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Data quality is one of the most important problems in data management,
since dirty data often leads to inaccurate data analytics results and
incorrect business decisions. Poor data across businesses and the U.S.
government are reported to cost trillions of dollars a year. Multiple surveys
show that dirty data is the most common barrier faced by data scientists.
Not surprisingly, developing effective and efficient data cleaning solutions
is challenging and is rife with deep theoretical and engineering problems.
This book is about data cleaning, which is used to refer to all kinds
of tasks and activities to detect and repair errors in the data. Rather than
focus on a particular data cleaning task, we give an overview of the end-
to-end data cleaning process, describing various error detection and repair
methods, and attempt to anchor these proposals with multiple taxonomies
and views. Specifically, we cover four of the most common and important
data cleaning tasks, namely, outlier detection, data transformation,
error repair (including imputing missing values), and data deduplication.
Furthermore, due to the increasing popularity and applicability of machine
learning techniques, we include a chapter that specifically explores how
machine learning techniques are used for data cleaning, and how data
cleaning is used to improve machine learning models.
This book is intended to serve as a useful reference for researchers
and practitioners who are interested in the area of data quality and data
cleaning. It can also be used as a textbook for a graduate course. Although
we aim at covering state-of-the-art algorithms and techniques, we
recognize that data cleaning is still an active field of research and therefore
provide future directions of research whenever appropriate.

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Data Cleaning
ACM Books

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Data Cleaning
Ihab F. Ilyas, University of Waterloo
Xu Chu, Georgia Institute of Technology
2019

Conversational UX Design: A Practitioner’s Guide to the Natural

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Heterogeneous Computing: Hardware and Software Perspectives

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Hardness of Approximation Between P and NP

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Verified Functional Programming in Agda
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Ada’s Legacy: Cultures of Computing from the Victorian to the Digital Age
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Edmund Berkeley and the Social Responsibility of Computer Professionals
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Data Cleaning

Ihab F. Ilyas
University of Waterloo

Xu Chu
Georgia Institute of Technology

ACM Books #28

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Data Cleaning
Ihab F. Ilyas
Xu Chu
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A publication in the ACM Books series, #28

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To my family: Francis, Aida, Mirette, Andrew and Marina

To my wife Jianmei and my daughter Hannah

 Contents

Preface xiii
Figure and Table Credits xv

Chapter 1 Introduction 1
1.1 Data Cleaning Workflow 3
1.2 Book Scope 4

Chapter 2 Outlier Detection 11

2.1 A Taxonomy of Outlier Detection Methods 12
2.2 Statistics-Based Outlier Detection 15
2.3 Distance-Based Outlier Detection 26
2.4 Model-Based Outlier Detection 30
2.5 Outlier Detection in High-Dimensional Data 32
2.6 Conclusion 44

Chapter 3 Data Deduplication 47

3.1 Similarity Metrics 49
3.2 Predicting Duplicate Pairs 54
3.3 Clustering 57
3.4 Blocking for Deduplication 60
3.5 Distributed Data Deduplication 66
3.6 Record Fusion and Entity Consolidation 73
3.7 Human-Involved Data Deduplication 81
3.8 Data Deduplication Tools 85
3.9 Conclusion 88

Chapter 4 Data Transformation 91

4.1 Syntactic Data Transformations 93
xii Contents

4.2 Semantic Data Transformations 107

4.3 ETL Tools 117
4.4 Conclusion 118

Chapter 5 Data Quality Rule Definition and Discovery 121

5.1 Functional Dependencies 124
5.2 Conditional Functional Dependencies 130
5.3 Denial Constraints 133
5.4 Other Types of Constraints 138
5.5 Conclusion 147

Chapter 6 Rule-Based Data Cleaning 149

6.1 Violation Detection 149
6.2 Error Repair 161
6.3 Conclusion 193

Chapter 7 Machine Learning and Probabilistic Data Cleaning 195

7.1 Machine Learning for Data Deduplication 196
7.2 Machine Learning for Data Repair 203
7.3 Data Cleaning for Analytics and Machine Learning 214

Chapter 8 Conclusion and Future Thoughts 223

References 227
Index 247
Author Biographies 259
Preface

Data quality is one of the most important problems in data management, since
dirty data often leads to inaccurate data analytics results and incorrect business
decisions. Poor data across businesses and the U.S. government are reported to
cost trillions of dollars a year. Multiple surveys show that dirty data is the most
common barrier faced by data scientists. Not surprisingly, developing effective and
efficient data cleaning solutions is challenging and is rife with deep theoretical and
engineering problems.
Data cleaning is used to refer to all kinds of tasks and activities to detect and
repair errors in the data. Rather than focus on a particular data cleaning task, in
this book, we give an overview of the end-to-end data cleaning process, describing
various error detection and repair methods, and attempt to anchor these propos-
als with multiple taxonomies and views. Specifically, we cover four of the most
common and important data cleaning tasks, namely, outlier detection, data trans-
formation, error repair (including imputing missing values), and data deduplica-
tion. Furthermore, due to the increasing popularity and applicability of machine
learning techniques, we include a chapter that specifically explores how machine
learning techniques are used for data cleaning, and how data cleaning is used to
improve machine learning models.
This book is intended to serve as a useful reference for researchers and practi-
tioners who are interested in the area of data quality and data cleaning. It can also
be used as a textbook for a graduate course. Although we aim at covering state-of-
the-art algorithms and techniques, we recognize that data cleaning is still an active
field of research and therefore provide future directions of research whenever ap-
propriate.

Ihab Ilyas
Xu Chu
March 2019
Figure and Table Credits

Figures
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Article 1 (January 2009), 41 pages. DOI: 10.1145/1456650.1456651.
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David. Modeling and querying possible repairs in duplicate detection. Proc. VLDB Endowment,
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David. Modeling and querying possible repairs in duplicate detection. Proc. VLDB Endowment,
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Figure 3.11 Jiannan Wang, Tim Kraska, Michael J. Franklin, and Jianhua Feng. Crowder:
Crowdsourcing entity resolution. Proc. VLDB Endowment, 5(11): 1483–1494, DOI: 10.14778/
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Crowdsourcing entity resolution. Proc. VLDB Endowment, 5(11): 1483–1494, DOI: 10.14778/
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xvi Figure and Table Credits

Figure 3.13 Chaitanya Gokhale, Sanjib Das, AnHai Doan, Jeffrey F. Naughton, Narasimhan
Rampalli, Jude Shavlik, and Xiaojin Zhu. 2014. Corleone: hands-off crowdsourcing for entity
matching. In Proceedings of the 2014 ACM SIGMOD International Conference on Management of
Data (SIGMOD ’14). ACM, New York, NY, USA, 601–612. DOI: 10.1145/2588555.2588576.
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R. Ballard, Han Li, Fatemah Panahi, Haojun Zhang, Jeff Naughton, et al. Magellan: Toward
building entity matching management systems. Proc. VLDB Endowment, 9(12): 1197–1208,
2016.
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Mitch Cherniack, Stanley B. Zdonik, Alexander Pagan, and Shan Xu. Data curation at scale:
The data tamer system. In Proc. 6th Biennial Conf. on Innovative Data Systems Research, 2013.
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Kaufmann Publishers Inc., San Francisco, CA, USA, 381–390.
Figure 4.4 Philip J. Guo, Sean Kandel, Joseph M. Hellerstein, and Jeffrey Heer. 2011.
Proactive wrangling: mixed-initiative end-user programming of data transformation scripts.
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Hellerstein, and Sean Kandel. Predictive interaction for data transformation. In Proc. 7th
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Joseph Hellerstein, and Jeffrey Heer. 2011. Wrangler: interactive visual specification of data
transformation scripts. In Proceedings of the SIGCHI Conference on Human Factors in Computing
Systems (CHI ’11). ACM, New York, NY, USA, 3363–3372. DOI: 10.1145/1978942.1979444.
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Figure 4.6 Sumit Gulwani. 2011. Automating string processing in spreadsheets using
input-output examples. In Proceedings of the 38th annual ACM SIGPLAN-SIGACT symposium
on Principles of programming languages (POPL ’11). ACM, New York, NY, USA, 317–330.
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Proactive wrangling: mixed-initiative end-user programming of data transformation scripts.
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’11). ACM, New York, NY, USA, 65–74. DOI: 10.1145/2047196.2047205.
Figure 4.8 Z. Abedjan, J. Morcos, I. F. Ilyas, M. Ouzzani, P. Papotti and M. Stonebraker,
DataXFormer: A robust transformation discovery system, 2016 IEEE 32nd International
Conference on Data Engineering (ICDE), Helsinki, 2016, pp. 1134–1145. DOI: 10.1109/ICDE
.2016.7498319.
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M. Stonebraker, DataXFormer: A robust transformation discovery system, 2016 IEEE
32nd International Conference on Data Engineering (ICDE), Helsinki, 2016, pp. 1134–1145.
DOI: 10.1109/ICDE.2016.7498319.
 Figure and Table Credits xvii

Figure 4.10 Z. Abedjan, J. Morcos, I. F. Ilyas, M. Ouzzani, P. Papotti and M. Stonebraker,

DataXFormer: A robust transformation discovery system, 2016 IEEE 32nd International
Conference on Data Engineering (ICDE), Helsinki, 2016, pp. 1134–1145. DOI: 10.1109/ICDE
.2016.7498319.
Figure 4.11 Based On: Z. Abedjan, J. Morcos, I. F. Ilyas, M. Ouzzani, P. Papotti and
M. Stonebraker, DataXFormer: A robust transformation discovery system, 2016 IEEE
32nd International Conference on Data Engineering (ICDE), Helsinki, 2016, pp. 1134–1145.
DOI: 10.1109/ICDE.2016.7498319.
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Dependency Discovery. In Proceedings of the 2016 International Conference on Management of
Data (SIGMOD ’16). ACM, New York, NY, USA, 821–833. DOI: 10.1145/2882903.2915203.
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In Proc. 15th Int. Conf. on Web-Age Information Management, pages 125–137. Springer, 2014a.
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Proc. 31st Int. Conf. on Data Engineering, 2015.
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Proc. 31st Int. Conf. on Data Engineering, 2015.
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Proc. 31st Int. Conf. on Data Engineering, 2015.
Figure 6.2 Based On: Anup Chalamalla, Ihab F. Ilyas, Mourad Ouzzani, and Paolo Papotti.
Descriptive and prescriptive data cleaning. In Proc. ACM SIGMOD Int. Conf. on Management of
Data, pages 445–456, 2014. DOI: 10.1145/2588555.2610520.
Figure 6.3 Alexandra Meliou, Wolfgang Gatterbauer, Suman Nath, and Dan Suciu. 2011.
Tracing data errors with view-conditioned causality. In Proceedings of the 2011 ACM SIGMOD
International Conference on Management of data (SIGMOD ’11). ACM, New York, NY, USA, 505–
516. DOI: 10.1145/1989323.1989376.
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queries. Proceedings of the VLDB Endowment, Vol. 6, No. 8. Copyright 2013 VLDB Endowment
2150-8097/13/06 553–564.
Figure 6.5 Anup Chalamalla, Ihab F. Ilyas, Mourad Ouzzani, and Paolo Papotti. Descriptive
and prescriptive data cleaning. In Proc. ACM SIGMOD Int. Conf. on Management of Data, pages
445–456, 2014. DOI: 10.1145/2588555.2610520.
Figure 6.6 Anup Chalamalla, Ihab F. Ilyas, Mourad Ouzzani, and Paolo Papotti. Descriptive
and prescriptive data cleaning. In Proc. ACM SIGMOD Int. Conf. on Management of Data, pages
445–456, 2014. DOI: 10.1145/2588555.2610520.
xviii Figure and Table Credits

Figure 6.7 Based On: Anup Chalamalla, Ihab F. Ilyas, Mourad Ouzzani, and Paolo Papotti.
Descriptive and prescriptive data cleaning. In Proc. ACM SIGMOD Int. Conf. on Management of
Data, pages 445–456, 2014. DOI: 10.1145/2588555.2610520.
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all folks! LLUNATIC goes open source. Proceedings of the VLDB Endowment, Vol. 7, No. 13.
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Figure 6.16 Mohamed Yakout, Ahmed K. Elmagarmid, Jennifer Neville, Mourad Ouzzani,
and Ihab F. Ilyas. Guided data repair. Proc. VLDB Endowment, 4(5): 279–289, DOI: 10.14778/
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and Ihab F. Ilyas. Guided data repair. Proc. VLDB Endowment, 4(5): 279–289, DOI: 10.14778/
1952376.1952378.
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Tang, and Yin Ye. 2015. KATARA: A Data Cleaning System Powered by Knowledge Bases
and Crowdsourcing. In Proceedings of the 2015 ACM SIGMOD International Conference on
Management of Data (SIGMOD ’15). ACM, New York, NY, USA, 1247–1261. DOI: 10.1145/
2723372.2749431.
Figure 6.20 Xu Chu, John Morcos, Ihab F. Ilyas, Mourad Ouzzani, Paolo Papotti, Nan
Tang, and Yin Ye. 2015. KATARA: A Data Cleaning System Powered by Knowledge Bases
and Crowdsourcing. In Proceedings of the 2015 ACM SIGMOD International Conference on
Management of Data (SIGMOD ’15). ACM, New York, NY, USA, 1247–1261. DOI: 10.1145/
2723372.2749431.
Figure 6.23 George Beskales, Ihab F. Ilyas, and Lukasz Golab. Sampling the repairs of
functional dependency violations under hard constraints. Proc. VLDB Endowment, 3(1–2):
197–207, DOI: 10.14778/1920841.1920870.
Figure 7.1 Sunita Sarawagi and Anuradha Bhamidipaty. 2002. Interactive deduplication using
active learning. In Proceedings of the eighth ACM SIGKDD international conference on Knowledge
discovery and data mining (KDD ’02). ACM, New York, NY, USA, 269–278. DOI: 10.1145/775047
.775087.
Figure 7.2 Sidharth Mudgal, Han Li, Theodoros Rekatsinas, AnHai Doan, Youngchoon Park,
Ganesh Krishnan, Rohit Deep, Esteban Arcaute, and Vijay Raghavendra. 2018. Deep learning for
Visit https://textbookfull.com
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 Figure and Table Credits xix

entity matching: A design space exploration. In Proceedings of the 2018 International Conference
on Management of Data (SIGMOD ’18). ACM, New York, NY, USA, 19–34. DOI: 10.1145/3183713
.3196926.
Figure 7.3 Sidharth Mudgal, Han Li, Theodoros Rekatsinas, AnHai Doan, Youngchoon Park,
Ganesh Krishnan, Rohit Deep, Esteban Arcaute, and Vijay Raghavendra. 2018. Deep learning for
entity matching: A design space exploration. In Proceedings of the 2018 International Conference
on Management of Data (SIGMOD ’18). ACM, New York, NY, USA, 19–34. DOI: 10.1145/3183713
.3196926.
Figure 7.8 Jiannan Wang, Sanjay Krishnan, Michael J. Franklin, Ken Goldberg, Tim Kraska,
and Tova Milo. A sample-and-clean framework for fast and accurate query processing on
dirty data. In Proc. ACM SIGMOD Int. Conf. on Management of Data, pages 469–480, 2014. DOI:
10.1145/2588555.2610505.
Figure 7.9 Sanjay Krishnan, Jiannan Wang, Eugene Wu, Michael J. Franklin, and Ken Gold-
berg. Activeclean: Interactive data cleaning for statistical modeling. Proc. VLDB Endowment,
9(12, August 2016): 948–959. DOI: 10.14778/2994509.2994514.

Tables
Table 3.2 Jens Bleiholder and Felix Naumann. 2009. Data fusion. ACM Comput. Surv. 41, 1,
Article 1 (January 2009), 41 pages. DOI: 10.1145/1456650.1456651 and Xin Luna Dong and Felix
Naumann. Data fusion: resolving data conflicts for integration. Proc. VLDB Endowment, 2(2):
1654–1655, 2009.
Table 4.1 Based On: Sean Kandel, Andreas Paepcke, Joseph Hellerstein, and Jeffrey Heer.
2011. Wrangler: interactive visual specification of data transformation scripts. In Proceedings
of the SIGCHI Conference on Human Factors in Computing Systems (CHI ’11). ACM, New York, NY,
USA, 3363–3372. DOI: 10.1145/1978942.1979444.
Table 5.2 Lukasz Golab, Howard Karloff, Flip Korn, Divesh Srivastava, and Bei Yu. On
generating near-optimal tableaux for conditional functional dependencies. Proc. VLDB
Endowment, 1(1): 376–390, DOI: 10.14778/1453856.1453900.
Table 6.1 Based On: Xu Chu, Ihab F. Ilyas, and Paolo Papotti. Holistic data cleaning: Putting
violations into context. In Proc. 29th Int. Conf. on Data Engineering, pages 458–469, 2013b.
Table 6.3 Wenfei Fan, Jianzhong Li, Shuai Ma, Nan Tang, and Wenyuan Yu. 2011. Interaction
between record matching and data repairing. In Proceedings of the 2011 ACM SIGMOD
International Conference on Management of data (SIGMOD ’11). ACM, New York, NY, USA, 469–
480. DOI: 10.1145/1989323.1989373.
Table 7.1 Theodoros Rekatsinas, Xu Chu, Ihab F. Ilyas, and Christopher Ré. 2017. HoloClean:
holistic data repairs with probabilistic inference. Proc. VLDB Endow. 10, 11 (August 2017),
1190–1201. DOI: 10.14778/3137628.3137631.
1
Introduction
Enterprises have been acquiring large amounts of data from a variety of sources in
order to build large data repositories that power their applications, with the goal of
enabling richer and more informed analytics. Data collection and acquisition often
introduce errors in data, e.g., missing values, typos, mixed formats, replicated en-
tries for the same real-world entity, and violations of business and data integrity
rules. A survey about the state of data science and machine learning (ML) reveals
that dirty data is the most common barrier faced by workers dealing with data.1
With the popularity of data science, it has become increasingly evident that data
curation, unification, preparation, and cleaning are key enablers in unleashing the
value of data.2 According to another survey of about 80 data scientists conducted
by CrowdFlower and published in Forbes,3 data scientists spend more than 60% of
their time in cleaning and organizing data, and 57% of data scientists regard clean-
ing and organizing data as the least enjoyable part of their work. Not surprisingly,
developing effective and efficient data cleaning solutions is challenging and is rife
with deep theoretical and engineering problems.
Regardless of the type of data errors to be fixed, data cleaning activities usually
consist of two phases: (1) error detection, where various errors and violations are
identified and possibly validated by experts; and (2) error repair, where updates to
the database are applied (or suggested to human experts) to bring the data to a
cleaner state suitable for downstream applications and analytics. Error detection
techniques can be either quantitative or qualitative. Specifically, quantitative error
detection techniques often involve statistical methods to identify abnormal behav-
iors and errors [Hellerstein 2008] (e.g., “a salary that is three standard deviations

1. https://www.kaggle.com/surveys/2017
2. https://www.nytimes.com/2014/08/18/technology/for-big-data-scientists-hurdle-to-insights-is-
janitor-work.html
3. https://www.forbes.com/sites/gilpress/2016/03/23/data-preparation-most-time-consuming-
least-enjoyable-data-science-task-survey-says/
2 Chapter 1 Introduction

away from the mean salary is an error”), and hence have been mostly studied in the
context of outlier detection [Aggarwal 2013]. On the other hand, qualitative error de-
tection techniques rely on descriptive approaches to specify patterns or constraints
of a consistent data instance, and for that reason these techniques identify those
data that violate such patterns or constraints as errors. For example, in a descrip-
tive statement about a company HR database, “for two employees working at the same
branch of the company, the senior employee cannot earn less salary than the junior em-
ployee,” if we find two employees with a violation of the rule, it is likely that there
is an error in at least one of them.
Various surveys and books detail specific aspects of data quality and data clean-
ing. For example, Rahm and Do [2000] classify different types of errors occurring in
an Extract-Transform-Load (ETL) process, and survey the tools available for clean-
ing data in an ETL process. Some work focuses on the effect of incompleteness data
on query answering [Grahne 1991] and the use of a Chase procedure [Maier et al.
1979] for dealing with incomplete data [Greco et al. 2012]. Hellerstein [2008] fo-
cuses on cleaning quantitative numerical data using mainly statistical techniques.
Bertossi [2011] provides complexity results for repairing inconsistent data and per-
forming consistent query answering on inconsistent data. Fan and Geerts [2012]
discuss the use of data quality rules in data consistency, data currency, and data
completeness, and their interactions. Dasu and Johnson [2003] summarize how
techniques in exploratory data mining can be integrated with data quality manage-
ment. Ganti and Sarma [2013] focus on an operator-centric approach for developing
a data cleaning solution, involving the development of customizable operators that
can be used as building blocks for developing common solutions. Ilyas and Chu
[2015] provide taxonomies and example algorithms for qualitative error detection
and repairing techniques. Multiple surveys and tutorials have been published to
summarize different definitions of outliers and the algorithms for detecting them
[Hodge and Austin 2004, Chandola et al. 2009, Aggarwal 2013]. Data deduplica-
tion, a long-standing problem that has been studied for decades [Fellegi and Sunter
1969], has also been extensively surveyed [Koudas et al. 2006, Elmagarmid et al.
2007, Herzog et al. 2007, Dong and Naumann 2009, Naumann and Herschel 2010,
Getoor and Machanavajjhala 2012].
This book, however, focuses on the end-to-end data cleaning process, describing
various error detection and repair methods, and attempts to anchor these proposals
with multiple taxonomies and views. Our goals are (1) to allow researchers and
general readers to understand the scope of current techniques and highlight gaps
and possible new directions of research; and (2) to give practitioners and system
implementers a variety of choices and solutions for their data cleaning activities.
 1.1 Data Cleaning Workflow 3

External sources

Knowledge
bases

PDFs, rules,
patterns, etc.
Error Error
Discovery detection Errors repair

Data

Figure 1.1 A typical data cleaning workflow with an optional discovery step, error detection step, and
error repair step.

In what follows, we give a brief overview of the book’s scope as well as a chapter
outline.

Data Cleaning Workflow

1.1 Figure 1.1 shows a typical data cleaning workflow, consisting of an optional discov-
ery and profiling step, an error detection step, and an error repair step. To clean
a dirty dataset, we often need to model various aspects of this data, e.g., schema,
patterns, probability distributions, and other metadata. One way to obtain such
metadata is by consulting domain experts, typically a costly and time-consuming
process. The discovery and profiling step is used to discover these metadata auto-
matically. Given a dirty dataset and the associated metadata, the error detection
step finds part of the data that does not conform to the metadata, and declares this
subset to contain errors. The errors surfaced by the error detection step can be in
various forms, such as outliers, violations, and duplicates. Finally, given the errors
detected and the metadata that generate those errors, the error repair step produces
data updates that are applied to the dirty dataset. Since there are many uncertainties
in the data cleaning process, external sources such as knowledge bases and human
experts are consulted whenever possible and feasible to ensure the accuracy of the
cleaning workflow.

Example 1.1 Consider Table 1.1 containing employee records for a U.S. company. Every tuple
specifies a person in a company with her id (GID), name (FN, LN), level (LVL),
Random documents with unrelated
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"Fantastic!" said the Secretary of Defense.
"Will it work with anybody?" the President asked.
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said the President.
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Some months later, two men arrived by air in the city of Moscow.
One of them went directly to the American Embassy. In his brief case
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The Ambassador shook his hand warmly. "The President told me to
give you the run of the place, Dr. Wolstadt. What are you going to
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room in the Embassy which faces the Kremlin."
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"But he can't do that!" the Ambassador said. "The President said he
was the most valuable man on Earth! He might get arrested."
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room, I'll go about my business."
Some distance away, on the opposite side of the Kremlin from the
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He smiled happily. This was the life!
THE END
*** END OF THE PROJECT GUTENBERG EBOOK THE MAN WHO
KNEW EVERYTHING ***

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