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  • 7.1.0 - CluProcessor now contains a MEMM model for syntactic chunking.
  • 7.1.0 - CluProcessor now produces both universal and Stanford dependencies, both basic and enhanced.
  • 7.0.2 - The ensemble parsing model in CluProcessor is now guaranteed to produce cycle-free outputs.
  • 7.0.1 - Added feature to Odin to import variables from a file. Works similarly to taxonomies.
  • 7.0.0 - Updated library to use Scala 2.12 by default. Add ability to remove lexicon members.
  • 7.0.0 - Retrained our two discourse parsers (constituent- and dependency-syntax based) to work with universal dependencies.
  • 7.0.0 - Switched to CoreNLP 3.8.0 and universal dependencies.
  • 6.3.0 - Branched released version 6.3.0 as base for future Reach development (branch name 'reach').
  • 6.3.0 - Renamed modification trait to Attachment.
  • 6.2.0 - Added ability to add Modifications to mentions.
  • 6.2.0 - Added openie package, which contains EntityFinder.
  • 6.2.0 - Added wrappers for the regression functions in liblinear and libsvm.
  • 6.2.0 - Added functionality to use a serialized model to LexiconNER.
  • 6.1.4 - Added org.clulab.sequences.LexiconNER to match known entity names efficiently.
  • 6.1.4 - Allow for odin variable use in import paths.
  • 6.1.3 - Update core server parameters. Increment Akka version to 2.5.4.
  • 6.1.3 - Added BioCluProcessor, which has all the functionality of BioNLPProcessor, with the exception of the bio NER (to be added later).
  • 6.1.3 - Separated the models jar in two jars: modelsmain, which contains data relevant for processors-main, and modelscorenlp, which contains data relevant for processors-corenlp.
  • 6.1.3 - Bug fix: fixed model loading for the maltparser models, which were not loading properly from the processors-models jar.
  • 6.1.3 - CluProcessor can now be configured through Config.
  • 6.1.2 - Update to use Bioresources 1.1.24 which includes the Harvard BioEntities updates of 8/22/2017.
  • 6.1.2 - Bug fix: made Counter.keySet efficient (again). This severely affected the performance of the discourse parser, which was extremely slow.
  • 6.1.2 - Replaced the CRF model based on Mallet with an in-house BiMEMM model. Performance is 97% on WSJ and 98% on Genia.
  • 6.1.0/1 - Added the word-by-word voting ensemble model to the CluProcessor parser. Performance (with gold POS tags) is: LAS on WSJ: 89.2%, LAS on Genia: 87.4%.
  • 6.1.0/1 - Added collapsed Stanford dependencies to CluProcessor. See org.clulab.processors.clu.syntax.EnhancedDependencies for details.
  • 6.1.0/1 - Bug fix: the parsing model in CluProcessor was broken (maltparser was trained incorrectly).
  • 6.0.7 - Implement Akka-based processors server, with default configuration for BioNLP.
  • 6.0.7 - Added basic Stanford dependencies to CluProcessor. These are implemented using maltparser trained on WSJ + Genia. Note that currently the CluProcessor POS tagger is trained just on WSJ.
  • 6.0.6 - Rename Odin subproject library artifact to processors-odin, for consistency.
  • 6.0.6 - Added CluProcessor, which contains only in-house tools under the Apache license. Currently contains English tokenization, lemmatization, and POS tagging.
  • 6.0.6 - Added graph field to Odin rules, which denotes the graph (ex. stanford collapsed dependencies) used within the pattern (incoming, outgoing, etc.).
  • 6.0.6 - Added ranged quantifiers to Odin graph pattern arguments.
  • 6.0.5 - Added charset parameter to ExtractorEngine methods.
  • 6.0.5 - The FastBioNLPProcessor is available in the ProcessorsShell.
  • 6.0.4 - Use consistent SBT version across projects. Fix lib clash: allow ai.lum.common to dicate typesafe.config version.
  • 6.0.3 - Added FastBioNLPProcessor. Update for Bioresources 1.1.22 containing updated MITRE Phase3 override KB.
  • 6.0.3 - The rule NER is now a singleton object, so it can be shared between different processor objects.
  • 6.0.3 - Remove use of Phase3 override file to phase3 branch only.
  • 6.0.2 - Update to use Bioresources 1.1.21 containing updated MITRE PhaseIII override KB.
  • 6.0.2 - Enhance NER to load multiple override files. Update to use Bioresources 1.1.20 containing MITRE PhaseIII override KB.
  • 6.0.2 - file I/O fix related to json deserialization.
  • 6.0.2 - Fixed odin bug related to ^ in lookbehinds. Update to use Bioresources 1.1.19 containing Bioentities project KBs.
  • 6.0.1 - Added support to odin for redefining variables.
  • 6.0.1 - Added support to odin for matching mention arguments.
  • 6.0.1 - Added support to odin for cross-sentence patterns.
  • 6.0.1 - Fixed odin bug when matching overlapping entities with same end at the beginning of a pattern.
  • 6.0.1 - Improved validation of named entities in RuleNER.
  • 6.0.1 - Added automated lexical variations to the BioNLPProcessor RuleNER.
  • 6.0.1 - Bug fix in multi-world entity matching in the RuleNER.
  • 6.0.0 - Reorganization into 3 subprojects with different licenses: main, corenlp, models.
  • 6.0.0 - Optimizations to json serialization/deserialization.
  • 5.9.6 - Serialize/deserialize Document, Mention, etc. to/from json.
  • 5.9.5 - Bug fix release: do not tag XML tags such as XREF... as named entities.
  • 5.9.4 - Update to use bioresources 1.1.15.
  • 5.9.3 - Improved support for multi-token triggers in dependency patterns in Odin.
  • 5.9.3 - Improved tokenization of n-ary complexes for BioNLPProcessor. Reverts some of CoreNLP's aggressive tokenization.
  • 5.9.2 - Add numeric comparisons and distributional similarity comparisons via word embeddings to Odin (word2vec).
  • 5.9.2 - Ensure amino acid abbreviations parse correctly. Tokenize sites that appear as prefixes; e.g. "Tyr-phosphorylated". Use Bioresources 1.1.13.
  • 5.9.1 - Bug fixes for KBLoader and X/Y heterodimer bugs. Update some BioNLP* tests.
  • 5.9.1 - Added override capability to the rule NER in BioNLPProcessor.
  • 5.9.1 - Improved tokenization of protein families and other edge cases.
  • 5.9.1 - Bug fix in the RF classifier: handle features that appear only with 0 values during training.
  • 5.9.1 - Updated to use bioresources 1.1.10.
  • 5.9.0 - Changed top package from edu.arizona.sista to org.clulab.
  • 5.8.6 - Global tokenization for complexes in BioNLPProcessor. Added support for sentiment analysis in CoreNLPSentimentAnalyzer.
  • 5.8.5 - Updated to bioresources 1.1.9. Improved the handling of stop-list entities in the bio NER.
  • 5.8.4 - Updated to bioresources 1.1.6. Add and load TissueType KB. Synch the KBLoader with NER configuration in Bioresources.
  • 5.8.3 - Updated to bioresources 1.1.4. The BioNLPProcessor POS tagger now correctly tags verbs for biochemical interactions as verbs.
  • 5.8.2 - Implemented unrestricted lookbehind for Odin's surface patterns. Updated to bioresources 1.1.1. Added support for unbalanced data to LibLinearClassifier. Incremental improvements to the SRL system.
  • 5.8.1 - Improved Odin's variables compatibility with YAML. Switched BioNLPProcessor to using bioresources rather than the local resources. Bug fix: RuleNER was not producing the longest possible match all the time.
  • 5.8.0 - Added in-house random forest implementation. Removed Weka dependency and its RF classifier. Removed RF reranking classifier. Bug fix in Odin: allow $ and \ in variable values. Restricted Odin variable names to valid Java identifiers. Added object Serializer. We no longer intern Strings by default in BioNLPProcessor.
  • 5.7.3 - Added support for context entities: species, organs, cell lines, cell types.
  • 5.7.2 - Keep matched syntactic paths in event/relation mentions. Added support for trigger matching from the state.
  • 5.7.1 - Made Odin event mentions friendlier for event coreference.
  • 5.7.0 - Added chunker for shallow syntax based on the CoNLL-2000 shared task. Improved Odin's Java API. Several bugfixes.
  • 5.6.0 - Changed organization to org.clulab. Changed to 3-number versions. Changed resource loader behavior for the Odin "import" command.
  • 5.5 - Added support for rule templates, importing grammar files, and taxonomies in Odin.
  • 5.4 - The Sentence class now stores all available dependency types generated by a processor, e.g., both basic and collapsed Stanford dependencies. Multiple improvements to the Odin language.
  • 5.3 - Many incremental improvements to ODIN and BioNLPProcessor, including better tokenization of biomedical text, and a revamped bio NER, which now combines an in-house CRF with a rule-based system, with rules derived from multiple knowledge bases such as Uniprot.
  • 5.2 - Version 2 of ODIN, including a cleaner (more declarative) rule language, which minimizes the need for custom actions. See edu.arizona.sista.odin.domains.toydomain for an example of a toy domain, and edu.arizona.sista.odin.domains.bigmechanism.dryrun2015 for a complete biomedical domain.
  • 5.1 - Improved tokenization for the bio domain. Replaced the BANNER NER for the bio domain with our own implementation. Installing BANNER is thus no longer necessary.
  • 5.0 - changed to Java 8, Scala 2.11, and CoreNLP 3.5.1. First public release of ODIN (domain-independent event extraction) framework, in the edu.arizona.sista.odin package. First release of ODIN's DARPA biomedical grammar. FastNLPProcessor now supports both the Malt and the new Stanford NN dependency parser (the Stanford parser is now the default setting).
  • 4.0 - added BioNLPProcessor. Install our fork of the BANNER named entity recognizer before!
  • 3.3 - bug fix: make sure DocumentSerializer.load() works when multiple documents are serialized into the same file.
  • 3.2 - Added a discourse parser to FastNLPProcessor. This performs marginally worse than the one in CoreNLPProcessor, but it is much faster for end-to-end processing, due to the shift-reduce syntactic parser.
  • 3.1 - Minimal functionality added to the learning package. Changed to CoreNLP 3.3.1.
  • 3.0 - Added a RST discourse parser to CoreNLPProcessor. Added the edu.arizona.sista.learning package. Utils classes are now under edu.arizona.sista.utils rather than edu.arizona.sista.processors.utils.
  • 2.2 - Various bug fixes. Added support for basic dependencies to CoreNLPProcessor.
  • 2.1 - Bug fix in FastNLPProcessor: better root detection algorithm, robust to malt inconsistencies.
  • 2.0 - We now support two processors: CoreNLPProcessor and FastNLPProcessor. Changed the package name from e.a.s.processor to e.a.s.processors. Added Java usage example to README. Updated to CoreNLP 3.3.0. Added better unit tests to check for thread safetiness.
  • 1.5 - Bug fixing. Made the string interning process (see Processor.in) local to each thread to avoid concurrency issues in multi-threaded programs. Added new unit tests. Added minor functionality to Lexicon.
  • 1.4 - Code cleanup. Added some minor new functionality such as finding base NPs in the Trees class.
  • 1.3 - Reverted back to the 1.x version numbers, since we will add other software here not just CoreNLP. Added correct mvn dependencies for the CoreNLP jars. Removed the install*.sh scripts, which are no longer needed.
  • 3.2.0 - Updated to Scala 2.10.1 and CoreNLP 3.2.0. Changed versioning system to be identical to CoreNLP's, so it's clear which CoreNLP version is used.
  • 1.0 - Initial release