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| |____tests
| | |____sample-matrix-file.txt
| | |____test_clusters.py
| | |____test_sanitycheck.py
| | |____test_ebc.py
| | |____test_benchmark_ebc.py
| | |____test_benchmark_ebc2d.py
| | |____test_matrix.py
| |____ebc.py
| |______init__.py
| |______pycache__
| | |______init__.cpython-38.pyc
| | |____ebc.cpython-38.pyc
| | |____matrix.cpython-38.pyc
| |____README.md
| |____.gitignore
| |____ebc2d.py
| |____.ipynb_checkpoints
| |____clusters-repeat.py
| |____.git
| | |____config
| | |____objects
| | | |____info
| | |____HEAD
| | |____info
| | | |____exclude
| | |____logs
| | | |____HEAD
| | | |____refs
| | | | |____heads
| | | | | |____master
| | | | |____remotes
| | | | | |____origin
| | | | | | |____HEAD
| | |____description
| | | |____heads
| | | | |____master
| | | |____tags
| | | |____remotes
| | | | |____origin
| | | | | |____HEAD
| | |____index
| | |____packed-refs
| | |____FETCH_HEAD
| |____LICENSE.txt
|____.DS_Store
|____LICENSE
|____module4
| |____test_ebc_scoring.py
| |____implement_ebc_scoring.py
| |____ebc_scoring_walkthrough.ipynb
| |____ebc_scoring.py
| |____drugbank_pairs.tsv
| |______pycache__
| | |____ebc_scoring.cpython-38.pyc
| | |____auc.cpython-38.pyc
| | |____visualize.cpython-38.pyc
| |____visualize.py
| |____.ipynb_checkpoints
| |____auc_walkthrough.ipynb
| |____temp-plot.html
| |____drugbank.py
| |____auc.py
|____module3
| |____ebc
| | |____matrix.py
| | |____ebc.py
| | |______pycache__
| | | |____ebc.cpython-38.pyc
| | | |____matrix.cpython-38.pyc
| |____Co-occurrency Matrix
| | |____Co-occurrency.ipynb
| | |____Co-occurrency_Matrix.csv
| |____biomedical_eda.py
| |____implement_itcc.py
| |______init__.py
| |______pycache__
| | |______init__.cpython-38.pyc
| | |____itcc.cpython-38.pyc
| | |____visualize.cpython-38.pyc
| |____visualize.py
| |____itcc.py
| |____pair_path_mappings.ipynb
| |____itcc_test.py
| |____Pair_Path_Mapping_Sparse.csv
| |____cXY.csv
| |____.ipynb_checkpoints
| |____druggene_mappings.csv
| |____path_mappings.csv
| |____Pair_Path_Mapping_Dense.csv
|____module2
| |____prepare_pubmed_data.py
| |____.coverage
| |______init__.py
| |______pycache__
| | |____stanford.cpython-38.pyc
| | |____prepare_pubmed_data.cpython-38.pyc
| |____module2attempt.py
| |____stanford.py
| |____path_parse.py
| |____prepare_pubmed_data_test.py
| |____test_stanford.py
| |____module2 dependency matrix.ipynb
| |____depedency_matrix_synthesis.py
|____module5
| |____artifact_itcc.csv
| |____cluster_dendrogram.jpeg
| |____agglomerative_clustering.py
| |____dendrogram.jpeg
| |____Stem dendrogram.Rmd
|____stanford-parser-full-2014-10-31
| |____edu
| | |____stanford
| | | |____nlp
| | | | |____models
| | | | | |____lexparser
| | | | | | |____xinhuaPCFG.ser.gz
| | | | | | |____xinhuaFactoredSegmenting.ser.gz
| | | | | | |____englishPCFG.ser.gz
| | | | | | |____wsjFactored.ser.gz
| | | | | | |____englishRNN.ser.gz
| | | | | | |____germanFactored.ser.gz
| | | | | | |____chinesePCFG.ser.gz
| | | | | | |____chineseFactored.ser.gz
| | | | | | |____germanPCFG.ser.gz
| | | | | | |____englishPCFG.caseless.ser.gz
| | | | | | |____englishFactored.ser.gz
| | | | | | |____frenchFactored.ser.gz
| | | | | | |____xinhuaFactored.ser.gz
| | | | | | |____wsjRNN.ser.gz
| | | | | | |____wsjPCFG.ser.gz
| | | | | | |____spanishPCFG.ser.gz
| | | | | | |____arabicFactored.ser.gz
| | | | | |____parser
| | | | | | |____nndep
| | | | | | | |____CTB_CoNLL_params.txt.gz
| | | | | | | |____PTB_Stanford_params.txt.gz
| | | | | | | |____PTB_CoNLL_params.txt.gz
| |____lexparser.bat
| |____DependencyParserDemo.java
| |____biomedical_typed_dependencies.txt
| |____.DS_Store
| |____stanford-parser-3.5.0-sources.jar
| |____ejml-0.23.jar
| |____bin
| | |____makeSerialized.csh
| | |____run-tb-preproc
| |____lexparser-gui.command
| |____stanford-parser-3.5.0-javadoc.jar
| |____build.xml
| |____demo_dependency_output.txt
| |____.jython_cache
| | |____packages
| | | |____sunec.pkc
| | | |____jfr.pkc
| | | |____jsse.pkc
| | | |____jfxrt.pkc
| | | |____rt.pkc
| | | |____nashorn.pkc
| | | |____cldrdata.pkc
| | | |____localedata.pkc
| | | |____stanford-parser.pkc
| | | |____sunjce_provider.pkc
| | | |____dnsns.pkc
| | | |____charsets.pkc
| | | |____resources.pkc
| | | |____jaccess.pkc
| | | |____sunpkcs11.pkc
| | | |____jython.pkc
| | | |____zipfs.pkc
| | | |____jce.pkc
| | | |____packages.idx
| |____first_dependency_output.txt
| |____ParserDemo2.java
| |____Makefile
| |____target
| | |____test-classes
| | |____classes
| |____lexparser-lang-train-test.sh
| |____stanford-parser-3.5.0-models.jar
| |____lexparser-gui.sh
| |____pom.xml
| |____META-INF
| | |____MANIFEST.MF
| |____.classpath
| |____ParserDemo.java
| |____demo_dependency.txt
| |____README_dependencies.txt
| |____.settings
| | |____org.eclipse.jdt.core.prefs
| | |____org.eclipse.jdt.apt.core.prefs
| | |____org.eclipse.m2e.core.prefs
| |____dependency_parsing_instructions.txt
| |____.project
| |____lexparser-gui.bat
| |____stanford-parser.jar
| |____README.txt
| |____lexparser-lang.sh
| |____ShiftReduceDemo.java
| |____ejml-0.23-src.zip
| |____LICENSE.txt
| |____data
| | |____pos-sentences.txt
| | |____english-onesent.txt
| | |____german-onesent.txt
| | |____testsent.txt
| | |____chinese-onesent-unseg-gb18030.txt
| | |____french-onesent.txt
| | |____chinese-onesent-gb18030.txt
| | |____chinese-onesent-unseg-utf8.txt
| | |____arabic-onesent-utf8.txt
| | |____chinese-onesent-utf8.txt
| |____conf
| | |____ftb-latest.conf
| | |____atb-latest.conf
| |____lexparser.sh
| |____lexparser_lang.def
| |____StanfordDependenciesManual.pdf
|____stem_away.egg-info
| |____PKG-INFO
| |____SOURCES.txt
| |____top_level.txt
| |____dependency_links.txt
|____README.md
|____utilities
|____visualizations
| |____.DS_Store
| |____Biomedical Data Lengths.png
|____setup.py
|____embeddings.py
|____.gitignore
|____.gitattributes
|____stemaway.egg-info
| |____PKG-INFO
| |____SOURCES.txt
| |____top_level.txt
| |____dependency_links.txt
|____history.txt
|____.ipynb_checkpoints
|____.git
| |____ORIG_HEAD
| |____config
| |____objects
| | |____61
| | | |____dd5b290add2dbac48087dd3487272a63adb416
| | |____0d
| | | |____b103610cc86e0b22dd98b065c236d58d02fad3
| | | |____6f7892ef347f5de8f54885b2024c7085282285
| | | |____3dc0e16e6cb5fc350c95cdeb4d153fa9add8fb
| | |____95
| | | |____23635b9dd9099b2a0c887b0d730120affa745b
| | |____59
| | | |____c382fea63cead5d32eb24fa92f2ccaa0326214
| | |____92
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| | |____0c
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| | | |____e3c798c0fd2b4230722f61c5357e1cab10d5f2
| | |____66
| | | |____21ec4531de36b26ae60fea26c3666e7f27666c
| | | |____0f78fcd5265157ae901df0e064e976e93318bc
| | |____50
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| | | |____7865c5f29f1ce4796baecbf032fc31852e254a
| | |____57
| | | |____eea4d8657d083a5c25a12108832dd91a11fed7
| | | |____bd210f238ba058232c9bac1a3b517fa02e2e1e
| | | |____11a1eac2d96c2ad856608ff499b280d0162519
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| | | |____8677deebb3a8954af9658dd37d55e6f3b340bc
| | |____9b
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| | | |____72b0d09e661d21b3154bd28333b80f760375c9
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| | |____35
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| | |____69
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| | |____3d
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| | | |____40ab651587aa2c2478ff45e5f19dcc51341272
| | |____34
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| | |____5f
| | | |____5fc2e14db9fb54f16bc5cf442cfec9e18851b8
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| | |____33
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| | | |____f7fbc5df6af7912b1c2c306bcf5f8d60e6e581
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| | | |____seed_test_sets_2021-08-16,21:27.txt
| | | |____seed_test_sets_2021-08-18,19:00.txt
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| | |____CREATED_2021-06-05.txt
| | |____LICENSE.txt
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