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5.2 KiB

STS

codes for membrane transporter paper:

  1. model_training_*.py are codes for parameter tuning in a server.
  2. all the tables and figs can be reproduced via jupyter notebooks.
  3. Regarding the raw feature extraction pipeline, these codes and data are provided upon request.
  4. iterstrat.py is the implementation of iterative stratification.

Dependencies:

  1. alabaster==0.7.12
  2. anaconda-client==1.7.2
  3. anaconda-navigator==1.9.7
  4. anaconda-project==0.8.3
  5. arff==0.9
  6. asn1crypto==0.24.0
  7. astroid==2.2.5
  8. astropy==3.2.1
  9. atomicwrites==1.3.0
  10. attrs==19.1.0
  11. Babel==2.7.0
  12. backcall==0.1.0
  13. backports.functools-lru-cache==1.5
  14. backports.os==0.1.1
  15. backports.shutil-get-terminal-size==1.0.0
  16. backports.tempfile==1.0
  17. backports.weakref==1.0.post1
  18. beautifulsoup4==4.7.1
  19. bitarray==0.9.3
  20. bkcharts==0.2
  21. bleach==3.1.0
  22. bokeh==1.2.0
  23. boto==2.49.0
  24. boto3==1.9.220
  25. botocore==1.12.220
  26. Bottleneck==1.2.1
  27. certifi==2019.6.16
  28. cffi==1.12.3
  29. chardet==3.0.4
  30. Click==7.0
  31. cloudpickle==1.2.1
  32. clyent==1.2.2
  33. colorama==0.4.1
  34. comtypes==1.1.7
  35. conda==4.7.10
  36. conda-build==3.18.8
  37. conda-package-handling==1.3.11
  38. conda-verify==3.4.2
  39. contextlib2==0.5.5
  40. cryptography==2.7
  41. cycler==0.10.0
  42. Cython==0.29.12
  43. cytoolz==0.10.0
  44. dask==2.1.0
  45. decorator==4.4.0
  46. defusedxml==0.6.0
  47. distributed==2.1.0
  48. docutils==0.14
  49. entrypoints==0.3
  50. et-xmlfile==1.0.1
  51. fastcache==1.1.0
  52. filelock==3.0.12
  53. Flask==1.1.1
  54. future==0.17.1
  55. gensim==3.8.0
  56. gevent==1.4.0
  57. glob2==0.7
  58. greenlet==0.4.15
  59. h5py==2.9.0
  60. heapdict==1.0.0
  61. html5lib==1.0.1
  62. idna==2.8
  63. imageio==2.5.0
  64. imagesize==1.1.0
  65. importlib-metadata==0.17
  66. ipykernel==5.1.1
  67. ipython==7.6.1
  68. ipython-genutils==0.2.0
  69. ipywidgets==7.5.0
  70. isort==4.3.21
  71. itsdangerous==1.1.0
  72. jdcal==1.4.1
  73. jedi==0.13.3
  74. Jinja2==2.10.1
  75. jmespath==0.9.4
  76. joblib==0.13.2
  77. json5==0.8.4
  78. jsonschema==3.0.1
  79. jupyter==1.0.0
  80. jupyter-client==5.3.1
  81. jupyter-console==6.0.0
  82. jupyter-core==4.5.0
  83. jupyterlab==1.0.2
  84. jupyterlab-server==1.0.0
  85. keyring==18.0.0
  86. kiwisolver==1.1.0
  87. lazy-object-proxy==1.4.1
  88. libarchive-c==2.8
  89. lightgbm==2.2.3
  90. llvmlite==0.29.0
  91. locket==0.2.0
  92. lxml==4.3.4
  93. MarkupSafe==1.1.1
  94. matplotlib==3.1.0
  95. mccabe==0.6.1
  96. menuinst==1.4.16
  97. mistune==0.8.4
  98. mkl-fft==1.0.12
  99. mkl-random==1.0.2
  100. mkl-service==2.0.2
  101. mlxtend==0.17.0
  102. mock==3.0.5
  103. mol2vec==0.1
  104. MolVS==0.1.1
  105. more-itertools==7.0.0
  106. mpmath==1.1.0
  107. msgpack==0.6.1
  108. multipledispatch==0.6.0
  109. navigator-updater==0.2.1
  110. nbconvert==5.5.0
  111. nbformat==4.4.0
  112. networkx==2.3
  113. nltk==3.4.4
  114. nose==1.3.7
  115. notebook==6.0.0
  116. numba==0.44.1
  117. numexpr==2.6.9
  118. numpy==1.16.4
  119. numpydoc==0.9.1
  120. olefile==0.46
  121. openpyxl==2.6.2
  122. packaging==19.0
  123. pandas==0.24.2
  124. pandocfilters==1.4.2
  125. parso==0.5.0
  126. partd==1.0.0
  127. path.py==12.0.1
  128. pathlib2==2.3.4
  129. patsy==0.5.1
  130. pep8==1.7.1
  131. pickleshare==0.7.5
  132. Pillow==6.1.0
  133. pkginfo==1.5.0.1
  134. pluggy==0.12.0
  135. ply==3.11
  136. prometheus-client==0.7.1
  137. prompt-toolkit==2.0.9
  138. psutil==5.6.3
  139. py==1.8.0
  140. pycairo==1.18.1
  141. pycodestyle==2.5.0
  142. pycosat==0.6.3
  143. pycparser==2.19
  144. pycrypto==2.6.1
  145. pycurl==7.43.0.3
  146. pyflakes==2.1.1
  147. Pygments==2.4.2
  148. pylint==2.3.1
  149. pyodbc==4.0.26
  150. pyOpenSSL==19.0.0
  151. pyparsing==2.4.0
  152. pyreadline==2.1
  153. pyrsistent==0.14.11
  154. PySocks==1.7.0
  155. pytest==5.0.1
  156. pytest-arraydiff==0.3
  157. pytest-astropy==0.5.0
  158. pytest-doctestplus==0.3.0
  159. pytest-openfiles==0.3.2
  160. pytest-remotedata==0.3.1
  161. python-dateutil==2.8.0
  162. python-louvain==0.13
  163. pytz==2019.1
  164. PyWavelets==1.0.3
  165. pywin32==223
  166. pywinpty==0.5.5
  167. PyYAML==5.1.1
  168. pyzmq==18.0.0
  169. QtAwesome==0.5.7
  170. qtconsole==4.5.1
  171. QtPy==1.8.0
  172. requests==2.22.0
  173. rope==0.14.0
  174. ruamel-yaml==0.15.46
  175. s3transfer==0.2.1
  176. scikit-image==0.15.0
  177. scikit-learn==0.20.3
  178. scikit-multilearn==0.2.0
  179. scipy==1.2.1
  180. seaborn==0.9.0
  181. Send2Trash==1.5.0
  182. simplegeneric==0.8.1
  183. singledispatch==3.4.0.3
  184. six==1.12.0
  185. smart-open==1.8.4
  186. snowballstemmer==1.9.0
  187. sortedcollections==1.1.2
  188. sortedcontainers==2.1.0
  189. soupsieve==1.8
  190. Sphinx==2.1.2
  191. sphinxcontrib-applehelp==1.0.1
  192. sphinxcontrib-devhelp==1.0.1
  193. sphinxcontrib-htmlhelp==1.0.2
  194. sphinxcontrib-jsmath==1.0.1
  195. sphinxcontrib-qthelp==1.0.2
  196. sphinxcontrib-serializinghtml==1.1.3
  197. sphinxcontrib-websupport==1.1.2
  198. spyder==3.3.6
  199. spyder-kernels==0.5.1
  200. SQLAlchemy==1.3.5
  201. statsmodels==0.10.0
  202. sympy==1.4
  203. tables==3.5.2
  204. tblib==1.4.0
  205. terminado==0.8.2
  206. testpath==0.4.2
  207. toolz==0.10.0
  208. tornado==6.0.3
  209. tqdm==4.32.1
  210. traitlets==4.3.2
  211. unicodecsv==0.14.1
  212. urllib3==1.24.2
  213. wcwidth==0.1.7
  214. webencodings==0.5.1
  215. Werkzeug==0.15.4
  216. widgetsnbextension==3.5.0
  217. win-inet-pton==1.1.0
  218. win-unicode-console==0.5
  219. wincertstore==0.2
  220. wrapt==1.11.2
  221. xgboost==0.90
  222. xlrd==1.2.0
  223. XlsxWriter==1.1.8
  224. xlwings==0.15.8
  225. xlwt==1.3.0
  226. zict==1.0.0
  227. zipp==0.5.1