Generalizable and scalable visualization of single-cell data using neural networks

H Cho, B Berger, J Peng - Cell systems, 2018 - cell.com
Visualization algorithms are fundamental tools for interpreting single-cell data. However,
standard methods, such as t-stochastic neighbor embedding (t-SNE), are not scalable to …

ivga: A fast force-directed method for interactive visualization of complex networks

W Dzwinel, R Wcisło, W Czech - Journal of Computational Science, 2017 - Elsevier
Complex networks play a very important role in various fields of science as data structures,
which aggregate information about mutual relationships between numerous objects. The …

PAM: particle automata in modeling of multiscale biological systems

W Dzwinel, R Wcisło, DA Yuen, S Miller - ACM Transactions on …, 2016 - dl.acm.org
Serious problems with bridging multiple scales in the scope of a single numerical model
make computer simulations too demanding computationally and highly unreliable. We …

2-d embedding of large and high-dimensional data with minimal memory and computational time requirements

W Dzwinel, R Wcislo, S Matwin - arXiv preprint arXiv:1902.01108, 2019 - arxiv.org
In the advent of big data era, interactive visualization of large data sets consisting of M* 10^
5+ high-dimensional feature vectors of length N (N~ 10^ 3+), is an indispensable tool for …

Visualization and analysis of local and distant population flows on the Qinghai-Tibet Plateau using crowd-sourced data

J Xu, J Liu, Y Xu, T Pei - Journal of Geographical Sciences, 2021 - Springer
Human migration between cities is one important aspect of spatial interaction that not only
reflects urban attractiveness but also denotes interactions amongst agglomerations. We …

Visualization of big high dimensional data in a three dimensional space

Y Xie, P Chenna, J He, L Le, J Planteen - Proceedings of the 3rd IEEE …, 2016 - dl.acm.org
This paper studies feasibility and scalable computing processes for visualizing big high
dimensional data in a 3 dimensional space by using dimension reduction techniques. More …

Multi-gpu k-nearest neighbor search in the context of data embedding

A Kłusek, W Dzwinel - Parallel Computing is Everywhere, 2018 - ebooks.iospress.nl
The k-nearest neighbor (k-NN) search is the rudimentary procedure widely used in machine
learning and data embedding techniques. Herein we present a new multi-GPU/CUDA …

Distributed computing of distance‐based graph invariants for analysis and visualization of complex networks

W Czech, W Mielczarek… - … and Computation: Practice …, 2017 - Wiley Online Library
We present a new framework for analysis and visualization of complex networks based on
structural information retrieved from their distance k‐graphs and B‐matrices. The …

Neural data visualization for scalable and generalizable single cell analysis

H Cho, B Berger, J Peng - bioRxiv, 2018 - biorxiv.org
Single-cell RNA sequencing is becoming effective and accessible as emerging technologies
push its scale to millions of cells and beyond. Visualizing the landscape of single cell …

Comparative study of dimension reduction approaches with respect to visualization in 3-dimensional space

P Chenna - 2016 - digitalcommons.kennesaw.edu
In the present big data era, there is a need to process large amounts of unlabeled data and
find some patterns in the data to use it further. If data has many dimensions, it is very hard to …