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diversitysel [2012/10/13 20:11] rkissdiversitysel [2016/12/27 21:16] (current) – [Algorithm] rkiss
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 ====== Diversity selection ====== ====== Diversity selection ======
  
 +{{:divsel_new2.png?800|}}
  
 This filter selects the most diverse (dissimilar) molecules from collections by eliminating the closest analogs. Diversity selection reduces the size of the input collection and maximizes the coverage of the chemical space at the same time. This filter selects the most diverse (dissimilar) molecules from collections by eliminating the closest analogs. Diversity selection reduces the size of the input collection and maximizes the coverage of the chemical space at the same time.
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 ===== Algorithm ===== ===== Algorithm =====
  
-Diversity selection utilizes an optimized implementation of the {{ref|stepwise elimination algorithm}}, which can be described as follows:+Diversity selection utilizes an optimized implementation of the stepwise elimination algorithm (R. J. Taylor, J. Chem. Inf. Comput. Sci., 1995, 35, 59-67.), which can be described as follows:
  
-Calculate the similarity matrix of the molecules in the input collection +  * Calculate the similarity matrix of the molecules in the input collection 
-Process the matrix elements as follows: +  Process the matrix elements as follows: 
-Select the largest off-diagonal element in the similarity matrix +  Select the largest off-diagonal element in the similarity matrix 
-Eliminate one molecule of the most similar molecule pair randomly +  - Eliminates one molecule of the most similar molecule pair randomly 
-Go to step I. if off-diagonal elements remained +  Go to step 1. if off-diagonal elements remained 
-Sort the list of eliminated molecules by similarity values associated to the elimination steps in increasing order +  Sort the list of eliminated molecules by similarity values associated to the elimination steps in increasing order
-During this process, the size of the collection is reduced while the diversity of the collection is increased. Each elimination step filters out one molecule that has close analogues in the remaining set. As a result, the remaining molecules will have a decreased similarity (increased diversity).+
  
-The average run time for 10,000 input molecules is about minute.+During this processthe size of the collection is reduced while the diversity of the collection is increased. Each elimination step filters out one molecule that has close analogues in the remaining set. As a result, the remaining molecules will have decreased similarity (increased diversity).
  
-1) http://en.wikipedia.org/wiki/Jaccard_index 
-2) Open Babel v2.3.90 http://openbabel.sourceforge.net/ 
-4) R. J. Taylor, J. Chem. Inf. Comput. Sci., 1995, 35, 59-67. 
diversitysel.1350159095.txt.gz · Last modified: 2012/10/13 20:11 by rkiss