COBI-GRINE: A Tool for Visualization and Advanced Evaluation of Communities in Mass Channel Similarity Graphs

09/24/2020
by   Karsten Wüllems, et al.
0

The detection of groups of molecules that co-localize with histopathological patterns or sub-structures is an important step to combine the rich high-dimensional content of mass spectrometry imaging (MSI) with classic histopathological staining. Here we present the evolution of GRINE to COBI-GRINE, an interactive web tool that maps MSI data onto a graph structure to detect communities of laterally similar distributed molecules and co-visualizes the communities with Hematoxylin and Eosin (HE) stained images. Thereby the tool enables biologists and pathologists to examine the MSI image graph in a target-oriented manner and links molecular co-localization to pathology. Another feature is the manual optimization of cluster results with the assist of graph statistics in order to improve the community results. As the graphs can become very complex, those statistics provide good heuristics to support and accelerate the detection of sub-clusters and misclusterings. This kind of edited cluster optimization allows the integration of expert background knowledge into the clustering result and a more precise analysis of links between molecular co-localization and pathology.

READ FULL TEXT

Authors

page 2

page 3

page 4

07/12/2018

A new graph modelisation for molecule similarity

In order to define the process of restrosynthesis of a new organic molec...
09/24/2020

SoRC – Evaluation of Computational Molecular Co-Localization Analysis in Mass Spectrometry Images

The computational analysis of Mass Spectrometry Imaging (MSI) data aims ...
09/01/2020

VeRNAl: A Tool for Mining Fuzzy Network Motifs in RNA

Motivation: RNAs are ubiquitous molecules involved in many regulatory an...
10/24/2019

Deep Learning for Molecular Graphs with Tiered Graph Autoencoders and Graph Classification

Tiered graph autoencoders provide the architecture and mechanisms for le...
02/09/2019

Clustering Bioactive Molecules in 3D Chemical Space with Unsupervised Deep Learning

Unsupervised clustering has broad applications in data stratification, p...
03/22/2019

Principal nested shape space analysis of molecular dynamics data

Molecular dynamics simulations produce huge datasets of temporal sequenc...
02/28/2021

Clustering Schemes on the Torus with Application to RNA Clashes

Molecular structures of RNA molecules reconstructed from X-ray crystallo...
This week in AI

Get the week's most popular data science and artificial intelligence research sent straight to your inbox every Saturday.