diff --git a/readme.md b/readme.md index 439de7a..63fdbd3 100644 --- a/readme.md +++ b/readme.md @@ -77,7 +77,7 @@ author--has not yet been necessary. There have been some studies which show that [auction algorithms](https://en.wikipedia.org/wiki/Auction_algorithm) for the assignment problem can have superior performance in real-world implementations, due to their simplicity, than more complex algorithms with better theoretical asymptotic performance. The author has implemented a basic forward auction algorithm, which produces optimal assignment for unbalanced bipartite graphs with -integer weights. To allow for unbalanced assignment, this algorithim eschews epsilon-scaling, +integer weights. To allow for unbalanced assignment, this algorithm eschews epsilon-scaling, and as a result is prone to "bidding-wars" which increase run time, making it less efficient than the implementation of the Fredman-Tarjan algorithm in JGraphT. A forward/reverse auction algorithm as developed by Bertsekas and CastaƱon should be able to handle unbalanced (or, as they call it, asymmetric) assignment much more efficiently, but has yet to be @@ -483,8 +483,9 @@ Several BiGpairSEQ simulations were performed on a home computer with the follow * Linux Mint 21 (5.15 kernel) ### SAMPLE PLATES WITH VARYING NUMBERS OF CELLS PER WELL -NOTE: these results were obtained with an earlier version of BiGpairSEQ_Sim, and should be re-run with the current version. -The observed behavior is not believed to be likely to change, however. + +The probability calculations used by pairSEQ require that every well on the sample plate contain the same number of T cells. +BiGpairSEQ does not share this limitation; it is robust to variations in the number of cells per well. A series of BiGpairSEQ simulations were conducted using a cell sample file of 3.5 million unique T cells. From these cells, 10 sample plate files were created. All of these sample plates had 96 wells, used an exponential distribution with a lambda of 0.6, and @@ -501,6 +502,9 @@ The well populations of the plates were: All BiGpairSEQ simulations were run with a low overlap threshold of 3 and a high overlap threshold of 94. No optional filters were used, so pairing was attempted for all sequences with overlaps within the threshold values. +NOTE: these results were obtained with an earlier version of BiGpairSEQ_Sim, and should be re-run with the current version. +The observed behavior is not believed to be likely to change, however. + Constant well population plate results: | |1000 Cell/Well Plate|2000 Cell/Well Plate|3000 Cell/Well Plate|4000 Cell/Well Plate|5000 Cell/Well Plate