Gephi

Open Source Software for Exploring and Manipulating Networks

download and install at

gephi.org

slides.com/danilsko/gephi

Plan

  1. Introducing Gephi
  2. Hands-on session

Gephi intro

Basics

  • About Gephi
  • Importing  graph data
  • Interface overview
  • Graph layouts

Advanced

  • Statistics in Gephi
  • Filters
  • Clustering
  • Dynamic networks

About Gephi

Gephi is

  • an open source software for exploring and manipulating networks 
  • "like Photoshop but for graph data" (gephi.org)
  • written in Java and runs on most OS's
  • extensible (plugins with additional features)
  • ...a bit buggy :) 

Let's get it started!

Do you have Gephi installed?

gephi.org

Importing data to Gephi

  1. Specific graph formats (GEXF, GraphML, Pajek NET, GDF, GML, TLP)
    • File->Open 
  2. Edges table in CSV
    • ​​File -> Import spreadsheet

Intermission: CSV

  • Comma-separated values 
  • The simplest table format
  • Not limited to comma (anything can serve as a separator — ;$: etc)
  • Can be opened in Excel/OpenOffice

Let's try it

Importing

  • File (Файл) -> Import spreadsheet
  • Important: Edges table (Таблица рёбер)
  • Далее -> Готово

Main windows

  • Preview (Обработка)
    • layout and all the calculations
  • Data laboratory (Лаборатория данных)
    • your original data (can be modified)
  • Overview (Просмотр)
    • for pretty pictures :)

Let's make Gephi show labels

  • Data Laboratory (Лаборатория данных)
    • Copy data to another column
      (Скопировать значения в другой столбец)
      • 'Id'
        • Copy to: 'Label'
          (Укажите целевой столбец: Label)

Graph layouts

Graph drawing 

укладка графа

  • is a complex scientific area on its own
  • lies at the intersection of computer science and some heavy-weight mathematics
  • can emphasize different features of a graph

Layouts in Gephi

Layouts in Gephi

Let's try some layouts!

Layout/укладка

Advanced part

Statistics

(and how to vizualize it)

Statistics 

  • Window -> Context  (Окно -> Контекст)
    • Number of nodes and edges
  • Window -> Statistics (Окно -> Статистика)
    • ​Click 'Run' to calculate metrics

Now let's see who has the highest degree!

Go to Data Laboratory 

Vizualizing statistics

  • Appearance
    • Size
      • Attribute
        • Degree

Filtering

  • Windows -> Filters
    • Attributes
      • Degree (or other attribute of your choice)
        • Equal (for exact values)
        • Range

Clustering

Clustering in Gephi

  • Louvain algorithm (Blondel et al, 2008) 
  • The value to be optimized is modularity
  • modularity measures the density of links inside communities compared to links between communities.

Formal definition

Intuition behind it

Modularity parameter

  • >1 to get less clusters
  • <1 (e.g. 0,5) to get more clusters 

Let us try and cluster Hamlet now

Bonus: directed Hamlet graph

for those who want to try it:

Dynamic graphs

  • Can be processed in Gephi
  • Feel free to explore at your own risk

Title Text

Assignment for next week

Choose one:

  1. Encode drama using 'Simple formalization'
  2. Bring some data (CSV or Graph formats). Some sources:
    • https://github.com/gephi/gephi/wiki/Datasets
    • http://snap.stanford.edu/data/
    • or whatever you find. Remember you can convert XLS(X) table to CSV using (Open/Libre)Office or Excel

Gephi

By danilsko

Gephi

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