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Posted to dev@ctakes.apache.org by Steven Bethard <st...@Colorado.EDU> on 2013/05/31 00:45:01 UTC
upgrade ClearTK dependency to 1.4.0?
I just released ClearTK 1.4.0 and there are a couple of reasons we should probably consider updating the cTAKES dependency:
(1) ClearTK 1.4.0 can now load trained models from the classpath, so we could get rid of the workaround org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.allowClassifierModelOnClasspath.
(2) ClearTK 1.4.0 has wrappers for multi-class classification with LIBLINEAR which is orders of magnitude faster than LIBSVM.
The main downside is that models will have to be re-trained. (It's not necessarily the case that all models would need to be retrained, depending on exactly which classes they were using, but it's probably safer to do so.)
I believe this would mostly affect ctakes-temporal, ctakes-relation-extractor and ctakes-assertion.
Thoughts?
Steve
P.S. I noticed that ctakes-assertion declares a dependency on cleartk-examples. The cleartk-examples module was never intended for release, and has not been released as part of ClearTK 1.4.0. Looking at the code, it seems like the dependency in cleartk-examples is not needed, but perhaps a ctakes-assertion person could weigh in on why this dependency was there?
Re: upgrade ClearTK dependency to 1.4.0?
Posted by Tim Miller <ti...@childrens.harvard.edu>.
Yeah, Pei, you're right, I was able to remove it w/o causing any errors.
I'll check it in with the dependency and imports removed.
Tim
On 05/31/2013 03:39 PM, Chen, Pei wrote:
> Regarding the cleartk-examples dependency from the assertion module:
> I think there were some commits on this already [1].
> There is only a reference to the example classes in the imports now, but it's actually never used.
> Perhaps Matt could chime. Maybe it's as simple as just removing the examples from the pom and imports.
>
> [1] http://mail-archives.apache.org/mod_mbox/incubator-ctakes-dev/201210.mbox/%3CF085F637EA9843429DA7A267BBB709A01E8402EF%40IMCMBX04.MITRE.ORG%3E
>
>
>> -----Original Message-----
>> From: Steven Bethard [mailto:steven.bethard@Colorado.EDU]
>> Sent: Thursday, May 30, 2013 6:46 PM
>> To: ctakes-dev@incubator.apache.org
>> Subject: upgrade ClearTK dependency to 1.4.0?
>>
>> I just released ClearTK 1.4.0 and there are a couple of reasons we should
>> probably consider updating the cTAKES dependency:
>>
>> (1) ClearTK 1.4.0 can now load trained models from the classpath, so we
>> could get rid of the workaround
>> org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.allowClas
>> sifierModelOnClasspath.
>>
>> (2) ClearTK 1.4.0 has wrappers for multi-class classification with LIBLINEAR
>> which is orders of magnitude faster than LIBSVM.
>>
>> The main downside is that models will have to be re-trained. (It's not
>> necessarily the case that all models would need to be retrained, depending
>> on exactly which classes they were using, but it's probably safer to do so.)
>>
>> I believe this would mostly affect ctakes-temporal, ctakes-relation-extractor
>> and ctakes-assertion.
>>
>> Thoughts?
>>
>> Steve
>>
>> P.S. I noticed that ctakes-assertion declares a dependency on cleartk-
>> examples. The cleartk-examples module was never intended for release,
>> and has not been released as part of ClearTK 1.4.0. Looking at the code, it
>> seems like the dependency in cleartk-examples is not needed, but perhaps a
>> ctakes-assertion person could weigh in on why this dependency was there?
RE: upgrade ClearTK dependency to 1.4.0?
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Regarding the cleartk-examples dependency from the assertion module:
I think there were some commits on this already [1].
There is only a reference to the example classes in the imports now, but it's actually never used.
Perhaps Matt could chime. Maybe it's as simple as just removing the examples from the pom and imports.
[1] http://mail-archives.apache.org/mod_mbox/incubator-ctakes-dev/201210.mbox/%3CF085F637EA9843429DA7A267BBB709A01E8402EF%40IMCMBX04.MITRE.ORG%3E
> -----Original Message-----
> From: Steven Bethard [mailto:steven.bethard@Colorado.EDU]
> Sent: Thursday, May 30, 2013 6:46 PM
> To: ctakes-dev@incubator.apache.org
> Subject: upgrade ClearTK dependency to 1.4.0?
>
> I just released ClearTK 1.4.0 and there are a couple of reasons we should
> probably consider updating the cTAKES dependency:
>
> (1) ClearTK 1.4.0 can now load trained models from the classpath, so we
> could get rid of the workaround
> org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.allowClas
> sifierModelOnClasspath.
>
> (2) ClearTK 1.4.0 has wrappers for multi-class classification with LIBLINEAR
> which is orders of magnitude faster than LIBSVM.
>
> The main downside is that models will have to be re-trained. (It's not
> necessarily the case that all models would need to be retrained, depending
> on exactly which classes they were using, but it's probably safer to do so.)
>
> I believe this would mostly affect ctakes-temporal, ctakes-relation-extractor
> and ctakes-assertion.
>
> Thoughts?
>
> Steve
>
> P.S. I noticed that ctakes-assertion declares a dependency on cleartk-
> examples. The cleartk-examples module was never intended for release,
> and has not been released as part of ClearTK 1.4.0. Looking at the code, it
> seems like the dependency in cleartk-examples is not needed, but perhaps a
> ctakes-assertion person could weigh in on why this dependency was there?
Re: upgrade ClearTK dependency to 1.4.0?
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
+1
Sounds like a good plan.
On Jun 1, 2013, at 7:54 AM, "Miller, Timothy" <Ti...@childrens.harvard.edu> wrote:
> Maybe a good way to do this is to create a big jira and break it up into
> module-level jira's, then assign a person to each, and for each module:
> 1) Upgrade pom to latest release for modules being used
> 2) Recompile/retrain/retest and check in
> 3) Close jira for that module
>
> Then have one last issue that is to
> 1) upgrade project-level pom managed versions to latest release
> 2) revert module-level poms to use managed versions
> 3) run tests and checkin
>
> How does that plan sound?
> Tim
>
> On 05/30/2013 11:06 PM, Steven Bethard wrote:
>> On May 30, 2013, at 8:38 PM, "Masanz, James J." <Ma...@mayo.edu> wrote:
>>> As a first pass, can we update the dependency to ClearTK 1.4.0 without retraining the models -- would retraining be necessary even if we didn't switch to LIBLINEAR.
>> Retraining might still be necessary for anything that uses CleartkExtractor, since generation of out-of-bounds features has improved:
>>
>> https://groups.google.com/forum/#!topic/cleartk-users/KS2BLQcT-ds
>>
>> But anything not using CleartkExtractor should be safe. And even the things that are using CleartkExtractor may not degrade much if the out-of-bounds features aren't very important. But we'd need to test it a bit to see.
>>
>> Steve
>>
>>
>>> Just wonder if we have an option for staging this, in case we can't tackle it all now.
>>>
>>> -----Original Message-----
>>> From: dev-return-1646-Masanz.James=mayo.edu@ctakes.apache.org [mailto:dev-return-1646-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of Steven Bethard
>>> Sent: Thursday, May 30, 2013 5:45 PM
>>> To: ctakes-dev@incubator.apache.org
>>> Subject: upgrade ClearTK dependency to 1.4.0?
>>>
>>> I just released ClearTK 1.4.0 and there are a couple of reasons we should probably consider updating the cTAKES dependency:
>>>
>>> (1) ClearTK 1.4.0 can now load trained models from the classpath, so we could get rid of the workaround org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.allowClassifierModelOnClasspath.
>>>
>>> (2) ClearTK 1.4.0 has wrappers for multi-class classification with LIBLINEAR which is orders of magnitude faster than LIBSVM.
>>>
>>> The main downside is that models will have to be re-trained. (It's not necessarily the case that all models would need to be retrained, depending on exactly which classes they were using, but it's probably safer to do so.)
>>>
>>> I believe this would mostly affect ctakes-temporal, ctakes-relation-extractor and ctakes-assertion.
>>>
>>> Thoughts?
>>>
>>> Steve
>>>
>>> P.S. I noticed that ctakes-assertion declares a dependency on cleartk-examples. The cleartk-examples module was never intended for release, and has not been released as part of ClearTK 1.4.0. Looking at the code, it seems like the dependency in cleartk-examples is not needed, but perhaps a ctakes-assertion person could weigh in on why this dependency was there?
>
Re: upgrade ClearTK dependency to 1.4.0?
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
Maybe a good way to do this is to create a big jira and break it up into
module-level jira's, then assign a person to each, and for each module:
1) Upgrade pom to latest release for modules being used
2) Recompile/retrain/retest and check in
3) Close jira for that module
Then have one last issue that is to
1) upgrade project-level pom managed versions to latest release
2) revert module-level poms to use managed versions
3) run tests and checkin
How does that plan sound?
Tim
On 05/30/2013 11:06 PM, Steven Bethard wrote:
> On May 30, 2013, at 8:38 PM, "Masanz, James J." <Ma...@mayo.edu> wrote:
>> As a first pass, can we update the dependency to ClearTK 1.4.0 without retraining the models -- would retraining be necessary even if we didn't switch to LIBLINEAR.
> Retraining might still be necessary for anything that uses CleartkExtractor, since generation of out-of-bounds features has improved:
>
> https://groups.google.com/forum/#!topic/cleartk-users/KS2BLQcT-ds
>
> But anything not using CleartkExtractor should be safe. And even the things that are using CleartkExtractor may not degrade much if the out-of-bounds features aren't very important. But we'd need to test it a bit to see.
>
> Steve
>
>
>> Just wonder if we have an option for staging this, in case we can't tackle it all now.
>>
>> -----Original Message-----
>> From: dev-return-1646-Masanz.James=mayo.edu@ctakes.apache.org [mailto:dev-return-1646-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of Steven Bethard
>> Sent: Thursday, May 30, 2013 5:45 PM
>> To: ctakes-dev@incubator.apache.org
>> Subject: upgrade ClearTK dependency to 1.4.0?
>>
>> I just released ClearTK 1.4.0 and there are a couple of reasons we should probably consider updating the cTAKES dependency:
>>
>> (1) ClearTK 1.4.0 can now load trained models from the classpath, so we could get rid of the workaround org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.allowClassifierModelOnClasspath.
>>
>> (2) ClearTK 1.4.0 has wrappers for multi-class classification with LIBLINEAR which is orders of magnitude faster than LIBSVM.
>>
>> The main downside is that models will have to be re-trained. (It's not necessarily the case that all models would need to be retrained, depending on exactly which classes they were using, but it's probably safer to do so.)
>>
>> I believe this would mostly affect ctakes-temporal, ctakes-relation-extractor and ctakes-assertion.
>>
>> Thoughts?
>>
>> Steve
>>
>> P.S. I noticed that ctakes-assertion declares a dependency on cleartk-examples. The cleartk-examples module was never intended for release, and has not been released as part of ClearTK 1.4.0. Looking at the code, it seems like the dependency in cleartk-examples is not needed, but perhaps a ctakes-assertion person could weigh in on why this dependency was there?
>
Re: upgrade ClearTK dependency to 1.4.0?
Posted by Steven Bethard <st...@Colorado.EDU>.
On May 30, 2013, at 8:38 PM, "Masanz, James J." <Ma...@mayo.edu> wrote:
> As a first pass, can we update the dependency to ClearTK 1.4.0 without retraining the models -- would retraining be necessary even if we didn't switch to LIBLINEAR.
Retraining might still be necessary for anything that uses CleartkExtractor, since generation of out-of-bounds features has improved:
https://groups.google.com/forum/#!topic/cleartk-users/KS2BLQcT-ds
But anything not using CleartkExtractor should be safe. And even the things that are using CleartkExtractor may not degrade much if the out-of-bounds features aren't very important. But we'd need to test it a bit to see.
Steve
>
> Just wonder if we have an option for staging this, in case we can't tackle it all now.
>
> -----Original Message-----
> From: dev-return-1646-Masanz.James=mayo.edu@ctakes.apache.org [mailto:dev-return-1646-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of Steven Bethard
> Sent: Thursday, May 30, 2013 5:45 PM
> To: ctakes-dev@incubator.apache.org
> Subject: upgrade ClearTK dependency to 1.4.0?
>
> I just released ClearTK 1.4.0 and there are a couple of reasons we should probably consider updating the cTAKES dependency:
>
> (1) ClearTK 1.4.0 can now load trained models from the classpath, so we could get rid of the workaround org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.allowClassifierModelOnClasspath.
>
> (2) ClearTK 1.4.0 has wrappers for multi-class classification with LIBLINEAR which is orders of magnitude faster than LIBSVM.
>
> The main downside is that models will have to be re-trained. (It's not necessarily the case that all models would need to be retrained, depending on exactly which classes they were using, but it's probably safer to do so.)
>
> I believe this would mostly affect ctakes-temporal, ctakes-relation-extractor and ctakes-assertion.
>
> Thoughts?
>
> Steve
>
> P.S. I noticed that ctakes-assertion declares a dependency on cleartk-examples. The cleartk-examples module was never intended for release, and has not been released as part of ClearTK 1.4.0. Looking at the code, it seems like the dependency in cleartk-examples is not needed, but perhaps a ctakes-assertion person could weigh in on why this dependency was there?
RE: upgrade ClearTK dependency to 1.4.0?
Posted by "Masanz, James J." <Ma...@mayo.edu>.
As a first pass, can we update the dependency to ClearTK 1.4.0 without retraining the models -- would retraining be necessary even if we didn't switch to LIBLINEAR.
Just wonder if we have an option for staging this, in case we can't tackle it all now.
-----Original Message-----
From: dev-return-1646-Masanz.James=mayo.edu@ctakes.apache.org [mailto:dev-return-1646-Masanz.James=mayo.edu@ctakes.apache.org] On Behalf Of Steven Bethard
Sent: Thursday, May 30, 2013 5:45 PM
To: ctakes-dev@incubator.apache.org
Subject: upgrade ClearTK dependency to 1.4.0?
I just released ClearTK 1.4.0 and there are a couple of reasons we should probably consider updating the cTAKES dependency:
(1) ClearTK 1.4.0 can now load trained models from the classpath, so we could get rid of the workaround org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.allowClassifierModelOnClasspath.
(2) ClearTK 1.4.0 has wrappers for multi-class classification with LIBLINEAR which is orders of magnitude faster than LIBSVM.
The main downside is that models will have to be re-trained. (It's not necessarily the case that all models would need to be retrained, depending on exactly which classes they were using, but it's probably safer to do so.)
I believe this would mostly affect ctakes-temporal, ctakes-relation-extractor and ctakes-assertion.
Thoughts?
Steve
P.S. I noticed that ctakes-assertion declares a dependency on cleartk-examples. The cleartk-examples module was never intended for release, and has not been released as part of ClearTK 1.4.0. Looking at the code, it seems like the dependency in cleartk-examples is not needed, but perhaps a ctakes-assertion person could weigh in on why this dependency was there?