Add ms2deepscore - for finalization #1958

robinschmid · 2024-07-15T04:40:51Z

Based on #1737

Just to finalize it

# Conflicts: # gradle/libs.versions.toml

utilities for pair processing in parallel stream

…epscore

…ectra and convert everything to float (since the model only runs with the same datatype)

…2deepscore

…2deepscore_robin

…2deepscore_robin # Conflicts: # mzmine-community/src/main/java/io/github/mzmine/gui/mainwindow/MainMenu.fxml # mzmine-community/src/main/java/io/github/mzmine/modules/dataprocessing/group_spectral_networking/SpectralNetworkingModule.java # mzmine-community/src/main/java/io/github/mzmine/modules/visualization/spectra/simplespectra/mirrorspectra/MirrorScanWindowController.java

SteffenHeu · 2024-07-29T08:59:40Z

javafx-framework/src/main/java/io/github/mzmine/javafx/components/factories/FxTexts.java


  public static final Text mzminePaper = hyperlinkText(
-      "Schmid, R., Heuckeroth, S., Korf, A. et al. Nat Biotechnol 41, 447–449 (2023).",
+      "Schmid R, Heuckeroth S, Korf A et al. Nat Biotechnol 41, 447–449 (2023).",


changing all this manually just forces us to change new citations manually as well. imo we could jsut keep the original style from the respective journal

Problem was that all the citations were very different. I would prefer just a single citation style.
I chose the nature style which can be just copied from any tool like paperpile.

I'm pretty sure the nature journals use the nature style. and paperpile is the worst tool in existence to manage citations

ok sorry was PLOS citation style. I thought it was nature

At least I think it is good to stick to one style and so far it was mixed.

...ub/mzmine/modules/dataprocessing/group_spectral_networking/MainSpectralNetworkingModule.java

SteffenHeu · 2024-07-29T09:09:26Z

...ng/group_spectral_networking/modified_cosine/ModifiedCosineSpectralNetworkingParameters.java

-      "Check MS2 neutral loss similarity",
-      "Generates a list of m/z differences and calculates cosine similarity",
-      new NeutralLossSimilarityParameters(), false);
+//  public static final OptionalModuleParameter<NeutralLossSimilarityParameters> CHECK_NEUTRAL_LOSS_SIMILARITY = new OptionalModuleParameter<>(


what's this?

this was an old option to run spectral networking also by comparing neutral losses between signals.
Basically took the top N signals and computed the delta m/z between all of them.

I removed it because this was never really used. Also we should rethink this approach and then just add another algorithm to the options that we now have.

i removed the commented code now

.../dataprocessing/group_spectral_networking/ms2deepscore/MS2DeepscoreNetworkingParameters.java

...odules/dataprocessing/group_spectral_networking/ms2deepscore/MS2DeepscoreNetworkingTask.java

SteffenHeu · 2024-07-29T09:32:35Z

.../java/io/github/mzmine/util/scans/similarity/impl/ms2deepscore/EmbeddingBasedSimilarity.java

+  }
+
+  /**
+   * TODO add documentation


todo (and below)

Best if @niekdejonge adds the documentation here

I have added some documentation in #2014

…mboParameter

…2deepscore_robin # Conflicts: # utils/src/main/java/io/github/mzmine/util/files/ExtensionFilters.java

…2deepscore_robin

robinschmid · 2024-07-29T15:20:57Z

Ready from my side and updated to master

niekdejonge · 2024-08-05T09:49:49Z

@robinschmid Thanks for finalizing the PR!

niekdejonge and others added 30 commits March 22, 2024 13:39

Initialise MS2Deepscore class

8266404

Add djl to dependencies

86044e2

Added first version of MS2DeepscoreModel

73a5222

Add constructor to MS2DeepscoreModel

eacf8c6

Add tests for MS2DeepscoreModel and test model

25c69bc

Remove MS2DeepscoreSpectralSimilarity.java

757f6b5

Remove MS2DeepscoreSpectralSimilarityParameters.java.java

9b5a4dc

Change String to Uri type

9ab1fed

utilities for pair processing in parallel stream

3c86819

Merge remote-tracking branch 'mzmine/master' into add_ms2deepscore

ca2e70d

# Conflicts: # gradle/libs.versions.toml

Merge pull request #1 from robinschmid/add_ms2deepscore

910ec3a

utilities for pair processing in parallel stream

Merge remote-tracking branch 'origin/add_ms2deepscore' into add_ms2de…

0aba022

…epscore

First version of MS2DeepscoreModule

d03a411

Integrate ms2deepscore module in mzmine and spectral networking

b8142c2

Update model to work with embeddings instead of predicting similarity

69fcc62

Added the settings as well (not yet used)

0fb9f70

remove MassSpecTestData record

1ef965c

Do NDMAnager conversion within test_correct_prediction

dc9425c

Add SettingsMS2Deepscore

ed5c0f0

Replace assertEquals with assertArrayEquals

fd941e7

Update SettingsMS2Deepscore types

bc8beb4

Add SpectrumTensorizer and implement tensorizeFragments

547c96c

Add metadata tensorizer

5e03969

Add check that additionalMetadata is as expected.

78f07ee

Add TensorizedSpectra

0484435

Add tensorizeSpectra method to SpectrumTensorizer

fe47c90

integrate spectrumTensorizer in MS2DeepscoreModel

99f3a08

Move NDArray generation into MS2DeepscoreModel.predictEmbeddingFromSp…

1520495

…ectra and convert everything to float (since the model only runs with the same datatype)

Added intensity_scaling

29cb627

Added check for expected output matching python embeddings

3549c40

niekdejonge and others added 19 commits July 3, 2024 14:46

rename to Camel Case

aaadd29

update logging

022e7b0

Remove print statements leftover of testing

7c7c128

Added MS2Deepscore Paper and citation info.

33d3f16

Merge remote-tracking branch 'refs/remotes/mzmine/master' into add_ms…

0ac5925

…2deepscore

djl library added

c4edf9b

small adjustments

6d0c386

Merge remote-tracking branch 'refs/remotes/mzmine/master' into add_ms…

2cb96f0

…2deepscore_robin

Merge remote-tracking branch 'refs/remotes/mzmine/master' into add_ms…

afc5f7b

…2deepscore_robin

first version of ModuleOptionsEnumComboParameter

2246687

ModuleOptionsEnumComboParameter intermediate parameters set

868bb77

molecular networking in one module works

29866b4

clean up tensorizer allow spectral library entries

b72e0a5

fix parameter load

cde25a0

add documentation

d96379f

remove neutral loss similarity from modified cosine

041c3e4

move modified cosine to own package

d8ff81d

up version of mol net module

0d3b6b6

SteffenHeu reviewed Jul 29, 2024

View reviewed changes

robinschmid added 7 commits July 29, 2024 12:37

make ModuleOptionsEnumComboParameter xml compatible with old ModuleCo…

3d9f789

…mboParameter

review and use List<? extends MassSpectrum> in model

830d845

add mass list in MS2Deepscore test

f52d39d

Merge remote-tracking branch 'refs/remotes/mzmine/master' into add_ms…

594a9d4

…2deepscore_robin # Conflicts: # utils/src/main/java/io/github/mzmine/util/files/ExtensionFilters.java

push article references in ArticleReferences

06609f7

fix FxComboBox

4127f32

Merge remote-tracking branch 'refs/remotes/mzmine/master' into add_ms…

c60838a

…2deepscore_robin

SteffenHeu merged commit c95fcc2 into mzmine:master Jul 29, 2024

Add ms2deepscore - for finalization #1958

Add ms2deepscore - for finalization #1958

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robinschmid commented Jul 15, 2024

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robinschmid commented Jul 29, 2024

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niekdejonge commented Aug 5, 2024

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