hACP

Package for Hierarchical Advanced Color Passing

Source Code Structure

• docs/ Documentation
  • build/ contains build as HTML
  • src/ Markdown files and assets
  • Project.toml Docs Project Configuration
  • make.jl build script
• instances/ input files for scripts
  • input/
  • mimic/ mimic dataset
    • .gitkeep
    • patients.csv
    • procedures_icd.csv
  • ljt-v1.0-jar-with-dependencies.jar inference algorithm
• results/ results will be put here
  • plot.r script to generate plots
  • prepare_plot.jl
• scripts/ scripts that use the hACP package
• src/ code of the hACP package
  • color_passing/
  • database/ database / dataframe / learning fg
  • fg/ factor graph
  • pfg/ paramterized fg
  • hACP.jl package file
  • helper.jl helping methods
  • hierarchical_ordering.jl
  • queries.jl
• test/ tests for the hACP Package
• Project.toml Project Configuration for hACP

When dependecies were updates:

• build docker image new: in hACP folder (login with credentials for user)

docker login registry.git.nrw
docker build --platform linux/amd64 -t registry.git.nrw/jan.speller/hacp_eacp_julia .
docker push registry.git.nrw/jan.speller/hacp_eacp_julia

Getting started

prepare hACP project

cd hACP
julia --project=.
]
instantiate

prepare docs project

cd hACP/docs
julia --project=.
]
dev ../
add Documenter

cd hACP/docs
julia --project=. make.jl

add package

cd hACP
julia --project=.
]
add package_name

Luttermann et al

Moreover, we applied openjdk version 11.0.25 to run the (lifted) inference algorithms, which are provided in the .jar file located at instances/ljt-v1.0-jar-with-dependencies.jar.

Instance Generation

First, the input instances need to be generated. To do so, see how to run at instance_generator.jl and julia mimic_generator.jl in the scripts/ directory. To be able to run mimic_generator.jl, both patients.csv and procedures_icd.csv need to be present in the instances/mimic/ directory (can be downloaded at https://physionet.org/content/mimiciv/3.1/). The input instances are then written to instances/input/ and to instances/mimic/, respectively.

Experiments

In all Scripts file there is a statement at the top line how to run those files. All results are written into the results/ directory. To create the plots, run julia prepare_plot.jl in the results/ directory to combine the obtained run times into averages and afterwards execute the R script plot.r (also in the results/ directory). The R script will then create a bunch of .tex files containing the plots of the experiments in the results/ directory. To generate the plots as .pdf files instead, set use_tikz = FALSE in line 7 of plot.r before executing the R script plot.r.