HyREX

HyREX stands for Hybrid Relation Extractor. It is a multi-phase hybrid kernel based approach -

• combines a feature based kernel (Chowdhury and Lavelli, EACL 2012), Shallow Linguistic kernel (Giuliano et al., EACL 2006), Path-enclosed Tree kernel (Moschitti, ACL 2004)
• exploits scope of negations (Chowdhury and Lavelli, NAACL 2013)
• discards uninformative training instances using semantic roles and contextual evidence (Chowdhury and Lavelli, COLING 2012)

This software is distributed under Apache License 2.0.

Modification, redistribution or any other usage of this software is permitted without any restriction, given that the following papers are cited:

[1] Md Faisal Mahbub Chowdhury, Alberto Lavelli, "Exploiting Scopes of Negations and Heterogeneous Features for Relation Extraction: A Case Study for Drug-Drug Interaction Extraction", NAACL 2013
[2] Md Faisal Mahbub Chowdhury, Alberto Lavelli, "FBK-irst: A Multi-Phase Kernel Based Approach for Drug-Drug Interaction Detection and Classification that Exploits Linguistic Information", SemEval 2013

Disclaimer

All the 3rd party tools and libraries (e.g. SVM-Light-TK and the jar files under "lib" directory) used by this software have their own license type. Please check them if you intend to use them for commerical usage.

Required Libraries/jars

To run this software, please download the following jar files and place them under "lib" directory -

1. lvg2012api.jar
2. lvg2012dist.jar

(Download lvg2012.tgz from https://lexsrv3.nlm.nih.gov/LexSysGroup/Projects/lvg/2012/release/lvg2012.tgz , unzip it, go inside the lib folder inside the unzipped folder and you will find those 2 jars.)

3. stanford-parser-2012-03-09-models.jar
4. stanford-parser.jar

(Download stanford-parser-2012-03-09.tgz from https://nlp.stanford.edu/software/stanford-parser-2012-03-09.tgz , unzip it, the above 2 jars are inside the unzipped folder.)

Data to train the system

Please check data_format for input data format. There are 2 sample files inside sample-data folder according to that format.

To replicate the results of the SemEval-2013 DDI Extraction task, obtain annotated training data from https://www.cs.york.ac.uk/semeval-2013/task9/index.php%3Fid=data.html . Please convert them into the format of the sample files.

There are a number of data pre-processing classes insidesrc/DataProcessor for a number of benchmark datasets for different RE tasks. You can either use them or write your own custom codes to preprocess your input data.
You can use src/Utility/SyntacticParser.java to parse your input text into the desired format specified in the sample files.

How to run the system

To run it, open terminal, cd to the HypRex folder and run the following command -

sh hyrex_run.sh

Make sure hyrex_sen_run.sh and hyrex_run.sh have execution and write permission.

Also, please remember to provide values for the following parameters inside the hyrex_run.sh file -

• TRAIN_DATA_FULL: a single file containing your training data in the format like sample-data/sample.full

• TRAIN_DATA_PARSED: a single file containing parsed output of your training data in the format like sample-data/sample.parsed.bllip.complete

• HELDOUT_DATA_FULL: Same as TRAIN_DATA_FULL (or a seprate development dataset) to be used for parameter tuning.

• HELDOUT_DATA_PARSED: Same as TRAIN_DATA_PARSED (or a seprate development dataset) to be used for parameter tuning.

• TEST_DATA_FULL: Your test data in the format like sample-data/sample.full

• TEST_DATA_PARSED: Your test data in the format like sample-data/sample.parsed.bllip.complete

-- Faisal