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Add data on randomized well population behavior

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efischer
2022-03-02 18:55:19 -06:00
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@@ -279,6 +279,49 @@ Since this implementation of BiGpairSEQ writes intermediate results to disk (to
with different filtering options), the actual elapsed time was greater. File I/O time was not measured, but took with different filtering options), the actual elapsed time was greater. File I/O time was not measured, but took
slightly less time than the simulation itself. Real elapsed time from start to finish was under 30 minutes. slightly less time than the simulation itself. Real elapsed time from start to finish was under 30 minutes.
## BEHAVIOR WITH RANDOMIZED WELL POPULATIONS
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
had a sequence dropout rate of 10%.
The well populations of the plates were:
* One sample plate with 1000 T cells/well
* One sample plate with 2000 T cells/well
* One sample plate with 3000 T cells/well
* One sample plate with 4000 T cells/well
* One sample plate with 5000 T cells/well
* Five sample plates with each individual well's population randomized, from 1000 to 5000 T cells. (Average population ~3000 T cells/well.)
All BiGpairSEQ simulations were run with a low overlap threshold of 3 and a high overlap threshold of 94.
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
|---|---|---|---|---|---|
|Total Alphas Found|6407|7330|7936|8278|8553|
|Total Betas Found|6405|7333|7968|8269|8582|
|Pairing Attempt Rate|0.661|0.653|0.600|0.579|0.559|
|Correct Pairing Count|4231|4749|4723|4761|4750|
|Incorrect Pairing Count|3|34|40|26|29|
|Pairing Error Rate|0.000709|0.00711|0.00840|0.00543|0.00607|
|Simulation Time (Seconds)|500|643|700|589|598|
Randomized well population plate results:
| |Random Plate 1 | Random Plate 2|Random Plate 3|Random Plate 4|Random Plate 5|Average|
|---|---|---|---|---|---|---|
Total Alphas Found|7853|7904|7964|7898|7917|7907|
Total Betas Found|7851|7891|7920|7910|7894|7893|
Pairing Attempt Rate|0.607|0.610|0.601|0.605|0.603|0.605|
Correct Pairing Count|4718|4782|4721|4755|4731|4741|
Incorrect Pairing Count|51|35|42|27|29|37|
Pairing Error Rate|0.0107|0.00727|0.00882|0.00565|0.00609|0.00771|
Simulation Time (Seconds)|590|677|730|618|615|646|
From these results, it can be seen that BiGpairSEQ treats a sample plate with a highly variable number of T cells/well
roughly as though it had a constant well population equal to the average well population.
## TODO ## TODO
* ~~Try invoking GC at end of workloads to reduce paging to disk~~ DONE * ~~Try invoking GC at end of workloads to reduce paging to disk~~ DONE