Python toolkit to read and analyse TREC results.


License
BSD-3-Clause
Install
pip install trectools==0.0.39

Documentation

TREC TOOLS

TrecTools is an open-source Python library for assisting Information Retrieval (IR) practitioners with TREC-like campaigns.

If this package helps your research somehow, please reference our paper:

@inproceedings{palotti2019,
 author = {Palotti, Joao and Scells, Harrisen and Zuccon, Guido},
 title = {TrecTools: an open-source Python library for Information Retrieval practitioners involved in TREC-like campaigns},
 series = {SIGIR'19},
 year = {2019},
 location = {Paris, France},
 publisher = {ACM}
} 

Installing

pip install trectools

Background

IR practitioners tasked with activities like building test collections, evaluating systems, or analysing results from empirical experiments commonly have to resort to use a number of different software tools and scripts that each perform an individual functionality – and at times they even have to implement ad-hoc scripts of their own. TrecTools aims to provide a unified environment for performing these common activities.

Features

TrecTools is implemented in Python using standard data science libraries (NumPy, SciPy, Pandas, and Matplotlib) and using the object-oriented paradigm. Each of the key components of an evaluation campaign is mapped to a class: classes for runs (TrecRun),topics/queries (TrecTopic), assessment pools (TrecPools), relevance assessments (TrecQrel) and the evaluation results (TrecRes). See file format for each object below. Evaluation results can be produced by TrecTools itself using the evaluation metrics implemented in the tool, or be imported from the output file of trec_eval and derivatives. The features that are currently implemented in TrecTools are:

  • Querying IR Systems: Benchmark runs can be obtained di-rectly from one of the IR toolkits that are integrated in TrecTools. There is support for issuing full-text queries to Indri and Terrier toolkits. Future releases will include other toolkits (e.g., Elastic-search, Anserini, etc.) and support for specific query languages(Indri’s query language, Boolean queries). See code snipets in Example 1.

  • Pooling Techniques: The following techniques for assessment pool creation from a runs set are implemented: Depth@K, Comb[Min/Max/Med/Sum/ANZ/MNZ], Take@N, RRFTake@N, RBPTake@N. See Example 2.

  • Evaluation Measures: Currently implemented and verified measures include: Precision at depth K, Recall at depth K, MAP, NDCG, Bpref, uBpref, RBP, uRBP. Implemented in TrecTools is the option to break ties using document score (i.e., similar to trec_eval), or document ranking (i.e., similar to the original implementation of RBP). Additionally, TrecTools also allows to compute the residual of the evaluation measure and analyse the relative presence of unassessed documents. See Example 3.

  • Correlation and Agreement Analysis: The Pearson, Spearman, Kendall and τ-ap correlation between system rankings can be computed (see Example 4). Agreement measures between relevance assessment sets can be obtained with Kappa or Jaccard (see Example 5).

  • Fusion Techniques. Runs can be fused using the following techniques: Comb[Max/Min/Sum/Mnz/Anz/Med] - both using the scores and document rankings, RBPFusion, RRFFusion,or BordaCountFusion. Fusion techniques are provided for meta-analysis. See Example 6.

File Formats

The three main modules found in TrecTools are inspired by the main files created in TREC campaigns: a participant run (TrecRun), a qrel (TrecQrel) e a result file (TrecRes).

TrecRun format

qid Q0 docno rank score tag

where:

  • qid is the query number
  • Q0 is the literal Q0
  • docno is the id of a document returned for qid
  • rank (1-999) is the rank of this response for this qid
  • score is a system-dependent indication of the quality of the response
  • tag is the identifier for the system

Example:
1 Q0 nhslo3844_12_012186 1 1.73315273652 mySystem
1 Q0 nhslo1393_12_003292 2 1.72581054377 mySystem
1 Q0 nhslo3844_12_002212 3 1.72522727817 mySystem
1 Q0 nhslo3844_12_012182 4 1.72522727817 mySystem
1 Q0 nhslo1393_12_003296 5 1.71374426875 mySystem

TrecQrel format

qid 0 docno relevance

where:

  • qid is the query number
  • 0 is the literal 0
  • docno is the id of a document in your collection
  • relevance is how relevant is docno for qid

Example:
1 0 aldf.1864_12_000027 1
1 0 aller1867_12_000032 2
1 0 aller1868_12_000012 0
1 0 aller1871_12_000640 1
1 0 arthr0949_12_000945 0
1 0 arthr0949_12_000974 1

TrecRes format

label qid value

where:

  • label is any string, usually representing a metric
  • qid is the query number or 'all' to represent a aggregate value
  • value is numeral result of a metric

Example: num_rel_ret 7 77 map 7 0.4653 P_10 9 0.9000 num_rel_ret all 1180 map all 0.1323 gm_map all 0.0504

Code Examples

Example 0

Code Snippets and toy examples with TrecTools.

from trectools import TrecQrel, procedures

qrels_file = "./qrel/robust03_qrels.txt"
qrels = TrecQrel(qrels_file)

# Generates a P@10 graph with all the runs in a directory
path_to_runs = "./robust03/runs/"
runs = procedures.list_of_runs_from_path(path_to_runs, "*.gz")

results = procedures.evaluate_runs(runs, qrels, per_query=True)
p10 = procedures.extract_metric_from_results(results, "P_10")
procedures.plot_system_rank(p10, display_metric="P@10")
# Sample output with one run for each participating team in robust03:

Example 1

Code Snippets for manipulating topic formats and querying different IR toolkits (shown here: Terrier and Indri)

from trectools import TrecTopics, TrecTerrier, TrecIndri

# Loads some topics from a file (e.g., topics.txt)
"""
<topics>
<topic number="201" type="single">
<query>amazon raspberry pi</query>
<description> You have heard quite a lot about cheap computing as being the way of the future,
including one recent model called a Raspberry Pi. You start thinking about buying one, and wonder how much they cost.
</description>
</topic>
</topics>
"""
topics = TrecTopics().read_topics_from_file("topics.txt")
# Or...load topics from a Python dictionary
topics = TrecTopics(topics={'201': u'amazon raspberry pi'})
topics.printfile(fileformat="terrier")
#<topics>
# <top>
# <num>201</num>
# <title>amazon raspberry pi</title>
# </top>
#</topics>

topics.printfile(fileformat="indri")
#<parameters>
# <trecFormat>true</trecFormat>
# <query>
# <id>201</id>
# <text>#combine( amazon raspberry pi )</text>
# </query>
#</parameters>

topics.printfile(fileformat="indribaseline")
#<parameters>
# <trecFormat>true</trecFormat>
# <query>
# <id>201</id>
# <text>amazon raspberry pi</text>
# </query>
#</parameters>

tt = TrecTerrier(bin_path="<PATH>/terrier/bin/") # where trec_terrier.sh is located
# Runs PL2 model from Terrier with Query Expansion
tr = tt.run(index="<PATH>/terrier/var/index", topics="topics.xml.gz", qexp=True,
model="PL2", result_file="terrier.baseline", expTerms=5, expDocs=3, expModel="Bo1") 

ti = TrecIndri(bin_path="~/<PATH>/indri/bin/") # where IndriRunQuery is located
ti.run(index="<PATH>/indriindex", topics, model="dirichlet", parameters={"mu":2500}, 
result_file="trec_indri.run", ndocs=1000, qexp=True, expTerms=5, expDocs=3)

Example 2

Code Snippets for generating and exporting document pools using different pooling strategies.

from trectools import TrecPool, TrecRun

r1 = TrecRun("./robust03/runs/input.aplrob03a.gz")
r2 = TrecRun("./robust03/runs/input.UIUC03Rd1.gz")

len(r1.topics()) # 100 topics
 
# Creates document pools with r1 and r2 using different strategies:

# Strategy1: Creates a pool with top 10 documents of each run:
pool1 = TrecPool.make_pool([r1, r2], strategy="topX", topX=10) # Pool with 1636 unique documents.

# Strategy2: Creates a pool with 2000 documents (20 per topic) using the reciprocal ranking strategy by Gordon, Clake and Buettcher:
pool2 = TrecPool.make_pool([r1,r2], strategy="rrf", topX=20, rrf_den=60) # Pool with 2000 unique documents.

# Check to see which pool covers better my run r1
pool1.check_coverage(r1, topX=10) # 10.0
pool2.check_coverage(r1, topX=10) # 8.35 

# Export documents to be judged using Relevation! visual assessing system
pool1.export_document_list(filename="mypool.txt", with_format="relevation")

Example 3

Code snippets showing case evaluation options available in TrecTools.

from trectools import TrecQrel, TrecRun, TrecEval

# A typical evaluation workflow
r1 = TrecRun("./robust03/runs/input.aplrob03a.gz")
r1.topics()[:5] # Shows the first 5 topics: 601, 602, 603, 604, 605

qrels = TrecQrel("./robust03/qrel/robust03_qrels.txt")

te = TrecEval(r1, qrels)
rbp, residuals = te.getRBP()           # RBP: 0.474, Residuals: 0.001
p100 = te.getPrecisionAtDepth(100)     # P@100: 0.186

# Check if documents retrieved by the system were judged:
r1.get_mean_coverage(qrels, topX=10)   # 9.99
r1.get_mean_coverage(qrels, topX=1000) # 481.390 
# On average for system 'input.aplrob03a' participating in robust03, 480 documents out of 1000 were judged.

# Loads another run
r2 = TrecRun("./robust03/runs/input.UIUC03Rd1.gz")

# Check how many documents, on average, in the top 10 of r1 were retrieved in the top 10 of r2
r1.check_run_coverage(r2, topX=10) # 3.64

# Evaluates r1 and r2 using all implemented evaluation metrics
result_r1 = r1.evaluate_run(qrels, per_query=True) 
result_r2 = r2.evaluate_run(qrels, per_query=True)

# Inspect for statistically significant differences between the two runs for  P_10 using two-tailed Student t-test
pvalue = result_r1.compare_with(result_r2, metric="P_10") # pvalue: 0.0167 

Example 4

Code Snippets for obtaining correlation measures from a set of runs.

from trectools import misc, TrecRun, TrecQrel, procedures

qrels_file = "./robust03/qrel/robust03_qrels.txt"
path_to_runs = "./robust03/runs/"

qrels = TrecQrel(qrels_file)

runs = procedures.list_of_runs_from_path(path_to_runs, "*.gz")

results = procedures.evaluate_runs(runs, qrels, per_query=True)

# check the system correlation between P@10 and MAP using Kendall's tau for all systems participating in a campaign
misc.get_correlation( misc.sort_systems_by(results, "P_10"), 
                      misc.sort_systems_by(results, "map"), correlation = "kendall") # Correlation: 0.7647

# check the system correlation between P@10 and MAP using Tau's ap for all systems participating in a campaign
misc.get_correlation( misc.sort_systems_by(results, "P_10"), 
                      misc.sort_systems_by(results, "map"), correlation = "tauap") # Correlation: 0.77413

Example 5

Code Snippets for obtaining agreement measures from a pair of relevance assessments.

# Code snippet to check correlation between two sets of relevance assessment (e.g., made by different cohorts - assessments made by medical doctors Vs. crowdsourced assessments)
from trectools import  TrecQrel

original_qrels_file =  "./robust03/qrel/robust03_qrels.txt"
# Changed the first 10 assessments from 0 to 1
modified_qrels_file = "./robust03/qrel/mod_robust03_qrels.txt"

original_qrels = TrecQrel(original_qrels_file)
modified_qrels = TrecQrel(modified_qrels_file)

# Overall agreement 
original_qrels.check_agreement(modified_qrels) # 0.99
# Fleiss' kappa agreement
original_qrels.check_kappa(modified_qrels) # P0: 1.00, Pe = 0.90
# Jaccard similarity coefficient
original_qrels.check_jaccard(modified_qrels) # 0.99
# 3x3 confusion matrix (labels 0, 1 or 2) 
original_qrels.check_confusion_matrix(modified_qrels)
# [[122712     10      0]
# [     0   5667      0]
# [     0      0    407]]

Example 6

Code Snippets for generating fusing two runs (Reciprocal Rank fusion shown here)

from trectools import TrecRun, TrecEval, fusion

r1 = TrecRun("./robust03/runs/input.aplrob03a.gz")
r2 = TrecRun("./robust03/runs/input.UIUC03Rd1.gz")

# Easy way to create new baselines by fusing existing runs:
fused_run = fusion.reciprocal_rank_fusion([r1,r2])
TrecEval(r1, qrels).getPrecisionAtDepth(25)          # P@25: 0.3392
TrecEval(r2, qrels).getPrecisionAtDepth(25)          # P@25: 0.2872
TrecEval(fused_run, qrels).getPrecisionAtDepth(25)   # P@25: 0.3436

# Save run to disk with all its topics
fused_run.print_subset("my_fused_run.txt", topics=fused_run.topics())

ToDos

  • Upload examples with a famous Trec campaing (e.g., robust3)
  • Explain other file formats, such as TrecPool