Related papers: Visualizing hierarchies in scRNA-seq data using a …
We propose a novel method, scTree, for single-cell Tree Variational Autoencoders, extending a hierarchical clustering approach to single-cell RNA sequencing data. scTree corrects for batch effects while simultaneously learning a…
Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons invoke evolutionary histories, as…
Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity, enabling detailed analysis of complex biological systems at single-cell resolution. However, the high dimensionality and technical noise…
Learning hierarchical features in Sparse Autoencoders (SAEs) is essential for capturing the structured nature of real-world data and mitigating issues like feature absorption or splitting. Existing works attempt to identify hierarchical…
t-SNE and hierarchical clustering are popular methods of exploratory data analysis, particularly in biology. Building on recent advances in speeding up t-SNE and obtaining finer-grained structure, we combine the two to create tree-SNE, a…
Single-cell RNA sequencing (scRNA-seq) has emerged as a transformative technology, offering unparalleled insights into the intricate landscape of cellular diversity and gene expression dynamics. The analysis of scRNA-seq data poses…
Single-cell RNA sequencing (scRNA-seq) enables dissecting cellular heterogeneity in tissues, resulting in numerous biological discoveries. Various computational methods have been devised to delineate cell types by clustering scRNA-seq data…
We propose Tree Variational Autoencoder (TreeVAE), a new generative hierarchical clustering model that learns a flexible tree-based posterior distribution over latent variables. TreeVAE hierarchically divides samples according to their…
Clustering single-cell RNA sequence (scRNA-seq) data poses statistical and computational challenges due to their high-dimensionality and data-sparsity, also known as `dropout' events. Recently, Regularized Auto-Encoder (RAE) based deep…
Single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to analyze gene expression at the cellular level. By providing data on gene expression for each individual cell, scRNA-seq generates large datasets with thousands of…
This work presents StrAE: a Structured Autoencoder framework that through strict adherence to explicit structure, and use of a novel contrastive objective over tree-structured representations, enables effective learning of multi-level…
Single-cell RNA sequencing (scRNA-seq) provides a high throughput, quantitative and unbiased framework for scientists in many research fields to identify and characterize cell types within heterogeneous cell populations from various…
Tree data occurs in many forms, such as computer programs, chemical molecules, or natural language. Unfortunately, the non-vectorial and discrete nature of trees makes it challenging to construct functions with tree-formed output,…
In this paper we propose Structuring AutoEncoders (SAE). SAEs are neural networks which learn a low dimensional representation of data which are additionally enriched with a desired structure in this low dimensional space. While traditional…
In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…
Tree kernels have demonstrated their ability to deal with hierarchical data, as the intrinsic tree structure often plays a discriminative role. While such kernels have been successfully applied to various domains such as nature language…
Biomolecular graph analysis has recently gained much attention in the emerging field of geometric deep learning. Here we focus on organizing biomolecular graphs in ways that expose meaningful relations and variations between them. We…
Trajectory inference is a critical problem in single-cell transcriptomics, which aims to reconstruct the dynamic process underlying a population of cells from sequencing data. Of particular interest is the reconstruction of differentiation…
Sparse autoencoders (SAEs) have proven effective for extracting monosemantic features from large language models (LLMs), yet these features are typically identified in isolation. However, broad evidence suggests that LLMs capture the…
As a powerful tool for characterizing cellular subpopulations and cellular heterogeneity, single cell RNA sequencing (scRNA-seq) technology offers advantages of high throughput and multidimensional analysis. However, the process of data…