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EXP

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EXP

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EXP - surely, you must be joking

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EXP - from 50% to 80% probability of not have a meta-gene right before an exon

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EXP - right now the probability of no-meta / 0-meta / 1-meta was the same. Experimenting a bit with modifying it

Alessio committed [r367]

Still cleaning up jade.env.PatternTracking

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Getting jade.env.PatternTracking ready for experiments

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EXP - comparing DGA to FGA / FGA-named / SGA as part of baseline for cyclicpatterntracking

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Implementing DGA

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Getting the DGA package started as a copy of FGA

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EXP - tuned a bit the parameters of the baseline experiments on cyclic pattern tracking with FGA, FGA-naked, and SGA so that the latter would be able to find the first optimum. Results show that SGA beats both versions of FGA to the first optimum, but is then unable to keep tracking the new optima. As expected, FGA beat both SGA and FGA-naked. Reproduction of previous results successful.

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REFACTORING - This code was no longer used since we now handle all parameters setting in the CfgParser via meta-programming

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REFACTORING - just cleaning up things a bit

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EXP - ICTAI97 paper suggests values for mirroring and folding that are way below what we used here; i.e. 0.001 vs. 0.05 and 0.01. We tried these values and it lead to FGA baseline performance to finally beat the SGA. The FGA now also converges slightly faster than the FGA-naked version that did not use mirroring or folding. Et voila! :)

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EXP - uncommenting. The previous experiments showed that setting the rates to 0 indeed works

Alessio committed [r357]

EXP - trying to comment out both folding and mirroring

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experimenting - deactivating folding the hard way just to make sure we eliminate any side effects when comparing

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refactoring - keep separate the bogus gene expression just in case we need it later for debugging purposes

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Still not working; the FGA without any specific operators slightly outperform the SGA after the first epoch but when turning on mirroring and folding the FGA performance is crappy. Anyhow, here are the cfg files used for these experiments.

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Still working on fixing the folding operator

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Observed big differences between previous baseline results and this new version; tracked it down to bad implementations of the folding operator and, more specifically, its neutrality

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Forgot to put back the mirroring and folding in evolve

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ktSelect replaces recruitment and selection

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Replacing selection and recruitment by ktSelect

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Starting the merging of selection and recruitment in jade.ga.Algo

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BUG FIX

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BUG FIX sneaky bug preventing the Statistic objects to be given proper references to cfg and pop fields from Statistics

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updating cfg

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Implementing FGA

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The cfg file that goes with the previous commit

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Removing default class-level fields' initializations in jade.ga.Config

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Default for seed value is 0 and should trigger a time-based randomization

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readme.txt file for this branch never got committed

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Fields marked as @ExperimentParameter should not be initialized outside constructors; this led to bugs fixed in previous commits. They should not either be initialized in the constructor since super() now ends up triggering the load() in CfgParser. Trying to initialize them after this does not result in a "default" value assigned in the absence of values in the cfg file, it instead results in overwriting any configuration via the cfg file by these initialization values. Another bug that was h...

Alessio committed [r337]

updated the cfg file so we may test jade.fga. WARNING make sure to always use jade.fga.Config when using jade.fga.Algo

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Fixing lil problem with the reification process in Run.

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Placeholder implementation of FGA

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updated the cfg for the test experiment so that it actually runs for 1000 generations. Tested by comparing bst.exp to results.sum; the jade stats and the ones resulting from dumping ECJSimpleStats and then analyzing them with the exp-analyze.sh script are the same. woohoo.

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well that was stupid...

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ECJSimpleStats implemented to produce the results.all directly

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oops taking that back; jade.stats.ECJSimpleStats will provide us with the results.all directly

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Configuring exp-analyze.sh to expect the output of jade.stats.ECJSimpleStats to be a bunch of job-XXX.out.stat.bstonly files

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Adding jade.stats.ECJSimpleStats as a copy of BstStat to start off with

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adding scripts used with ECJ and adapting them. Not yet tested since we have not added ECJShortStatistics in Jade.stats

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Spring refactoring in preparation for FGA vs. McEA experiments

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Removing debugging System.out.println

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Integrating branch ITSP-2014-Davis improvements...

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Moving Paul Burton ITSP work from the trunk to ...

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US701 Broker verify garbage collection

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US507.2 Broker Load Genotypes

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US507.2 Load Genotypes Experiment

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US507.1 Broker Save Genotypes

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US507.1 Save Genotypes Experiment

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US506.2 Broker Load Student Data

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US506.2 Load Student Data Experiment

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US506.1 Broker Saving Student Data

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US506.1 Saving Student Data Experiment

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US504 Broker Display Summary Data

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US504 Display Summary Data Experiment

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US503 Broker Genotype Records

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US503 Genotype Records Experiment

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US502 PSI Keep Student records

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US502 Broker Keep Student Records

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US502 Keep Student Records Experiment

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US501 PSI Identify Genotypes

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US501 Broker Identify Genotypes

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US501 Identify Genotypes Experiment

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US500.2 PSI Identify Students

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US500.2 Broker Identify Students

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US500.2 Identify Students Experiment

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US500.1 PSI Get Student ID

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US500.1 Broker Get Student ID

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US500.1 Get Student ID Experiment

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US405 PSI Feedback to Users

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US405 Feedback to Users Experiment

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US404 PSI Applying Transforms

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US404 Broker Applying Transforms

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US404 Applying Transforms Experiment

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US403 Broker Model Transforms and answers key

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US403 Broker Model Transforms

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US403 Model Transforms Experiment folder

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US401 PSI Checking for Correct Order

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Broker consolidating common files in the broker

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US401 Checking for Correct Order Experiment

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US400 PSI Show Puzzle to user

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US400 Broker Show Puzzle to user

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US400 Show Puzzle to user

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US311 PSI Puzzle in PSI

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US311 Broker Puzzle in PSI

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US311 Puzzle in PSI Experiment

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US306.2 Broker reduced evaluation number for te...

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US306.2 Add Author Experiment

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Broker Fix Multiples

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Fix Multiples Experiment

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US310 Broker EA initialized from Broker

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US310 Jade EA Initialzed from Broker

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US310 EA initialize from Broker Experiment

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US309 PSI Real ParsonsPuzzle

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US309 Broker Real ParsonsPuzzle