[ML] Add decision path charts to exploration results table #73561

qn895 · 2020-07-28T21:57:57Z

Summary

This PR adds the decision path popover to the exploration table. Popover includes both the chart view and the JSON view.

Clicking on the ml.feature_importance cell will show both tabs.

If there's only 1 feature, no need to show the chart.
For regression jobs:
- Calculate the baseline, and add the feature importance values in order of ascending absolute importance to arrive at the final predicted value.

Show other which is the residual feature importance for when number of features included is less than number of feature importance set

For binary classification jobs:
- Show dropdown for user to pick what class name/path to visualize. By default pick the first option since option has highest probability and is the ml.prediction value.
For multiclass classification jobs: (pending on backend)

Checklist

Delete any items that are not applicable to this PR.

Any text added follows EUI's writing guidelines, uses sentence case text and includes i18n support
This was checked for cross-browser compatibility

walterra · 2020-07-29T08:34:40Z

I love where this is going! Some feedback:

Can we style the tabs to have smaller font and padding (for example same as the data grid header)?
Ideally we should dynamically adjust the popover height so the chart is viewable without scrolling.
Suggest to make the padding between features significantly smaller.

Here's a mockup with the suggestions: (For this one I set the multiplier for the row height like this: height: mappedFeatureImportance.length * 22)

walterra · 2020-07-29T08:39:32Z

The SHAP library calls this chart type a "Decision Plot", should we also go with this naming? In this case I'd rename the tab names in the popover to Decision Plot | JSON instead of just Chart | JSON. (Regardless of the name we decide to use, IMHO we should be more specific in the tab title than just saying Chart)

qn895 · 2020-07-29T13:59:56Z

The SHAP library calls this chart type a "Decision Plot", should we also go with this naming? In this case I'd rename the tab names in the popover to Decision Plot | JSON instead of just Chart | JSON. (Regardless of the name we decide to use, IMHO we should be more specific in the tab title than just saying Chart)

Will do!

I love where this is going! Some feedback:

Can we style the tabs to have smaller font and padding (for example same as the data grid header)?

Ideally we should dynamically adjust the popover height so the chart is viewable without scrolling.

Suggest to make the padding between features significantly smaller.

Here's a mockup with the suggestions: (For this one I set the multiplier for the row height like this: height: mappedFeatureImportance.length * 22)

That definitely looks much more neat and compact. Will try to make the tabs smaller.

peteharverson · 2020-07-29T14:16:19Z

This is looking good! A few extra comments in addition to the suggestions from @walterra:

For the point tooltips, limit the value to 3 sigfigs (I'm unsure if the values in the JSON tab should also be limited to 3 sigfigs):

Popover definitely needs to adjust to the number of features (up to a maximum, at which point having a scrollbar makes sense)
The features should be sorted from top to bottom in order of descending magnitude(importance). This doesn't seem to be the case for some of my jobs (classification ones possibly).
Add some brief explanation text and/or an info tooltip to the chart tab to explain what the chart is displaying (using the text for the decision path viz in https://www.elastic.co/blog/feature-importance-for-data-frame-analytics-with-elastic-machine-learning as a guide).
Is it possible to add gridlines to the chart? If so, would be interesting to see how it looks.
Add 'Prediction' x-axis label
Some of my jobs don't have a single feature_importance column, so I don't see the chart / JSON popover. Do we know why we don't get a single column for some jobs?

I guess this might be because the baseline calculation is still a WIP, but the x-axis value for the top point doesn't end up at the predicted value. The x-axis value should be I think Moving from the bottom of the plot to the top, SHAP values (= feature importance) for each feature are added to the model's base value. This shows how each feature contributes to the overall prediction. Which in this case would result I think in the top point be plotted at the predicted value of -0.059:

- Add grid lines - Adjust sorting for classification from biggest at the top to smallest at the bottom - Change chart to using cumulative values

# Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit.

qn895 · 2020-07-29T20:18:12Z

@walterra I renamed the tab to Decision Plot, updated the height (small and compact if num features > 3). Unfortunately, I have confirmed with the Eui team that there's not a way right now for us to override the padding of that EuiContentPopover. Also there seems to be a bug with the overflow so I'm working with the Eui team to figure out the fix.

Example: 3 features vs 8 features

@Pete I have also

Added sorting for the classification results, although I think this is temporary as
Added gridlines
Added Prediction as x axis label
Changed tooltips to 3 significant figures
Corrected the prediction decision plot where it will start at the baseline and add the feature importance until it reaches the predicted value at the top. Although I'm not sure if it's due to the significant figures or what but I noticed some rows that didn't add up quite right.

Some of my jobs don't have a single feature_importance column, so I don't see the chart / JSON popover. Do we know why we don't get a single column for some jobs?

As for this I'm not too sure. I wasn't able to create this by setting num_features to 0 since it should hide the column automatically. Might need to look at what job config gives you that result.

pete · 2020-07-29T23:19:44Z

@qn895 Thank you, I think that is pretty cool to do but I don't have any strong opinions on this changeset, as I am completely unfamiliar with Kibana.

peteharverson · 2020-07-30T14:52:27Z

Looking at my job configs which give me two empty feature_importance columns in the data grid, I think it only happens when I have num_top_feature_importance_values=0.

I don't know if we want to / can hide those columns from the data grid column picker if num_top_feature_importance_values=0?

# Please enter a commit message to explain why this merge is necessary, # especially if it merges an updated upstream into a topic branch. # # Lines starting with '#' will be ignored, and an empty message aborts # the commit.

# Conflicts: # x-pack/plugins/ml/server/routes/data_frame_analytics.ts

peteharverson · 2020-09-04T17:03:26Z

This is looking good! Just wondered if it's possible to control the formatting on the x-axis and tooltip value depending on magnitude of the values, so for example, we'd display 1000 rather than 1.00e+3 here:

Update: Tested after edits in 5fd5ff4 and formatting looks good.

stevedodson · 2020-09-08T12:53:36Z

@peteharverson - reviewed this today with you and after going through some examples it looks good. My only concern is that the docs (linked to from the popup) have a clear concrete example of the chart with explanation.

An idea is that a specific prediction like AvgTicketPrice and show how the features are summed with the average to make the prediction + a similar concrete example for classification.

...gins/ml/public/application/components/data_grid/feature_importance/decision_path_popover.tsx

…sults fields

qn895 · 2020-09-08T14:20:00Z

This is looking good! Just wondered if it's possible to control the formatting on the x-axis and tooltip value depending on magnitude of the values, so for example, we'd display 1000 rather than 1.00e+3 here:

Updated here 5fd5ff4

We have DEFAULT_RESULTS_FIELD for this in plugins/ml/public/application/data_frame_analytics/common/constants.ts

Thanks @walterra! I have moved this DEFAULT_RESULTS_FIELD to x-pack/plugins/ml/common/constants/data_frame_analytics.ts so both the application and the server can share this constant here a93e740 and here 5fd5ff4

peteharverson

Tested latest edits and LGTM!

walterra · 2020-09-09T12:19:37Z

Latest code LGTM!

I noticed how the code is structured causes the ML page load bundle to grow in size because of the changes. My suspicion this is happening because part of the data grid code that's shared with the transforms plugin grew because of the decision plot code (even if the decision plot itself isn't used by the transform plugin).

I think this is something worth investigating in a follow up so I created an issue for it here #77041

qn895 · 2020-09-09T14:43:20Z

@elasticmachine merge upstream

kibanamachine · 2020-09-09T16:37:56Z

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continuous-integration/kibana-ci/pull-request
Commit: b857ffe

Build metrics

@kbn/optimizer bundle module count

id	value	diff	baseline
ml	1395	+9	1386

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id	value	diff	baseline
ml	8.0MB	-230.3KB	8.2MB

page load bundle size

id	value	diff	baseline
ml	847.8KB	⚠️ +263.4KB	584.4KB

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💚 Build #73126 succeeded 5fd5ff4
💚 Build #72653 succeeded 76488b6
💚 Build #72304 succeeded 09495e3
💔 Build #72281 failed a954cc6
💚 Build #70431 succeeded a71e190

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@elasticmachine merge upstream

…3561) Co-authored-by: Elastic Machine <[email protected]>

) (#77082) Co-authored-by: Elastic Machine <[email protected]> Co-authored-by: Elastic Machine <[email protected]>

* master: (25 commits) [bugfix] Replace panel flyout opens 2 flyouts (elastic#76931) clean up test (elastic#76887) [Enterprise Search] Update shared API request handler (elastic#77112) [Maps] convert ESAggSource to TS (elastic#76999) Add plugin status API - take 2 (elastic#76732) Adds lens as a readable saved object for read-only dashboard users (elastic#77067) Skip checking for the reserved realm (elastic#76687) Reporting/diagnostics (elastic#74314) Reporting/Test: unskip non-screenshot tests (elastic#77088) Move metrics to setup and add cgroup metrics (elastic#76730) [Enterprise Search] Add Overview landing page/plugin (elastic#76734) First pass. Change TS type. Update OpenAPI (elastic#76434) [CI] Balance xpack ci groups a bit (elastic#77068) [Security_solution][Detections] Refactor signal ancestry to allow multiple parents (elastic#76531) [Maps] convert MetricsEditor to TS (elastic#76727) IndexMigrator: fix non blocking migration wrapper promise rejection (elastic#77018) [Enterprise Search] Update config data endpoint to v2 (elastic#76970) [ML] Add decision path charts to exploration results table (elastic#73561) Bump eventemitter3 from 4.0.0 to 4.0.7 (elastic#77016) [Ingest Pipelines] Add descriptions for ingest processors K-S (elastic#76981) ...

* master: (41 commits) [bugfix] Replace panel flyout opens 2 flyouts (elastic#76931) clean up test (elastic#76887) [Enterprise Search] Update shared API request handler (elastic#77112) [Maps] convert ESAggSource to TS (elastic#76999) Add plugin status API - take 2 (elastic#76732) Adds lens as a readable saved object for read-only dashboard users (elastic#77067) Skip checking for the reserved realm (elastic#76687) Reporting/diagnostics (elastic#74314) Reporting/Test: unskip non-screenshot tests (elastic#77088) Move metrics to setup and add cgroup metrics (elastic#76730) [Enterprise Search] Add Overview landing page/plugin (elastic#76734) First pass. Change TS type. Update OpenAPI (elastic#76434) [CI] Balance xpack ci groups a bit (elastic#77068) [Security_solution][Detections] Refactor signal ancestry to allow multiple parents (elastic#76531) [Maps] convert MetricsEditor to TS (elastic#76727) IndexMigrator: fix non blocking migration wrapper promise rejection (elastic#77018) [Enterprise Search] Update config data endpoint to v2 (elastic#76970) [ML] Add decision path charts to exploration results table (elastic#73561) Bump eventemitter3 from 4.0.0 to 4.0.7 (elastic#77016) [Ingest Pipelines] Add descriptions for ingest processors K-S (elastic#76981) ...

* master: (38 commits) Reporting/Test: unskip non-screenshot tests (elastic#77088) Move metrics to setup and add cgroup metrics (elastic#76730) [Enterprise Search] Add Overview landing page/plugin (elastic#76734) First pass. Change TS type. Update OpenAPI (elastic#76434) [CI] Balance xpack ci groups a bit (elastic#77068) [Security_solution][Detections] Refactor signal ancestry to allow multiple parents (elastic#76531) [Maps] convert MetricsEditor to TS (elastic#76727) IndexMigrator: fix non blocking migration wrapper promise rejection (elastic#77018) [Enterprise Search] Update config data endpoint to v2 (elastic#76970) [ML] Add decision path charts to exploration results table (elastic#73561) Bump eventemitter3 from 4.0.0 to 4.0.7 (elastic#77016) [Ingest Pipelines] Add descriptions for ingest processors K-S (elastic#76981) [Metrics UI] Replace Snapshot API with Metrics API (elastic#76253) legacy utils cleanup (elastic#76608) [ML] Account for "properties" layer in find_file_structure mappings (elastic#77035) fixed typo Upgrade to Kea 2.2 (elastic#77047) a11y tests on spaces home page including feature control (elastic#76515) [ML] Transforms list: persist pagination through refresh interval (elastic#76786) [ML] Replace all use of date_histogram interval with fixed_interval (elastic#76876) ...

qn895 added 4 commits July 28, 2020 15:48

[ML] Add decision path charts

62e8918

[ML] Remove baseline div

031415f

[ML] Move baseline logic to exploration results table

40ef5e6

[ML] Fix type issues

7e47db9

qn895 added release_note:enhancement :ml v8.0.0 Feature:Data Frame Analytics ML data frame analytics features v7.10.0 labels Jul 28, 2020

qn895 requested review from walterra, alvarezmelissa87 and peteharverson July 28, 2020 21:57

qn895 self-assigned this Jul 28, 2020

qn895 added 5 commits July 29, 2020 10:36

[ML] Improvements to data viz charts

e8d0b41

- Add grid lines - Adjust sorting for classification from biggest at the top to smallest at the bottom - Change chart to using cumulative values

[ML] Add info text

5ad6690

[ML] Change size to pass as Chart props

ea12a63

[ML] Change to 3 sigfig instead of decimals

49a541c

[ML] Fix i18n issue

52964e5

qn895 added 4 commits August 10, 2020 15:27

[ML] Decision path popover improvement + importance summary

8b1e8c8

[ML] Change title to fit summary

19a1aae

qn895 added 6 commits August 25, 2020 22:48

[ML] Update grid and header

a71e190

Merge remote-tracking branch 'upstream/master' into feature-importance

9f435f6

# Conflicts: # x-pack/plugins/ml/server/routes/data_frame_analytics.ts

[ML] Update to new client & more strict conversion

a954cc6

[ML] Fix type

09495e3

[ML] Update tolerance to check for abs difference

1345cf2

Merge remote-tracking branch 'upstream/master' into feature-importance

76488b6

qn895 added 2 commits September 8, 2020 07:57

[ML] Change to DEFAULT_RESULTS_FIELD

a93e740

Merge remote-tracking branch 'upstream/master' into feature-importance

004518b

peteharverson reviewed Sep 8, 2020

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[ML] Update doc link, tick formatter, and baseline api for generic re…

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…sults fields

peteharverson approved these changes Sep 8, 2020

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walterra mentioned this pull request Sep 9, 2020

[ML] Improve bundles sizes related to shared code ml/transform #77041

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walterra approved these changes Sep 9, 2020

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Merge branch 'master' into feature-importance

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qn895 merged commit 619108c into elastic:master Sep 9, 2020

qn895 deleted the feature-importance branch September 9, 2020 16:41

qn895 mentioned this pull request Sep 9, 2020

[7.x] [ML] Add decision path charts to exploration results table (#73561) #77082

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qn895 added a commit to qn895/kibana that referenced this pull request Sep 9, 2020

[ML] Add decision path charts to exploration results table (elastic#7…

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…3561) Co-authored-by: Elastic Machine <[email protected]>

qn895 added a commit that referenced this pull request Sep 9, 2020

[7.x] [ML] Add decision path charts to exploration results table (#73561

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) (#77082) Co-authored-by: Elastic Machine <[email protected]> Co-authored-by: Elastic Machine <[email protected]>

lcawl mentioned this pull request Sep 10, 2020

[DOCS] Add feature importance to classification example elastic/stack-docs#1359

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lcawl mentioned this pull request Sep 11, 2020

[DOCS] Adds feature importance regression example elastic/stack-docs#1360

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[ML] Add decision path charts to exploration results table #73561

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