lazar
22 months agotentative random forest classification: hangs unpredictably during caret model genera... mutanew
helma@in-silico.ch [Tue, 9 Oct 2018 16:20:27 +0000 (18:20 +0200)]
tentative random forest classification: hangs unpredictably during caret model generation/optimization for some (inorganic?) compounds.

22 months agodataset merge with feature/value maps
helma@in-silico.ch [Sun, 7 Oct 2018 16:12:39 +0000 (18:12 +0200)]
dataset merge with feature/value maps

22 months agopartial pubchem classification import
helma@in-silico.ch [Fri, 5 Oct 2018 17:31:48 +0000 (19:31 +0200)]
partial pubchem classification import

22 months agosdf import, csv files with id column
helma@in-silico.ch [Fri, 5 Oct 2018 15:06:46 +0000 (17:06 +0200)]
sdf import, csv files with id column

22 months agosmiles as identifier for sdf export
helma@in-silico.ch [Mon, 17 Sep 2018 14:54:23 +0000 (16:54 +0200)]
smiles as identifier for sdf export

23 months agoadjusted classification similarities, dataset sdf export
helma@in-silico.ch [Thu, 6 Sep 2018 15:24:25 +0000 (17:24 +0200)]
adjusted classification similarities, dataset sdf export

23 months agoclassification min_sim=0.5, 5 repeated cvs
helma@in-silico.ch [Tue, 14 Aug 2018 12:02:03 +0000 (12:02 +0000)]
classification min_sim=0.5, 5 repeated cvs

2 years agoadd positive delog method
gebele [Thu, 26 Jul 2018 07:30:54 +0000 (07:30 +0000)]
add positive delog method

2 years agofixed version path
gebele [Fri, 27 Apr 2018 07:01:42 +0000 (09:01 +0200)]
fixed version path

2 years agofixed version path
gebele [Fri, 27 Apr 2018 06:59:10 +0000 (08:59 +0200)]
fixed version path

2 years agoversion bump v1.1.2
gebele [Thu, 26 Apr 2018 15:43:21 +0000 (17:43 +0200)]
version bump

2 years agoMerge branch 'development'
gebele [Thu, 26 Apr 2018 15:30:31 +0000 (17:30 +0200)]
Merge branch 'development'

2 years agoadd git or gem versioning to model
gebele [Thu, 26 Apr 2018 15:24:25 +0000 (17:24 +0200)]
add git or gem versioning to model

2 years agomerge development v1.1.1
gebele [Tue, 3 Apr 2018 15:14:45 +0000 (15:14 +0000)]
merge development

2 years agounmuted enm import; mute cleanup
gebele [Wed, 17 Jan 2018 13:49:01 +0000 (14:49 +0100)]
unmuted enm import; mute cleanup

2 years agoremoved libPath test
gebele [Wed, 17 Jan 2018 11:28:45 +0000 (12:28 +0100)]
removed libPath test

2 years agochanged assertion value
gebele [Wed, 17 Jan 2018 10:39:11 +0000 (11:39 +0100)]
changed assertion value

2 years agochanged assertion value
gebele [Wed, 17 Jan 2018 10:37:01 +0000 (11:37 +0100)]
changed assertion value

2 years agoadded R packages test
gebele [Mon, 15 Jan 2018 12:11:21 +0000 (12:11 +0000)]
added R packages test

2 years agoadded R packages test
gebele [Mon, 15 Jan 2018 12:05:43 +0000 (12:05 +0000)]
added R packages test

2 years agomuted enm import
gebele [Mon, 15 Jan 2018 10:52:09 +0000 (10:52 +0000)]
muted enm import

2 years agobumped version
gebele [Mon, 14 Aug 2017 11:19:37 +0000 (11:19 +0000)]
bumped version

2 years agobumped version
gebele [Mon, 14 Aug 2017 11:19:02 +0000 (11:19 +0000)]
bumped version

3 years agoadded model field for qmrf metadata
gebele [Tue, 8 Aug 2017 14:53:22 +0000 (14:53 +0000)]
added model field for qmrf metadata

3 years agoscript to convert mol to mmol -log10 in training dataset
gebele [Fri, 4 Aug 2017 14:02:40 +0000 (14:02 +0000)]
script to convert mol to mmol -log10 in training dataset

3 years agocleanup test db
gebele [Thu, 6 Jul 2017 08:44:18 +0000 (08:44 +0000)]
cleanup test db

3 years agoconsistend use of RestClientWrapper to import datasets
gebele [Fri, 30 Jun 2017 14:18:04 +0000 (14:18 +0000)]
consistend use of RestClientWrapper to import datasets

3 years agoadded addressable gem to avoid URI::InvalidURIError
gebele [Fri, 9 Jun 2017 11:08:45 +0000 (11:08 +0000)]
added addressable gem to avoid URI::InvalidURIError

3 years agobumped version to 1.1.0 v1.1.0
gebele [Fri, 26 May 2017 13:06:18 +0000 (13:06 +0000)]
bumped version to 1.1.0

3 years agoMerge branch 'development'
gebele [Fri, 26 May 2017 12:53:01 +0000 (12:53 +0000)]
Merge branch 'development'

3 years agoMerge branch 'master' of https://github.com/opentox/lazar
gebele [Fri, 26 May 2017 12:52:28 +0000 (12:52 +0000)]
Merge branch 'master' of https://github.com/opentox/lazar

3 years agofix for lower min sim threshold
gebele [Mon, 22 May 2017 12:45:32 +0000 (12:45 +0000)]
fix for lower min sim threshold

3 years agoadded warnings field for leave-one-out test fails
gebele [Fri, 5 May 2017 12:43:01 +0000 (12:43 +0000)]
added warnings field for leave-one-out test fails

3 years agocleanup and hack for mongos file size limit
gebele [Thu, 4 May 2017 09:59:37 +0000 (09:59 +0000)]
cleanup and hack for mongos file size limit

3 years agoensure always two probability values for classification
gebele [Thu, 4 May 2017 09:50:57 +0000 (09:50 +0000)]
ensure always two probability values for classification

3 years agoensure warnings for validation statistics
gebele [Thu, 4 May 2017 09:50:08 +0000 (09:50 +0000)]
ensure warnings for validation statistics

3 years agochanged compound to predict fixed test
gebele [Tue, 11 Apr 2017 08:03:15 +0000 (08:03 +0000)]
changed compound to predict fixed test

3 years agoadjusted classification tests for min sim 0.1
gebele [Fri, 31 Mar 2017 15:08:14 +0000 (15:08 +0000)]
adjusted classification tests for min sim 0.1

3 years agoset default min sim to 0.1 for classification and 0.5 for regression
gebele [Fri, 31 Mar 2017 15:07:28 +0000 (15:07 +0000)]
set default min sim to 0.1 for classification and 0.5 for regression

3 years agofixed wrong accuracy assertion to rmse
gebele [Tue, 28 Mar 2017 11:00:12 +0000 (11:00 +0000)]
fixed wrong accuracy assertion to rmse

3 years agoadjusted for higher default similarity min value
gebele [Fri, 24 Mar 2017 13:00:19 +0000 (13:00 +0000)]
adjusted for higher default similarity min value

3 years agoadjusted for higher similarity min value
gebele [Fri, 24 Mar 2017 12:51:12 +0000 (12:51 +0000)]
adjusted for higher similarity min value

3 years agofixed regression test for rf algorithm see: 'loael edit' commit;along with larger...
gebele [Tue, 21 Mar 2017 15:11:44 +0000 (15:11 +0000)]
fixed regression test for rf algorithm see: 'loael edit' commit;along with larger treining datasets

3 years agofixed endless loop; rescue for missing neighbors
gebele [Tue, 21 Mar 2017 15:08:38 +0000 (15:08 +0000)]
fixed endless loop; rescue for missing neighbors

3 years agofixed test_to_csv
gebele [Tue, 21 Mar 2017 09:18:49 +0000 (09:18 +0000)]
fixed test_to_csv

3 years agoMerge branch 'master' into development
gebele [Thu, 16 Mar 2017 12:57:38 +0000 (12:57 +0000)]
Merge branch 'master' into development

3 years agodetect and use a central mongodb
gebele [Thu, 16 Mar 2017 12:56:29 +0000 (12:56 +0000)]
detect and use a central mongodb

3 years agoMerge branch 'development' of github.com:opentox/lazar into development
gebele [Thu, 16 Mar 2017 12:54:10 +0000 (12:54 +0000)]
Merge branch 'development' of github.com:opentox/lazar into development

3 years agoloael edit
gebele [Thu, 16 Mar 2017 12:53:23 +0000 (12:53 +0000)]
loael edit

3 years agoMerge branch 'master' into development
gebele [Fri, 3 Mar 2017 11:54:55 +0000 (12:54 +0100)]
Merge branch 'master' into development

3 years agoworst predictions fixed for regression nano-lazar-paper.revision
Christoph Helma [Mon, 20 Feb 2017 08:41:05 +0000 (09:41 +0100)]
worst predictions fixed for regression

3 years agofixed header for nano-lazar correlation plots
Christoph Helma [Sat, 18 Feb 2017 08:49:48 +0000 (09:49 +0100)]
fixed header for nano-lazar correlation plots

3 years agoMerge branch 'master' of https://github.com/opentox/lazar
gebele [Fri, 10 Feb 2017 12:24:23 +0000 (12:24 +0000)]
Merge branch 'master' of https://github.com/opentox/lazar

3 years agoblock idents
Christoph Helma [Fri, 3 Feb 2017 13:43:29 +0000 (14:43 +0100)]
block idents

3 years agotypos fixed
Christoph Helma [Fri, 3 Feb 2017 13:40:21 +0000 (14:40 +0100)]
typos fixed

3 years agoalgorithm selection tutorial
Christoph Helma [Fri, 3 Feb 2017 13:36:07 +0000 (14:36 +0100)]
algorithm selection tutorial

3 years agoadded TODO for missing descriptor
gebele [Thu, 19 Jan 2017 16:39:46 +0000 (16:39 +0000)]
added TODO for missing descriptor

3 years agofixed feature test and unique_descriptors
gebele [Thu, 19 Jan 2017 12:41:55 +0000 (12:41 +0000)]
fixed feature test and unique_descriptors

3 years agobumped version v1.0.1
gebele [Wed, 18 Jan 2017 14:37:56 +0000 (14:37 +0000)]
bumped version

3 years agofixed merge
gebele [Wed, 18 Jan 2017 14:17:02 +0000 (14:17 +0000)]
fixed merge

3 years agomerge development
gebele [Mon, 16 Jan 2017 09:50:33 +0000 (09:50 +0000)]
merge development

3 years agosource uris for core and coating
Christoph Helma [Thu, 12 Jan 2017 16:57:03 +0000 (17:57 +0100)]
source uris for core and coating

3 years agodocumentation for all classes
Christoph Helma [Wed, 11 Jan 2017 15:00:07 +0000 (16:00 +0100)]
documentation for all classes

3 years agotraining test set validation documentation
Christoph Helma [Wed, 11 Jan 2017 08:57:36 +0000 (09:57 +0100)]
training test set validation documentation

3 years agoLOO documentation
Christoph Helma [Wed, 11 Jan 2017 08:25:33 +0000 (09:25 +0100)]
LOO documentation

3 years agovalidation documentation
Christoph Helma [Wed, 11 Jan 2017 08:20:40 +0000 (09:20 +0100)]
validation documentation

3 years agomodel documentation updated
Christoph Helma [Wed, 11 Jan 2017 07:24:23 +0000 (08:24 +0100)]
model documentation updated

3 years agomodel documentation
Christoph Helma [Tue, 10 Jan 2017 15:56:48 +0000 (16:56 +0100)]
model documentation

3 years agoinitial model documentation
Christoph Helma [Tue, 10 Jan 2017 15:29:02 +0000 (16:29 +0100)]
initial model documentation

3 years agoREADME.md CV information fixed
Christoph Helma [Tue, 10 Jan 2017 14:31:25 +0000 (15:31 +0100)]
README.md CV information fixed

3 years agoREADME.md headings fixed
Christoph Helma [Tue, 10 Jan 2017 14:27:56 +0000 (15:27 +0100)]
README.md headings fixed

3 years agoBrief tutorial in README.md
Christoph Helma [Tue, 10 Jan 2017 14:25:42 +0000 (15:25 +0100)]
Brief tutorial in README.md

3 years agoindependent_variables stored in GridFS to avoid Mongo database size limit problems
Christoph Helma [Tue, 10 Jan 2017 12:44:43 +0000 (13:44 +0100)]
independent_variables stored in GridFS to avoid Mongo database size limit problems

3 years agoMerge branch 'development' 1.0.0
gebele [Tue, 20 Dec 2016 16:26:09 +0000 (16:26 +0000)]
Merge branch 'development'

3 years agotrue_rate, predictivity stored in crossvalidation nano-lazar-paper.submission
Christoph Helma [Tue, 20 Dec 2016 15:28:36 +0000 (16:28 +0100)]
true_rate, predictivity stored in crossvalidation

3 years agomodena import modifications removed nano-lazar-paper.review
Christoph Helma [Sun, 18 Dec 2016 11:43:41 +0000 (12:43 +0100)]
modena import modifications removed

3 years ago5 repeated cvs for enm
Christoph Helma [Mon, 12 Dec 2016 12:02:29 +0000 (13:02 +0100)]
5 repeated cvs for enm

3 years agomodena import workarounds
Christoph Helma [Mon, 12 Dec 2016 11:46:24 +0000 (12:46 +0100)]
modena import workarounds

3 years agomerged development
gebele [Mon, 12 Dec 2016 09:15:48 +0000 (09:15 +0000)]
merged development

3 years agomerged origin/development
Christoph Helma [Thu, 8 Dec 2016 12:08:55 +0000 (13:08 +0100)]
merged origin/development

3 years agoOpenTox::Validation::RepeatedCrossValidation fixed, stringi R library added
Christoph Helma [Thu, 8 Dec 2016 12:04:38 +0000 (13:04 +0100)]
OpenTox::Validation::RepeatedCrossValidation fixed, stringi R library added

3 years agofull class name required
gebele [Tue, 6 Dec 2016 09:59:24 +0000 (09:59 +0000)]
full class name required

3 years agoremoved dependency gem version numbers
gebele [Mon, 5 Dec 2016 10:44:24 +0000 (10:44 +0000)]
removed dependency gem version numbers

3 years agoMerge branch 'development' of github.com:opentox/lazar into development
Christoph Helma [Fri, 25 Nov 2016 09:37:30 +0000 (10:37 +0100)]
Merge branch 'development' of github.com:opentox/lazar into development

3 years agoalgorithms accessor for Model::Validation
Christoph Helma [Fri, 25 Nov 2016 09:36:02 +0000 (10:36 +0100)]
algorithms accessor for Model::Validation

3 years agoalways convert to SMILES v9-nestec
gebele [Thu, 24 Nov 2016 07:16:54 +0000 (07:16 +0000)]
always convert to SMILES

3 years agoadded delog10;generalized mmol2-log10 eNM
gebele [Wed, 23 Nov 2016 15:10:58 +0000 (15:10 +0000)]
added delog10;generalized mmol2-log10

3 years agop-chem regression and enm import fixed
Christoph Helma [Fri, 11 Nov 2016 16:19:13 +0000 (17:19 +0100)]
p-chem regression and enm import fixed

3 years agoenm import fixed
Christoph Helma [Fri, 11 Nov 2016 12:07:53 +0000 (13:07 +0100)]
enm import fixed

3 years agoModel::NanoPrediction parameters
Christoph Helma [Thu, 10 Nov 2016 14:27:26 +0000 (15:27 +0100)]
Model::NanoPrediction parameters

3 years agoMerge branch 'development' of github.com:opentox/lazar into development
Christoph Helma [Thu, 10 Nov 2016 11:24:08 +0000 (12:24 +0100)]
Merge branch 'development' of github.com:opentox/lazar into development

3 years agointermediate commit, may be defunct
Christoph Helma [Thu, 10 Nov 2016 11:23:46 +0000 (12:23 +0100)]
intermediate commit, may be defunct

3 years agoMerge branch 'development' of https://github.com/opentox/lazar into development
gebele [Thu, 10 Nov 2016 11:07:03 +0000 (11:07 +0000)]
Merge branch 'development' of https://github.com/opentox/lazar into development

3 years agoadded nanomodel create
gebele [Thu, 10 Nov 2016 11:06:27 +0000 (11:06 +0000)]
added nanomodel create

3 years agoCDK 2.0
Christoph Helma [Wed, 9 Nov 2016 09:03:46 +0000 (10:03 +0100)]
CDK 2.0

3 years agoMerge branch 'development' of github.com:opentox/lazar into development
Christoph Helma [Tue, 8 Nov 2016 15:05:07 +0000 (16:05 +0100)]
Merge branch 'development' of github.com:opentox/lazar into development

3 years agoprobability plot for classification
Christoph Helma [Tue, 8 Nov 2016 15:04:49 +0000 (16:04 +0100)]
probability plot for classification

3 years agoreintroduced Gemfile
gebele [Fri, 4 Nov 2016 11:51:17 +0000 (11:51 +0000)]
reintroduced Gemfile

3 years agoadjusted r^2 removed (does not apply well to local models)
Christoph Helma [Fri, 28 Oct 2016 10:31:53 +0000 (12:31 +0200)]
adjusted r^2 removed (does not apply well to local models)

3 years agoGridFS storage for plots.
Christoph Helma [Thu, 27 Oct 2016 10:09:06 +0000 (12:09 +0200)]
GridFS storage for plots.