for Dynamical Systems, Signal Processing, and Data Analytics, Department of Electrical Engineering (ESAT), KU Leuven, 3001 Leuven, Belgium STADIUS Center for Dynamical Systems, Signal ...
eLife

Generating colorblind-friendly scatter plots for single-cell data

Reduced-dimension or spatial in situ scatter plots are widely employed in bioinformatics papers analyzing single-cell data to present phenomena or cell-conditions of interest in cell groups. When ...
Frontiers

deepMNN: Deep Learning-Based Single-Cell RNA Sequencing Data Batch Correction Using Mutual Nearest Neighbors

It is well recognized that batch effect in single-cell RNA sequencing (scRNA-seq) data remains a big challenge when integrating different datasets. Here, we proposed deepMNN, a novel deep ...