Files in krisrs1128/MSLF
Package accompanying "Bootstrap Confidence Regions for Learned Feature Embeddings"
.Rbuildignore
.dockerignore
.gitignore
CONDUCT.md
CONTRIBUTING.md
DESCRIPTION
Dockerfile
LFBCR.Rproj
LICENSE.md
NAMESPACE
R/bootstrap.R
R/file_manipulation.R
R/mibi.R
R/point_process.R
R/simulate.R
R/vis.R
README.Rmd
README.md
analysis/data/DO-NOT-EDIT-ANY-FILES-IN-HERE-BY-HAND
analysis/data/README.md
analysis/data/derived_data/README.md
analysis/data/raw_data/README.md
analysis/data_analysis/bootstrap-vis.Rmd
analysis/data_analysis/bootstrap.Rmd
analysis/data_analysis/learning/conf/tnbc_cnn-k128.yaml
analysis/data_analysis/learning/conf/tnbc_cnn-k32.yaml
analysis/data_analysis/learning/conf/tnbc_cnn-k64.yaml
analysis/data_analysis/learning/conf/tnbc_rcf-k1024.yaml
analysis/data_analysis/learning/conf/tnbc_rcf-k256.yaml
analysis/data_analysis/learning/conf/tnbc_rcf-k512.yaml
analysis/data_analysis/learning/conf/tnbc_vae-k128.yaml
analysis/data_analysis/learning/conf/tnbc_vae-k32.yaml
analysis/data_analysis/learning/conf/tnbc_vae-k64.yaml
analysis/data_analysis/learning/model_training.ipynb
analysis/data_analysis/learning/tnbc_baseline.ipynb
analysis/data_analysis/learning/tnbc_splits.ipynb
analysis/data_analysis/performance_eval.Rmd
analysis/data_analysis/prepare_mibi.Rmd
analysis/data_analysis/visualize_mibi.Rmd
analysis/figures/15_128_coordinates.png
analysis/figures/15_32_coordinates.png
analysis/figures/15_64_coordinates.png
analysis/figures/50_128_coordinates.png
analysis/figures/50_32_coordinates.png
analysis/figures/50_64_coordinates.png
analysis/figures/90_128_coordinates.png
analysis/figures/90_32_coordinates.png
analysis/figures/90_64_coordinates.png
analysis/figures/cnn_compromise_coordinates.png
analysis/figures/cnn_nonparametric_coordinates.png
analysis/figures/cnn_parametric_coordinates.png
analysis/figures/heatmaps/cnn-k64-50.yaml_0.png
analysis/figures/heatmaps/cnn-k64-50.yaml_1.png
analysis/figures/heatmaps/rcf-k512-50.yaml_0.png
analysis/figures/heatmaps/rcf-k512-50.yaml_1.png
analysis/figures/heatmaps/vae-k64-50.yaml_0.png
analysis/figures/heatmaps/vae-k64-50.yaml_1.png
analysis/figures/image_grid_tnbc_cnn.png
analysis/figures/image_grid_tnbc_rcf.png
analysis/figures/image_grid_tnbc_vae.png
analysis/figures/rcf_compromise_coordinates.png
analysis/figures/rcf_nonparametric_coordinates.png
analysis/figures/rcf_parametric_coordinates.png
analysis/figures/tnbc_cnn_compromise_coordinates.png
analysis/figures/tnbc_cnn_nonparametric_coordinates.png
analysis/figures/tnbc_cnn_parametric_coordinates.png
analysis/figures/tnbc_k_128_coordinates.png
analysis/figures/tnbc_k_32_coordinates.png
analysis/figures/tnbc_k_64_coordinates.png
analysis/figures/tnbc_rcf_compromise_coordinates.png
analysis/figures/tnbc_rcf_nonparametric_coordinates.png
analysis/figures/tnbc_rcf_parametric_coordinates.png
analysis/figures/tnbc_vae_compromise_coordinates.png
analysis/figures/tnbc_vae_nonparametric_coordinates.png
analysis/figures/tnbc_vae_parametric_coordinates.png
analysis/figures/vae_compromise_coordinates.png
analysis/figures/vae_nonparametric_coordinates.png
analysis/figures/vae_parametric_coordinates.png
analysis/simulations/low_rank_simulation/low_rank_model.Rmd
analysis/simulations/spatial_process_simulation/bootstrap-vis.Rmd
analysis/simulations/spatial_process_simulation/bootstrap.Rmd
analysis/simulations/spatial_process_simulation/generate.Rmd
analysis/simulations/spatial_process_simulation/heatmaps.Rmd
analysis/simulations/spatial_process_simulation/learning/conf/cnn-k128-15.yaml
analysis/simulations/spatial_process_simulation/learning/conf/cnn-k128-50.yaml
analysis/simulations/spatial_process_simulation/learning/conf/cnn-k128-90.yaml
analysis/simulations/spatial_process_simulation/learning/conf/cnn-k32-15.yaml
analysis/simulations/spatial_process_simulation/learning/conf/cnn-k32-50.yaml
analysis/simulations/spatial_process_simulation/learning/conf/cnn-k32-90.yaml
analysis/simulations/spatial_process_simulation/learning/conf/cnn-k64-15.yaml
analysis/simulations/spatial_process_simulation/learning/conf/cnn-k64-50.yaml
analysis/simulations/spatial_process_simulation/learning/conf/cnn-k64-90.yaml
analysis/simulations/spatial_process_simulation/learning/conf/rcf-k1024-15.yaml
analysis/simulations/spatial_process_simulation/learning/conf/rcf-k1024-50.yaml
analysis/simulations/spatial_process_simulation/learning/conf/rcf-k1024-90.yaml
analysis/simulations/spatial_process_simulation/learning/conf/rcf-k256-15.yaml
analysis/simulations/spatial_process_simulation/learning/conf/rcf-k256-50.yaml
analysis/simulations/spatial_process_simulation/learning/conf/rcf-k256-90.yaml
analysis/simulations/spatial_process_simulation/learning/conf/rcf-k512-15.yaml
analysis/simulations/spatial_process_simulation/learning/conf/rcf-k512-50.yaml
analysis/simulations/spatial_process_simulation/learning/conf/rcf-k512-90.yaml
analysis/simulations/spatial_process_simulation/learning/conf/vae-k128-15.yaml
analysis/simulations/spatial_process_simulation/learning/conf/vae-k128-50.yaml
analysis/simulations/spatial_process_simulation/learning/conf/vae-k128-90.yaml
analysis/simulations/spatial_process_simulation/learning/conf/vae-k32-15.yaml
analysis/simulations/spatial_process_simulation/learning/conf/vae-k32-50.yaml
analysis/simulations/spatial_process_simulation/learning/conf/vae-k32-90.yaml
analysis/simulations/spatial_process_simulation/learning/conf/vae-k64-15.yaml
analysis/simulations/spatial_process_simulation/learning/conf/vae-k64-50.yaml
analysis/simulations/spatial_process_simulation/learning/conf/vae-k64-90.yaml
analysis/simulations/spatial_process_simulation/learning/model_training.ipynb
analysis/simulations/spatial_process_simulation/learning/save_splits.ipynb
inst/python/__init__.py
inst/python/bootstrap.py
inst/python/data.py
inst/python/features.py
inst/python/infer.py
inst/python/models/__init__.py
inst/python/models/cnn.py
inst/python/models/random_features.py
inst/python/models/vae.py
inst/python/train.py
inst/python/train_rcf.py
man/align_to_list.Rd
man/arr_to_list.Rd
man/features.Rd
man/image_grid.Rd
man/inhomogeneous_process.Rd
man/mark_process.Rd
man/matern_kernel.Rd
man/matern_process.Rd
man/param_boot.Rd
man/param_boot_.Rd
man/param_boot_cmp.Rd
man/param_boot_cmp_.Rd
man/procrustes.Rd
man/relative_intensities.Rd
man/sim_wrapper.Rd
man/spatial_df.Rd
man/untar_all.Rd
runtime.txt
