From fd521bed1e12988bcc099ae0f58190f6ace01dfa Mon Sep 17 00:00:00 2001 From: Ariane Sasso Date: Thu, 15 Nov 2018 17:51:35 -0500 Subject: [PATCH 1/5] Update README.md Adding new features and examples on how to run experiments :). --- README.md | 32 +++++++++++++++++++++++++++++++- 1 file changed, 31 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 9ec86d20..ba6960ee 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ A repository containing support code and resources initially developed at the [Institute for Medical Informatics, Statistics and Documentation at the Medical University of Graz (Austria)](https://www.medunigraz.at/imi/en/) for participation at the [2017 TREC Precision Medicine Track](http://trec-cds.appspot.com/2017.html). For further information on this track and the final results please check the official [TREC-PM 2017 overview paper](https://trec.nist.gov/pubs/trec26/papers/Overview-PM.pdf). Team name: **imi_mug** -It was then further improved for participation at the [2018 TREC Precision Medicine Track](http://trec-cds.appspot.com/2018.html). +It was then further improved for participation at the [2018 TREC Precision Medicine Track](http://trec-cds.appspot.com/2018.html). Improvements include: support for subtemplates and the possibility to use disjunctive queries (_dis\_max_) allowing e.g. synonyms and hypernyms to have different weights. If you use data or code in your work, please cite our [TREC 2017 proceedings paper](https://trec.nist.gov/pubs/trec26/papers/imi_mug-PM.pdf): @@ -14,6 +14,8 @@ Also of interest: * [Our TREC 2017 presentation slides](https://github.com/bst-mug/trec2017/blob/master/docs/presentation.pdf) * [Our TREC 2017 Poster](https://github.com/bst-mug/trec2017/blob/master/docs/poster.pdf) +* [Our TREC 2018 presentation slides](https://github.com/hpi-dhc/trec-pm/blob/master/docs/2018/presentation.pdf) +* [Our TREC 2018 Poster](https://github.com/hpi-dhc/trec-pm/blob/master/docs/2018/poster.pdf) ## Code Dependencies @@ -24,6 +26,34 @@ Also of interest: - perl (for `sample_eval` tool) - Elasticsearch 5.4.0+ +# Some Examples on How to Run Experiments + +``` +# All executions should be run where the pom file is, usually the root of the project + +# How to run the pubmed experimenter +# Necessary to define the year and type of gold-standard (for evaluation) + +mvn clean install +mvn exec:java -Dexec.mainClass="at.medunigraz.imi.bst.trec.PubmedExperimenter" + +# How to run the clinical trials experimenter +# Necessary to define the year and type of gold-standard (for evaluation) + +mvn clean install +mvn exec:java -Dexec.mainClass="at.medunigraz.imi.bst.trec.ClinicalTrialsExperimenter" + +# How to run the KeywordExperimenter +# Necessary to define the year and type of gold-standard (for evaluation) +# For positive booster, in the keyword template leave boost = 1 +# For negative booster, in the keyword template leave boost = -1 +# Also, in the KeywordExperimenter the keywordsSource needs to be specified + +mvn clean install +mvn exec:java -Dexec.mainClass="at.medunigraz.imi.bst.trec.KeywordExperimenter" > out.txt & +cat out.txt | grep -e "\(^[0-9\.]*\)\(\;.*\)\(with.*\)\(\\[.*\\]\)\(.*\)" | sed -r "s/"\(^[0-9\.]*\)\(\;.*\)\(with.*\)\(\\[.*\\]\)\(.*\)"/\1 \2 \4/" > results.txt +``` + [![Codacy Badge](https://api.codacy.com/project/badge/Grade/00d52e98173d4629be22a4224a48a223)](https://www.codacy.com/app/michelole/trec-pm) [![Build Status](https://travis-ci.com/bst-mug/trec-pm.svg?branch=master)](https://travis-ci.com/bst-mug/trec-pm) [![Coverage Status](https://coveralls.io/repos/github/bst-mug/trec-pm/badge.svg?branch=master)](https://coveralls.io/github/bst-mug/trec-pm?branch=master) From 86e409e180bb1483189cdc609b5cf7164a388ce9 Mon Sep 17 00:00:00 2001 From: Ariane Sasso Date: Thu, 15 Nov 2018 17:52:06 -0500 Subject: [PATCH 2/5] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index ba6960ee..63a66239 100644 --- a/README.md +++ b/README.md @@ -26,7 +26,7 @@ Also of interest: - perl (for `sample_eval` tool) - Elasticsearch 5.4.0+ -# Some Examples on How to Run Experiments +## Some Examples on How to Run Experiments ``` # All executions should be run where the pom file is, usually the root of the project From e53e482aa26dfbd4ea7c5ae185eb2a430eda49e7 Mon Sep 17 00:00:00 2001 From: Ariane Sasso Date: Thu, 15 Nov 2018 17:56:27 -0500 Subject: [PATCH 3/5] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 63a66239..8f476c3e 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ A repository containing support code and resources initially developed at the [Institute for Medical Informatics, Statistics and Documentation at the Medical University of Graz (Austria)](https://www.medunigraz.at/imi/en/) for participation at the [2017 TREC Precision Medicine Track](http://trec-cds.appspot.com/2017.html). For further information on this track and the final results please check the official [TREC-PM 2017 overview paper](https://trec.nist.gov/pubs/trec26/papers/Overview-PM.pdf). Team name: **imi_mug** -It was then further improved for participation at the [2018 TREC Precision Medicine Track](http://trec-cds.appspot.com/2018.html). Improvements include: support for subtemplates and the possibility to use disjunctive queries (_dis\_max_) allowing e.g. synonyms and hypernyms to have different weights. +It was then further improved for participation at the [2018 TREC Precision Medicine Track](http://trec-cds.appspot.com/2018.html), team: **dhc-hpi**. Improvements include: support for subtemplates and the possibility to use disjunctive queries (_dis\_max_) allowing e.g. synonyms and hypernyms to have different weights. If you use data or code in your work, please cite our [TREC 2017 proceedings paper](https://trec.nist.gov/pubs/trec26/papers/imi_mug-PM.pdf): From 6b97debdeb7d5230b6edb5992a3dcd045f1f8f2d Mon Sep 17 00:00:00 2001 From: Ariane Sasso Date: Thu, 15 Nov 2018 18:45:09 -0500 Subject: [PATCH 4/5] Update README.md --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 8f476c3e..fdf419dd 100644 --- a/README.md +++ b/README.md @@ -16,6 +16,7 @@ Also of interest: * [Our TREC 2017 Poster](https://github.com/bst-mug/trec2017/blob/master/docs/poster.pdf) * [Our TREC 2018 presentation slides](https://github.com/hpi-dhc/trec-pm/blob/master/docs/2018/presentation.pdf) * [Our TREC 2018 Poster](https://github.com/hpi-dhc/trec-pm/blob/master/docs/2018/poster.pdf) +* [Our TREC 2018 Data Artifacts](https://figshare.com/projects/TREC_PM_2018_Data_dhc-hpi_/56882) ## Code Dependencies From 17b7617f10492f337577af267cde5abfbf09f3fc Mon Sep 17 00:00:00 2001 From: Ariane Sasso Date: Fri, 16 Nov 2018 06:40:29 -0500 Subject: [PATCH 5/5] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index fdf419dd..183ad5c2 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ Also of interest: * [Our TREC 2017 Poster](https://github.com/bst-mug/trec2017/blob/master/docs/poster.pdf) * [Our TREC 2018 presentation slides](https://github.com/hpi-dhc/trec-pm/blob/master/docs/2018/presentation.pdf) * [Our TREC 2018 Poster](https://github.com/hpi-dhc/trec-pm/blob/master/docs/2018/poster.pdf) -* [Our TREC 2018 Data Artifacts](https://figshare.com/projects/TREC_PM_2018_Data_dhc-hpi_/56882) +* [Our TREC 2018 Data Artifacts](https://figshare.com/projects/TREC_PM_2018_Data_hpi-dhc_/56882) ## Code Dependencies