# Class: OptimizationStage 


_A single stage in a multi-stage optimization workflow. Stages run sequentially, with each stage potentially using different parameters, shapes, learning rates, and algorithms._



<div data-search-exclude markdown="1">



URI: [tvbo:OptimizationStage](https://w3id.org/tvbo/OptimizationStage)





```{mermaid}
 classDiagram
    class OptimizationStage
    click OptimizationStage href "./OptimizationStage.html"
      OptimizationStage <|-- Optimization
        click Optimization href "./Optimization.html"
      
      OptimizationStage : algorithm
        
          
    
        
        
        OptimizationStage --> "0..1" String : algorithm
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      OptimizationStage : description
        
          
    
        
        
        OptimizationStage --> "0..1" String : description
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      OptimizationStage : free_parameters
        
          
    
        
        
        OptimizationStage --> "*" FreeParameter : free_parameters
        click FreeParameter href "./FreeParameter.html"
    

        
      OptimizationStage : freeze_parameters
        
          
    
        
        
        OptimizationStage --> "*" Parameter : freeze_parameters
        click Parameter href "./Parameter.html"
    

        
      OptimizationStage : hyperparameters
        
          
    
        
        
        OptimizationStage --> "*" Parameter : hyperparameters
        click Parameter href "./Parameter.html"
    

        
      OptimizationStage : label
        
          
    
        
        
        OptimizationStage --> "0..1" String : label
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      OptimizationStage : learning_rate
        
          
    
        
        
        OptimizationStage --> "0..1" Float : learning_rate
        click Float href "../http://www.w3.org/2001/XMLSchema#float.html"
    

        
      OptimizationStage : max_iterations
        
          
    
        
        
        OptimizationStage --> "0..1" Integer : max_iterations
        click Integer href "../http://www.w3.org/2001/XMLSchema#integer.html"
    

        
      OptimizationStage : name
        
          
    
        
        
        OptimizationStage --> "1" String : name
        click String href "../http://www.w3.org/2001/XMLSchema#string.html"
    

        
      OptimizationStage : warmup_from
        
          
    
        
        
        OptimizationStage --> "0..1" OptimizationStage : warmup_from
        click OptimizationStage href "./OptimizationStage.html"
    

        
      
```





## Inheritance
* **OptimizationStage**
    * [Optimization](../classes/Optimization.qmd)


## Class Properties

| Property | Value |
| --- | --- |
| Class URI | [tvbo:OptimizationStage](https://w3id.org/tvbo/OptimizationStage) |


## Slots

| Name | Cardinality and Range | Description | Inheritance |
| ---  | --- | --- | --- |
| [name](../slots/name.qmd) | 1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | Globally unique identifier for the entity | direct |
| [label](../slots/label.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) |  | direct |
| [description](../slots/description.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) |  | direct |
| [free_parameters](../slots/free_parameters.qmd) | * <br/> [FreeParameter](../classes/FreeParameter.qmd) | Parameters to optimize in this stage | direct |
| [algorithm](../slots/algorithm.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | Optimizer for this stage: 'adam', 'adamw', 'sgd', etc | direct |
| [learning_rate](../slots/learning_rate.qmd) | 0..1 <br/> [xsd:float](http://www.w3.org/2001/XMLSchema#float) |  | direct |
| [max_iterations](../slots/max_iterations.qmd) | 0..1 <br/> [xsd:integer](http://www.w3.org/2001/XMLSchema#integer) |  | direct |
| [hyperparameters](../slots/hyperparameters.qmd) | * <br/> [Parameter](../classes/Parameter.qmd) | Stage-specific hyperparameters (e | direct |
| [freeze_parameters](../slots/freeze_parameters.qmd) | * <br/> [Parameter](../classes/Parameter.qmd) | Parameters from previous stages to freeze (keep at optimized value but not up... | direct |
| [warmup_from](../slots/warmup_from.qmd) | 0..1 <br/> [OptimizationStage](../classes/OptimizationStage.qmd) | Previous stage to initialize from | direct |





## Usages

| used by | used in | type | used |
| ---  | --- | --- | --- |
| [OptimizationStage](../classes/OptimizationStage.qmd) | [warmup_from](../slots/warmup_from.qmd) | range | [OptimizationStage](../classes/OptimizationStage.qmd) |
| [Optimization](../classes/Optimization.qmd) | [stages](../slots/stages.qmd) | range | [OptimizationStage](../classes/OptimizationStage.qmd) |
| [Optimization](../classes/Optimization.qmd) | [warmup_from](../slots/warmup_from.qmd) | range | [OptimizationStage](../classes/OptimizationStage.qmd) |












## Identifier and Mapping Information





### Schema Source


* from schema: https://w3id.org/tvbo




## Mappings

| Mapping Type | Mapped Value |
| ---  | ---  |
| self | tvbo:OptimizationStage |
| native | tvbo:OptimizationStage |






## LinkML Source

<!-- TODO: investigate https://stackoverflow.com/questions/37606292/how-to-create-tabbed-code-blocks-in-mkdocs-or-sphinx -->

### Direct

<details>
```yaml
name: OptimizationStage
description: A single stage in a multi-stage optimization workflow. Stages run sequentially,
  with each stage potentially using different parameters, shapes, learning rates,
  and algorithms.
from_schema: https://w3id.org/tvbo
slots:
- name
- label
- description
attributes:
  free_parameters:
    name: free_parameters
    description: Parameters to optimize in this stage. Each entry is a FreeParameter
      that references an existing Parameter by dotted scope (e.g. "ReducedWongWang.w"
      or "FastLinearCoupling.G") and supplies optimization-specific metadata (heterogeneous,
      shape, bounds). No new Parameter is created here.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - OptimizationStage
    - Continuation
    range: FreeParameter
    multivalued: true
    inlined: true
    inlined_as_list: true
  algorithm:
    name: algorithm
    description: 'Optimizer for this stage: ''adam'', ''adamw'', ''sgd'', etc.'
    from_schema: https://w3id.org/tvbo
    ifabsent: string(adam)
    domain_of:
    - Digest
    - OptimizationStage
    - AlgorithmInclude
    - Continuation
    range: string
  learning_rate:
    name: learning_rate
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: float(0.001)
    domain_of:
    - OptimizationStage
    - Algorithm
    range: float
  max_iterations:
    name: max_iterations
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: integer(100)
    domain_of:
    - OptimizationStage
    range: integer
  hyperparameters:
    name: hyperparameters
    description: Stage-specific hyperparameters (e.g., b2=0.9999 for adam)
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - OptimizationStage
    - Algorithm
    range: Parameter
    multivalued: true
    inlined: true
    inlined_as_list: true
  freeze_parameters:
    name: freeze_parameters
    description: Parameters from previous stages to freeze (keep at optimized value
      but not update)
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - OptimizationStage
    range: Parameter
    multivalued: true
    inlined: false
  warmup_from:
    name: warmup_from
    description: Previous stage to initialize from. Final values from that stage become
      initial values for this stage.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - OptimizationStage
    range: OptimizationStage
    inlined: false
class_uri: tvbo:OptimizationStage

```
</details>

### Induced

<details>
```yaml
name: OptimizationStage
description: A single stage in a multi-stage optimization workflow. Stages run sequentially,
  with each stage potentially using different parameters, shapes, learning rates,
  and algorithms.
from_schema: https://w3id.org/tvbo
attributes:
  free_parameters:
    name: free_parameters
    description: Parameters to optimize in this stage. Each entry is a FreeParameter
      that references an existing Parameter by dotted scope (e.g. "ReducedWongWang.w"
      or "FastLinearCoupling.G") and supplies optimization-specific metadata (heterogeneous,
      shape, bounds). No new Parameter is created here.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: OptimizationStage
    domain_of:
    - OptimizationStage
    - Continuation
    range: FreeParameter
    multivalued: true
    inlined: true
    inlined_as_list: true
  algorithm:
    name: algorithm
    description: 'Optimizer for this stage: ''adam'', ''adamw'', ''sgd'', etc.'
    from_schema: https://w3id.org/tvbo
    ifabsent: string(adam)
    owner: OptimizationStage
    domain_of:
    - Digest
    - OptimizationStage
    - AlgorithmInclude
    - Continuation
    range: string
  learning_rate:
    name: learning_rate
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: float(0.001)
    owner: OptimizationStage
    domain_of:
    - OptimizationStage
    - Algorithm
    range: float
  max_iterations:
    name: max_iterations
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: integer(100)
    owner: OptimizationStage
    domain_of:
    - OptimizationStage
    range: integer
  hyperparameters:
    name: hyperparameters
    description: Stage-specific hyperparameters (e.g., b2=0.9999 for adam)
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: OptimizationStage
    domain_of:
    - OptimizationStage
    - Algorithm
    range: Parameter
    multivalued: true
    inlined: true
    inlined_as_list: true
  freeze_parameters:
    name: freeze_parameters
    description: Parameters from previous stages to freeze (keep at optimized value
      but not update)
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: OptimizationStage
    domain_of:
    - OptimizationStage
    range: Parameter
    multivalued: true
    inlined: false
  warmup_from:
    name: warmup_from
    description: Previous stage to initialize from. Final values from that stage become
      initial values for this stage.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: OptimizationStage
    domain_of:
    - OptimizationStage
    range: OptimizationStage
    inlined: false
  name:
    name: name
    description: Globally unique identifier for the entity.
    from_schema: https://w3id.org/tvbo/common
    slot_uri: schema:name
    identifier: true
    owner: OptimizationStage
    domain_of:
    - BrainAtlas
    - CommonCoordinateSpace
    - ParcellationEntity
    - StudyLayout
    - StudyTemplate
    - StudyDirectory
    - StudyFile
    - DBSProtocol
    - ClinicalScale
    - ClinicalScore
    - SoftwarePackage
    - SoftwareRequirement
    - SoftwareEnvironment
    - Figure
    - Event
    - Tractogram
    - ResultEntity
    - Activity
    - CachedArray
    - MeasureSpec
    - NamedArray
    - GraphGenerator
    - Binding
    - ProcedureStep
    - File
    - StateValue
    - Observation
    - Dynamics
    - StateVariable
    - Distribution
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - FunctionCall
    - Callable
    - DerivedParameter
    - DerivedVariable
    - DataSource
    - OptimizationStage
    - Exploration
    - Inference
    - Prior
    - Likelihood
    - UpdateRule
    - Algorithm
    - Option
    - BranchSwitch
    - Continuation
    - Coupling
    - EnvironmentVariable
    - SchedulerDirective
    - Reducer
    range: string
    required: true
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: rdfs:label
    owner: OptimizationStage
    domain_of:
    - ParcellationTerminology
    - Subject
    - Session
    - Dataset
    - Contact
    - SoftwareEnvironment
    - Figure
    - Panel
    - Inset
    - Layer
    - Colorbar
    - Rule
    - Equation
    - Stimulus
    - Event
    - Parcellation
    - Tractogram
    - Matrix
    - Phenotype
    - Network
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - Function
    - FunctionCall
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - ExplorationAxis
    - FreeParameter
    - Inference
    - AlgorithmStage
    - TuningObjective
    - Continuation
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - SimulationStudy
    - TimeSeries
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - DifferentialOperator
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    rank: 1000
    slot_uri: dcterms:description
    owner: OptimizationStage
    domain_of:
    - CommonCoordinateSpace
    - Dataset
    - StudyLayout
    - StudyTemplate
    - StudyDirectory
    - StudyFile
    - ClinicalScore
    - SoftwarePackage
    - SoftwareRequirement
    - SoftwareEnvironment
    - Figure
    - Panel
    - Equation
    - Stimulus
    - Event
    - Tractogram
    - Matrix
    - ResultEntity
    - Activity
    - Phenotype
    - MeasureSpec
    - NamedArray
    - Network
    - GraphGenerator
    - ProcedureStep
    - File
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - FunctionCall
    - Callable
    - DerivedParameter
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - ExplorationAxis
    - FreeParameter
    - Inference
    - Prior
    - Likelihood
    - UpdateRule
    - AlgorithmStage
    - TuningObjective
    - Algorithm
    - BranchSwitch
    - Continuation
    - Integrator
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - Study
    - ResultBinding
    - TimeSeries
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - BoundaryCondition
    - PDESolver
    - PDE
    - Reducer
    range: string
class_uri: tvbo:OptimizationStage

```
</details></div>