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Katherine1216
bcee5983c1
|
2 years ago | |
|---|---|---|
| MTS.tif | 2 years ago | |
| README | 2 years ago | |
| README.md | 2 years ago | |
| Supplementary Material.csv | 2 years ago | |
| Ys.csv | 2 years ago | |
| after_analysis.ipynb | 2 years ago | |
| correlation.csv | 2 years ago | |
| exploratory_analysis.ipynb | 2 years ago | |
| feature_similarity_chebi_ontology_DiShIn_2.csv | 2 years ago | |
| final_reports.csv | 2 years ago | |
| iterstrat.py | 2 years ago | |
| label_matrix.txt | 2 years ago | |
| model_training.ipynb | 2 years ago | |
| model_training.py | 2 years ago | |
| model_training_XGB.py | 2 years ago | |
| model_training_ext.py | 2 years ago | |
| model_training_lgb.py | 2 years ago | |
| model_training_mtsvm.py | 2 years ago | |
| model_training_rakeld-nb.py | 2 years ago | |
| model_training_rakeld-rf.py | 2 years ago | |
| model_training_rakeld.py | 2 years ago | |
| model_training_rf.py | 2 years ago | |
| model_training_template.py | 2 years ago | |
| query_smiles_feature_similarity_four_average.csv | 2 years ago | |
| single_label.ipynb | 2 years ago | |
README.md
STS
codes for membrane transporter paper:
- model_training_
*.py are codes for parameter tuning in a server. - all the tables and figs can be reproduced via jupyter notebooks.
- Regarding the raw feature extraction pipeline, these codes and data are provided upon request.
iterstrat.pyis the implementation of iterative stratification.
Dependencies:
- alabaster==0.7.12
- anaconda-client==1.7.2
- anaconda-navigator==1.9.7
- anaconda-project==0.8.3
- arff==0.9
- asn1crypto==0.24.0
- astroid==2.2.5
- astropy==3.2.1
- atomicwrites==1.3.0
- attrs==19.1.0
- Babel==2.7.0
- backcall==0.1.0
- backports.functools-lru-cache==1.5
- backports.os==0.1.1
- backports.shutil-get-terminal-size==1.0.0
- backports.tempfile==1.0
- backports.weakref==1.0.post1
- beautifulsoup4==4.7.1
- bitarray==0.9.3
- bkcharts==0.2
- bleach==3.1.0
- bokeh==1.2.0
- boto==2.49.0
- boto3==1.9.220
- botocore==1.12.220
- Bottleneck==1.2.1
- certifi==2019.6.16
- cffi==1.12.3
- chardet==3.0.4
- Click==7.0
- cloudpickle==1.2.1
- clyent==1.2.2
- colorama==0.4.1
- comtypes==1.1.7
- conda==4.7.10
- conda-build==3.18.8
- conda-package-handling==1.3.11
- conda-verify==3.4.2
- contextlib2==0.5.5
- cryptography==2.7
- cycler==0.10.0
- Cython==0.29.12
- cytoolz==0.10.0
- dask==2.1.0
- decorator==4.4.0
- defusedxml==0.6.0
- distributed==2.1.0
- docutils==0.14
- entrypoints==0.3
- et-xmlfile==1.0.1
- fastcache==1.1.0
- filelock==3.0.12
- Flask==1.1.1
- future==0.17.1
- gensim==3.8.0
- gevent==1.4.0
- glob2==0.7
- greenlet==0.4.15
- h5py==2.9.0
- heapdict==1.0.0
- html5lib==1.0.1
- idna==2.8
- imageio==2.5.0
- imagesize==1.1.0
- importlib-metadata==0.17
- ipykernel==5.1.1
- ipython==7.6.1
- ipython-genutils==0.2.0
- ipywidgets==7.5.0
- isort==4.3.21
- itsdangerous==1.1.0
- jdcal==1.4.1
- jedi==0.13.3
- Jinja2==2.10.1
- jmespath==0.9.4
- joblib==0.13.2
- json5==0.8.4
- jsonschema==3.0.1
- jupyter==1.0.0
- jupyter-client==5.3.1
- jupyter-console==6.0.0
- jupyter-core==4.5.0
- jupyterlab==1.0.2
- jupyterlab-server==1.0.0
- keyring==18.0.0
- kiwisolver==1.1.0
- lazy-object-proxy==1.4.1
- libarchive-c==2.8
- lightgbm==2.2.3
- llvmlite==0.29.0
- locket==0.2.0
- lxml==4.3.4
- MarkupSafe==1.1.1
- matplotlib==3.1.0
- mccabe==0.6.1
- menuinst==1.4.16
- mistune==0.8.4
- mkl-fft==1.0.12
- mkl-random==1.0.2
- mkl-service==2.0.2
- mlxtend==0.17.0
- mock==3.0.5
- mol2vec==0.1
- MolVS==0.1.1
- more-itertools==7.0.0
- mpmath==1.1.0
- msgpack==0.6.1
- multipledispatch==0.6.0
- navigator-updater==0.2.1
- nbconvert==5.5.0
- nbformat==4.4.0
- networkx==2.3
- nltk==3.4.4
- nose==1.3.7
- notebook==6.0.0
- numba==0.44.1
- numexpr==2.6.9
- numpy==1.16.4
- numpydoc==0.9.1
- olefile==0.46
- openpyxl==2.6.2
- packaging==19.0
- pandas==0.24.2
- pandocfilters==1.4.2
- parso==0.5.0
- partd==1.0.0
- path.py==12.0.1
- pathlib2==2.3.4
- patsy==0.5.1
- pep8==1.7.1
- pickleshare==0.7.5
- Pillow==6.1.0
- pkginfo==1.5.0.1
- pluggy==0.12.0
- ply==3.11
- prometheus-client==0.7.1
- prompt-toolkit==2.0.9
- psutil==5.6.3
- py==1.8.0
- pycairo==1.18.1
- pycodestyle==2.5.0
- pycosat==0.6.3
- pycparser==2.19
- pycrypto==2.6.1
- pycurl==7.43.0.3
- pyflakes==2.1.1
- Pygments==2.4.2
- pylint==2.3.1
- pyodbc==4.0.26
- pyOpenSSL==19.0.0
- pyparsing==2.4.0
- pyreadline==2.1
- pyrsistent==0.14.11
- PySocks==1.7.0
- pytest==5.0.1
- pytest-arraydiff==0.3
- pytest-astropy==0.5.0
- pytest-doctestplus==0.3.0
- pytest-openfiles==0.3.2
- pytest-remotedata==0.3.1
- python-dateutil==2.8.0
- python-louvain==0.13
- pytz==2019.1
- PyWavelets==1.0.3
- pywin32==223
- pywinpty==0.5.5
- PyYAML==5.1.1
- pyzmq==18.0.0
- QtAwesome==0.5.7
- qtconsole==4.5.1
- QtPy==1.8.0
- requests==2.22.0
- rope==0.14.0
- ruamel-yaml==0.15.46
- s3transfer==0.2.1
- scikit-image==0.15.0
- scikit-learn==0.20.3
- scikit-multilearn==0.2.0
- scipy==1.2.1
- seaborn==0.9.0
- Send2Trash==1.5.0
- simplegeneric==0.8.1
- singledispatch==3.4.0.3
- six==1.12.0
- smart-open==1.8.4
- snowballstemmer==1.9.0
- sortedcollections==1.1.2
- sortedcontainers==2.1.0
- soupsieve==1.8
- Sphinx==2.1.2
- sphinxcontrib-applehelp==1.0.1
- sphinxcontrib-devhelp==1.0.1
- sphinxcontrib-htmlhelp==1.0.2
- sphinxcontrib-jsmath==1.0.1
- sphinxcontrib-qthelp==1.0.2
- sphinxcontrib-serializinghtml==1.1.3
- sphinxcontrib-websupport==1.1.2
- spyder==3.3.6
- spyder-kernels==0.5.1
- SQLAlchemy==1.3.5
- statsmodels==0.10.0
- sympy==1.4
- tables==3.5.2
- tblib==1.4.0
- terminado==0.8.2
- testpath==0.4.2
- toolz==0.10.0
- tornado==6.0.3
- tqdm==4.32.1
- traitlets==4.3.2
- unicodecsv==0.14.1
- urllib3==1.24.2
- wcwidth==0.1.7
- webencodings==0.5.1
- Werkzeug==0.15.4
- widgetsnbextension==3.5.0
- win-inet-pton==1.1.0
- win-unicode-console==0.5
- wincertstore==0.2
- wrapt==1.11.2
- xgboost==0.90
- xlrd==1.2.0
- XlsxWriter==1.1.8
- xlwings==0.15.8
- xlwt==1.3.0
- zict==1.0.0
- zipp==0.5.1
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CSV Jupyter Notebook Text Python