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)
Using biocaddie_all indexes
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 "{}"
baselines/new/tfidf-lucene.sh short test biocaddie| parallel -j 20 bash -c "{}"
baselines/new/jm-lucene.sh short test biocaddie| parallel -j 20 bash -c "{}"
baselines/new/bm25-lucene.sh short test biocaddie| parallel -j 20 bash -c "{}"
baselines/new/rocchio-lucene.sh short test biocaddie| parallel -j 20 bash -c "{}"
Using biocaddie_all.snowball indexes
cd ~/biocaddie
baselines/new/<model>-lucene-snowball.sh <topics> <subset> <col>| parallel -j 20 bash -c "{}"
baselines/new/<model>-lucene-snowball.sh <topics> <subset> <col> <year>| parallel -j 20 bash -c "{}"
Eg: baselines/new/dir-lucene-snowball.sh short test biocaddie| parallel -j 20 bash -c "{}"
baselines/new/tfidf-lucene-snowball.sh short test biocaddie| parallel -j 20 bash -c "{}"
baselines/new/jm-lucene-snowball.sh short test biocaddie| parallel -j 20 bash -c "{}"
baselines/new/bm25-lucene-snowball.sh short test biocaddie| parallel -j 20 bash -c "{}"
baselines/new/rocchio-lucene-snowball.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
scripts/new/mkeval-lucene.sh tfidf short test biocaddie
scripts/new/mkeval-lucene.sh jm short test biocaddie
scripts/new/mkeval-lucene.sh bm25 short test biocaddie
scripts/new/mkeval-lucene.sh rocchio short test biocaddie
scripts/new/mkeval-lucene.sh dir-snowball short test biocaddie
scripts/new/mkeval-lucene.sh tfidf-snowball short test biocaddie
scripts/new/mkeval-lucene.sh jm-snowball short test biocaddie
scripts/new/mkeval-lucene.sh bm25-snowball short test biocaddie
scripts/new/mkeval-lucene.sh rocchio-snowball 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
Rscript scripts/new/compare.R test tfidf-snowball dir-snowball short biocaddie
4. Results
Using biocaddie_all indexes.
| Model | MAP | NDCG | P@20 | NDCG@20 | P@100 | NDCG@100 | Notes | Date |
|---|---|---|---|---|---|---|---|---|
| classic tfidf | 0.3282 | 0.5824 | 0.6867 | 0.5478 | 0.5013 | 0.5018 | No parameters | 07/05/17 |
| BM25 | 0.3543 | 0.6105+ | 0.7467+ | 0.5917+ | 0.506 | 0.5186 | Sweep b, k1 | 07/05/17 |
| QL (JM) | 0.3382 | 0.6022 | 0.7233 | 0.571 | 0.5 | 0.4996 | Sweep lambda | 07/05/17 |
| QL (Dir) | 0.3675 (p-value=0.0548) | 0.6163+ (p-value=0.0502) | 0.6567 | 0.5664 | 0.5213 | 0.522 | Sweep mu | 07/05/17 |
| Rocchio | 0.4044+ | 0.6417 (p-value=0.0533) | 0.6967 | 0.5403 | 0.492 | 0.4912 | Sweep b, k1, fbTerms, fbDocs, fbOrigWeight | 07/05/17 |
Using biocaddie_all.snowball indexes
| Model | MAP | NDCG | P@20 | NDCG@20 | P@100 | NDCG@100 | Notes | Date |
|---|---|---|---|---|---|---|---|---|
| classic tfidf (tfidf-snowball) | 0.3375 | 0.5944 | 0.6667 | 0.5256 | 0.4987 | 0.5002 | No parameters | 07/06/17 |
| BM25 (bm25-snowball) | 0.3764+ | 0.6239+ | 0.73+ | 0.6006+ | 0.5413+ | 0.539+ | Sweep b, k1 | 07/06/17 |
| QL (JM) (jm-snowball) | 0.3448 | 0.6058 | 0.67 | 0.5813+ | 0.4987 | 0.5289+ | Sweep lambda | 07/06/17 |
| QL (Dir) (dir-snowball) | 0.3776+ | 0.6315+ | 0.7033 | 0.6006+ | 0.5307 | 0.5365+ | Sweep mu | 07/06/17 |
| Rocchio (rocchio-snowball) | 0.3959 | 0.6052 | 0.7267 | 0.598+ | 0.5453 | 0.525 | Sweep b, k1, fbTerms, fbDocs, fbOrigWeight | 07/06/17 |
Difference between unstemmed and stemmed indexes
| Model | MAP | NDCG | P@20 | NDCG@20 | P@100 | NDCG@100 | Notes | Date |
|---|---|---|---|---|---|---|---|---|
| classic tfidf | 0.3282 | 0.5824 | 0.6867 | 0.5478 | 0.5013 | 0.5018 | No parameters | 07/10/17 |
| classic tfidf (tfidf-snowball) | 0.3375 | 0.5944 | 0.6667 | 0.5256 | 0.4987 | 0.5002 | No parameters | 07/10/17 |
| BM25 | 0.3543 | 0.6105 | 0.7467 | 0.5917 | 0.506 | 0.5186 | Sweep b, k1 | 07/10/17 |
| BM25 (bm25-snowball) | 0.3764+ | 0.6239 | 0.73 | 0.6006 | 0.5413+ | 0.539+ | Sweep b, k1 | 07/10/17 |
| QL (JM) | 0.3382 | 0.6022 | 0.7233 | 0.571 | 0.5 | 0.4996 | Sweep lambda | 07/10/17 |
| QL (JM) (jm-snowball) | 0.3448 | 0.6058 | 0.67 | 0.5813 | 0.4987 | 0.5289+ | Sweep lambda | 07/10/17 |
| QL (Dir) | 0.3675 | 0.6163 | 0.6567 | 0.5664 | 0.5213 | 0.522 | Sweep mu | 07/10/17 |
| QL (Dir) (dir-snowball) | 0.3776 | 0.6315 (p-value=0.0534) | 0.7033+ | 0.6006+ | 0.5307 | 0.5365 | Sweep mu | 07/10/17 |
| Rocchio | 0.4044 | 0.6417 | 0.6967 | 0.5403 | 0.492 | 0.4912 | Sweep b, k1, fbTerms, fbDocs, fbOrigWeight | 07/11/17 |
| Rocchio (rocchio-snowball) | 0.3959 | 0.6052- | 0.7267 | 0.598+ | 0.5453+ | 0.525 | Sweep b, k1, fbTerms, fbDocs, fbOrigWeight | 07/11/17 |
Verification
Using biocaddie_all indexes:
thphan@biocaddie-dev:/data/thphan/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 0.3282 0.3675 p= 0.0548"
[1] "ndcg 0.5824 0.6163 p= 0.0502"
[1] "P_20 0.6867 0.6567 p= 0.9461"
[1] "ndcg_cut_20 0.5478 0.5664 p= 0.186"
[1] "P_100 0.5013 0.5213 p= 0.2168"
[1] "ndcg_cut_100 0.5018 0.522 p= 0.1401"
thphan@biocaddie-dev:/data/thphan/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 0.3282 0.3382 p= 0.1719"
[1] "ndcg 0.5824 0.6022 p= 0.0932"
[1] "P_20 0.6867 0.7233 p= 0.0831"
[1] "ndcg_cut_20 0.5478 0.571 p= 0.145"
[1] "P_100 0.5013 0.5 p= 0.5301"
[1] "ndcg_cut_100 0.5018 0.4996 p= 0.5552"
thphan@biocaddie-dev:/data/thphan/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 0.3282 0.3543 p= 0.0846"
[1] "ndcg 0.5824 0.6105 p= 0.0148"
[1] "P_20 0.6867 0.7467 p= 0.0491"
[1] "ndcg_cut_20 0.5478 0.5917 p= 0.0496"
[1] "P_100 0.5013 0.506 p= 0.428"
[1] "ndcg_cut_100 0.5018 0.5186 p= 0.2195"
thphan@biocaddie-dev:/data/thphan/biocaddie$ Rscript scripts/new/compare.R test tfidf rocchio 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 0.3282 0.4044 p= 0.0188"
[1] "ndcg 0.5824 0.6417 p= 0.0533"
[1] "P_20 0.6867 0.6967 p= 0.3785"
[1] "ndcg_cut_20 0.5478 0.5403 p= 0.6276"
[1] "P_100 0.5013 0.492 p= 0.6184"
[1] "ndcg_cut_100 0.5018 0.4912 p= 0.6071"
Using biocaddie_all.snowball indexes
thphan@biocaddie-dev:/data/thphan/biocaddie$ Rscript scripts/new/compare.R test tfidf-snowball dir-snowball 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 0.3375 0.3776 p= 0.0387"
[1] "ndcg 0.5944 0.6315 p= 0.0072"
[1] "P_20 0.6667 0.7033 p= 0.1042"
[1] "ndcg_cut_20 0.5256 0.6006 p= 0.0046"
[1] "P_100 0.4987 0.5307 p= 0.0652"
[1] "ndcg_cut_100 0.5002 0.5365 p= 0.0207"
thphan@biocaddie-dev:/data/thphan/biocaddie$ Rscript scripts/new/compare.R test tfidf-snowball jm-snowball 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 0.3375 0.3448 p= 0.2782"
[1] "ndcg 0.5944 0.6058 p= 0.2069"
[1] "P_20 0.6667 0.67 p= 0.475"
[1] "ndcg_cut_20 0.5256 0.5813 p= 0.0161"
[1] "P_100 0.4987 0.4987 p= 0.5"
[1] "ndcg_cut_100 0.5002 0.5289 p= 0.0117"
thphan@biocaddie-dev:/data/thphan/biocaddie$ Rscript scripts/new/compare.R test tfidf-snowball bm25-snowball 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 0.3375 0.3764 p= 0.0284"
[1] "ndcg 0.5944 0.6239 p= 0.011"
[1] "P_20 0.6667 0.73 p= 0.0331"
[1] "ndcg_cut_20 0.5256 0.6006 p= 0.0045"
[1] "P_100 0.4987 0.5413 p= 0.0326"
[1] "ndcg_cut_100 0.5002 0.539 p= 0.0149"
thphan@biocaddie-dev:/data/thphan/biocaddie$ Rscript scripts/new/compare.R test tfidf rocchio-snowball 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 0.3282 0.3959 p= 0.0427"
[1] "ndcg 0.5824 0.6052 p= 0.2869"
[1] "P_20 0.6867 0.7267 p= 0.1189"
[1] "ndcg_cut_20 0.5478 0.598 p= 0.0424"
[1] "P_100 0.5013 0.5453 p= 0.1152"
[1] "ndcg_cut_100 0.5018 0.525 p= 0.2733"
Compare results between unstemmed and stemmed indexes:
thphan@biocaddie-dev:/data/thphan/biocaddie$ Rscript scripts/new/compare.R test tfidf tfidf-snowball 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 0.3282 0.3375 p= 0.1463"
[1] "ndcg 0.5824 0.5944 p= 0.1454"
[1] "P_20 0.6867 0.6667 p= 0.808"
[1] "ndcg_cut_20 0.5478 0.5256 p= 0.8715"
[1] "P_100 0.5013 0.4987 p= 0.5819"
[1] "ndcg_cut_100 0.5018 0.5002 p= 0.5652"
thphan@biocaddie-dev:/data/thphan/biocaddie$ Rscript scripts/new/compare.R test dir dir-snowball 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 0.3675 0.3776 p= 0.0842"
[1] "ndcg 0.6163 0.6315 p= 0.0534"
[1] "P_20 0.6567 0.7033 p= 0.0011"
[1] "ndcg_cut_20 0.5664 0.6006 p= 0.0222"
[1] "P_100 0.5213 0.5307 p= 0.1942"
[1] "ndcg_cut_100 0.522 0.5365 p= 0.0645"
thphan@biocaddie-dev:/data/thphan/biocaddie$ Rscript scripts/new/compare.R test jm jm-snowball 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 0.3382 0.3448 p= 0.2603"
[1] "ndcg 0.6022 0.6058 p= 0.3358"
[1] "P_20 0.7233 0.67 p= 0.8885"
[1] "ndcg_cut_20 0.571 0.5813 p= 0.2551"
[1] "P_100 0.5 0.4987 p= 0.55"
[1] "ndcg_cut_100 0.4996 0.5289 p= 0.0026"
thphan@biocaddie-dev:/data/thphan/biocaddie$ Rscript scripts/new/compare.R test bm25 bm25-snowball 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 0.3543 0.3764 p= 0.0317"
[1] "ndcg 0.6105 0.6239 p= 0.0945"
[1] "P_20 0.7467 0.73 p= 0.8548"
[1] "ndcg_cut_20 0.5917 0.6006 p= 0.2775"
[1] "P_100 0.506 0.5413 p= 0.0209"
[1] "ndcg_cut_100 0.5186 0.539 p= 0.0441"
thphan@biocaddie-dev:/data/thphan/biocaddie$ Rscript scripts/new/compare.R test rocchio rocchio-snowball 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 0.4044 0.3959 p= 0.6841"
[1] "ndcg 0.6417 0.6052 p= 0.9667"
[1] "P_20 0.6967 0.7267 p= 0.2037"
[1] "ndcg_cut_20 0.5403 0.598 p= 0.0465"
[1] "P_100 0.492 0.5453 p= 0.0035"
[1] "ndcg_cut_100 0.4912 0.525 p= 0.0625"