├── .gitignore ├── .server.log ├── Ab3P ├── WordData │ ├── Ab3P_prec.dat │ ├── Lf1chSf │ ├── SingTermFreq.dat │ ├── cshset_wrdset3.ad │ ├── cshset_wrdset3.ct │ ├── cshset_wrdset3.ha │ ├── cshset_wrdset3.nm │ ├── cshset_wrdset3.str │ ├── hshset_Lf1chSf.ad │ ├── hshset_Lf1chSf.ha │ ├── hshset_Lf1chSf.nm │ ├── hshset_Lf1chSf.str │ ├── hshset_stop.ad │ ├── hshset_stop.ha │ ├── hshset_stop.nm │ ├── hshset_stop.str │ └── stop └── identify_abbr ├── LICENSE ├── README.md ├── demo.py ├── eval.py ├── images ├── biosyn_demo.gif ├── biosyn_overview.png ├── logo_dmis.png └── logo_eng.gif ├── inference.py ├── instance └── config.py ├── path_Ab3P ├── preprocess ├── README.md ├── bc5cdr_preprocess.py ├── ctd_preprocess.py ├── dictionary_preprocess.py ├── meddra_preprocess.py ├── ncbi_disease_preprocess.py ├── path_Ab3P ├── query_preprocess.py ├── resources │ ├── ctd_chemical_04Nov2019.txt │ ├── medic_06Jul2012.txt │ └── ncbi-spell-check.txt └── tac2017adr_preprocess.py ├── setup.cfg ├── setup.py ├── src └── biosyn │ ├── __init__.py │ ├── abbr_resolver.py │ ├── biosyn.py │ ├── data_loader.py │ ├── preprocesser.py │ ├── rerankNet.py │ └── sparse_encoder.py ├── template └── index.html ├── train.py └── utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/.gitignore -------------------------------------------------------------------------------- /.server.log: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/.server.log -------------------------------------------------------------------------------- /Ab3P/WordData/Ab3P_prec.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/Ab3P/WordData/Ab3P_prec.dat -------------------------------------------------------------------------------- /Ab3P/WordData/Lf1chSf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/Ab3P/WordData/Lf1chSf -------------------------------------------------------------------------------- /Ab3P/WordData/SingTermFreq.dat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/Ab3P/WordData/SingTermFreq.dat -------------------------------------------------------------------------------- /Ab3P/WordData/cshset_wrdset3.ad: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/Ab3P/WordData/cshset_wrdset3.ad -------------------------------------------------------------------------------- /Ab3P/WordData/cshset_wrdset3.ct: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/Ab3P/WordData/cshset_wrdset3.ct -------------------------------------------------------------------------------- /Ab3P/WordData/cshset_wrdset3.ha: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/Ab3P/WordData/cshset_wrdset3.ha -------------------------------------------------------------------------------- /Ab3P/WordData/cshset_wrdset3.nm: -------------------------------------------------------------------------------- 1 | 94718 524287 918071 2 | -------------------------------------------------------------------------------- /Ab3P/WordData/cshset_wrdset3.str: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/Ab3P/WordData/cshset_wrdset3.str -------------------------------------------------------------------------------- /Ab3P/WordData/hshset_Lf1chSf.ad: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/Ab3P/WordData/hshset_Lf1chSf.ad -------------------------------------------------------------------------------- /Ab3P/WordData/hshset_Lf1chSf.ha: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/Ab3P/WordData/hshset_Lf1chSf.ha -------------------------------------------------------------------------------- /Ab3P/WordData/hshset_Lf1chSf.nm: -------------------------------------------------------------------------------- 1 | 4991 32767 48126 2 | -------------------------------------------------------------------------------- /Ab3P/WordData/hshset_Lf1chSf.str: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/Ab3P/WordData/hshset_Lf1chSf.str -------------------------------------------------------------------------------- /Ab3P/WordData/hshset_stop.ad: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/Ab3P/WordData/hshset_stop.ad -------------------------------------------------------------------------------- /Ab3P/WordData/hshset_stop.ha: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/Ab3P/WordData/hshset_stop.ha -------------------------------------------------------------------------------- /Ab3P/WordData/hshset_stop.nm: -------------------------------------------------------------------------------- 1 | 313 2047 1870 2 | -------------------------------------------------------------------------------- /Ab3P/WordData/hshset_stop.str: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/Ab3P/WordData/hshset_stop.str -------------------------------------------------------------------------------- /Ab3P/WordData/stop: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/Ab3P/WordData/stop -------------------------------------------------------------------------------- /Ab3P/identify_abbr: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/Ab3P/identify_abbr -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/README.md -------------------------------------------------------------------------------- /demo.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/demo.py -------------------------------------------------------------------------------- /eval.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/eval.py -------------------------------------------------------------------------------- /images/biosyn_demo.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/images/biosyn_demo.gif -------------------------------------------------------------------------------- /images/biosyn_overview.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/images/biosyn_overview.png -------------------------------------------------------------------------------- /images/logo_dmis.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/images/logo_dmis.png -------------------------------------------------------------------------------- /images/logo_eng.gif: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/images/logo_eng.gif -------------------------------------------------------------------------------- /inference.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/inference.py -------------------------------------------------------------------------------- /instance/config.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /path_Ab3P: -------------------------------------------------------------------------------- 1 | ./Ab3P/WordData/ 2 | -------------------------------------------------------------------------------- /preprocess/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/preprocess/README.md -------------------------------------------------------------------------------- /preprocess/bc5cdr_preprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/preprocess/bc5cdr_preprocess.py -------------------------------------------------------------------------------- /preprocess/ctd_preprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/preprocess/ctd_preprocess.py -------------------------------------------------------------------------------- /preprocess/dictionary_preprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/preprocess/dictionary_preprocess.py -------------------------------------------------------------------------------- /preprocess/meddra_preprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/preprocess/meddra_preprocess.py -------------------------------------------------------------------------------- /preprocess/ncbi_disease_preprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/preprocess/ncbi_disease_preprocess.py -------------------------------------------------------------------------------- /preprocess/path_Ab3P: -------------------------------------------------------------------------------- 1 | ../Ab3P/WordData/ 2 | -------------------------------------------------------------------------------- /preprocess/query_preprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/preprocess/query_preprocess.py -------------------------------------------------------------------------------- /preprocess/resources/ctd_chemical_04Nov2019.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/preprocess/resources/ctd_chemical_04Nov2019.txt -------------------------------------------------------------------------------- /preprocess/resources/medic_06Jul2012.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/preprocess/resources/medic_06Jul2012.txt -------------------------------------------------------------------------------- /preprocess/resources/ncbi-spell-check.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/preprocess/resources/ncbi-spell-check.txt -------------------------------------------------------------------------------- /preprocess/tac2017adr_preprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/preprocess/tac2017adr_preprocess.py -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | [metadata] 2 | description-file = README.md -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/setup.py -------------------------------------------------------------------------------- /src/biosyn/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/src/biosyn/__init__.py -------------------------------------------------------------------------------- /src/biosyn/abbr_resolver.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/src/biosyn/abbr_resolver.py -------------------------------------------------------------------------------- /src/biosyn/biosyn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/src/biosyn/biosyn.py -------------------------------------------------------------------------------- /src/biosyn/data_loader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/src/biosyn/data_loader.py -------------------------------------------------------------------------------- /src/biosyn/preprocesser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/src/biosyn/preprocesser.py -------------------------------------------------------------------------------- /src/biosyn/rerankNet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/src/biosyn/rerankNet.py -------------------------------------------------------------------------------- /src/biosyn/sparse_encoder.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/src/biosyn/sparse_encoder.py -------------------------------------------------------------------------------- /template/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/template/index.html -------------------------------------------------------------------------------- /train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/train.py -------------------------------------------------------------------------------- /utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dmis-lab/BioSyn/HEAD/utils.py --------------------------------------------------------------------------------