Data Curation and Debugging for Data Centric AI

Data Curation and Debugging
for Data Centric AI
Prof. Paul Groth | @pgroth | pgroth.com | indelab.org

Thanks to Stefan Grafberger, Dr. Julia Stoyanovich,
Dr. Sebastian Schelter, Dr. Laura Koesten, Prof.
Elena Simperl, Dr. Pavlos Vougiouklis, Madelon
Hulsebos, Dr. Çağatay Demiralp, Dr. Juan Sequeda,
Prof. George Fletcher

DBML - May 8, 2022

The making of data is important

Finding digital truth—that is, identifying
and combining data that accurately
represent reality—is becoming more
difficult and more important.

More difficult because data and their
sources are multiplying.

And more important because firms need to
get their data house in order to benefit
from AI, which they must to stay
competitive.

-- The Economist, February 2020

Data interoperability and quality, as well
as their structure, authenticity and
integrity are key for the exploitation of the
data value, especially in the context of AI
deployment

-- European Commission, “A European strategy
for data”, February 2020
(andrio/Shutterstock)

Source:

http://veekaybee.github.io/2019/02/13/data-science-is-di
ff
erent/

Source: https://www.youtube.com/watch?v=06-AZXmwHjo

Bottlenecks
• Manual

• Di
ffi
culty in creating
fl
exible reusable work
fl
ows

• Lack of transparency
Paul Groth."The Knowledge-Remixing Bottleneck," Intelligent
Systems, IEEE , vol.28, no.5, pp.44,48, Sept.-Oct. 2013 doi:
10.1109/MIS.2013.138

Paul Groth, "Transparency and Reliability in the Data Supply
Chain," Internet Computing, IEEE, vol.17, no.2, pp.69,71,
March-April 2013 doi: 10.1109/MIC.2013.41

Debugging
Sebastian Schelter

UvA
Julia Stoyanovich

NYU
Stefan Grafberger
UvA
Credits

ML Pipelines in the Real World
9
Integration & Cleaning 
of Data
Feature Encoding Pipelines 
& Data Augmentation
Model Training & 
Evaluation
Heterogeneous 
Datasources
⋈
σ
π
⋈
The “last mile” of end-to-end ML
make_pipeline([
(‘encoding’, ColumnTransformer([
('num', StandardScaler, …),
(‘cat', OneHotEncoder, …)])), 
’learner’, KerasClassifier(…))
1 2 3

10
of Data
& Data Augmentation
Model Training & 
Evaluation
Heterogeneous 
Datasources
⋈
σ
π
⋈
make_pipeline([
1 2 3
Data Representation  
Bugs

11
of Data
& Data Augmentation
Model Training & 
Evaluation
Heterogeneous 
Datasources
⋈
σ
π
⋈
make_pipeline([
1 2 3
Bugs
Schema Violations 
& Missing Data

12
of Data
& Data Augmentation
Model Training & 
Evaluation
Heterogeneous 
Datasources
⋈
σ
π
⋈
make_pipeline([
1 2 3
Bugs
Schema Violations 
& Missing Data
Unsound 
Experimentation

The Way Forward
• First approach: invent new programming languages + runtime systems to regain control
(e.g. SystemDS) -> would require to rewrite all existing code

• Second approach: manually annotate and instrument existing code (ml
fl
ow) -> does
not happen in practice

• Our approach: retro
fi
t inspection techniques into the existing DS landscape
• Observation: declarative speci
fi
cation of operations for preprocessing present in some
popular ML libraries:

• Pandas mostly applies relational operations

• Estimator / Transformer pipelines (scikit-learn / SparkML / Tensor
fl
ow Transform)
o
ff
er nestable and composable way to declaratively specify feature transformations
13

Example
14
Can we
fi
nd ways to automatically hint data  
scientists at potentially problematic operations  
in the preprocessing code of their ML pipelines?

Inspiration from software engineering, e.g.  
code inspection in modern IDE’s

mlinspect
• Library to instrument ML preprocessing code with custom inspections

• available on GitHub: https://github.com/stefan-grafberger/mlinspect
• Works with “native” preprocessing pipelines (no annotation / manual
instrumentation required) in pandas / sklearn

• Representation of preprocessing operations based on data
fl
ow graph

• Allows users to implement inspections as user-de
fi
ned functions which
are automatically applied to the inputs and outputs of certain
operations

• Allow for the propagation of annotations per record through the
program
16
Grafberger, S., Groth, P., Stoyanovich, J., & Schelter, S. (2022). Data
distribution debugging in machine learning pipelines. The VLDB Journal, 1-24.

Example Inspections
• Change detection for the proportions of protected groups: compute histograms of operator outputs 
 
 
 
 
17
age_group county
60 CountyA
60 CountyA
20 CountyA
60 CountyB
20 CountyB
20 CountyB
data = data[data.county = “CountyA”]
age_group county
60 CountyA
60 CountyA
20 CountyA
• Lineage tracking: generate identi
fi
er annotations for records and propagate them through operators
50% vs 50%
66% vs 33%
ssn smoke
123 Y
456 N
789 Y
ssn cost
123 100
789 200
ssn smoke cost
123 Y 100
789 N 200
smoke cost
Y 100
N 200
data = pd.merge([patient, cost], 
on=“ssn”)
data = data[[“smoke”, “cost”]]
[p1]
[p2]
[p3]
[c1]
[c2]
[p1, c1]
[p3, c2]
[p1, c1]
[p3, c2]

Summary
• mlinspect is a general runtime for ML pipeline
analysis available on GitHub:  
https://github.com/stefan-grafberger/mlinspect
• Limitation: Our approach relies on“declaratively”
written ML pipelines, where we can identify the
semantics of the operations
• Enables many use cases like ArgusEyes, a CI tool 
https://github.com/schelterlabs/arguseyes
18

Curation
Prof. Elena Simperl
King’s College London
Dr. Laura Koesten
King’s College London /
University of Vienna
Dr. Pavlos Vougiouklis
Huawei
Credits
Madelon Hulsebos
UvA
Sigma Computing
Çağatay Demiralp
Sigma Computing

What curation should data providers prioritise to facilitate reuse?

Lots of good advice
Editorial
Ten Simple Rules for the Care and Feeding of Scientific
Data
Alyssa Goodman1
, Alberto Pepe1
*, Alexander W. Blocker1
, Christine L. Borgman2
, Kyle Cranmer3
,
Merce Crosas1
, Rosanne Di Stefano1
, Yolanda Gil4
, Paul Groth5
, Margaret Hedstrom6
, David W. Hogg3
,
Vinay Kashyap1
, Ashish Mahabal7
, Aneta Siemiginowska1
, Aleksandra Slavkovic8
1 Harvard University, Cambridge, Massachusetts, United States of America, 2 University of California, Los Angeles, Los Angeles, California, United States of America, 3 New
York University, New York, New York, United States of America, 4 University of Southern California, Los Angeles, Los Angeles, California, United States of America, 5 Vrije
Universiteit Amsterdam, Amsterdam, The Netherlands, 6 University of Michigan, Ann Arbor, Michigan, United States of America, 7 California Institute of Technology,
Pasadena, California, United States of America, 8 Pennsylvania State University, State College, Pennsylvania, United States of America
Introduction
In the early 1600s, Galileo Galilei
turned a telescope toward Jupiter. In his
log book each night, he drew to-scale
schematic diagrams of Jupiter and some
oddly moving points of light near it.
Galileo labeled each drawing with the
date. Eventually he used his observations
to conclude that the Earth orbits the Sun,
just as the four Galilean moons orbit
Jupiter. History shows Galileo to be much
more than an astronomical hero, though.
His clear and careful record keeping and
publication style not only let Galileo
understand the solar system, they continue
to let anyone understand how Galileo did it.
Galileo’s notes directly integrated his data
(drawings of Jupiter and its moons), key
metadata (timing of each observation,
weather, and telescope properties), and
text (descriptions of methods, analysis,
and conclusions). Critically, when Galileo
included the information from those notes
in Sidereus Nuncius [1], this integration of
text, data, and metadata was preserved, as
shown in Figure 1. Galileo’s work ad-
vanced the ‘‘Scientific Revolution,’’ and
his approach to observation and analysis
contributed significantly to the shaping of
today’s modern ‘‘scientific method’’ [2,3].
Today, most research projects are
considered complete when a journal
article based on the analysis has been
written and published. The trouble is,
unlike Galileo’s report in Sidereus Nuncius,
the amount of real data and data descrip-
tion in modern publications is almost
never sufficient to repeat or even statisti-
cally verify a study being presented.
Worse, researchers wishing to build upon
and extend work presented in the litera-
ture often have trouble recovering data
associated with an article after it has been
published. More often than scientists
would like to admit, they cannot even
recover the data associated with their own
published works.
Complicating the modern situation, the
words ‘‘data’’ and ‘‘analysis’’ have a wider
variety of definitions today than at the
time of Galileo. Theoretical investigations
can create large ‘‘data’’ sets through
simulations (e.g., The Millennium Simu-
lation Project: http://www.mpa-garching.
mpg.de/galform/virgo/millennium/).
Large-scale data collection often takes
place as a community-wide effort (e.g.,
The Human Genome project: http://
www.genome.gov/10001772), which leads
to gigantic online ‘‘databases’’ (organized
collections of data). Computers are so
essential in simulations, and in the pro-
cessing of experimental and observational
data, that it is also often hard to draw a
dividing line between ‘‘data’’ and ‘‘analy-
sis’’ (or ‘‘code’’) when discussing the care
and feeding of ‘‘data.’’ Sometimes, a copy
of the code used to create or process data
is so essential to the use of those data that
the code should almost be thought of as
part of the ‘‘metadata’’ description of the
data. Other times, the code used in a
scientific study is more separable from the
data, but even then, many preservation
and sharing principles apply to code just as
well as they do to data.
So how do we go about caring for and
feeding data? Extra work, no doubt, is
associated with nurturing your data, but
care up front will save time and increase
insight later. Even though a growing number
of researchers, especially in large collabora-
tions, know that conducting research with
sharing and reuse in mind is essential, it still
requires a paradigm shift. Most people are
still motivated by piling up publications and
by getting to the next one as soon as possible.
But, the more we scientists find ourselves
wishing we had access to extant but now
unfindable data [4], the more we will realize
why bad data management is bad for
science. How can we improve?
This article offers a short guide to
the steps scientists can take to
ensure that their data and associat-
ed analyses continue to be of value
and to be recognized. In just the past
few years, hundreds of scholarly papers
and reports have been written on ques-
tions of data sharing, data provenance,
research reproducibility, licensing, attribu-
tion, privacy, and more—but our goal
here is not to review that literature.
Instead, we present a short guide intended
for researchers who want to know why it is
important to ‘‘care for and feed’’ data,
with some practical advice on how to do
that. The final section at the close of this
work (Links to Useful Resources) offers
links to the types of services referred to
throughout the text. Boldface lettering
below highlights actions one can take to
follow the suggested rules.
Rule 1. Love Your Data, and
Help Others Love It, Too
Data management is a repeat-play
game. If you take care to make your data
Citation: Goodman A, Pepe A, Blocker AW, Borgman CL, Cranmer K, et al. (2014) Ten Simple Rules for the Care
and Feeding of Scientific Data. PLoS Comput Biol 10(4): e1003542. doi:10.1371/journal.pcbi.1003542
Published April 24, 2014
Copyright: ! 2014 Goodman et al. This is an open-access article distributed under the terms of the Creative
Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium,
provided the original author and source are credited.
Funding: The authors received no specific funding for writing this manuscript.
Competing Interests: The authors have declared that no competing interests exist.
* E-mail: alberto.pepe@gmail.com
Editor: Philip E. Bourne, University of California San Diego, United States of America
PLOS Computational Biology | www.ploscompbiol.org 1 April 2014 | Volume 10 | Issue 4 | e1003542

Article
Dataset Reuse: Toward Translating
Principles to Practice
Laura Koesten,1,* Pavlos Vougiouklis,2 Elena Simperl,1 and Paul Groth3,4,*
1King’s College London, London WC2B 4BG, UK
2Huawei Technologies, Edinburgh EH9 3BF, UK
3University of Amsterdam, Amsterdam 1090 GH, the Netherlands
4Lead Contact
*Correspondence: laura.koesten@kcl.ac.uk (L.K.), p.groth@uva.nl (P.G.)
https://doi.org/10.1016/j.patter.2020.100136
SUMMARY
The web provides access to millions of datasets that can have additional impact when used beyond their
original context. We have little empirical insight into what makes a dataset more reusable than others and
which of the existing guidelines and frameworks, if any, make a difference. In this paper, we explore potential
reuse features through a literature review and present a case study on datasets on GitHub, a popular open
platform for sharing code and data. We describe a corpus of more than 1.4 million data files, from over
65,000 repositories. Using GitHub’s engagement metrics as proxies for dataset reuse, we relate them to
reuse features from the literature and devise an initial model, using deep neural networks, to predict a data-
set’s reusability. This demonstrates the practical gap between principles and actionable insights that allow
data publishers and tools designers to implement functionalities that provably facilitate reuse.
1 INTRODUCTION
There has been a gradual shift in the last years from viewing da-
tasets as byproducts of (digital) work to critical assets, whose
value increases the more they are used.1,2
However, our under-
standing of how this value emerges, and of the factors that
demonstrably affect the reusability of a dataset is still limited.
Using a dataset beyond the context where it originated re-
mains challenging for a variety of socio-technical reasons, which
have been discussed in the literature;3,4
the bottom line is that
simply making data available, even when complying with existing
guidance and best practices, does not mean it can be easily
used by others.5
At the same time, making data reusable to a diverse audience,
in terms of domain, skill sets, and purposes, is an important way
to realize its potential value (and recover some of the, sometimes
considerable, resources invested in policy and infrastructure
support). This is one of the reasons why scientific journals and
research-funding organizations are increasingly calling for
further data sharing6
or why industry bodies, such as the Interna-
tional Data Spaces Association (IDSA) (https://www.
internationaldataspaces.org/) are investing in reference archi-
tectures to smooth data flows from one business to another.
There is plenty of advice on how to make data easier to
reuse, including technical standards, legal frameworks, and
guidelines. Much work places focus on machine readability
THE BIGGER PICTURE The web provides access to millions of datasets. These data can have additional
impact when it is used beyond the context for which it was originally created. We have little empirical insight
into what makes a dataset more reusable than others, and which of the existing guidelines and frameworks,
if any, make a difference. In this paper, we explore potential reuse features through a literature review and
present a case study on datasets on GitHub, a popular open platform for sharing code and data. We
describe a corpus of more than 1.4 million data files, from over 65,000 repositories. Using GitHub’s engage-
ment metrics as proxies for dataset reuse, we relate them to reuse features from the literature and devise an
initial model, using deep neural networks, to predict a dataset’s reusability. This work demonstrates the
practical gap between principles and actionable insights that allow data publishers and tools designers
to implement functionalities that provably facilitate reuse.
Proof-of-Concept: Data science output has been formulated,
implemented, and tested for one domain/problem
Patterns 1, 100136, November 13, 2020 ª 2020 The Author(s). 1
ll
OPEN ACCESS
Lots of good advice
• Maybe a bit too much….

• Currently, 140 policies on fairsharing.org as
of April 5, 2021

• We reviewed 40 papers

• Cataloged 39 di
ff
erent features of datasets
that enable data reuse

Where should a data provider start?
• Lots of good advice!

• It would be great to do all these things

• But it’s all a bit overwhelming

• Can we help prioritize?

Getting some data
• Used Github as a case study

• ~1.4 million datasets (e.g. CSV, excel) from
~65K repos

• Use engagement metrics as proxies for data
reuse

• Map literature features to both dataset and
repository features

• Train a predictive model to see what are
features are good predictors

Dataset Features
Missing values
Size
Columns + Rows
Readme features
Issue features
Age
Description
Parsable

Where to start?
• Some ideas from this study if you’re publishing data
with Github

• provide an informative short textual summary of the
dataset  
• provide a comprehensive README
fi
le in a
structured form and links to further information  
• datasets should not exceed standard processable
fi
le sizes  
• datasets should be possible to open with a standard
con
fi
guration of a common library (such as Pandas) 
Trained a Recurrent Neural Network. Might be better models but useful for
handling text, Not the greatest predicator (good for classifying not reuse)
but still useful for helping us tease out features

Can we help automate curation?

Madelon Hulsebos
https://madelonhulsebos.github.io

Example: semantic column type detection
Sherlock [Hulsebos et al., KDD, 2019]

DL method for semantic data type detection of table columns

https://github.com/mitmedialab/sherlock-project

Need for a new corpora
• Database-like table content and structure (semantics, data types, size).

• Large-scale to facilitate table representation models.

• Broad coverage to generalize to a diversity of domains.

• Table semantics (e.g. column types).

CSVs from Github
https://gittables.github.io

Tools to improve data supply chains
Groth, Paul, "Transparency and Reliability in the Data Supply Chain,"
Internet Computing, IEEE, vol.17, no.2, pp.69,71, March-April 2013 doi:
10.1109/MIC.2013.41

Conclusion
• AI is data centric

• Need tools that help users debug and curate their data for ML

• Way forward: Conversation between ML, DB, and HCI research

• We are hiring :-)
Paul Groth | @pgroth | pgroth.com | indelab.org

Data Curation and Debugging for Data Centric AI

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