DeepGOPlus-stability

• The perturbed results aren't provided, but the original data and pre-trained model can be found at can be found at http://deepgoplus.bio2vec.net/data labelled as version 1.0.6.
• The original DeepGOPlus GitHub repository is located here.
• The built DeepGOPlus docker image for Verrou and IEEE can be pulled using docker pull inesgp/deepgoplus_verrou_vprec and docker pull inesgp/deepgoplus_ieee

Instructions

• In order to run the full set of experiments, the DeepGOPlus repository and the significant_digits (v.0.0) repository will have to be cloned
  • compute_sig_protein.py is to be added to the significant_digits package
  • main.py and evaluate_deepgoplus.py are to replace the files of the same name in the DeepGOPlus package
• In order to create the Verificarlo Python, Verrou TF or Verrou All containers, select the appropriate Dockerfile in the Dockerfiles folder
• User docker build -t imageName . to build the image for deepgoplus fuzzy model and convert if needed to Singularity
• Run a container of the image
• DeepGOPlus is already installed in the image, but to get further details on how to run the model consult here
• For Verificarlo Python, set echo "libinterflop_mca.so -m MODE --precision-binary32=FLOAT_PRECISION --precision-binary64=DOUBLE_PRECISION" > $VFC_BACKENDS_FROM_FILE to preferred mode or precision, however the results for Verificarlo Python were obtained with the default settings
  • To obtain the protein predictions, run the below command python3 /deepgoplus/deepgoplus/main.py -dr /workdir/data-1.0.6/data -if INPUT_FILE -of OUTPUT_FILE
• For Verrou, simply run the below command and pass in the appropriate exclusion file to instrument either the entire program or just Tensorflow valgrind --tool=verrou --rounding-mode=random --mca-mode=rr -s --check-nan=no --exclude=ABSOLUTE_EXCLUSION_FILEPATH --mca-precision-double=53 --mca-precision-float=24 python3 /deepgoplus/deepgoplus/main.py -dr /workdir/data-1.0.6/data -if INPUT_FILE -of OUTPUT_FILE
• In order to experiment with reduced precision using Verrou, use the below command valgrind --tool=verrou --backend=vprec --rounding-mode=random -s --check-nan=no --exclude=ABSOLUTE_EXCLUSION_FILEPATH --vprec-precision-binary64=DOUBLE_PRECISION --vprec-range-binary64=DOUBLE_RANGE --vprec-precision-binary32=FLOAT_PRECISION --vprec-range-binary32=FLOAT_RANGE python3 /deepgoplus/deepgoplus/main.py -dr /workdir/data-1.0.6/data -if INPUT_FILE -of OUTPUT_FILE
• Metrics are calculated as shown below in an IEEE environment and so should not be run in any of the perturbed containers python3 /deepgoplus/evaluate_deepgoplus.py -dr /workdir/data-1.0.6 -tsdf INPUT_PREDICTIONS -o ONTOLOGY_CLASS
• To calculate significant digits, run python3 compute_sig.py METRIC_OUTPUT_NAME REFERENCE_FILE_NAME SAMPLE_FILE to calculate the metrics and python3 compute_sig_protein.py PROTEIN_OUTPUT_NAME REFERENCE_FILE_NAME SAMPLE_FILE to calculate the significant digits of the protein predictions
• Copy the relevant files out of the container and set the paths to them in the Jupyter notebook
• From this point, run the code in the notebooks to generate statistics on the perturbed results and metrics in order to see if any perturbation can be found
• For additional information on instrumenting the code, consult Fuzzy and Verrou
• For additional information on methodology, consult this paper