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MMRS & Reproducibility MULTIMODAL REMOTE SENSING BENJAMIN KELLENBERGER {@GEO.UZH.CH}

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Page 1: My experiences with reproducible research - UZH€¦ · Reproducibility? INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 2 Data Persistence Method Description & Reconstruction

MMRS&ReproducibilityMULTIMODAL REMOTE SENSING

BENJAMIN KELLENBERGER {@ GEO.UZH.CH}

Page 2: My experiences with reproducible research - UZH€¦ · Reproducibility? INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 2 Data Persistence Method Description & Reconstruction

Reproducibility?

2INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1

Data Persistence

Method Description &

Reconstruction

Collaboration

Code Distribution

Versioning

Comparability

Page 3: My experiences with reproducible research - UZH€¦ · Reproducibility? INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 2 Data Persistence Method Description & Reconstruction

We work with data (a lot)•We produce a lot of code

•We experiment with several parametrizations

•We often use the same data

We need to keep track of it all!

We need to be consistent among papers!

We need to become comparable too!

INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 3

Page 4: My experiences with reproducible research - UZH€¦ · Reproducibility? INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 2 Data Persistence Method Description & Reconstruction

Data PersistenceTypes of Datasets:

INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 4

Proprietary

✓ Tailored to research✓ Sometimes the only option

✗ Hardly repeatable setting✗ Rarely distributed✗ No comparability

Page 5: My experiences with reproducible research - UZH€¦ · Reproducibility? INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 2 Data Persistence Method Description & Reconstruction

Data PersistenceTypes of Datasets:

INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 5

Public, custom-built

Proprietary

✓ Easily obtainable✓ Often well-defined✓ Open: comparative work possible

✗ No separate test dataset

Examples

Page 6: My experiences with reproducible research - UZH€¦ · Reproducibility? INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 2 Data Persistence Method Description & Reconstruction

Data PersistenceTypes of Datasets:

INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 6

Public,evaluation server

Proprietary

✓ Publicly available✓Well-defined✓ Separate, hidden test set✓ Online evaluation server: you get your accuracy scores only

✗ Extensive & expensive for host

Example

Public, custom-built

Page 7: My experiences with reproducible research - UZH€¦ · Reproducibility? INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 2 Data Persistence Method Description & Reconstruction

Data PersistenceAt MMRS:

• We have an internal data server

• We maintain publicly available datasets: examples

• We are also occasionally involved in public contests (with evaluation servers)

INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 7

Page 8: My experiences with reproducible research - UZH€¦ · Reproducibility? INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 2 Data Persistence Method Description & Reconstruction

Method ReconstructionWe want our methods to bereproducible, too!

This involves:

• Detailed description in publication

• A lot of code, including (intuitive) examples

At MMRS, we do exactly that!

• All details in paper

• Distribution of code:• MMRS webpage

• Individual researchers‘ webpages:link1, link2, etc.

• Github: link

• We include parameter settings

INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 8

Page 9: My experiences with reproducible research - UZH€¦ · Reproducibility? INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 2 Data Persistence Method Description & Reconstruction

Method ReconstructionIn addition: we share useful general-purpose scripts on our server

INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 9

Page 10: My experiences with reproducible research - UZH€¦ · Reproducibility? INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 2 Data Persistence Method Description & Reconstruction

VersioningInvaluable paradigm for everything research-related!

• We collaborate

• Our projects evolve as we work on them

• We cannot avoid hardware failures ( backups!)

• We all make mistakes

INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 10

Page 11: My experiences with reproducible research - UZH€¦ · Reproducibility? INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 2 Data Persistence Method Description & Reconstruction

VersioningIdea:

• Relevant files lie on a server (e.g. scripts, LaTeX documents, etc.)

1. Every collaborator has a local copy he workson

2. Once finished, they submit their changes tothe server

3. Every (incremental) update is saved andrevertible if needed

4. Conflicts are easily resolvable

At MMRS:

• Paper collaboration: SVN

• Code: Github

• With outer world: collaborative systems(e.g. Overleaf, ShareLaTeX)

INNOPOOL WORKSHOP REPRODUCIBLE RESEARCH: SESSION 1 11