Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Linear regression subpackage added to linear dynamical systems #8

Merged
merged 15 commits into from
May 22, 2024
Merged

Linear regression subpackage added to linear dynamical systems #8

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
15 commits
Select commit Hold shift + click to select a range
936b229
Updated main.py and added LR sub package
ncguilbeault Mar 8, 2024
923b8e6
Merge remote-tracking branch 'upstream/main' into linear-regression
ncguilbeault Mar 8, 2024
2073562
Merge remote-tracking branch 'upstream/main' into linear-regression
ncguilbeault Mar 11, 2024
7310c1c
Added heatmap visualizers and linear regression model
ncguilbeault Mar 12, 2024
8b10292
Added linear regression nodes and workflows
ncguilbeault Mar 22, 2024
5933895
Added lds linear regression to readme
ncguilbeault Mar 25, 2024
0e72f52
Updated name of external property in workflow
ncguilbeault Apr 5, 2024
3b005d9
Updated package version number to new minor release
ncguilbeault May 20, 2024
7b46664
Added new documentation and comments
ncguilbeault May 20, 2024
eb31906
Updated package version
ncguilbeault May 20, 2024
f689496
Changed ColorPalettes to ColorPalette
ncguilbeault May 20, 2024
24a9829
Updated documentation and minor code refactoring
ncguilbeault May 20, 2024
2b15f0f
Updated descriptions and replaced tabs with spaces
ncguilbeault May 20, 2024
5a380ad
Converted tabs to spaces
ncguilbeault May 20, 2024
b0508a1
Minor code refactoring
ncguilbeault May 20, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@ The Bonsai.ML project is a collection of packages with reactive infrastructure f
* Bonsai.ML - provides core functionality across all Bonsai.ML packages.
* Bonsai.ML.LinearDynamicalSystems - package for performing inference of linear dynamical systems. Interfaces with the [lds_python](https://github.com/joacorapela/lds_python) package.
- *Bonsai.ML.LinearDynamicalSystems.Kinematics* - subpackage included in the LinearDynamicalSystems package which supports using the Kalman Filter to infer kinematic data.
- *Bonsai.ML.LinearDynamicalSystems.LinearRegression* - subpackage included in the LinearDynamicalSystems package which supports using the Kalman Filter to perform Bayesian linear regression.
* Bonsai.ML.Visualizers - provides a set of visualizers for dynamic graphing/plotting.

> [!NOTE]
Expand Down
2 changes: 1 addition & 1 deletion src/Bonsai.ML.LinearDynamicalSystems/Bonsai.ML.LinearDynamicalSystems.csproj
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
<Description>A Bonsai package for implementing the Kalman Filter using python.</Description>
<PackageTags>Bonsai Rx ML KalmanFilter LinearDynamicalSystems</PackageTags>
<TargetFrameworks>net472;netstandard2.0</TargetFrameworks>
<Version>0.1.0</Version>
<Version>0.2.0</Version>
</PropertyGroup>
<ItemGroup>
<PackageReference Include="Bonsai.Core" Version="2.8.1" />
Expand Down
112 changes: 112 additions & 0 deletions src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/CreateKFModel.bonsai
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,112 @@
<?xml version="1.0" encoding="utf-8"?>
<WorkflowBuilder Version="2.8.1"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:p1="clr-namespace:Bonsai.ML.LinearDynamicalSystems.LinearRegression;assembly=Bonsai.ML.LinearDynamicalSystems"
xmlns:p2="clr-namespace:Bonsai.ML.LinearDynamicalSystems;assembly=Bonsai.ML.LinearDynamicalSystems"
xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python"
xmlns="https://bonsai-rx.org/2018/workflow">
<Workflow>
<Nodes>
<Expression xsi:type="WorkflowInput">
<Name>Source1</Name>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="LikelihoodPrecisionCoefficient" Category="Parameters" />
<Property Name="PriorPrecisionCoefficient" Category="Parameters" />
<Property Name="NumFeatures" Category="Parameters" />
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="X" Category="ModelState" />
<Property Name="P" Category="ModelState" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p1:KFModelParameters">
<p1:LikelihoodPrecisionCoefficient>25</p1:LikelihoodPrecisionCoefficient>
<p1:PriorPrecisionCoefficient>2</p1:PriorPrecisionCoefficient>
<p1:NumFeatures>2</p1:NumFeatures>
</Combinator>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" Category="ModelReference" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p2:CreateModelReference">
<p2:Name>model</p2:Name>
</Combinator>
</Expression>
<Expression xsi:type="rx:BehaviorSubject">
<Name>model</Name>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>Name</Selector>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:Zip" />
</Expression>
<Expression xsi:type="rx:Sink">
<Name>InitModel</Name>
<Workflow>
<Nodes>
<Expression xsi:type="WorkflowInput">
<Name>Source1</Name>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="py:ObserveOnGIL" />
</Expression>
<Expression xsi:type="Format">
<Format>{0} = KalmanFilterLinearRegression({1})</Format>
<Selector>it.Item2, it.Item1</Selector>
</Expression>
<Expression xsi:type="InputMapping">
<PropertyMappings>
<Property Name="Script" Selector="it" />
</PropertyMappings>
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>LDSModule</Name>
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="Module" />
</PropertyMappings>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="py:Exec">
<py:Script>model = KalmanFilterLinearRegression(likelihood_precision_coef=25, prior_precision_coef=2, n_features=2, x=None, P=None)</py:Script>
</Combinator>
</Expression>
<Expression xsi:type="WorkflowOutput" />
</Nodes>
<Edges>
<Edge From="0" To="1" Label="Source1" />
<Edge From="1" To="2" Label="Source1" />
<Edge From="2" To="3" Label="Source1" />
<Edge From="3" To="6" Label="Source1" />
<Edge From="4" To="5" Label="Source1" />
<Edge From="5" To="6" Label="Source2" />
<Edge From="6" To="7" Label="Source1" />
</Edges>
</Workflow>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>Item1</Selector>
</Expression>
<Expression xsi:type="WorkflowOutput" />
</Nodes>
<Edges>
<Edge From="0" To="3" Label="Source1" />
<Edge From="1" To="3" Label="Source2" />
<Edge From="2" To="3" Label="Source3" />
<Edge From="3" To="8" Label="Source1" />
<Edge From="4" To="5" Label="Source1" />
<Edge From="4" To="6" Label="Source2" />
<Edge From="5" To="6" Label="Source1" />
<Edge From="6" To="7" Label="Source1" />
<Edge From="7" To="8" Label="Source2" />
<Edge From="8" To="9" Label="Source1" />
<Edge From="9" To="10" Label="Source1" />
<Edge From="10" To="11" Label="Source1" />
</Edges>
</Workflow>
</WorkflowBuilder>
136 changes: 136 additions & 0 deletions src/Bonsai.ML.LinearDynamicalSystems/LinearRegression/CreateMultivariatePDF.bonsai
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,136 @@
<?xml version="1.0" encoding="utf-8"?>
<WorkflowBuilder Version="2.8.1"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python"
xmlns:p1="clr-namespace:Bonsai.ML.LinearDynamicalSystems;assembly=Bonsai.ML.LinearDynamicalSystems"
xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
xmlns:p2="clr-namespace:Bonsai.ML.LinearDynamicalSystems.LinearRegression;assembly=Bonsai.ML.LinearDynamicalSystems"
xmlns="https://bonsai-rx.org/2018/workflow">
<Workflow>
<Nodes>
<Expression xsi:type="WorkflowInput">
<Name>Source1</Name>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="py:ObserveOnGIL" />
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="Name" DisplayName="Name" Category="ModelReference" />
</Expression>
<Expression xsi:type="SubscribeSubject" TypeArguments="p1:ModelReference">
<Name>model</Name>
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>Name</Selector>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:WithLatestFrom" />
</Expression>
<Expression xsi:type="MemberSelector">
<Selector>Item2</Selector>
</Expression>
<Expression xsi:type="ExternalizedMapping">
<Property Name="X0" Category="GridParameters" />
<Property Name="X1" Category="GridParameters" />
<Property Name="XSteps" Category="GridParameters" />
<Property Name="Y0" Category="GridParameters" />
<Property Name="Y1" Category="GridParameters" />
<Property Name="YSteps" Category="GridParameters" />
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p2:GridParameters">
<p2:X0>-1</p2:X0>
<p2:X1>1</p2:X1>
<p2:XSteps>100</p2:XSteps>
<p2:Y0>-1</p2:Y0>
<p2:Y1>1</p2:Y1>
<p2:YSteps>100</p2:YSteps>
</Combinator>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="rx:WithLatestFrom" />
</Expression>
<Expression xsi:type="rx:Sink">
<Name>PDF</Name>
<Workflow>
<Nodes>
<Expression xsi:type="WorkflowInput">
<Name>Source1</Name>
</Expression>
<Expression xsi:type="Format">
<Format>{0}.pdf({1})</Format>
<Selector>it.Item1, it.Item2</Selector>
</Expression>
<Expression xsi:type="InputMapping">
<PropertyMappings>
<Property Name="Script" Selector="it" />
</PropertyMappings>
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>LDSModule</Name>
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="Module" />
</PropertyMappings>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="py:Exec">
<py:Script>model.pdf(x0=-1, x1=1, xsteps=100, y0=-1, y1=1, ysteps=100)</py:Script>
</Combinator>
</Expression>
<Expression xsi:type="WorkflowOutput" />
</Nodes>
<Edges>
<Edge From="0" To="1" Label="Source1" />
<Edge From="1" To="2" Label="Source1" />
<Edge From="2" To="5" Label="Source1" />
<Edge From="3" To="4" Label="Source1" />
<Edge From="4" To="5" Label="Source2" />
<Edge From="5" To="6" Label="Source1" />
</Edges>
</Workflow>
</Expression>
<Expression xsi:type="InputMapping">
<PropertyMappings>
<Property Name="VariableName" Selector="it.Item1" />
</PropertyMappings>
</Expression>
<Expression xsi:type="SubscribeSubject">
<Name>LDSModule</Name>
</Expression>
<Expression xsi:type="PropertyMapping">
<PropertyMappings>
<Property Name="Module" />
</PropertyMappings>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="py:Get">
<py:VariableName>model</py:VariableName>
</Combinator>
</Expression>
<Expression xsi:type="Combinator">
<Combinator xsi:type="p2:MultivariatePDF" />
</Expression>
<Expression xsi:type="WorkflowOutput" />
</Nodes>
<Edges>
<Edge From="0" To="1" Label="Source1" />
<Edge From="1" To="5" Label="Source1" />
<Edge From="2" To="3" Label="Source1" />
<Edge From="3" To="4" Label="Source1" />
<Edge From="4" To="5" Label="Source2" />
<Edge From="5" To="6" Label="Source1" />
<Edge From="6" To="9" Label="Source1" />
<Edge From="7" To="8" Label="Source1" />
<Edge From="8" To="9" Label="Source2" />
<Edge From="9" To="10" Label="Source1" />
<Edge From="10" To="11" Label="Source1" />
<Edge From="11" To="14" Label="Source1" />
<Edge From="12" To="13" Label="Source1" />
<Edge From="13" To="14" Label="Source2" />
<Edge From="14" To="15" Label="Source1" />
<Edge From="15" To="16" Label="Source1" />
</Edges>
</Workflow>
</WorkflowBuilder>
Loading