Class: Optimization

Configuration for parameter optimization. Inherits single-stage fields from OptimizationStage. For multi-stage workflows, use ‘stages’ (ignores inherited single-stage fields). Loss equation references observations directly by name.

URI: tvbo:class/Optimization

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

        
      Optimization : depends_on
        
          
    
        
        
        Optimization --> "0..1" Algorithm : depends_on
        click Algorithm href "./Algorithm.html"
    

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

        
      Optimization : execution
        
          
    
        
        
        Optimization --> "0..1" ExecutionConfig : execution
        click ExecutionConfig href "./ExecutionConfig.html"
    

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

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

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

        
      Optimization : integration
        
          
    
        
        
        Optimization --> "0..1" Integrator : integration
        click Integrator href "./Integrator.html"
    

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

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

        
      Optimization : loss
        
          
    
        
        
        Optimization --> "0..1" FunctionCall : loss
        click FunctionCall href "./FunctionCall.html"
    

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

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

        
      Optimization : stages
        
          
    
        
        
        Optimization --> "*" OptimizationStage : stages
        click OptimizationStage href "./OptimizationStage.html"
    

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

        
      

Inheritance

• OptimizationStage
  • Optimization

Slots

Name	Cardinality and Range	Description	Inheritance
execution	0..1 ExecutionConfig	Per-optimization execution configuration (overrides experiment-level defaults…	direct
integration	0..1 Integrator	Integration settings for optimization simulations (overrides experiment defau…	direct
loss	0..1 FunctionCall	Loss function call	direct
stages	* OptimizationStage	Ordered list of optimization stages	direct
depends_on	0..1 Algorithm	Algorithm to use as starting point for optimization	direct
name	1 xsd:string		OptimizationStage
label	0..1 xsd:string		OptimizationStage
description	0..1 xsd:string		OptimizationStage
free_parameters	* Parameter	Parameters to optimize in this stage	OptimizationStage
algorithm	0..1 xsd:string	Optimizer for this stage: ‘adam’, ‘adamw’, ‘sgd’, etc	OptimizationStage
learning_rate	0..1 xsd:float		OptimizationStage
max_iterations	0..1 xsd:integer		OptimizationStage
hyperparameters	* Parameter	Stage-specific hyperparameters (e	OptimizationStage
freeze_parameters	* Parameter	Parameters from previous stages to freeze (keep at optimized value but not up…	OptimizationStage
warmup_from	0..1 OptimizationStage	Previous stage to initialize from	OptimizationStage

Usages

used by	used in	type	used
SimulationExperiment	optimization	range	Optimization

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/tvbo

Mappings

Mapping Type	Mapped Value
self	tvbo:Optimization
native	tvbo:Optimization

LinkML Source

Direct

name: Optimization
description: Configuration for parameter optimization. Inherits single-stage fields
  from OptimizationStage. For multi-stage workflows, use 'stages' (ignores inherited
  single-stage fields). Loss equation references observations directly by name.
from_schema: https://w3id.org/tvbo
is_a: OptimizationStage
attributes:
  execution:
    name: execution
    description: Per-optimization execution configuration (overrides experiment-level
      defaults). Useful for setting random_seed, precision, or hardware for optimization
      phase.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Optimization
    - Exploration
    - Algorithm
    - SimulationExperiment
    range: ExecutionConfig
    inlined: true
  integration:
    name: integration
    description: Integration settings for optimization simulations (overrides experiment
      defaults). If specified, creates a fresh model_fn and state with prepare() before
      optimization. Can specify different duration, step_size, method than the experiment.
      If not specified, uses experiment-level integration settings.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Optimization
    - SimulationExperiment
    range: Integrator
    inlined: true
  loss:
    name: loss
    description: 'Loss function call. Uses FunctionCall to either: 1. Reference existing
      function: function: rmse 2. Inline callable: callable: {module: ..., name: ...}
      Arguments specify inputs (simulated_fc, empirical_fc, etc.)'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Optimization
    range: FunctionCall
    inlined: true
  stages:
    name: stages
    description: Ordered list of optimization stages. Stages run sequentially. Stage
      n+1 starts from optimized values of stage n. When defined, inherited single-stage
      fields are ignored.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Optimization
    range: OptimizationStage
    multivalued: true
    inlined: true
    inlined_as_list: true
  depends_on:
    name: depends_on
    description: Algorithm to use as starting point for optimization. If specified,
      optimization starts from algorithm's result state. If not specified, optimization
      starts from initial simulation state.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Optimization
    - Algorithm
    range: Algorithm
    inlined: false

Induced

name: Optimization
description: Configuration for parameter optimization. Inherits single-stage fields
  from OptimizationStage. For multi-stage workflows, use 'stages' (ignores inherited
  single-stage fields). Loss equation references observations directly by name.
from_schema: https://w3id.org/tvbo
is_a: OptimizationStage
attributes:
  execution:
    name: execution
    description: Per-optimization execution configuration (overrides experiment-level
      defaults). Useful for setting random_seed, precision, or hardware for optimization
      phase.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: execution
    owner: Optimization
    domain_of:
    - Optimization
    - Exploration
    - Algorithm
    - SimulationExperiment
    range: ExecutionConfig
    inlined: true
  integration:
    name: integration
    description: Integration settings for optimization simulations (overrides experiment
      defaults). If specified, creates a fresh model_fn and state with prepare() before
      optimization. Can specify different duration, step_size, method than the experiment.
      If not specified, uses experiment-level integration settings.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: integration
    owner: Optimization
    domain_of:
    - Optimization
    - SimulationExperiment
    range: Integrator
    inlined: true
  loss:
    name: loss
    description: 'Loss function call. Uses FunctionCall to either: 1. Reference existing
      function: function: rmse 2. Inline callable: callable: {module: ..., name: ...}
      Arguments specify inputs (simulated_fc, empirical_fc, etc.)'
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: loss
    owner: Optimization
    domain_of:
    - Optimization
    range: FunctionCall
    inlined: true
  stages:
    name: stages
    description: Ordered list of optimization stages. Stages run sequentially. Stage
      n+1 starts from optimized values of stage n. When defined, inherited single-stage
      fields are ignored.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: stages
    owner: Optimization
    domain_of:
    - Optimization
    range: OptimizationStage
    multivalued: true
    inlined: true
    inlined_as_list: true
  depends_on:
    name: depends_on
    description: Algorithm to use as starting point for optimization. If specified,
      optimization starts from algorithm's result state. If not specified, optimization
      starts from initial simulation state.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    alias: depends_on
    owner: Optimization
    domain_of:
    - Optimization
    - Algorithm
    range: Algorithm
    inlined: false
  name:
    name: name
    from_schema: https://w3id.org/tvbo
    rank: 1000
    key: true
    alias: name
    owner: Optimization
    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: Optimization
    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: Optimization
    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
  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: Optimization
    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: Optimization
    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: Optimization
    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: Optimization
    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: Optimization
    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: Optimization
    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: Optimization
    domain_of:
    - OptimizationStage
    range: OptimizationStage
    inlined: false