Recent changes to feature-requests-improvements

Change distances to similarities in Base Matchers

Juergen Bock — Fri, 07 Oct 2011 14:47:00 -0000

For all base matchers, the distance metric (0 is best, 1 is worst) must be changed to similarities (0 is worst, 1 is best).

Implement correspondence evaluation cache

Juergen Bock — Fri, 07 Oct 2011 14:41:34 -0000

Some base matchers could cache the evaluations of correspondences.

Refactor cloud deployment code to harmonia-commons or kadmos

Juergen Bock — Wed, 18 May 2011 08:18:52 -0000

It should be evaluated how the cloud deployment implementation can be generalised in order to be available for several population-based alignment algorithms. In particular, the code should then be part of harmonia-commons or kadmos.

Refactor fitness calaculation to harmonia-commons

Juergen Bock — Wed, 18 May 2011 08:13:32 -0000

The fitness calculation should be provided by the harmonia-commons fitness calculator project since it is a shared functionality for this and other alignment algorithms. Fitness calculation means the aggregation of an alignment fitness from the individual correspondences' fitnesses and other global fitnes criteria.

Maven WAR packaging

Juergen Bock — Wed, 18 May 2011 07:56:12 -0000

In order to enable MapPSO to be deployed as a web service, we need a WAR file to be deployed in an application server e.g. Tomcat. Maven must be configured to package such a WAR file.

Switch to KADMOS API

Juergen Bock — Wed, 18 May 2011 07:51:04 -0000

The KADMOS API (https://sourceforge.net/projects/kadmos/) should replace the Alignment API.

Switch to Commons Logging

Juergen Bock — Wed, 18 May 2011 07:47:23 -0000

Apache Commons Logging is the better logging framework for library-like software components like MapPSO. It should be used throughout the project apart from any entry points (which should not exist anyway).

Refactor particle length adjustment

Juergen Bock — Mon, 02 May 2011 14:12:10 -0000

The particle length adjustment procedure is rather obscure and probably buggy. In order to make it easier to test, the single method should be refactored into several that provide the different core functionalities required for length adjustment, i.e. computation of change probability, computation of actual length change, and performing the adding and removal of correspondences. The different methods should be designed for easy testing, and as decoupled as possible from the rest of MapPSO.

Read WordNet dictionary and version from system variables

Juergen Bock — Fri, 20 Aug 2010 09:24:34 -0000

Before WordNet initialisation, read the dictionary and version parameters from system variables to make it easier to run MapPSO on a distributed environment with different WordNet locations. The parameters coming from params.xml should override the system variables though.

Enable confidence values in alignment

Juergen Bock — Sun, 13 Jun 2010 20:54:36 -0000

The final alignment should contain confidence values for each correspondence. This means the "strength" value in Cell objects should be used, where
strength = 1 - dist
Setting the strength value in AlignmentParticle immediately after distance computation results in a ConcurrentModificationException using two large ontologies with 4 particles in only 2 iterations.

Exception in thread "0" java.util.ConcurrentModificationException
at java.util.HashMap$HashIterator.nextEntry(HashMap.java:810)
at java.util.HashMap$EntryIterator.next(HashMap.java:851)
at java.util.HashMap$EntryIterator.next(HashMap.java:849)
at de.fzi.mappso.align.impl.AlignmentParticle.proportionalLikelihoodUpdate(AlignmentParticle.java:756)
at de.fzi.mappso.align.impl.AlignmentParticle.updateVelocity(AlignmentParticle.java:724)
at de.fzi.mappso.align.impl.AlignmentParticle.update(AlignmentParticle.java:455)
at de.fzi.mappso.align.impl.AlignmentParticle.step(AlignmentParticle.java:256)
at de.fzi.mappso.align.impl.AlignmentParticle.run(AlignmentParticle.java:230)
at java.lang.Thread.run(Thread.java:636)
Exception in thread "2" java.util.ConcurrentModificationException
at java.util.HashMap$HashIterator.nextEntry(HashMap.java:810)
at java.util.HashMap$EntryIterator.next(HashMap.java:851)
at java.util.HashMap$EntryIterator.next(HashMap.java:849)
at de.fzi.mappso.align.impl.AlignmentParticle.proportionalLikelihoodUpdate(AlignmentParticle.java:756)
at de.fzi.mappso.align.impl.AlignmentParticle.updateVelocity(AlignmentParticle.java:724)
at de.fzi.mappso.align.impl.AlignmentParticle.update(AlignmentParticle.java:455)
at de.fzi.mappso.align.impl.AlignmentParticle.step(AlignmentParticle.java:256)
at de.fzi.mappso.align.impl.AlignmentParticle.run(AlignmentParticle.java:230)
at java.lang.Thread.run(Thread.java:636)
Exception in thread "3" java.util.ConcurrentModificationException
at java.util.HashMap$HashIterator.nextEntry(HashMap.java:810)
at java.util.HashMap$EntryIterator.next(HashMap.java:851)
at java.util.HashMap$EntryIterator.next(HashMap.java:849)
at de.fzi.mappso.align.impl.AlignmentParticle.proportionalLikelihoodUpdate(AlignmentParticle.java:756)
at de.fzi.mappso.align.impl.AlignmentParticle.updateVelocity(AlignmentParticle.java:724)
at de.fzi.mappso.align.impl.AlignmentParticle.update(AlignmentParticle.java:455)
at de.fzi.mappso.align.impl.AlignmentParticle.step(AlignmentParticle.java:256)
at de.fzi.mappso.align.impl.AlignmentParticle.run(AlignmentParticle.java:230)
at java.lang.Thread.run(Thread.java:636)
Exception in thread "1" java.util.ConcurrentModificationException
at java.util.HashMap$HashIterator.nextEntry(HashMap.java:810)
at java.util.HashMap$EntryIterator.next(HashMap.java:851)
at java.util.HashMap$EntryIterator.next(HashMap.java:849)
at de.fzi.mappso.align.impl.AlignmentParticle.proportionalLikelihoodUpdate(AlignmentParticle.java:756)
at de.fzi.mappso.align.impl.AlignmentParticle.updateVelocity(AlignmentParticle.java:724)
at de.fzi.mappso.align.impl.AlignmentParticle.update(AlignmentParticle.java:455)
at de.fzi.mappso.align.impl.AlignmentParticle.step(AlignmentParticle.java:256)
at de.fzi.mappso.align.impl.AlignmentParticle.run(AlignmentParticle.java:230)
at java.lang.Thread.run(Thread.java:636)