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eugenefischer
2025-04-09 11:31:05 -05:00
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@@ -9,18 +9,21 @@
2. [COMMAND LINE OPTIONS](#command-line-options)
3. [INTERACTIVE INTERFACE](#interactive-interface)
4. [INPUT/OUTPUT](#input-output)
1. Cell Sample Files
2. Sample Plate Files
3. Graph/Data Files
4. Matching Results Files
1. [Cell Sample Files](#cell-sample-files)
2. [Sample Plate Files](#sample-plate-files)
3. [Graph/Data Files](#graph-data-files)
4. [Matching Results Files](#matching-results-files)
5. [RESULTS](#results)
1. SAMPLE PLATES WITH VARYING NUMBERS OF CELLS PER WELL
2. SIMULATING EXPERIMENTS FROM pairSEQ PAPER
1. [SAMPLE PLATES WITH VARYING NUMBERS OF CELLS PER WELL](#sample-plates-with-varying-numbers-of-cells-per-well)
2. [SIMULATING EXPERIMENTS FROM THE 2015 pairSEQ PAPER](#simulating-experiments-from-the-2015-pairseq-paper)
1. [EXPERIMENT 1](#experiment-1)
2. [EXPERIMENT 3](#experiment-3)
6. [TODO](#todo)
7. [CITATIONS](#citations)
8. [ACKNOWLEDGEMENTS](#acknowledgements)
9. [AUTHOR](#author)
10. [DISCLOSURE](#disclosure)
8. [EXTERNAL LIBRARIES USED](#external-libraries-used)
9. [ACKNOWLEDGEMENTS](#acknowledgements)
10. [AUTHOR](#author)
11. [DISCLOSURE](#disclosure)
## ABOUT
@@ -600,7 +603,7 @@ the file of distinct cells may enable better simulated replication of this exper
* ~~Test whether pairing heap (currently used) or Fibonacci heap is more efficient for priority queue in current matching algorithm~~ DONE
* ~~in theory Fibonacci heap should be more efficient, but complexity overhead may eliminate theoretical advantage~~
* ~~Add controllable heap-type parameter?~~
* Parameter implemented. Fibonacci heap the current default.
* Parameter implemented. Pairing heap the current default.
* ~~Implement sample plates with random numbers of T cells per well.~~ DONE
* Possible BiGpairSEQ advantage over pairSEQ: BiGpairSEQ is resilient to variations in well population sizes on a sample plate; pairSEQ is not due to nature of probability calculations.
* preliminary data suggests that BiGpairSEQ behaves roughly as though the whole plate had whatever the *average* well concentration is, but that's still speculative.
@@ -625,13 +628,13 @@ the file of distinct cells may enable better simulated replication of this exper
* Add frequency distribution details to metadata output
* need to make an enum for the different distribution types and refactor the Plate class and user interfaces, also add the necessary fields to GraphWithMapData and then call if from Simulator
* Update performance data in this readme
* Add section to ReadMe describing data filtering methods.
* ~~Add section to ReadMe describing data filtering methods.~~ DONE, now part of algorithm description
* Re-implement CDR1 matching method
* ~~Refactor simulator code to collect all needed data in a single scan of the plate~~ DONE
* ~~Currently it scans once for the vertices and then again for the edge weights. This made simulating read depth awkward, and incompatible with caching of plate files.~~
* ~~This would be a fairly major rewrite of the simulator code, but could make things faster, and would definitely make them cleaner.~~
* Implement Duan and Su's maximum weight matching algorithm
* Add controllable algorithm-type parameter?
* ~~Add controllable algorithm-type parameter?~~ DONE
* This would be fun and valuable, but probably take more time than I have for a hobby project.
* ~~Implement an auction algorithm for maximum weight matching~~ DONE
* Implement a forward/reverse auction algorithm for maximum weight matching