Reproducibility challenges in computational settings: what are they, why should we address them, and how?

Reproducibility Challenges in Computational Settings:

What are they, why should we address them, and how?

Andreas Rauber

Vienna University of [email protected]

http://www.ifs.tuwien.ac.at/~andi

mailto:[email protected]

http://www.ifs.tuwien.ac.at/~andi

Outline

What are the challenges in reproducibility? What do we gain from reproducibility?

(and: why is non-reproducibility interesting?)

How to address the challenges of complex processes?

How to deal with “Big Data”?

Summary

Challenges in Reproducibility

Challenges in reproducibility or: Why data sharing is not enough

FAIR principles are a necessity Data Management and DMPs are a necessity But they are not sufficient if we want to

- Ensure reproducibility

- Enable metastudies

- Benefit from efficient eScience

…unless we define data broader than we commonly tend to do


http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038234

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038234


Excursion: Scientific Processes

Challenges in Reproducibility Excursion: scientific processes

set1_freq440Hz_Am12.0Hz



Java Matlab


Excursion: Scientific Processes

Bug? Psychoacoustic transformation tables? Forgetting a transformation? Different implementation of filters? Limited accuracy of calculation? Difference in FFT implementation? ...?


Workflows

Taverna


Challenges in Reproducibility Large scale quantitative analysis Obtain workflows from MyExperiments.org

- March 2015: almost 2.700 WFs (approx. 300-400/year)- Focus on Taverna 2 WFs: 1.443 WFs- Published by authors should be „better quality“

Try to re-execute the workflows- Record data on the reasons for failure along

Analyse the most common reasons for failures

Re-Execution resultsMajority of workflows failsOnly 23.6 % are successfully executed

- No analysis yet on correctness of results…


Rudolf Mayer, Andreas Rauber, “A Quantitative Study on the Re-executability of Publicly Shared Scientific Workflows”, 11th IEEE Intl. Conference on e-Science, 2015.

Computer Science 613 papers in 8 ACM conferences Process

- download paper and classify- search for a link to code (paper, web, email twice)- download code- build and execute

Christian Collberg and Todd Proebsting. “Repeatability in Computer Systems Research,” CACM 59(3):62-69.2016

In a nutshell – and another aspect of reproducibility:


Source: xkcd

http://xkcd.com/

Reproducibility – solved! (?)

Reproducibility is more than just sharing the data! Provide source code, parameters, data, … Ensure that it works:

Wrap it up in a container/virtual machine, …

…

done?LXC

Outline

What are the challenges in reproducibility?

What do we gain by aiming for reproducibility?


How to deal with dynamic data?

Summary


Provide source code, parameters, data, … Wrap it up in a container/virtual machine, …

…

Why do we want reproducibility? Which levels or reproducibility are there? What do we gain by different levels of reproducibility?

LXC


Dagstuhl Seminar: Reproducibility of Data-Oriented Experiments in e-ScienceJanuary 2016, Dagstuhl, Germany

Types of Reproducibility

The PRIMAD1 model: which attributes can we “prime”? - Data

• Parameters• Input data

- Plattform- Implementation- Method- Research Objective- Actors

What do we gain by priming one or the other?

[1] Juliana Freire, Norbert Fuhr, and Andreas Rauber. Reproducibility of Data-Oriented Experiments in eScience. Dagstuhl Reports, 6(1), 2016.

Types of Reproducibility and Gains

Reproducibility Papers

Aim for reproducibility: for one’s own sake – and as Chairs of conference tracks, editor, reviewer, superviser, …- Review of reproducibility of submitted work (material provided)

- Encouraging reproducibility studies

- (Messages to stakeholders in Dagstuhl Report)

Consistency of results, not identity! Reproducibility studies and papers

- Not just re-running code / a virtual machine

- When is a reproducibility paper worth the effort / worth being published?

Reproducibility Papers When is a Reproducibility paper worth being published?

Learning from Non-Reproducibility

Do we always want reproducibility?

- Scientifically speaking: yes! Research is addressing challenges:

- Looking for and learning from non-reproducibility! Non-reproducibility if

- Some (un-known) aspect of a study influences results

- Technical: parameter sweep, bug in code, OS, … -> fix it!

- Non-technical: input data! (specifically: “the user”)

Learning from Non-Reproducibility

Challenges in MIR – “things sometimes don’t seem to work”Virtual Box, Github, <your favourite tool> are starting pointsSame features, same algorithm, different data -> Same data, different listeners -> Understanding “the rest”:

- Isolating unknown influence factors

- Generating hypotheses

- Verifying these to understand the “entire system”, cultural and other biases, …

Benchmarks and Meta-Studies


Provide source code, parameters, data, … Wrap it up in a container/virtual machine,

Provide context information Encourage reproducibility studies beyond re-running Use it to establish trust in your research & gain new insights

done?

LXC

Outline





Summary

Deja-vue…

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0038234

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038234

And the solution is…

Standardization and Documentation- Standardized components, procedures, workflows- Documenting complete system set-up across

entire provenance chain How to do this – efficiently?

Alexander Graham Bell’s Notebook, March 9 1876https://commons.wikimedia.org/wiki/File:Alexander_Graham_Bell's_notebook,_March_9,_1876.PNG

Pieter Bruegel the Elder: De Alchemist (British Museum, London)

Documenting a Process

Context Model: establish what to document and how Meta-model for describing process & context

- Extensible architecture integrated by core model- Reusing existing models as much as possible- Based on ArchiMate, implemented using OWL

Extracted by static and dynamic analysis

Context Model – Static Analysis

Analyses steps, platforms, services, tools called Dependencies (packages, libraries) HW, SW Licenses, …

Taverna Workflow ArchiMate model Context Model(OWL ontology)

#!/bin/bash

# fetch datajava -jar GestBarragensWSClientIQData.jarunzip -o IQData.zip

# fix encoding#iconv -f LATIN1 -t UTF-8 iq.r > iq_utf8.r

# generate referencesR --vanilla < iq_utf8.r > IQout.txt

# create pdfpdflatex iq.texpdflatex iq.tex

Script

Context Model – Dynamic Analysis

Process Migration Framework (PMF)

- designed for automatic redeployments into virtual machines

- uses strace to monitor system calls

- complete log of all accessed resources (files, ports)

- captures and stores process instance data

- analyse resources (file formats via PRONOM, PREMIS)

Context Model – Dynamic Analysis

Taverna Workflow

VFramework

Are these processes the same?

Original environment Redeployment environmentRepository

Preserve Redeploy

VFramework

VFramework

#!/bin/bash





VFramework

#!/bin/bash





VFramework

#!/bin/bash





#!/bin/bash





VFramework

ADDED

NOT USED


Provide source code, parameters, data, … Wrap it up in a container/virtual machine, Provide context information Encourage reproducibility studies beyond re-running Use it to establish trust in your research & gain new insights

(automatically) capture process execution context Verify re-executions

done?

LXC

Outline





Summary

Research Data Alliance WG on Data Citation:

Making Dynamic Data Citeable WG endorsed in March 2014

- Concentrating on the problems of large, dynamic (changing) datasets

- Focus! Identification of data!Not: PID systems, metadata, citation string, attribution, …

- Liaise with other WGs and initiatives on data citation (CODATA, DataCite, Force11, …)

- https://rd-alliance.org/working-groups/data-citation-wg.html

RDA WG Data Citation

https://rd-alliance.org/working-groups/data-citation-wg.html

Data Citation – Output

14 Recommendationsgrouped into 4 phases:- Preparing data and query store- Persistently identifying specific data sets- Resolving PIDs- Upon modifications to the data

infrastructure 2-page flyer

https://rd-alliance.org/recommendations-working-group-data-citation-revision-oct-20-2015.html

More detailed report: IEEE TCDL 2016http://www.ieee-tcdl.org/Bulletin/v12n1/papers/IEEE-TCDL-DC-2016_paper_1.pdf




http://www.ieee-tcdl.org/Bulletin/v12n1/papers/IEEE-TCDL-DC-2016_paper_1.pdf



Data Citation – Output

14 Recommendationsgrouped into 4 phases:- Preparing data and query store- Persistently identifying specific data sets- Resolving PIDs- Upon modifications to the data

infrastructure 2-page flyer


More detailed report: IEEE TCDL 2016http://www.ieee-tcdl.org/Bulletin/v12n1/papers/IEEE-TCDL-DC-2016_paper_1.pdf

Detailed presentation on

Tuesday, Session 9,

12:00-13:30

3 Take-Away Messages

Message 1Aim at achieving reproducibility at different levels

- Re-run, ask others to re-run

- Re-implement

- Port to different platforms

- Test on different data, vary parameters (and report!)

If something is not reproducible -> investigate!(you might be onto something!)Encourage reproducibility studies!


Message 2Aim for better procedures and documentationDocument the research process, environment, interim results, …(preferably automatically, 80:20, …)The process is part of the data (and vice versa)

Source: xkdc Pieter Bruegel the Elder: De Alchemist (British Museum, London)

Research Objects, Context Models, VFramework


Message 3Aim for proper (research) data management(not just in academia!)Data Management Plans, Research Infrastructure Services

Source: http://www.phdcomics.com/comics.php?f=1323 RDA WGDC: Dynamic Data Citation

Detailed presentation on

Tuesday, Session 9,

12:00-13:30

Summary

Trustworthy and efficient e-Science Need to move beyond preserving code + data Need to move beyond the focus on description Capture Process and entire execution context Precisely identify data used in process Verification of re-execution Data and process re-use as basis for data driven science

- evidence- investment- efficiency

Trust!!

Summary

Preaching and eating…

Do we do all this in our lab for our experiments?

No! (not yet?)

Researchers (also in CS) need assistance

Institutions and Research Infrastructures

… and some research on open questions on how to best do

all of this (but mind the infamous 80:20 rule)

Summary

C. Glenn Begley, Alastair M. Buchan, Ulrich Dirnagl: Robust research: Institutions must do their part for reproducibility, Nature 525(7567), Sep 3 2015, Illustration by David Parkinshttp://www.nature.com/news/robust-research-institutions-must-do-their-part-for-reproducibility-1.18259?WT.mc_id=SFB_NNEWS_1508_RHBox

Acknowledgements

Johannes Binder Rudolf Mayer Tomasz Miksa Stefan Pröll Stephan Strodl Marco Unterberger

TIMBUS SBA: Secure Business Austria RDA: Research Data Alliance WGDC

References Juliana Freire, Norbert Fuhr, and Andreas Rauber. Reproducibility of Data-Oriented

Experiments in eScience. Dagstuhl Reports, 6(1), 2016. Andreas Rauber, Ari Asmi, Dieter van Uytvanck and Stefan Proell. Identification of

Reproducible Subsets for Data Citation, Sharing and Re-Use. Bulletin of IEEE Technical Committee on Digital Libraries (TCDL), vol. 12, 2016.

Andreas Rauber, Tomasz Miksa, Rudolf Mayer and Stefan Proell. Repeatability and Re-Usability in Scientific Processes: Process Context, Data Identification and Verification. In Proceedings of the 17th International Conference on Data Analytics and Management in Data Intensive Domains (DAMDID), 2015.

Tomasz Miksa, Rudolf Mayer and Andreas Rauber. Ensuring sustainability of web services dependent processes. International Journal of Computational Science and Engineering (IJCSE). 2015 Vol.10, No.1/2, pp.70 – 81

Rudolf Mayer and Andreas Rauber, A Quantitative Study on the Re-executability ofPublicly Shared Scientific Workflows. 11th IEEE Intl. Conference on e-Science, 2015.

Rudolf Mayer, Tomasz Miksa and Andreas Rauber. Ontologies for describing the context of scientific experiment processes. 10th IEEE Intl. Conference on e-Science, 2014.

Tomasz Miksa, Stefan Proell, Rudolf Mayer, Stephan Strodl, Ricardo Vieira, Jose Barateiro and Andreas Rauber, Framework for verification of preserved and redeployed processes. 10th International Conference on Preservation of Digital Objects (IPRES2013), 2013.

Tomasz Miksa, Stephan Strodl and Andreas Rauber, Process Management Plans. International Journal of Digital Curation, Vol 9, No 1 (2014),pp. 83-97.

Thank you!

http://www.ifs.tuwien.ac.at/imp

Data & Analytics

Reproducibility challenges in computational settings: what are they, why should we address them, and how?