BaderLab / saber

Saber is a deep-learning based tool for information extraction in the biomedical domain. Pull requests are welcome! Note: this is a work in progress. Many things are broken, and the codebase is not stable.
https://baderlab.github.io/saber/
MIT License
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Pretrained_model #93

Closed rishabh279 closed 5 years ago

rishabh279 commented 5 years ago

Can you please provide pretrained_model for DISO as you have provided for PRGE.

JohnGiorgi commented 5 years ago

Yes! I will try to have that done before the end of the week.

rishabh279 commented 5 years ago

Thank you!

JohnGiorgi commented 5 years ago

Training... ⏲

JohnGiorgi commented 5 years ago

Okay, the model has be added. You can play around with it in a jupyter notebook with:

from saber import Saber()
saber = Saber()
saber.load('DISO')
text = '''Chronic kidney disease is a worldwide public health problem with an increasing incidence and prevalence, poor outcomes, and high cost. Outcomes of chronic kidney disease include not only kidney failure but also complications of decreased kidney function and cardiovascular disease. Current evidence suggests that some of these adverse outcomes can be prevented or delayed by early detection and treatment. Unfortunately, chronic kidney disease is underdiagnosed and undertreated, in part as a result of lack of agreement on a definition and classification of its stages of progression.'''
saber.annotate(text, jupyter=True)

which gives:

screen shot 2018-12-01 at 7 07 14 pm

or use the local web-service.

Just a few things to note:

Please let me know if that works!

rishabh279 commented 5 years ago

Sure and thanks a lot!! . I will try the model and let you know.