Monopartite graph

As explained in Knowledge Graphs and LLMs in Action

A monopartite subnetwork is a network containing one type of node, with connections only between nodes of that type.

A monopartite graph contains one node type, so every connection joins nodes of that same type. A protein–protein interaction (PPI) network is a practical example: proteins form the nodes and interactions form the edges. section 4.2.1 section 4.2.3

Use the structure to analyze a disease-specific protein subnetwork:

• Select proteins associated with a disease from the knowledge graph. section 4.2.3
• Retain PPI edges between the selected proteins, producing an undirected disease pathway. section 4.2.3
• Measure internal connectivity, density, largest-component size, and boundary connections to the full PPI network. section 4.2.3

Disease pathway

For celiac disease, associated proteins are collected and their PPI relationships extracted. The resulting monopartite subnetwork excludes disease nodes, although disease pathways can overlap through shared proteins. section 4.2.1 section 4.2.3

Figure 4.4 A disease pathway is a subgraph of the PPI network defined by a set of proteins associated with the disease.

Visualizes a disease pathway as a protein-defined subgraph of the PPI network. section 4.2.1

How Knowledge Graphs and LLMs in Action covers it

How deep it goes

Defines the structure and demonstrates extraction, density, component, and boundary analysis, but defers formal metric derivations.

Examples

Uses human proteins, celiac disease, disease-associated protein sets, and extracted PPI pathways.

What it assumes

Assumes familiarity with nodes, edges, subnetworks, knowledge graphs, and protein–disease associations.

What you can do after

Evaluate disease pathways by extracting their protein subnetworks and measuring internal and external connectivity.

How it connects

Connects knowledge graphs, protein–protein interaction networks, bipartite graphs, disease pathways, density, and conductance.

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Also explained in

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  Graph Algorithms for Data ScienceA monopartite graph is a graph containing one type of node, with relationships connecting nodes within that single node set.

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Related concepts

• network projectionproduced by · Network projection is the transformation of a multipartite graph into a graph containing one selected node type by inferring connections through shared neighbors.
• bipartite graphcontrasts with · A bipartite graph is a graph whose vertices can be partitioned into two disjoint sets, with edges only between the sets.
• protein-protein interaction networkhas part · A protein-protein interaction network is a graph whose nodes represent proteins and whose edges represent experimentally observed physical or functional interactions between them.
• graph algorithmused by · A graph algorithm is a computational procedure that operates on graph vertices, edges, and relationships to compute properties or solve problems.

This explainer was generated by Manning's knowledge graph from the text of Knowledge Graphs and LLMs in Action. The section links point to the parts of the book it draws on.