├── .gitattributes ├── ExtrinsicEva.sh ├── README.md ├── createModel.sh ├── create_shf_low_text.sh ├── evaluate.py ├── geniass ├── CVS │ ├── Entries │ ├── Repository │ └── Root ├── Classifying2Splitting.rb ├── EventExtracter.rb ├── LICENSE ├── Makefile ├── README ├── blmvm.cpp ├── blmvm.h ├── blmvm.o ├── geniass ├── makeMapping ├── makeMapping.C ├── makeMapping.o ├── maxent.cpp ├── maxent.h ├── maxent.o ├── model1-0.0 ├── model1-1.0 ├── model2-0.0 ├── model2-0.5 ├── model2-1.0 ├── model2-1.5 ├── model2-2.0 ├── model2c.cpp ├── remapStandOff ├── remapStandOff.C ├── remapStandOff.o ├── run_geniass.sh ├── sample.cpp ├── sample.o ├── segmentText │ ├── 1.txt │ └── 2.txt └── sentence2standOff.rb ├── intrinsicEva.sh ├── keras ├── data │ └── ner │ │ ├── BC2GM-IOB │ │ ├── devel.tsv │ │ ├── test.tsv │ │ └── train.tsv │ │ ├── BC2GM-narrow │ │ ├── README │ │ ├── devel.tsv │ │ ├── test.tsv │ │ └── train.tsv │ │ ├── BC2GM │ │ ├── devel.tsv │ │ ├── original-data │ │ │ └── test │ │ │ │ ├── ALTGENE.eval │ │ │ │ ├── GENE.eval │ │ │ │ ├── README │ │ │ │ ├── alt_eval.perl │ │ │ │ ├── test.idmap │ │ │ │ └── test.in │ │ ├── test.tsv │ │ └── train.tsv │ │ └── JNLPBA │ │ ├── devel.tsv │ │ ├── original-data │ │ ├── test │ │ │ ├── Genia4EReval1.iob2 │ │ │ └── LICENSE │ │ └── train │ │ │ ├── Genia4ERtask1.iob2 │ │ │ └── LICENSE │ │ ├── test.tsv │ │ ├── tools │ │ ├── 1978-1989.lst │ │ ├── 1990-1999.lst │ │ ├── 2000-2001.lst │ │ ├── Genia4EReval.ref │ │ ├── ReadMe.txt │ │ ├── S1998-2001.lst │ │ ├── SharedTaskEval.pl │ │ ├── combine-and-eval.sh │ │ ├── combine.py │ │ ├── evalIOB2.pl │ │ └── fixbio.py │ │ └── train.tsv └── ner │ ├── batch-ner.sh │ ├── common.pyc │ ├── conv.py │ ├── convall.sh │ ├── input_data.pyc │ ├── layers.py │ ├── layers.pyc │ ├── mlp.py │ ├── rnn.py │ ├── settings.py │ └── settings.pyc ├── lower_shuffled_combine_tokenized.txt ├── pre-process.sh ├── tokenize_Text.py ├── tools ├── __init__.py ├── __init__.pyc ├── utilities.py └── utilities.pyc ├── word2vec ├── LICENSE ├── LICENSE.txt ├── README.txt ├── compute-accuracy ├── compute-accuracy.c ├── data-phrase.txt ├── demo-analogy.sh ├── demo-classes.sh ├── demo-phrase-accuracy.sh ├── demo-phrases.sh ├── demo-train-big-model-v1.sh ├── demo-word-accuracy.sh ├── demo-word.sh ├── distance ├── distance.c ├── makefile ├── questions-words.txt ├── word-analogy ├── word-analogy.c ├── word2phrase ├── word2phrase.c ├── word2phrase.c.1 ├── word2vec ├── word2vec.c └── word2vec.c.1 └── wvlib ├── LICENSE ├── README.md ├── __init__.py ├── __init__.pyc ├── analogy.py ├── analogy.pyc ├── common.py ├── common.pyc ├── compat ├── __init__.py ├── argparse.py └── ordereddict.py ├── convert.py ├── dbscan.py ├── eval-all-classes.sh ├── eval-all-ranks.sh ├── evalclass.py ├── evalclass.pyc ├── evalrank.py ├── evalrank.pyc ├── evalset.py ├── kmeans.py ├── nearest.py ├── output ├── output1 ├── pairdist.py ├── relation.py ├── similarity.py ├── similarity.pyc ├── tools └── convert-senna-embeddings.sh ├── word-classes ├── AP-05 │ ├── README │ ├── animal.txt │ ├── assets.txt │ ├── atmospheric_phenomenon.txt │ ├── chemical_element.txt │ ├── creator.txt │ ├── district.txt │ ├── edible_fruit.txt │ ├── feeling.txt │ ├── game.txt │ ├── illness.txt │ ├── legal_document.txt │ ├── monetary_unit.txt │ ├── motivation.txt │ ├── pain.txt │ ├── physical_property.txt │ ├── social_occasion.txt │ ├── social_unit.txt │ ├── solid.txt │ ├── time.txt │ ├── tree.txt │ └── vehicle.txt ├── BLESS-classes │ ├── README │ ├── amphibian_reptile.txt │ ├── appliance.txt │ ├── bird.txt │ ├── building.txt │ ├── clothing.txt │ ├── container.txt │ ├── fruit.txt │ ├── furniture.txt │ ├── ground_mammal.txt │ ├── insect.txt │ ├── musical_instrument.txt │ ├── tool.txt │ ├── tree.txt │ ├── vegetable.txt │ ├── vehicle.txt │ ├── water_animal.txt │ └── weapon.txt ├── McIC-09 │ ├── ANTI.txt │ ├── CELL.txt │ ├── CLNE.txt │ ├── DISE.txt │ ├── DRUG.txt │ ├── FUNC.txt │ ├── MUTN.txt │ ├── PROT.txt │ ├── README │ ├── SIGN.txt │ └── TUMR.txt └── Ohta-10-bio-words │ ├── README │ ├── antibiotic.txt │ ├── biotoxin.txt │ ├── cell-type.txt │ ├── multi-tissue-structure.txt │ ├── nationality.txt │ ├── oncogene.txt │ ├── organ-system.txt │ ├── organism-subdiv-animal.txt │ ├── organism-subdiv-plant.txt │ ├── process-function.txt │ ├── property-color.txt │ └── tissue.txt ├── word-sets └── Ohta-bio-sets │ ├── README │ ├── bacteria.txt │ ├── chemical-elements.txt │ ├── human-bones.txt │ ├── human-cancers.txt │ ├── human-organs.txt │ ├── livestock.txt │ ├── protein-ptms.txt │ ├── standard-amino-acids.txt │ └── tumor-suppressor-genes.txt ├── word-similarities ├── MC-30 │ └── EN-MC-30.txt ├── MEM-TR-3k │ └── EN-MEN-TR-3k.txt ├── MTurk-287 │ └── EN-MTurk-287.txt ├── MTurk-771 │ └── EN-MTurk-771.txt ├── MayoSRS │ ├── MayoSRS.txt │ ├── MiniMayoSRS.txt │ └── README ├── RG-65 │ └── EN-RG-65.txt ├── RW-STANFORD │ └── EN-RW-STANFORD.txt ├── SimLex-999 │ ├── README │ └── SimLex-999.txt ├── UMNSRS │ ├── README │ ├── UMNSRS-rel.txt │ ├── UMNSRS-sim.txt │ └── 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