Data Quality

In Machine Learning
Production Systems
Felix Biessmann,
Sebastian Schelter,
Sebastian Jäger
Why Data Quality for Machine Learning?

1. Manager’s Perspective:

Legal requirement

Biased data (gender, ethnicity)

Quality standards (e.g. Autopilots)

2. Scientist’s Perspective:

Better data quality, better predictive performance

3. Engineer’s Perspective:

Data quality problems worst hidden technical debt in AI systems

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Better Data Quality, Better Predictive Performance

Classi cation Horror vs Comedy from plot:

Misconception 2. Parameter tuning
Data quality most important hyper parameter
is the most important problem
Data Cleaning 0.91

TFIDF, PoS, Stop Words 0.695 Python Hyperopt 0.73

Scikit Learn Default 0.69

Accuracy

Horror vs. Comedy From Plot

Krishnan and Wang, “Data Cleaning - a Statistical Perspective”,
82

SIGMOD Tutorial on Data Cleaning, 2016

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AI in Academia

Machine
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Learning

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AI in Production Systems

Machine
Learning

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AI in Production Systems

Dat
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AI in Production Systems

Dat
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Machine
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Featur
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AI in Production Systems

Dat Dat
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Machine
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Featur
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AI in Production Systems

Monitoring

Dat Dat
Collection Veri cation

Con guration
Machine
Learning Analysis Tools
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Featur
Extraction Machine
Resource
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Adapted from Sculley et al,
“Hidden Technical Debt in ML Systems” NIPS 2015

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Automation for Data Quality

• Data Quality is important for responsible usage of ML

• Automated Data Quality Monitoring is difficult
• Lack of automation for Data Quality leads to
• Slow transfer from research to applications
• Poor scalability
• Difficult maintenance

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Automation for Data Quality

• Responsible usage of ML requires novel tooling

• We develop solutions for scalable and automated
• Monitoring of data quality
• Improvement of data quality
• Prediction of data quality impact on ML models
• Modelling Data Errors

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Automated Monitoring of Data Quality

Research Question:
Can we measure Data Quality problems automatically?

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Automated DQ Monitoring: Unit Tests for Data

• So ware systems are testable

• Unit tests
• Integration tests

• Machine Learning systems depend on data

• Data quality is essential for ML systems

➡ Unit tests for Data Quality

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Automated DQ Monitoring: Unit Tests for Data

val verificationResult = VerificationSuite(

.onData(data
.addCheck
Check(CheckLevel.Error, "unit testing my data")
.hasSize(_ == 5) // we expect 5 row
.isComplete("id") // should never be NULL
.isUnique("id") // should not contain duplicate
.isComplete("name") // should never be NUL
// should only contain the values "high" and "low"
.isContainedIn("priority", Array("high", "low"))
// should not contain negative value
.isNonNegative("numViews"
// at least half of the descriptions should contain a url
.containsURL("description", _ >= 0.5)
// half of the items should have less than 10 views
.hasApproxQuantile("numViews", 0.5, _ <= 10))
.run(

Schelter et al, VLDB, 2018 https://github.com/awslabs/deequ

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Automated DQ Monitoring: Unit Tests for Data
Check(Level.Error)
.isUnique("product_id")
.isComplete("name", "description")
.satisfies("price > 0")
.hasValidValueRange("priority",
("high", "low"))
.hasCountDistinct("brand",
verifyBrandCount(_))
Check(Level.Warning, scope=SERIES)
.hasNoAnomalies(Size,
OnlineNormal(stdDevs=3))
Check(Level.Warning)
.isPredictable("brand",
("name", "description"), f1=.98)
user-defined declarative
1 2 data quality metrics
checks and constraints
Schelter et al, VLDB, 2018
SELECT AVG(NOT_NULL(name)),
AVG(NOT_NULL(description)),
AVG(price > 0),…
FROM data
Uniqueness("product_id")
SELECT SUM(COUNT(*))
Completeness("name")
FROM data
Completeness("description")
GROUP BY asin
Compliance("price > 0")
HAVING COUNT(*) = 1
Compliance("priority IN (...)")
Histogram("brand")
...
Predictability("brand", ...)
Size
aggregation queries
3 4
on Apache Spark
https://github.com/awslabs/deequ
Success("isUnique(product_id)",
Uniqueness("product_id") == 1.0)
Failure("isComplete(name)",
Completeness("name") == 1.0,
0.987)
Success("isComplete(description)",
Completeness("description") == 1.0)
Success("hasCountDistinct(brand, ...)",
verifyBrandCount(Histogram("brand")
.numDistinct)))
...
metrics and validation
results
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Automated Improvement of Data Quality

Research Question:
Can we fix Data Quality problems automatically?

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Data Quality Problems
• Correctness (Di cult to measure)
• Unknown schemas / data types
• Wrong entries

• Consistency
• Duplicates
• Invalid values

• Statistical properties
• Anomalies
• Are value distributions changing over time?
• Is a column predictable from another column?

• Completeness
• How many missing values?

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Table 2: F1 scores on held-out data for imputation task product attributes for mode imputation, string
matching, LSTM and character n-gram featurizers. For single product attributes, we report F1 scores relative
to the result obtained with the best model. We also report the median of absolute F1 across all product
attributes. Compared to baselines, our imputation approach is better in all cases, achieving on average a
Imputation for Tables
23-fold increase (compared to Mode imputation) and a 3-fold increase (compared to a rule-based system) in
imputation quality.

Dataset Attribute Mode String matching LSTM N-gram

brand 0.4% 80.3% best 99.9%
dress, English manufacturer 1.0% 22.7% 99.4% best
size 4.8% 0.1% best 96.1%
brand 13.3% 44.5% best 94.5%
monitor, English display technology 30.6% 13.5% 99.8% best
manufacturer 15.1% 33.6% best 95.3%
brand 3.9% 48.5% best 99.1%
notebook, English cpu model manufacturer 82.7% 88.0% 98.9% best
manufacturer 4.3% 35.9% 99.8% best
brand 0.5% 91.5% 99.9% best
shoes, English manufacturer 0.5% 79.2% 98.8% best
size 2.2% 0.0% best 82.7%
toe style 13.1% 23.5% 96.5% best
brand 2.6% 19.3% 98.8% best
shoes, Japanese color 20.4% 58.3% 94.5% best
size 76.7% 2.6% best 99.2%
style 61.3% 13.4% 92.6% best
Median of absolute F1 scores 4.1% 30.1% 92.8% 93.0%

Simple imputation models on par with or better than LSTMs

Table 3: F1 scores on held-out data for imputation task DBpedia. See Table 2 for a description of columns.
In contrast to the relative results for single product attributes, all numbers for the DBpedia dataset are
absolute F1 scores.

Dataset Attribute Mode String matching LSTM N-gram

birth place 0.3% 16.3% 54.1% 60.2%
DBpedia, English genre 1.5% 6.4% 43.2% 72.4% 16
location 0.7% 7.5% 41.8% 60.0%
.
Automated Monitoring of Data Quality Impact

Research Questions:

Can we predict performance of ML systems

• In the presence of covariate shi

• Without access to ML system internals

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 ML Production Systems
Classical ML Production Setting

Training / Validation Serving

black box
ML model
Cloud ML Auto ML
Service

Customer
(Engineers without
ML expertise)

24

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Predicting ML Performance

• Many Data Quality problems will be not detected / xed

• Errors in preprocessing
• Covariate shi s
• Adversarial attacks

• Some errors will not have impact on downstream ML model

• Only looking at input data leads to false alarms
• Other errors are di cult to detect in input
• Only looking at input data will miss some errors

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Predicting ML Performance
Training Data Performance Estimate
Model
Predicting ML Performance
Training Data Performance Estimate
Model

Apply typical*
perturbations
Perturbed Datasets

Predicting ML Performance
Training Data Performance Estimate
Model

Apply typical*
perturbations Performance Estimates
Perturbed Datasets

Predicting ML Performance
Training Data Performance Estimate
Model

Apply typical*
perturbations Performance Estimates
Perturbed Datasets
Featurized model
output

Predicting ML Performance
Training Data Performance Estimate
Model

Apply typical*
perturbations Performance Estimates
Perturbed Datasets
Featurized model
output

Meta Regression
Model

Predicting ML Performance
Training Data Performance Estimate
Model

Apply typical*
perturbations Performance Estimates
Perturbed Datasets
Featurized model
output

Meta Regression
Model

Production Data Prod Performance

Estimate

Predicting ML Performance
Training Data Performance Estimate
Model

Apply typical*
perturbations Performance Estimates
Perturbed Datasets
Featurized model
output

Meta Regression
Model

Production Data Prod Performance

Estimate

Predicting ML Performance under Covariate Shifts

Simple Method to
estimate ML Model
Performance under
realistic covariate shifts /
data quality issues

Sebastian Schelter, Tammo Rukat, Felix Bießmann JENGA-A Framework to Study the Impact of Data Errors on
the Predictions of Machine Learning Models, EDBT, 2021

Sebastian Schelter, Tammo Rukat, Felix Bießmann, Learning to Validate the Predictions of Black Box Classi ers
on Unseen Data, SIGMOD, 2020

21
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Works for unknown errors

Sebastian Schelter, Tammo Rukat, Felix Bießmann JENGA-A Framework to Study the Impact of Data Errors on
the Predictions of Machine Learning Models, EDBT, 2021

Sebastian Schelter, Tammo Rukat, Felix Bießmann, Learning to Validate the Predictions of Black Box Classi ers
on Unseen Data, SIGMOD, 2020

22
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 ure 4. We observe in all cases that the performance predictor
achieves low prediction errors after having access to a few
hundred
Works with fewexamples.
samples

Figure
and o
datase
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slices

Sebastian Schelter, Tammo Rukat, Felix Bießmann JENGA-A Framework to Study the Impact of Data Errors on
Figure 4: Sensitivity of our performance predictors to
the Predictions of Machine Learning Models, EDBT, 2021
the sample
Sebastian Schelter, size
Tammo Rukat, |D
Felix test | for
Bießmann, different
Learning to Validateerrors andof Black
the Predictions modelsBox Classi ers presen
on Unseen on
Data, the income and heart datasets. The performance
SIGMOD, 2020
of slice
predictor achieves low prediction errors after having the inc
23
access to a few hundred examples. .

be stro

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Modelling Data Quality Problems

Research Question:

Can we generate realistic errors?

24
.
The Importance of Errors in Machine Learning

• Injecting errors in data has many applications

• Regularization
• Differential Privacy
• Adversarial training
• Self-Supervised Training
• But which errors are useful and realistic?

All clean data sets are alike; All dirty data is dirty in its own way
Charles Sutton 2019 (AIDA workshop), after Leo Tolstoi

25
.
Jenga - A Framework to Study the Impact of Data Errors on
the Predictions of Machine Learning Models

• So ware systems are tested

• ML applications are di cult to test
▪ ML models depend on data
▪ Real test data is limited, models overparametrized
◦ Google's underspeci ation paper (D'Amour et al., 2020)
◦ Stochastic Parrots paper (Bender et al., 2021)

26
.
ft
fi
ffi
How to test ML Systems?

• A lot of data sets with convenient API (OpenML, Vanschoren et al. 2014)
• Data corruptions (Schelter, Rukat, Biessmann, SIGMOD, 2020)

Jenga leverages both to ensure:

• automation
• reproducibility

27
.
 SIGMOD, 2020, Portland, OR Sebasti
d ML Pipeline Performance Prediction2
ors compute predictions
SIGMOD, 2020, Portland, OR and scores for the S
Apply User De ned
corrupted examples corruptImpact
Evaluate examples
on
Error Generators to labeled data Trained ML Model
user-defined
error generators
2
compute predictions from the blackbox
Missing Values,
and scores for the
model
rupt 1
age
Scaling, …
user-defined
income
corrupted examples loan?
corrupt examples
from the blackbox
2
3
learn a performance
s
model predictor from mode
age income loan? compute predictions
h error generators
generate corrupt statistics of
scores p
predictions and scor
18 250,000 no
examples with and scores for the
18 250,000 corrupted
no predictions 3
user-defined examples corrupt examples on corrupt
on corrupt
error generators1 N/A 5,000 yes
black box
from
model
the blackbox
examples
examples learned
o
learn a
predict
performance
ors N/A
generate corrupt
5,000
examples withN/A 2,800
age income
no
loan?
yesML model
statistics of
scores Predictor predict
labeled test examples user-defined
error generators
18 250,000 no
Trained
black
predictions
box
on corrupt
on corrupt
examples
age income loan? N/A 5,000 yes examples0.67

18 2,500 no N/A
age income
2,800
loan?
N/A -2,500 N/Ano 2,800
nono black box
ML model ML Model
model per
P
mples
40 5,000
labeled test examples
yes
age income 40
loan? 5,000 ageyesincome loan?
0.52
0.67
37 2,800 18no 2,500 37 -2,800 N/Ano -2,500
loan? 40 5,000
no
ageyes income
40 5,000
loan?
yes
no
0.52

(a) Learning 37a performance

2,800 no predictor
37 for a pretrained
-2,800 no black box classi�er, using synthetic
nocorrupted data to explore
N/A how-2,500 no the resulting prediction quality.
data errors impact
(a) Learning a performance predictor for a pretrained black box classi�er, using s
yes corrupted40 5,000how datayes
data to explore errors impact the resulting prediction quality.
noFigure 1: Overview
37
of our proposed approach: (a) We learn a perform
-2,800 no 28

input data to estimate the prediction quality of a black box mode .

Figure 1: Overview of our proposed approach: (a) We learn a pe

fi
Jenga - Example

29
.
Jenga - Example

30
.
Jenga - Example

31
.
Jenga - Example

32
.
Jenga - Core Components

Tasks:
▪ binary/multiclass classi cation
▪ regression

Corruptions:
▪ Text
▪ Images
▪ Tabular data

Evaluators:
▪ Applies corruptions and tests ML model on task

33
.
fi
Jenga - Available Data Errors

• Text: leetspee
• Images: standard augmentation
• Structured data (tables)
▪ missing dat
◦ missing completely at rando
◦ missing at rando
◦ missing not at rando
▪ swapping column
▪ numerical data
◦ additive Gaussian nois
◦ scaling

34
.
a

Jenga - Available Error Sampling Schemes

• Inspired by Imputation literature, error probability is sampled

• Completely at rando
• For each value, we draw error probability from uniform distributio

• At random
• Error probability depends on values in other column

• Not at random
• Error probability depends on values themselves

35
.
:

Jenga - Error Example

36
.
Summary

• Data Quality is fundamental to responsible usage of ML

• Automation is key to scalable DQ management
• We work on automation of Data Quality
• Monitoring
• Improvement
• Modelling

• Limitations:
• Adoption of DQ tooling remains difficult
• Many DQ problems are difficult to model
• Data on errors is scarce (but see AIAAIC error DB)

37
.
Open Source

Measuring Data Quality:

https://github.com/awslabs/deequ
Fixing Data Quality issues
https://github.com/awslabs/datawi
Predicting Data Quality issues
https://github.com/schelterlabs/jenga

38
.
g

References

• Felix Bießmann, Jacek Golebiowski, Tammo Rukat, Dustin Lange, Philipp Schmidt, Automated data validation in machine learning
systems, Bulletin of the IEEE Computer Society Technical Committee on Data Engineering, 2021

• Sebastian Schelter, Tammo Rukat, Felix Bießmann, Towards Automated Data Quality Management for Machine Learning,
Proceedings of the 2020 ML Ops workshop at the Conference on Machine Learning and Systems (MLSys), 2020

• Sebastian Schelter, Felix Biessmann, Dustin Lange, Tammo Rukat, Phillipp Schmidt, Stephan Seufert, Pierre Brunelle, Andrey
Taptunov Unit Testing Data with Deequ Proceedings of the International Conference on Management of Data, 2019

• Sebastian Schelter, Stefan Grafberger, Philipp Schmidt, Tammo Rukat, Mario Kiessling, Andrey Taptunov, Felix Biessmann, Dustin
Lange Di erential Data Quality Veri cation on Partitioned Data IEEE 35th International Conference on Data Engineering (ICDE), 2019

• Stefan Grafberger, Philipp Schmidt, Tammo Rukat Mario Kiessling, Andrey Tap- tunov, Felix Bießmann, Dustin Lange Deequ - Data
Quality Validation for Machine Learning Pipelines ML Systems Workshop, NeurIPS 2018

• Sebastian Schelter, Dustin Lange, Philipp Schmidt, Meltem Celikel, Felix Bießmann, Andreas Grafberger Automating Large-Scale
Data Quality Veri cation Very Large Databases (VLDB), 2018

• Felix Biessmann, David Salinas, Sebastian Schelter, Philipp Schmidt, Dustin Lange, “Deep Learning for Missing Value Imputation in
Tables with Non-Numerical Data”, CIKM 2018

• Biessmann et al. Journal of Machine Learning Research, 2019

• Jaeger, Allhorn, Biessmann., Frontiers in Big Data, 2021

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ff
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Fair ML Automated

• Many data sets are biased

• Resulting ML Model predictions are biased
• Building fair ML models requires domain expertise
• Automating application of fairness constraints important

40
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Fair ML Automated: Declarative Feature Selection

Neutatz, Biessmann, Abedjan, SIGMOD, 2021

41
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Fair ML Automated: Declarative Feature Selection

Neutatz, Biessmann, Abedjan, SIGMOD, 2021

41
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