Seminar 01  Introduction to network visualization tools

Prerequisites

Please install gephi https://gephi.org/users/download/ for today's seminar and set up English Language.

Materials

• NetworkX  colab 

Data

• edges  
• nodes 

Форматы файлов и средства работы с графами

Graph data sources classification

1. Graph Databases

•     Graph Query languages

3. Relational Databases

•     SQL

3. Files

•     Common tables
•     Specific graph formats
•     Domain-oriented formats

File formats

Main formats

1. Description of graph6, sparse6 and digraph6 encodings
2. DOT (graph-description,language)
3. GraphML
4. GXL (Graph eXchange Language)
5. GML (Graph Modelling Language)

• from yFiles
• from Gephi

## Domain specific graph formats

1. OpenBabel
github, file formats

Data collection file formats

1. UCI Network Data Repository Download formats

a. Pajek

b. GML

c. GraphML

d. DyNetML

Python packages

1. graph-tool

2. Snap от Стенфордской группы

3. JGraphT - java библиотека с питоновской обвязкой.

4. NetworkX - a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. Converting to and from other data formats

5. IGraph - Network analysis software

Reading and Writing Graphs from and to Files

6. PyG

7. DGL, attention visualization

Main implementations

1. Graphviz - Graph Visualization Software. The DOT Language

2. Gephi - the leading visualization and exploration software for all kinds of graphs and networks. Supported Graph Formats

3. Cytoscape - an open source software platform for visualizing complex networks 

4. Graphjstry - has a list of connectors

5. ngraph

6. forcegraph, cool 3d viz

Other implementations

1. stellargraph для эббеддингов [obsolete]

2. ibm i2

3. CASOS ORA

4. ReGraph - a Python package for advanced graph visualisation

ReGraph tutorial

5. NodeXL - add-in for Microsoft Excel that support social network and content analysis. Moreover, it has some build-in importers of social-web data (Flickr, Twitter, Youtube) and you are able to download additional importers.

6. Socnetv: social network analysis and visualization software Supported Formats

Other implementations

7. vosviewer - a software tool for constructing and visualizing bibliometric networks

8. CitNetExplorer - a software tool for visualizing and analyzing citation networks of scientific publications

9. yworks yed - online demo

10. ogma, sigma graph

11. d3. 

12. Pajek

13. neo4j

Интересное сравнение бенчмарков есть в статье Benchmark of popular graph/network packages v2

Publications and prototypes

1. LargeViz, github, Visualizing Large-scale and High-dimensional Data
2. mars - a graph drawing tool for large graph visualization
3. Interactive Graph Layout of a Million Nodes

Graph Vizualization

Network Repository
Cora in Network Repository

- julesvernestrilogy.com
- internet-map.net / webverse.org

Статья по визуализации графов от iggisv9t хабр, towardsdatascience
Еще одна визуализация от Deep Graph Library блог

Хороший гайд по yFiles Automatic Graph Layout
yEd - Live Graph Editor

Layout-Styles Demo(offers more settings)

References

"A survey of two-dimensional graph layout techniques for information visualisation" [@gibsonSurveyTwodimensionalGraph2013]
 "[What Would a Graph Look Like in This Layout? A Machine Learning Approach to Large Graph Visualization" [@kwonWhatWouldGraph2018]

- Understanding How Dimension Reduction Tools Work: An Empirical Approach to Deciphering t-SNE, UMAP, TriMap, and PaCMAP for Data Visualization. 
- Graph Exploration With Embedding-Guided Layouts, pdf