cambridgeltl / mtl-bioinformatics-2016 Goto Github PK
View Code? Open in Web Editor NEWLicense: Creative Commons Attribution 4.0 International
License: Creative Commons Attribution 4.0 International
Hi,
Where is this standoff2conll script and how can we use it?
Hi,
Thanks for providing these useful resources!
While we were using the resources, we got to know that sentences in JNLPBA-IOBES dataset might be incorrectly split.
MTL-Bioinformatics-2016/data/JNLPBA-IOBES/test.tsv
starts with
Number O
of O
glucocorticoid B-protein
receptors E-protein
in O
lymphocytes S-cell_type
and O
their O
sensitivity O
to O
hormone O
action O
. O
The O
study O
demonstrated O
while MTL-Bioinformatics-2016/data/JNLPBA/test.tsv
starts with
-DOCSTART- O
Number O
of O
glucocorticoid B-protein
receptors I-protein
in O
lymphocytes B-cell_type
and O
their O
sensitivity O
to O
hormone O
action O
. O
The O
study O
We used our own post-preprocessing script to fix this and used the fixed dataset in our experiments.
Once again, thank you so much for sharing these useful resources!
Dear @GamalC ,
This is to first and foremost thank you sincerly for preparing the dataset. I wonder which tokenizer did you use when splitting raw sentences to tokens.?
Looking forward to your answer.
Running the baseline.py
I get the error in the title. More precisely the log is the following
models/baseline:using ConllEvaluator for NCBI-disease-IOB-train
models/baseline:using ConllEvaluator for NCBI-disease-IOB-test
Epoch 1/20
135701/135701 [==============================] - 8s - loss: 0.1265 - acc: 0.9620
models/baseline:Ep: 1 8s (start 2018-01-26 13:31:20, end 2018-01-26 13:31:29)
Traceback (most recent call last):
File "models/baseline.py", line 71, in <module>
verbose=config.verbosity
File "/home/aris/py_envs/py2/local/lib/python2.7/site-packages/keras/engine/training.py", line 1196, in fit
initial_epoch=initial_epoch)
File "/home/aris/py_envs/py2/local/lib/python2.7/site-packages/keras/engine/training.py", line 867, in _fit_loop
callbacks.on_epoch_begin(epoch)
File "/home/aris/py_envs/py2/local/lib/python2.7/site-packages/keras/callbacks.py", line 62, in on_epoch_begin
callback.on_epoch_begin(epoch, logs)
File "/home/aris/biotools/MTL-Bioinformatics-2016/models/ltlib/callbacks.py", line 54, in on_epoch_begin
callback.on_epoch_begin(*args, **kwargs)
File "/home/aris/biotools/MTL-Bioinformatics-2016/models/ltlib/callbacks.py", line 31, in on_epoch_begin
self.after_epoch_end(self.epoch)
File "/home/aris/biotools/MTL-Bioinformatics-2016/models/ltlib/callbacks.py", line 137, in after_epoch_end
predictions = self.model.predict(self.dataitems.inputs)
AttributeError: 'Predictor' object has no attribute 'model'
Indeed in line 137 of the callbacks.py
there is an attempt to use self.model
but call Predictor
is never assigned a model in the token_evaluator
function, line 200.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.