1. Variables and notations
| Term | Meaning | Variable in script | Scripts |
|---|---|---|---|
| collection | name of the collection/dataset (biocaddie, ohsumed, treccds, trecgenomics) | col | all |
| subset | set of data used for running baselines (combined, test, train) | subset | all |
| topics | name of the topics file (short, orig, stopped, etc) | topics | all |
| year | year of the collection/dataset, available for few collections such as trecgenomics (2006, 2007) | year | all |
| model | retrieval model (dir, rm3, jm, pubmed, etc) | model | mkeval.sh, mkeval-lucene.sh |
| from model | retrieval model (dir, rm3, jm, pubmed, etc), for comparison (t-test) | from | compare.R |
| to model | retrieval model (dir, rm3, jm, pubmed, etc), for comparison (t-test) | to | compare.R |
| metric | evaluation metric (map, ndcg, P_20, ndcg_cut_20, etc) | metric | mkeval.sh, mkeval-lucene.sh, compare.R |
| run method | running method (indri, lucene) | run | compare.R |
2. Files and their locations
Collections without year: biocaddie, ohsumed
Collections with year: treccds (2015), trecgenomics (2006, 2007)
| Type | Location | Example |
|---|---|---|
| Indexes | /data/<col>/lucene/<col>_all/shard0 /data/<col>/lucene/<col><year>_all/shard0 | /data/biocaddie/lucene/biocaddie_all/shard0 /data/trecgenomics/lucene/trecgenomics2006_all/shard0 |
| Queries | /data/<col>/queries/queries.<subset>.<topics> /data/<col>/queries/queries.<subset>.<topics>.<year> | /data/biocaddie/queries/queries.test.short /data/trecgenomics/queries/queries.combined.orig.2006 |
| Qrels | /data/<col>/qrels/<col>.qrels.<subset> /data/<col>/qrels/<col>.qrels.<subset>.<year> | /data/biocaddie/qrels/biocaddie.qrels.test /data/trecgenomics/qrels/trecgenomics.qrels.combined.2006 |
| Output | /data/<col>/lucene-output/<model>/<subset>/<topics> /data/<col>/lucene-output/<year>/<model>/<subset>/<topics> | /data/biocaddie/lucene-output/dir/test/short /data/trecgenomics/lucene-output/2006/dir/combined/orig |
| Eval | /data/<col>/lucene-eval/<model>/<subset>/<topics> /data/<col>/lucene-eval/<year>/<model>/<subset>/<topics> | /data/biocaddie/lucene-eval/dir/test/short /data/trecgenomics/lucene-eval/2006/dir/combined/orig |
| Loocv | /data/<col>/loocv/<model>.<subset>.<topics>.<metric>.lucene.out /data/<col>/loocv/<year>/<model>.<subset>.<topics>.<metric>.lucene.out | /data/biocaddie/loocv/dir.test.short.ndcg.lucene.out /data/trecgenomics/loocv/2006/dir.combined.orig.ndcg.lucene.out |
*** Note: both Lucene and Indri's loocv results are saved in the same location for easy comparison across different runs.
3. Run Lucene baselines
a) Lucene Run (lucene-output)
cd ~/biocaddie
baselines/new/<model>-lucene.sh <topics> <subset> <col>| parallel -j 20 bash -c "{}"
baselines/new/<model>-lucene.sh <topics> <subset> <col> <year>| parallel -j 20 bash -c "{}"
Eg: baselines/new/dir-lucene.sh short test biocaddie | parallel -j 20 bash -c "{}"
b) Evaluation and Cross-validation (lucene-eval, loocv)
cd ~/biocaddie scripts/new/mkeval-lucene.sh <model> <topics> <subset> <col> scripts/new/mkeval-lucene.sh <model> <topics> <subset> <col> <year>
Eg: scripts/new/mkeval-lucene.sh dir short test biocaddie
c) Compare models
We have to input running method for comparison:
0 - both from and to models are from Indri run
1 - both from and to models are from Lucene run
2 - from model is from Indri run, to model is from Lucene run
3 - from model is from Lucene run, to model is from Indri run
cd ~/biocaddie Rscript scripts/new/compare.R <subset> <from> <to> <topics> <col> Rscript scripts/new/compare.R <subset> <from> <to> <topics> <col> <year>
Eg: Rscript scripts/new/compare.R test tfidf dir short biocaddie
4. Results
| Model | MAP | NDCG | P@20 | NDCG@20 | P@100 | NDCG@100 | Notes | Date |
|---|---|---|---|---|---|---|---|---|
| classic tfidf | 0.3283 | 0.5816 | 0.6933 | 0.5462 | 0.5007 | 0.4996 | No parameters | 06/30/17 |
| BM25 | 0.3544 | 0.6061+ | 0.75 | 0.5958+ | 0.5067 | 0.5182 | Sweep b, k1 | 06/30/17 |
| QL (JM) | 0.3367 | 0.6016 | 0.7233 | 0.5713 | 0.5007 | 0.5017 | Sweep lambda | 06/30/17 |
| QL (Dir) | 0.3677 (p-value=0.0526) | 0.6169+ | 0.6667 | 0.5676 | 0.5213 | 0.5221 | Sweep mu | 06/30/17 |
root@integration-1:~/biocaddie# Rscript scripts/new/compare.R test tfidf dir short biocaddie
Please enter run methods for comparison:
0: both are Indri
1: both are Lucene
2: from is Indri, to is Lucene
3: from is Lucene, to is Indri
1
[1] "map 0.3283 0.3677 p= 0.0526"
[1] "ndcg 0.5816 0.6169 p= 0.0408"
[1] "P_20 0.6933 0.6667 p= 0.9251"
[1] "ndcg_cut_20 0.5462 0.5676 p= 0.1533"
[1] "P_100 0.5007 0.5213 p= 0.2053"
[1] "ndcg_cut_100 0.4996 0.5221 p= 0.1162"
root@integration-1:~/biocaddie# Rscript scripts/new/compare.R test tfidf bm25 short biocaddie
Please enter run methods for comparison:
0: both are Indri
1: both are Lucene
2: from is Indri, to is Lucene
3: from is Lucene, to is Indri
1
[1] "map 0.3283 0.3544 p= 0.0825"
[1] "ndcg 0.5816 0.6061 p= 0.0239"
[1] "P_20 0.6933 0.75 p= 0.0612"
[1] "ndcg_cut_20 0.5462 0.5958 p= 0.0302"
[1] "P_100 0.5007 0.5067 p= 0.4072"
[1] "ndcg_cut_100 0.4996 0.5182 p= 0.1975"
root@integration-1:~/biocaddie# Rscript scripts/new/compare.R test tfidf jm short biocaddie
Please enter run methods for comparison:
0: both are Indri
1: both are Lucene
2: from is Indri, to is Lucene
3: from is Lucene, to is Indri
1
[1] "map 0.3283 0.3367 p= 0.2231"
[1] "ndcg 0.5816 0.6016 p= 0.0753"
[1] "P_20 0.6933 0.7233 p= 0.1356"
[1] "ndcg_cut_20 0.5462 0.5713 p= 0.1312"
[1] "P_100 0.5007 0.5007 p= 0.5"
[1] "ndcg_cut_100 0.4996 0.5017 p= 0.4441"