Get TMCompression and make the project, using:
git clone https://github.com/jorgeMFS/TMCompression.git;
cd TMCompression;
make;
make ioStNormalize;
make ioAverage2;
make ioGrowthAverage;
make bdmAvg;
make TMsimulator;Folder organization:
./src : Source Code of the TMCompression Program;
./val : Source Code of program used in Turing Tape Validation;
./scripts : Bash Scripts to Process Results and plot them
./resultText : Textual results obtained from the usage of TMCompression;
./resultPlots : Plots of some results obtained;
./profiles : Normal Profiles and Dynamic Temporal Profiles of Turing Machine Tapes.
There are many ways to run this program see help for clarification :
./tm --help;
#-----------------------------------------------------------------------------
#Program that creates Turing machines and Measures its Statistical Complexity.
#-----------------------------------------------------------------------------
#Arguments to set flags:
--verbose #Indicates programs that will receive inputs in a verbose form.
--brief #Indicates programs that will receive inputs in a brief form.
--tmverbose #Indicates programs that tm output will be send to the user.
--tmgrowth #Indicates programs that output a list of Turing machines with an increase in the number of states and a alphabet size of 2
--replicate #Indicates programs that will replicate experiment to determine the best k and it for a given number of states and alphabet size.
--profile #Indicates programs that will receive through the tm number through the flag tm and will create a profile of that turing
--dynprofile #Indicates programs that will receive through the tm number through the flag tm and will create a dynamical temporal profile of that turing
--ruleProfile #Indicates programs to create a Compression profile of the rules for a given Turing Machine
--ruleMetrics #Indicates programs to compute the rule metrics of a given TMs
--StMatrix #Indicates programs to print the StateMatrix of a given TMs
--mutate #Indicates programs to print the nc of the mutation of a string (starting with all zeros and ending with all ones) and performing mutations until its 100% mutated
--mutateVirus #Indicates programs perform the edition and permutation of a virus DNA sequence and print NC results
--MethodI #Indicates programs to recreate similar list of results used in plots of the article using MethodI
--MethodII #Indicates programs to recreate similar list of results used in plots of the article using MethodII
--3DgraphMethodII #Indicates programs to recreate similar list of results used in 3D plots of the article using MethodII
#Mandatory Arguments:
-s, --number_states #Number of States the Turing Machine has.
-a, --alphabet_size #Alphabet size the Turing Machine considers.
-i, --iterations #Number of iterations the Turing Machine makes in the tape.
-k, --context #k indexes to consider as a context to fill the Markov Table.
-t, --tm #Speciffy turing to obtain results, can only be activated with --profile flag.
#Other Optional Arguments:
-S, --strategy #Turing Machine traversal strategy (default: sequential)
-N, #Number of Turing Machines to traverse
-v, --version #Outputs the version of the program.
-h, --help #Describes program.
#-----------------------------------------------------------------------------
#Examples:
#-----------------------------------------------------------------------------
#Run all tms
./tm -s 2 -a 2 -i 10 -k 1
./tm --brief -s 2 -a 2 -i 10 -k 1
./tm --verbose --number_states=2 --alphabet_size=2 --iterations=20 --context=2
#----------------
#Run all tms with multithreads
./tm -s 2 -a 2 -i 10 -k 1 -j 7
./tm --brief -s 2 -a 2 -i 10 -k 1 -j 7
#----------------
#Strategies of running TM Machines
#By default strategy is Sequential:
./tm --brief -s 2 -a 2 -i 10 -k 1 -j 7
./tm --brief -s 2 -a 2 -i 10 -k 1 -N 10 -j 4 -S sequential
#Monte Carlo:
./tm --brief -s 2 -a 2 -i 10 -k 1 -N 10 -j 4 -S monte_carlo
#----------------
#Run specific TM and obtain profile:
./tm --brief --profile -s 2 -a 2 -i 100 -k 2 -t 5
#----------------
#Run a specific TM and obtain their rules normal complexity profile
./tm --brief --ruleProfile -s 2 -a 2 -i 100 -k 2 -t 5
#----------------
#Run specific tm and obtain dynamical temporal profile:
./tm --brief --dynprofile -s 2 -a 2 -i 100 -k 2 -t 5
#----------------
# Run specific tm and obtain their Rule Compression Profile:
#----------------
./tm --brief --ruleMetrics -s 2 -a 2 -i 100 -t 5
# ----------------
#Replicate k and it determination:
./tm --brief --replicate -s 2 -a 2 -j 10
#----------------
#turing machine growth with alphabet size of 2 and increase in state cardinality:
./tm --tmgrowth
#----------------
#Run specific tm and print tape
./tm --brief --printTape -s 2 -a 2 -i 100 -t 1
#----------------
#Run StMatrix of the tm
./tm --brief --StMatrix -s 2 -a 2 -t 1
#----------------
#Obtain nc of the substitutions and permutations of a string
./tm --mutate
#----------------
#Obtain nc of Virus genome sequence with substitutions and permutations
echo "./resultText/Parvovirus_virus_genome.txt" | ./tm --mutateVirus
#----------------
#Obtain list of graph of Method I
./tm --MethodI
#----------------
#Obtain list of graph of Method II
./tm --MethodII
#----------------
#Obtain list of 3d graphs of Method II
./tm --3DgraphMethodII
#----------------To recreate the plots shown in the article (bellow example):
chmod +x run.sh;
bash run.sh;Virus and String edition and Permutation Plots:
# Command to create list:
echo "./resultText/Parvovirus_virus_genome.txt" | ./tm --mutateVirus;
# Recreate Edition and permutation plots...";
bash reprArticlePlot.sh 0 0 1 1 1 1;TMs Plots:
# Recreating plots of Cardinality Growth and TMs...;
bash processResults.sh 0 1 1 1 1 1 1 1;Profile Plots:
# Recreate Plots of Normal and Dynamic Profiles...";
bash reprArticlePlot.sh 1 1 0 0 0 0;Inside and outside Region Plots:
# Recreating Plot of Inside vs Outside region of TM Tapes...;
bash getRegionTapeValues.sh;
# Recreating Plot of Inside vs Outside region of TM Rules...
bash getRegionRuleValues.sh 1 0 1 1;Average Rule Complexity Profiles plots:
# Obtain Average Rule Profiles...
bash avg_rule_profile.sh 1 1;Block Decomposition Method comparation with NC plots:
#Compare BDM with NC for #Q={6,8,10}...
bash bdm_NC_comparisson.sh 1 0 1 1;Method I and II plots:
# Command to create list:
./tm --MethodI;
./tm --MethodII;
# Recreate Plots of Method I and II.
bash evolve_tm_plot.sh Method_I_200;
bash evolve_tm_plot.sh Method_II_2000;3D Method II Plots:
# Command to create list:
./tm --3DgraphMethodII;
# Recreate 3D Plot of Method II...
bash 3d_evolve_graph.sh;Note: This downloads the files Containing the results from running all TMs for a given State and Alphabet Cardinality, since this can take from several minutes to several days. If you wish to recreate the Results use TM program. Example:
./tm --brief -s 2 -a 4 -i 50000 -k 2:10 -N 30000000 -j 20 -S monte_carlo > 2sts4alp.txt;There are two main scripts:
./processResults.sh : "Plots graphics shown in Folder ./resultPlot"
./filteringResults.sh :"Plots Profiles shown in Folder ./profiles"There are many ways to the scripts, see help for clarification:
bash scripts/processResults.sh;
bash scripts/filteringResults.sh;Please cite the followings, if you use TMCompression:
Silva, J. M., Pinho, E., Matos, S., & Pratas, D. (2020). Statistical Complexity Analysis of Turing Machine tapes with Fixed Algorithmic Complexity Using the Best-Order Markov Model. Entropy, 22(1), 105.
@article{silva2020statistical,
title={Statistical Complexity Analysis of Turing Machine tapes with Fixed Algorithmic Complexity Using the Best-Order Markov Model},
author={Silva, Jorge M and Pinho, Eduardo and Matos, S{\'e}rgio and Pratas, Diogo},
journal={Entropy},
volume={22},
number={1},
pages={105},
year={2020},
publisher={Multidisciplinary Digital Publishing Institute}
}
Please let us know if there is any issues.
TMCompression is under GPL v3 license. For more information, click here.