Comments (3)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3307026/
"""
In order to obtain an appropriate null distribution on causal graphs, it is important to require that the randomized graphs share basic structural properties with the original causal graph, yet have enough flexibility to reflect the space of reasonable graphical models. We propose to fix the vertex set V of our original graph G = (V, E) and randomize the edges, requiring that the randomized versions G' = (V, E') maintain three properties:
-
Vertex degrees. We require that each vertex a ∈ V have the same positive and negative in- and out-degrees in G' as in G. This requirement is important as biological networks typically have long-tailed degree distributions that include highly connected "hubs" as well as vertices with few incident edges.
-
Simplicity. We disallow self-edges and parallel edges in G' as these are not present in G. In other words, for any two vertices a, b ∈ V, there cannot be an edge from a to itself and there can be at most one directed edge from a to b, either positive or negative.
-
Connectedness. We require that G' be connected, as is the case for our original biological network G. For our signed directed graphs, we take connectedness to mean that the graph induced by ignoring edge signs and directions is connected.
"""
from pybel-tools.
Awesome, thanks. This is a low priority but good to have on the to-do list
from pybel-tools.
Definitely
from pybel-tools.
Related Issues (20)
- Better citation tests
- Testing on OLSNamespace HOT 1
- Auto class expansion HOT 1
- Export a BELGraph to SCAIView format HOT 2
- Implement pseudo-topological sort
- Add argument that defines how to process multiple values overlaying to the same node
- Cache intermediate NeuroMMSig results
- Edge summary double counts two way edges
- HGVS Validator
- Direct Interaction Validator
- Upstream controller recursive implementation HOT 1
- Validator with sitemapper
- Fix SPIA script
- Implement assembler with reified edges HOT 1
- Collapse nodes with the same name (doesnt matter to which one) HOT 2
- HTML assembler can't find index.html
- Add chemical similarity calculator
- pybel-tools should have a new documentation?
- module 'pybel_tools' has no attribute 'summary'
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from pybel-tools.