7,508 research outputs found
Deep generative modeling for single-cell transcriptomics.
Single-cell transcriptome measurements can reveal unexplored biological diversity, but they suffer from technical noise and bias that must be modeled to account for the resulting uncertainty in downstream analyses. Here we introduce single-cell variational inference (scVI), a ready-to-use scalable framework for the probabilistic representation and analysis of gene expression in single cells ( https://github.com/YosefLab/scVI ). scVI uses stochastic optimization and deep neural networks to aggregate information across similar cells and genes and to approximate the distributions that underlie observed expression values, while accounting for batch effects and limited sensitivity. We used scVI for a range of fundamental analysis tasks including batch correction, visualization, clustering, and differential expression, and achieved high accuracy for each task
Simultaneous Coherent Structure Coloring facilitates interpretable clustering of scientific data by amplifying dissimilarity
The clustering of data into physically meaningful subsets often requires
assumptions regarding the number, size, or shape of the subgroups. Here, we
present a new method, simultaneous coherent structure coloring (sCSC), which
accomplishes the task of unsupervised clustering without a priori guidance
regarding the underlying structure of the data. sCSC performs a sequence of
binary splittings on the dataset such that the most dissimilar data points are
required to be in separate clusters. To achieve this, we obtain a set of
orthogonal coordinates along which dissimilarity in the dataset is maximized
from a generalized eigenvalue problem based on the pairwise dissimilarity
between the data points to be clustered. This sequence of bifurcations produces
a binary tree representation of the system, from which the number of clusters
in the data and their interrelationships naturally emerge. To illustrate the
effectiveness of the method in the absence of a priori assumptions, we apply it
to three exemplary problems in fluid dynamics. Then, we illustrate its capacity
for interpretability using a high-dimensional protein folding simulation
dataset. While we restrict our examples to dynamical physical systems in this
work, we anticipate straightforward translation to other fields where existing
analysis tools require ad hoc assumptions on the data structure, lack the
interpretability of the present method, or in which the underlying processes
are less accessible, such as genomics and neuroscience
Gravity-Inspired Graph Autoencoders for Directed Link Prediction
Graph autoencoders (AE) and variational autoencoders (VAE) recently emerged
as powerful node embedding methods. In particular, graph AE and VAE were
successfully leveraged to tackle the challenging link prediction problem,
aiming at figuring out whether some pairs of nodes from a graph are connected
by unobserved edges. However, these models focus on undirected graphs and
therefore ignore the potential direction of the link, which is limiting for
numerous real-life applications. In this paper, we extend the graph AE and VAE
frameworks to address link prediction in directed graphs. We present a new
gravity-inspired decoder scheme that can effectively reconstruct directed
graphs from a node embedding. We empirically evaluate our method on three
different directed link prediction tasks, for which standard graph AE and VAE
perform poorly. We achieve competitive results on three real-world graphs,
outperforming several popular baselines.Comment: ACM International Conference on Information and Knowledge Management
(CIKM 2019
- …