All modules for which code is available
153 |- gslr 154 |
├── .gitignore ├── README.md ├── docs ├── .nojekyll ├── Makefile ├── README.md ├── doctrees │ ├── environment.pickle │ └── index.doctree ├── html │ ├── .buildinfo │ ├── .nojekyll │ ├── _modules │ │ ├── gslr.html │ │ └── index.html │ ├── _sources │ │ └── index.rst.txt │ ├── _static │ │ ├── ajax-loader.gif │ │ ├── basic.css │ │ ├── comment-bright.png │ │ ├── comment-close.png │ │ ├── comment.png │ │ ├── css │ │ │ ├── badge_only.css │ │ │ └── theme.css │ │ ├── doctools.js │ │ ├── down-pressed.png │ │ ├── down.png │ │ ├── file.png │ │ ├── fonts │ │ │ ├── Inconsolata-Bold.ttf │ │ │ ├── Inconsolata-Regular.ttf │ │ │ ├── Lato-Bold.ttf │ │ │ ├── Lato-Regular.ttf │ │ │ ├── RobotoSlab-Bold.ttf │ │ │ ├── RobotoSlab-Regular.ttf │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ └── fontawesome-webfont.woff │ │ ├── jquery-3.1.0.js │ │ ├── jquery.js │ │ ├── js │ │ │ ├── modernizr.min.js │ │ │ └── theme.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ ├── underscore.js │ │ ├── up-pressed.png │ │ ├── up.png │ │ └── websupport.js │ ├── genindex.html │ ├── index.html │ ├── objects.inv │ ├── py-modindex.html │ ├── search.html │ └── searchindex.js ├── index.html └── source │ ├── .nojekyll │ ├── conf.py │ └── index.rst ├── examples └── Example_Usage.ipynb ├── experiments ├── KEGG │ ├── KEGG_df.filtered.with_correlates.pickle │ ├── KEGG_df.pickle │ ├── Pathway_Curation_and_Correlates_Discovery.ipynb │ ├── README.md │ └── download_KEGG.ipynb ├── README.md ├── algorithms │ ├── Logit_PR_vs_GSLR_pr.ipynb │ ├── Logit_vs_GSLR.ipynb │ ├── PLS-DA.ipynb │ ├── README.md │ ├── figures │ │ ├── easy.pdf │ │ ├── hard.pdf │ │ ├── hsa04110_easy.pdf │ │ └── hsa04110_hard.pdf │ ├── gslr │ │ ├── GSLR.ipynb │ │ ├── GSLR2.ipynb │ │ ├── GSLR_gmm_results.ipynb │ │ ├── GSLR_results.ipynb │ │ ├── TCGA_BRCA.ipynb │ │ ├── TCGA_OV.ipynb │ │ ├── TOBI_MEDULLO.ipynb │ │ ├── gslr_gmm_pr_results.ipynb │ │ ├── gslr_gmm_results.pickle │ │ ├── gslr_pr_results.ipynb │ │ ├── gslr_results.pickle │ │ ├── ludwig │ │ │ ├── graph_proj_test.ipynb │ │ │ ├── gslr_test.ipynb │ │ │ └── softmax_test.ipynb │ │ ├── medullo_coefs.pickle │ │ ├── ovarian_coefs.pickle │ │ ├── real_data.py │ │ ├── run_GSLR.py │ │ ├── run_gslr_gmm.py │ │ ├── run_gslr_gmm_pr.py │ │ ├── run_gslr_pr.py │ │ └── run_xor_GSLR.py │ ├── logit │ │ ├── logit.ipynb │ │ ├── logit_gmm_pr_results.ipynb │ │ ├── logit_gmm_results.ipynb │ │ ├── logit_gmm_results.pickle │ │ ├── logit_l2_gmm_pr_results.ipynb │ │ ├── logit_l2_pr_results.ipynb │ │ ├── logit_pr_results.ipynb │ │ ├── logit_results.ipynb │ │ ├── logit_results.pickle │ │ ├── run_logit.py │ │ ├── run_logit_gmm.py │ │ ├── run_logit_gmm_pr.py │ │ ├── run_logit_pr.py │ │ ├── run_xor_logit.py │ │ ├── xor_logit_results.ipynb │ │ └── xor_logit_results.pickle │ ├── netreg │ │ ├── GX.tsv │ │ ├── NetReg.ipynb │ │ ├── X.tsv │ │ ├── Y.tsv │ │ ├── netreg.sh │ │ ├── outfile_coefficients.tsv │ │ └── outfile_intercepts.tsv │ ├── pcsf │ │ ├── PCSF.ipynb │ │ ├── hsa04110_inbiomap_exp.pcsf.prizes │ │ └── inbiomap_temp.tsv │ └── srig │ │ ├── SRIG.ipynb │ │ ├── Test_PyLearn_ParsimonY.ipynb │ │ ├── run_srig_pr.py │ │ └── test_SPAMS.ipynb ├── data_generation │ ├── 1_multivariate_normal │ │ ├── README.md │ │ ├── multivariate_normal.ipynb │ │ └── multivariate_normal.py │ ├── 2_independent_normals │ │ ├── README.md │ │ ├── independent_normals.ipynb │ │ └── independent_normals.py │ ├── 3_multivariate_normal_svd_covariance │ │ ├── README.md │ │ ├── ludwig.ipynb │ │ ├── ludwig_svd_covariance.ipynb │ │ ├── ludwig_svd_covariance.py │ │ ├── updated_kegg_ludwig_svd_covariance.ipynb │ │ └── xor_kegg_pathways.py │ ├── 4_multivariate_normal_svd_covariance_greater_shift │ │ ├── README.md │ │ └── ludwig_svd_covariance_gaussian_mixture.py │ ├── 5_conditional_multivariate_normal │ │ ├── README.md │ │ └── hypothesis.ipynb │ ├── README.md │ └── synthetic_vs_real.ipynb └── real_data │ ├── brca_inbiomap_exp.tsv │ ├── medullo_inbiomap_exp.tsv │ └── ovarian_inbiomap_exp.tsv ├── gslr ├── __init__.py ├── __main__.py └── gslr.py ├── poster ├── beamerthemeI6dv.sty ├── graph_sparsity_picture.tex ├── images │ ├── 1.pdf │ ├── 2.pdf │ ├── 3.pdf │ ├── 4.pdf │ ├── algo.pdf │ ├── graph.pdf │ ├── matrix.pdf │ ├── mit-cropped.pdf │ └── selected.pdf ├── middle-col-low.tex ├── poster.out ├── poster.pdf └── poster.tex ├── requirements.txt └── setup.py /.gitignore: -------------------------------------------------------------------------------- 1 | *.xlsx 2 | sftp-config.json 3 | experiments/generated_data 4 | **/**_pr_**.pickle 5 | .venv 6 | 7 | poster/*.aux 8 | poster/*.fdb_latexmk 9 | poster/*.fls 10 | poster/*.nav 11 | poster/*.toc 12 | poster/*snm 13 | 14 | 15 | # Byte-compiled / optimized / DLL files 16 | __pycache__/ 17 | *.py[cod] 18 | *$py.class 19 | 20 | # C extensions 21 | *.so 22 | 23 | # Distribution / packaging 24 | .Python 25 | env/ 26 | build/ 27 | develop-eggs/ 28 | dist/ 29 | downloads/ 30 | eggs/ 31 | .eggs/ 32 | lib64/ 33 | parts/ 34 | sdist/ 35 | var/ 36 | *.egg-info/ 37 | .installed.cfg 38 | *.egg 39 | 40 | # PyInstaller 41 | # Usually these files are written by a python script from a template 42 | # before PyInstaller builds the exe, so as to inject date/other infos into it. 43 | *.manifest 44 | *.spec 45 | 46 | # Installer logs 47 | pip-log.txt 48 | pip-delete-this-directory.txt 49 | 50 | # Unit test / coverage reports 51 | htmlcov/ 52 | .tox/ 53 | .coverage 54 | .coverage.* 55 | .cache 56 | nosetests.xml 57 | coverage.xml 58 | *,cover 59 | .hypothesis/ 60 | 61 | # Translations 62 | *.mo 63 | *.pot 64 | 65 | # Django stuff: 66 | *.log 67 | local_settings.py 68 | 69 | # Flask stuff: 70 | instance/ 71 | .webassets-cache 72 | 73 | # Scrapy stuff: 74 | .scrapy 75 | 76 | # Sphinx documentation 77 | docs/_build/ 78 | 79 | # PyBuilder 80 | target/ 81 | 82 | # IPython Notebook 83 | .ipynb_checkpoints 84 | 85 | # pyenv 86 | .python-version 87 | 88 | # celery beat schedule file 89 | celerybeat-schedule 90 | 91 | # dotenv 92 | .env 93 | 94 | # virtualenv 95 | venv/ 96 | ENV/ 97 | 98 | # Spyder project settings 99 | .spyderproject 100 | 101 | # Rope project settings 102 | .ropeproject 103 | 104 | # Vim swap files 105 | *.swp 106 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | 2 | [](https://pypi.python.org/pypi/gslr) 3 | 4 | # Graph-Sparse Logistic Regression 5 | 6 | ## Motivation 7 | 8 | The motivation for Graph-Sparse Logistic Regression is to constrain classification to predict a label from a graph-sparse support. More in [the paper](https://arxiv.org/abs/1712.05510) or [the poster](https://github.com/fraenkel-lab/GSLR/raw/master/poster/poster.pdf). 9 | 10 | 11 | ## Installation 12 | 13 | From [pypi](https://pypi.python.org/pypi/gslr). 14 | ``` 15 | pip install gslr 16 | ``` 17 | ## Documentation 18 | 19 | See the [docs](https://fraenkel-lab.github.io/GSLR/). 20 | 21 | ## Example Usage 22 | 23 | See the [`examples`](examples) directory 24 | -------------------------------------------------------------------------------- /docs/.nojekyll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fraenkel-lab/GSLR/7a10e8823a7edb7f0eb1f5f1801e711002560b09/docs/.nojekyll -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | SPHINXPROJ = GSLR 8 | SOURCEDIR = source 9 | BUILDDIR = . 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 21 | -------------------------------------------------------------------------------- /docs/README.md: -------------------------------------------------------------------------------- 1 | ## Docs 2 | 3 | In order to actually change the documentation that shows up, change the docstrings in `gslr/gslr.py`. 4 | 5 | Docs are automatically generated by sphinx with autodoc and napoleon. 6 | 7 | ## Compilation Instructions: 8 | 9 | from `./docs` do `make html`. 10 | 11 | 12 | -------------------------------------------------------------------------------- /docs/doctrees/environment.pickle: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fraenkel-lab/GSLR/7a10e8823a7edb7f0eb1f5f1801e711002560b09/docs/doctrees/environment.pickle -------------------------------------------------------------------------------- /docs/doctrees/index.doctree: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fraenkel-lab/GSLR/7a10e8823a7edb7f0eb1f5f1801e711002560b09/docs/doctrees/index.doctree -------------------------------------------------------------------------------- /docs/html/.buildinfo: -------------------------------------------------------------------------------- 1 | # Sphinx build info version 1 2 | # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. 3 | config: f3a98b159e10e282be31920e978cb9b0 4 | tags: 645f666f9bcd5a90fca523b33c5a78b7 5 | -------------------------------------------------------------------------------- /docs/html/.nojekyll: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fraenkel-lab/GSLR/7a10e8823a7edb7f0eb1f5f1801e711002560b09/docs/html/.nojekyll -------------------------------------------------------------------------------- /docs/html/_modules/index.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 |
7 | 8 | 9 | 10 | 11 |' + _('Hide Search Matches') + '
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296 | if (nextHref) { 297 | window.location.href = nextHref; 298 | return false; 299 | } 300 | } 301 | } 302 | }); 303 | } 304 | }; 305 | 306 | // quick alias for translations 307 | _ = Documentation.gettext; 308 | 309 | $(document).ready(function() { 310 | Documentation.init(); 311 | }); -------------------------------------------------------------------------------- /docs/html/_static/down-pressed.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fraenkel-lab/GSLR/7a10e8823a7edb7f0eb1f5f1801e711002560b09/docs/html/_static/down-pressed.png -------------------------------------------------------------------------------- /docs/html/_static/down.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fraenkel-lab/GSLR/7a10e8823a7edb7f0eb1f5f1801e711002560b09/docs/html/_static/down.png -------------------------------------------------------------------------------- /docs/html/_static/file.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fraenkel-lab/GSLR/7a10e8823a7edb7f0eb1f5f1801e711002560b09/docs/html/_static/file.png -------------------------------------------------------------------------------- /docs/html/_static/fonts/Inconsolata-Bold.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fraenkel-lab/GSLR/7a10e8823a7edb7f0eb1f5f1801e711002560b09/docs/html/_static/fonts/Inconsolata-Bold.ttf -------------------------------------------------------------------------------- /docs/html/_static/fonts/Inconsolata-Regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fraenkel-lab/GSLR/7a10e8823a7edb7f0eb1f5f1801e711002560b09/docs/html/_static/fonts/Inconsolata-Regular.ttf -------------------------------------------------------------------------------- /docs/html/_static/fonts/Lato-Bold.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fraenkel-lab/GSLR/7a10e8823a7edb7f0eb1f5f1801e711002560b09/docs/html/_static/fonts/Lato-Bold.ttf -------------------------------------------------------------------------------- /docs/html/_static/fonts/Lato-Regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fraenkel-lab/GSLR/7a10e8823a7edb7f0eb1f5f1801e711002560b09/docs/html/_static/fonts/Lato-Regular.ttf -------------------------------------------------------------------------------- /docs/html/_static/fonts/RobotoSlab-Bold.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fraenkel-lab/GSLR/7a10e8823a7edb7f0eb1f5f1801e711002560b09/docs/html/_static/fonts/RobotoSlab-Bold.ttf -------------------------------------------------------------------------------- /docs/html/_static/fonts/RobotoSlab-Regular.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fraenkel-lab/GSLR/7a10e8823a7edb7f0eb1f5f1801e711002560b09/docs/html/_static/fonts/RobotoSlab-Regular.ttf -------------------------------------------------------------------------------- /docs/html/_static/fonts/fontawesome-webfont.eot: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fraenkel-lab/GSLR/7a10e8823a7edb7f0eb1f5f1801e711002560b09/docs/html/_static/fonts/fontawesome-webfont.eot -------------------------------------------------------------------------------- /docs/html/_static/fonts/fontawesome-webfont.ttf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fraenkel-lab/GSLR/7a10e8823a7edb7f0eb1f5f1801e711002560b09/docs/html/_static/fonts/fontawesome-webfont.ttf -------------------------------------------------------------------------------- /docs/html/_static/fonts/fontawesome-webfont.woff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/fraenkel-lab/GSLR/7a10e8823a7edb7f0eb1f5f1801e711002560b09/docs/html/_static/fonts/fontawesome-webfont.woff -------------------------------------------------------------------------------- /docs/html/_static/js/theme.js: -------------------------------------------------------------------------------- 1 | require=(function e(t,n,r){function s(o,u){if(!n[o]){if(!t[o]){var a=typeof require=="function"&&require;if(!u&&a)return a(o,!0);if(i)return i(o,!0);var f=new Error("Cannot find module '"+o+"'");throw f.code="MODULE_NOT_FOUND",f}var l=n[o]={exports:{}};t[o][0].call(l.exports,function(e){var n=t[o][1][e];return s(n?n:e)},l,l.exports,e,t,n,r)}return n[o].exports}var i=typeof require=="function"&&require;for(var o=0;o
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