├── LICENSE ├── README.md ├── bert ├── file_utils.py ├── modeling.py ├── optimization.py └── tokenization.py ├── configs ├── brat │ ├── cg │ │ └── annotation.conf │ └── pc │ │ ├── annotation.conf │ │ └── visual.conf ├── cg.yaml ├── default.yaml ├── epi.yaml ├── ge11.yaml ├── ge13.yaml ├── id.yaml └── mlee.yaml ├── data └── my-pubmed │ ├── pmid.txt │ └── text │ ├── PMID-1370299.txt │ └── PMID-1670994.txt ├── download.sh ├── eval ├── evalEV.py ├── evalRE.py ├── evaluate.py └── scripts │ ├── eval-ev-cg.py │ └── eval-ev-pc.py ├── img └── PMID-1370299.png ├── install.sh ├── loader ├── prepData │ ├── brat.py │ ├── entity.py │ ├── prepdata.py │ └── sentence.py └── prepNN │ ├── ent2net.py │ ├── prep4nn.py │ ├── sent2net.py │ └── span4nn.py ├── nets ├── EVGen.py ├── EVNet.py ├── NERNet.py ├── RELNet.py └── deepEM.py ├── predict.py ├── preprocess.sh ├── pubmed.sh ├── pubmed ├── med2text.py └── pubmed2text.py ├── requirements.txt ├── run.sh ├── scripts ├── file_utils.py ├── generate_configs.py 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