Building off of the findings of "Validating Causal Diagrams of Human Health Risks for Spaceflight: An Example Using Bone Data from Rodents," this project explores, in collaboration with the authors of this study, to explore Machine Learning approaches to generate Directed Acyclic Graphs using the Grow-Shrink Algorithm.
You can get started by cloning the repository and running notebooks/growshrink_notebook.Rmd in RStudio or VS Code. The file notebooks/growshrink_notebook.nb.html can also be downloaded to read through the file as a learning resource in your web browser.
The output graphs of Grow-Shrink, and an Exploratory Data Analysis are available in the graphs/ directory.
-
Generate a DAG that can be validated or invalidated by a domain expert
-
Identify or develop a validity score that can measure the degree of congruency with another graph
-
Determine Grow-Shrink's level of adaptability to generate DAGs for HSRB medical risk assessment for astronauts
-
Ensure that DAGs are ML-ready -- can they be used to fit the parameters to a Bayesian Network?
- Rewrite
notebooks/growshrink_notebook.Rmdas an R Script file - Convert source code to Python or C++ for further reusability
- Generalize code for any dataset that meets standards for OSDR's TRANSFORMED datasets
- Rewrite
All data from this project is publicly available through NASA's Open Science Data Repositories. If you would like to automate the use of data please download the following CSV files and place them in a directory called data/ on the same level as the notebooks/ directory. The notebook will use this structure to load the files relatively from the R Notebook file for you. Otherwise, you will be prompted to load the files through a file explorer.
- Quantifying Cancellous Bone Structural Changes in Microgravity: Axial Skeleton Results from the RR-1 Mission (Dubeé, 2022)
- Effects of Spaceflight on Bone Microarchitecture in the Axial and Appendicular Skeleton in Growing Ovariectomized Rats from STS-62 (Keune, 2015)
- Spaceflight-induced (STS-62) vertebral bone loss in ovariectomized rats is associated with increased bone marrow adiposity and no change in bone formation (Keune, 2016)
- Dose-dependent skeletal deficits due to varied reductions in mechanical loading in rats (Tibia - pQCT) (Ko, 2020) 1/2
- Use of this data is TBD by findings of microCT data below
- Dose-dependent skeletal deficits due to varied reductions in mechanical loading in rats (Femur - microCT, three-point bending, histomorphometry) (Ko, 2020) 2/2
The following libraries are used in the notebooks associated with the project