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.

URI: tvbo:class/OptimizationStage

 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 --> "*" Parameter : free_parameters
        click Parameter href "./Parameter.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

Slots

Name	Cardinality and Range	Description	Inheritance
name	1 xsd:string		direct
label	0..1 xsd:string		direct
description	0..1 xsd:string		direct
free_parameters	* Parameter	Parameters to optimize in this stage	direct
algorithm	0..1 xsd:string	Optimizer for this stage: ‘adam’, ‘adamw’, ‘sgd’, etc	direct
learning_rate	0..1 xsd:float		direct
max_iterations	0..1 xsd:integer		direct
hyperparameters	* Parameter	Stage-specific hyperparameters (e	direct
freeze_parameters	* Parameter	Parameters from previous stages to freeze (keep at optimized value but not up…	direct
warmup_from	0..1 OptimizationStage	Previous stage to initialize from	direct

Usages

used by	used in	type	used
OptimizationStage	warmup_from	range	OptimizationStage
Optimization	stages	range	OptimizationStage
Optimization	warmup_from	range	OptimizationStage

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

Direct

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. Use ''shape'' attribute to
      specify scalar vs regional. Example: {name: w, shape: "(n_nodes,)"} for heterogeneous.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - OptimizationStage
    range: Parameter
    multivalued: true
    inlined: false
  algorithm:
    name: algorithm
    description: 'Optimizer for this stage: ''adam'', ''adamw'', ''sgd'', etc.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(adam)
    domain_of:
    - OptimizationStage
    - AlgorithmInclude
    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

Induced

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. Use ''shape'' attribute to
      specify scalar vs regional. Example: {name: w, shape: "(n_nodes,)"} for heterogeneous.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: free_parameters
    owner: OptimizationStage
    domain_of:
    - OptimizationStage
    range: Parameter
    multivalued: true
    inlined: false
  algorithm:
    name: algorithm
    description: 'Optimizer for this stage: ''adam'', ''adamw'', ''sgd'', etc.'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(adam)
    alias: algorithm
    owner: OptimizationStage
    domain_of:
    - OptimizationStage
    - AlgorithmInclude
    range: string
  learning_rate:
    name: learning_rate
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: float(0.001)
    alias: learning_rate
    owner: OptimizationStage
    domain_of:
    - OptimizationStage
    - Algorithm
    range: float
  max_iterations:
    name: max_iterations
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: integer(100)
    alias: max_iterations
    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
    alias: hyperparameters
    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
    alias: freeze_parameters
    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
    alias: warmup_from
    owner: OptimizationStage
    domain_of:
    - OptimizationStage
    range: OptimizationStage
    inlined: false
  name:
    name: name
    from_schema: https://w3id.org/tvbo
    rank: 1000
    key: true
    alias: name
    owner: OptimizationStage
    domain_of:
    - BrainAtlas
    - CommonCoordinateSpace
    - ParcellationEntity
    - DBSProtocol
    - ClinicalScale
    - ClinicalScore
    - Tractogram
    - File
    - Observation
    - Dynamics
    - StateVariable
    - Distribution
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - Callable
    - DerivedParameter
    - DerivedVariable
    - DataSource
    - OptimizationStage
    - Exploration
    - UpdateRule
    - Algorithm
    - Coupling
    - SoftwareEnvironment
    - SoftwareRequirement
    - SoftwarePackage
    range: string
    required: true
  label:
    name: label
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: label
    owner: OptimizationStage
    domain_of:
    - ParcellationTerminology
    - Dataset
    - Contact
    - Equation
    - Stimulus
    - Parcellation
    - Tractogram
    - Matrix
    - Network
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - Function
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - TuningObjective
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - SimulationStudy
    - TimeSeries
    - SoftwareEnvironment
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - DifferentialOperator
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string
  description:
    name: description
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: description
    owner: OptimizationStage
    domain_of:
    - ClinicalScore
    - Equation
    - Stimulus
    - Tractogram
    - Matrix
    - Network
    - File
    - Node
    - Edge
    - Observation
    - Dynamics
    - StateVariable
    - Parameter
    - CouplingInput
    - Argument
    - Function
    - Callable
    - DerivedParameter
    - DerivedVariable
    - RandomStream
    - DataSource
    - OptimizationStage
    - Exploration
    - UpdateRule
    - TuningObjective
    - Algorithm
    - Integrator
    - Coupling
    - RegionMapping
    - SimulationExperiment
    - SimulationStudy
    - TimeSeries
    - SoftwareEnvironment
    - SoftwareRequirement
    - SoftwarePackage
    - NDArray
    - SpatialDomain
    - Mesh
    - SpatialField
    - FieldStateVariable
    - BoundaryCondition
    - PDESolver
    - PDE
    range: string