ATriaJava

Java implementation of the Ablatio Triadum (ATria) centrality algorithm for PluMA.

Based on the original C++ implementation by movingpictures83/ATria and the algorithm described in Cickovski et al, 2015, 2017.

ATria (Ablatio Triadum) is a centrality algorithm for analyzing microbial interaction networks. It identifies the most central nodes in a network by iteratively:

1. Computing shortest paths using a modified Floyd-Warshall algorithm
2. Calculating payoff scores for each node
3. Removing triads associated with the highest-scoring node
4. Repeating until all nodes are ranked

CSV format with nodes as rows and columns, where entry (i,j) represents the weight of the edge from node i to node j.

Example:

"","NodeA","NodeB","NodeC"
"NodeA",1,0.8,-0.5
"NodeB",0.8,1,0.6
"NodeC",-0.5,0.6,1

Tab-separated file with columns: Name, Centrality, Rank

scons

javac ATriaJavaPlugin.java

Run the unit tests:

javac -cp . ATriaJavaPluginTest.java
java -cp . ATriaJavaPluginTest

1. Place the plugin in PluMA's plugins/ directory
2. Create a config file:

Prefix plugins/ATriaJava/example/
Plugin ATriaJava inputfile corrP.never.csv outputfile output.noa

3. Run PluMA:

./pluma config.txt

The plugin is optimized for performance with:

• Precomputed row offsets for array indexing
• Early termination in Floyd-Warshall for zero paths
• Bitwise operations for even/odd checks
• Loop hoisting and reduced bounds checking

Typical execution time: ~9ms for a 126-node network.

MIT License

• Cickovski, T., & Narasimhan, G. (2018). Constructing Lightweight and Flexible Pipelines Using Plugin-Based Microbiome Analysis (PluMA). Bioinformatics, 34(17), 2881-2888.