#PERank

This research aims to tackle this issue by supporting an inter-topic search to improve the search with the inputs, keywords and preferences, under the different topics.

This study developed an effective algorithm in which the relations between the biomedical entities are used in tandem with the current keyword-based entity search, Siren. The algorithm, called PERank, an adapted variation of Personalized PageRank (PPR), uses a pair of input: (1) search preferences, and (2) entities from any keyword-based entity search with keywords, to formalize the search results on-the-fly based on the index of the precomputed Individual Personalized PageRank Vectors.

1. generate ppv initials for all the entities (PERankFingerPrintIni.java)
2. run java -cp edu.ucsd.dbmi.perank.data.ComputationBatchJob ./config_c.xml ./config_100 for computation
3. counter all IPPV and index (IPPVCounter.java, IPPV Indexer.java)
4. search, input(keyword query, preference) PERankSearcher.java

find in https://drive.google.com/drive/folders/0B9VbMHIr1fkZOWlua0JKVURNUE0?usp=sharing