lazar
4 years agolocal pls regression as default regression algorithm fminer
Christoph Helma [Sat, 27 Feb 2016 15:47:48 +0000 (16:47 +0100)]
local pls regression as default regression algorithm

4 years agoimproved handling of duplicates in validations
Christoph Helma [Sat, 13 Feb 2016 12:15:29 +0000 (13:15 +0100)]
improved handling of duplicates in validations

4 years agopls regression
Christoph Helma [Tue, 9 Feb 2016 10:04:00 +0000 (11:04 +0100)]
pls regression

4 years agomg-mmol conversion fixed
Christoph Helma [Fri, 8 Jan 2016 10:00:20 +0000 (11:00 +0100)]
mg-mmol conversion fixed

4 years agoleave one out validation implemented
Christoph Helma [Mon, 9 Nov 2015 13:58:34 +0000 (14:58 +0100)]
leave one out validation implemented

4 years agoaccuracy threshold for prediction model test adjusted
Christoph Helma [Wed, 4 Nov 2015 17:07:15 +0000 (18:07 +0100)]
accuracy threshold for prediction model test adjusted

4 years agoMerge branch 'development' of github.com:opentox/lazar into development
Christoph Helma [Wed, 4 Nov 2015 16:50:32 +0000 (17:50 +0100)]
Merge branch 'development' of github.com:opentox/lazar into development

4 years agoneighbor search delegated to database backend
Christoph Helma [Wed, 4 Nov 2015 16:50:17 +0000 (17:50 +0100)]
neighbor search delegated to database backend

4 years agoerror methods do only accept 1 argument
Micha Rautenberg [Fri, 30 Oct 2015 13:08:56 +0000 (14:08 +0100)]
error methods do only accept 1 argument

4 years agoerror methods do only accept 1 argument
Micha Rautenberg [Fri, 30 Oct 2015 11:58:17 +0000 (12:58 +0100)]
error methods do only accept 1 argument

4 years agoadded csv encode option windows-1251:utf-8 v7-nestec
gebele [Fri, 30 Oct 2015 10:09:49 +0000 (10:09 +0000)]
added csv encode option windows-1251:utf-8

4 years agoRemoved comment.
davor [Thu, 29 Oct 2015 14:42:53 +0000 (15:42 +0100)]
Removed comment.

4 years agoAdded molecular weight to compound and mg conversions
davor [Thu, 29 Oct 2015 13:33:30 +0000 (13:33 +0000)]
Added molecular weight to compound and mg conversions

Added tests

4 years agocheck for whitespaces in smiles
Christoph Helma [Thu, 29 Oct 2015 11:45:49 +0000 (12:45 +0100)]
check for whitespaces in smiles

4 years agoavoid duplicated obconversion in from_smiles
gebele [Thu, 29 Oct 2015 09:56:37 +0000 (09:56 +0000)]
avoid duplicated obconversion in from_smiles

4 years agoalways collect neighbors even if database hit
gebele [Wed, 28 Oct 2015 09:12:20 +0000 (09:12 +0000)]
always collect neighbors even if database hit

4 years agoadded files and test for create dataset from file (smiles/inchi) without features...
gebele [Thu, 22 Oct 2015 11:35:32 +0000 (11:35 +0000)]
added files and test for create dataset from file (smiles/inchi) without features, used for batch prediction

4 years agoGridFS storage for data_entries removed (will break kazius/fminer models), lazy creat...
Christoph Helma [Mon, 19 Oct 2015 09:42:16 +0000 (11:42 +0200)]
GridFS storage for data_entries removed (will break kazius/fminer models), lazy creation of classification confidence plots.

4 years agonew environment variable LAZAR_ENV for databases and log levels
Christoph Helma [Thu, 8 Oct 2015 12:10:00 +0000 (14:10 +0200)]
new environment variable LAZAR_ENV for databases and log levels

4 years agonew master branch
Christoph Helma [Thu, 8 Oct 2015 08:43:43 +0000 (10:43 +0200)]
new master branch

4 years agoversion bump, experiment tests skipped
Christoph Helma [Thu, 8 Oct 2015 08:36:34 +0000 (10:36 +0200)]
version bump, experiment tests skipped

4 years agocrossvalidation plots, original classification confidence
Christoph Helma [Thu, 8 Oct 2015 08:32:31 +0000 (10:32 +0200)]
crossvalidation plots, original classification confidence

4 years agoMerge branch 'development' of github.com:opentox/lazar into development
Christoph Helma [Wed, 7 Oct 2015 10:45:48 +0000 (12:45 +0200)]
Merge branch 'development' of github.com:opentox/lazar into development

4 years agoconfidence = similarity to nearest neighbor
Christoph Helma [Wed, 7 Oct 2015 10:45:10 +0000 (12:45 +0200)]
confidence = similarity to nearest neighbor

4 years agogeneralised fingerprints
Christoph Helma [Wed, 7 Oct 2015 10:34:02 +0000 (12:34 +0200)]
generalised fingerprints

4 years agofixed typo
gebele [Wed, 30 Sep 2015 12:49:08 +0000 (14:49 +0200)]
fixed typo

4 years agoadded helper method 'dimension' for nested arrays
gebele [Fri, 25 Sep 2015 09:09:35 +0000 (11:09 +0200)]
added helper method 'dimension' for nested arrays

4 years agomean method for Arrays
Christoph Helma [Thu, 24 Sep 2015 13:41:18 +0000 (15:41 +0200)]
mean method for Arrays

4 years agofixed missing model_algorithm in experiments
Christoph Helma [Thu, 24 Sep 2015 11:09:20 +0000 (13:09 +0200)]
fixed missing model_algorithm in experiments

4 years agovalidations fixed (all models were executed with default parameters)
Christoph Helma [Wed, 23 Sep 2015 12:51:41 +0000 (14:51 +0200)]
validations fixed (all models were executed with default parameters)

4 years agoimport of datasets without features fixed
Christoph Helma [Fri, 18 Sep 2015 12:48:39 +0000 (14:48 +0200)]
import of datasets without features fixed

4 years agoMerge branch 'development' of github.com:opentox/lazar into development
gebele [Fri, 18 Sep 2015 11:31:13 +0000 (13:31 +0200)]
Merge branch 'development' of github.com:opentox/lazar into development

4 years agointroduced batch prediction file and test
gebele [Fri, 18 Sep 2015 11:31:05 +0000 (13:31 +0200)]
introduced batch prediction file and test

4 years agofix for empty values
Christoph Helma [Fri, 18 Sep 2015 11:01:59 +0000 (13:01 +0200)]
fix for empty values

4 years agoneighbor calculation moved to Compound class
Christoph Helma [Thu, 17 Sep 2015 12:56:25 +0000 (14:56 +0200)]
neighbor calculation moved to Compound class

4 years agogeneric openbabel fingerprints
Christoph Helma [Wed, 16 Sep 2015 14:52:18 +0000 (16:52 +0200)]
generic openbabel fingerprints

4 years agorepeated crossvalidations, improved experiment reports
Christoph Helma [Wed, 16 Sep 2015 11:11:45 +0000 (13:11 +0200)]
repeated crossvalidations, improved experiment reports

4 years agotests for Model::Prediction.[classification|regression]?
Christoph Helma [Mon, 14 Sep 2015 11:44:51 +0000 (13:44 +0200)]
tests for Model::Prediction.[classification|regression]?

4 years agotraining_dataset moved to base Model class
Christoph Helma [Mon, 14 Sep 2015 11:40:11 +0000 (13:40 +0200)]
training_dataset moved to base Model class

4 years agoattr_accessor :training_dataset removed in Lazar models
Christoph Helma [Mon, 14 Sep 2015 11:15:46 +0000 (13:15 +0200)]
attr_accessor :training_dataset removed in Lazar models

4 years agoclassification? and regression? methods for Model::Prediction
Christoph Helma [Mon, 14 Sep 2015 09:44:34 +0000 (11:44 +0200)]
classification? and regression? methods for Model::Prediction

4 years agotests fixed (crossvalidations may fail due to memory constraints)
Christoph Helma [Thu, 10 Sep 2015 10:54:18 +0000 (12:54 +0200)]
tests fixed (crossvalidations may fail due to memory constraints)

4 years agofminer classification fixed
Christoph Helma [Wed, 9 Sep 2015 12:49:35 +0000 (14:49 +0200)]
fminer classification fixed

4 years agoundo ruby version
gebele [Tue, 1 Sep 2015 10:11:25 +0000 (12:11 +0200)]
undo ruby version

4 years agoset required RUBY version
gebele [Mon, 31 Aug 2015 10:05:20 +0000 (12:05 +0200)]
set required RUBY version

4 years agoInitial GUI for Nestec models
Christoph Helma [Thu, 27 Aug 2015 18:28:25 +0000 (20:28 +0200)]
Initial GUI for Nestec models

4 years agoParallel Crossvalidations
Christoph Helma [Wed, 26 Aug 2015 12:20:23 +0000 (14:20 +0200)]
Parallel Crossvalidations

4 years agoExperiments added
Christoph Helma [Tue, 25 Aug 2015 15:20:55 +0000 (17:20 +0200)]
Experiments added

4 years agoModel::Prediction with tests, initial indexes v0.0.8
Christoph Helma [Mon, 24 Aug 2015 10:17:07 +0000 (12:17 +0200)]
Model::Prediction with tests, initial indexes

4 years agocrossvalidation fixes v0.0.7
Christoph Helma [Thu, 20 Aug 2015 12:02:04 +0000 (14:02 +0200)]
crossvalidation fixes

4 years agonew development HEAD v0.0.6
Christoph Helma [Wed, 19 Aug 2015 16:04:22 +0000 (18:04 +0200)]
new development HEAD

4 years agogit calls reintroduced into lazar.gemspec to avoid file losses. Seems to work with...
Christoph Helma [Wed, 19 Aug 2015 15:29:33 +0000 (17:29 +0200)]
git calls reintroduced into lazar.gemspec to avoid file losses. Seems to work with require 'lazar' in irb.

4 years agogit calls removed from lazar.gemspec (git does not work when installed as a gem)
Christoph Helma [Wed, 19 Aug 2015 14:48:43 +0000 (16:48 +0200)]
git calls removed from lazar.gemspec (git does not work when installed as a gem)

4 years agoVERSION bumped to 0.0.4 v0.0.4
Christoph Helma [Wed, 19 Aug 2015 13:41:38 +0000 (15:41 +0200)]
VERSION bumped to 0.0.4

4 years agoVERSION bumped to 0.0.4 v0.0.5
Christoph Helma [Wed, 19 Aug 2015 13:41:05 +0000 (15:41 +0200)]
VERSION bumped to 0.0.4

4 years agoMakefile fixed
Christoph Helma [Wed, 19 Aug 2015 13:40:34 +0000 (15:40 +0200)]
Makefile fixed

4 years agoVERSION bumped to 0.0.3 v0.0.3
Christoph Helma [Wed, 19 Aug 2015 13:39:05 +0000 (15:39 +0200)]
VERSION bumped to 0.0.3

4 years agoext/lazar/Makefile added
Christoph Helma [Wed, 19 Aug 2015 13:36:20 +0000 (15:36 +0200)]
ext/lazar/Makefile added

4 years agoVERSION bumped to 0.0.2 v0.0.2
Christoph Helma [Wed, 19 Aug 2015 13:28:01 +0000 (15:28 +0200)]
VERSION bumped to 0.0.2

4 years agodummy Makefile for ext/lazar/extconf.rb
Christoph Helma [Wed, 19 Aug 2015 13:27:20 +0000 (15:27 +0200)]
dummy Makefile for ext/lazar/extconf.rb

4 years agoversioning started at 0.0.1 v0.0.1
Christoph Helma [Wed, 19 Aug 2015 12:24:30 +0000 (14:24 +0200)]
versioning started at 0.0.1

4 years agoname conversion fixed v1.0.0beta1
Christoph Helma [Wed, 19 Aug 2015 12:17:44 +0000 (14:17 +0200)]
name conversion fixed

4 years agohydrogens added for 3d generation
Christoph Helma [Wed, 19 Aug 2015 12:00:55 +0000 (14:00 +0200)]
hydrogens added for 3d generation

4 years agoob_{include|lib} paths fixed
Christoph Helma [Wed, 19 Aug 2015 11:37:14 +0000 (13:37 +0200)]
ob_{include|lib} paths fixed

4 years agolibfminer rpath fixed, installation instructions
Christoph Helma [Wed, 19 Aug 2015 10:57:23 +0000 (12:57 +0200)]
libfminer rpath fixed, installation instructions

4 years agoinitial installation fixes, installs on Debian 3.16.7
ch [Tue, 18 Aug 2015 14:37:09 +0000 (16:37 +0200)]
initial installation fixes, installs on Debian 3.16.7

4 years agofirst attempt at installing openbabel from github
Christoph Helma [Tue, 18 Aug 2015 11:19:37 +0000 (13:19 +0200)]
first attempt at installing openbabel from github

4 years agoopenbabel and fminer installation added
Christoph Helma [Sat, 15 Aug 2015 12:57:16 +0000 (14:57 +0200)]
openbabel and fminer installation added

4 years agojava libraries added
Christoph Helma [Sat, 15 Aug 2015 09:52:18 +0000 (11:52 +0200)]
java libraries added

4 years agoinitial installation script
Christoph Helma [Sat, 15 Aug 2015 09:21:26 +0000 (11:21 +0200)]
initial installation script

4 years agomajority of tests working
Christoph Helma [Thu, 13 Aug 2015 16:57:11 +0000 (18:57 +0200)]
majority of tests working

4 years agoOpenBabel can (canonical smiles) instead of inchi as internal identifier to avoid...
Christoph Helma [Thu, 13 Aug 2015 09:56:40 +0000 (11:56 +0200)]
OpenBabel can (canonical smiles) instead of inchi as internal identifier to avoid OpenBabel InChi bug.

5 years agoalgorithm libraries added, fminer tests pass
Christoph Helma [Mon, 10 Aug 2015 11:26:06 +0000 (13:26 +0200)]
algorithm libraries added, fminer tests pass

5 years agotransfer to new git project started
Christoph Helma [Mon, 10 Aug 2015 07:48:57 +0000 (09:48 +0200)]
transfer to new git project started

5 years agoInitial commit
Christoph Helma [Sun, 9 Aug 2015 11:54:26 +0000 (13:54 +0200)]
Initial commit

5 years agocustomized prediction algorithms implemented
Christoph Helma [Sun, 9 Aug 2015 11:42:54 +0000 (13:42 +0200)]
customized prediction algorithms implemented

5 years agoSMARTS_InteLigand.txt added
Christoph Helma [Fri, 7 Aug 2015 17:50:48 +0000 (19:50 +0200)]
SMARTS_InteLigand.txt added

5 years agoinitial k-nn weighted average implementation
Christoph Helma [Fri, 7 Aug 2015 17:50:09 +0000 (19:50 +0200)]
initial k-nn weighted average implementation

5 years agoinitial classification validation
Christoph Helma [Mon, 3 Aug 2015 16:04:58 +0000 (18:04 +0200)]
initial classification validation

5 years ago50 times faster bbrc setup by eliminating @fminer.add_fminer_data
Christoph Helma [Sat, 1 Aug 2015 16:03:09 +0000 (18:03 +0200)]
50 times faster bbrc setup by eliminating @fminer.add_fminer_data

5 years agointermediary commit
Christoph Helma [Fri, 31 Jul 2015 17:25:13 +0000 (19:25 +0200)]
intermediary commit

5 years agodescriptor tests working
Christoph Helma [Fri, 31 Jul 2015 08:59:53 +0000 (10:59 +0200)]
descriptor tests working

5 years agokazius lazar predictions working
Christoph Helma [Wed, 29 Jul 2015 15:10:25 +0000 (17:10 +0200)]
kazius lazar predictions working

5 years agobbrc features for kazius with minfreq 20 successfully created and stored
Christoph Helma [Wed, 29 Jul 2015 13:05:02 +0000 (15:05 +0200)]
bbrc features for kazius with minfreq 20 successfully created and stored

5 years agosave data_entries in GridFS (fastest method up to now)
Christoph Helma [Wed, 29 Jul 2015 10:39:07 +0000 (12:39 +0200)]
save data_entries in GridFS (fastest method up to now)

5 years agoreasonable query performace for data_entries
Christoph Helma [Mon, 27 Jul 2015 18:51:25 +0000 (20:51 +0200)]
reasonable query performace for data_entries

5 years agomongo batch import workaround
Christoph Helma [Wed, 22 Jul 2015 18:08:12 +0000 (20:08 +0200)]
mongo batch import workaround

5 years agointermediary commit before switching to generalised storage model
Christoph Helma [Tue, 21 Jul 2015 08:52:03 +0000 (10:52 +0200)]
intermediary commit before switching to generalised storage model

5 years agolazar predictions working in principle
Christoph Helma [Sun, 19 Jul 2015 19:26:03 +0000 (21:26 +0200)]
lazar predictions working in principle

5 years agoinitial algorithm changes
Christoph Helma [Sat, 18 Jul 2015 08:14:16 +0000 (10:14 +0200)]
initial algorithm changes

5 years agodataset tests pass
Christoph Helma [Sat, 18 Jul 2015 06:52:39 +0000 (08:52 +0200)]
dataset tests pass

5 years agotask tests passed
Christoph Helma [Thu, 16 Jul 2015 17:07:29 +0000 (19:07 +0200)]
task tests passed

5 years agofeature tests for standalone version
Christoph Helma [Thu, 16 Jul 2015 14:54:48 +0000 (16:54 +0200)]
feature tests for standalone version

5 years agostorage of uris instead of objects
Christoph Helma [Thu, 16 Jul 2015 08:06:24 +0000 (10:06 +0200)]
storage of uris instead of objects

5 years agoinitial dataset tests
ch [Sun, 12 Jul 2015 10:14:13 +0000 (12:14 +0200)]
initial dataset tests

5 years agofeature, error and task (almost) working
ch [Wed, 8 Jul 2015 08:58:24 +0000 (10:58 +0200)]
feature, error and task (almost) working

5 years agoavoid data_entries nil error
gebele [Thu, 26 Mar 2015 16:09:00 +0000 (17:09 +0100)]
avoid data_entries nil error

5 years agoreintroduce percentageCompleted for task progress;added method to generate a task...
gebele [Mon, 9 Mar 2015 09:42:32 +0000 (10:42 +0100)]
reintroduce percentageCompleted for task progress;added method to generate a task uri for pass to object to update progress

5 years agoMerge branch 'development' of github.com:opentox/opentox-client into development
rautenberg [Wed, 5 Nov 2014 15:44:54 +0000 (16:44 +0100)]
Merge branch 'development' of github.com:opentox/opentox-client into development

5 years agoadd missing opening body tag in to_html method / remove autologin to avoid confusion...
rautenberg [Wed, 5 Nov 2014 15:44:41 +0000 (16:44 +0100)]
add missing opening body tag in to_html method / remove autologin to avoid confusion with configuration errors