# Class: Inference 


_Bayesian inference of model parameters from an observation, via MCMC. A standalone, first-class concept (NOT an Optimization): it produces a POSTERIOR, not a point estimate, using priors + a likelihood + a sampler instead of a loss + optimizer. It runs the SAME differentiable forward model, wrapped in a probabilistic model (sample priors -> forward -> likelihood)._



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



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





```{mermaid}
 classDiagram
    class Inference
    click Inference href "./Inference.html"
      Inference : depends_on
        
          
    
        
        
        Inference --> "0..1" Algorithm : depends_on
        click Algorithm href "./Algorithm.html"
    

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

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

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

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

        
      Inference : likelihood
        
          
    
        
        
        Inference --> "1" Likelihood : likelihood
        click Likelihood href "./Likelihood.html"
    

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

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

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

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

        
      Inference : priors
        
          
    
        
        
        Inference --> "*" Prior : priors
        click Prior href "./Prior.html"
    

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

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

        
      
```




<!-- no inheritance hierarchy -->

## Class Properties

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


## 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 |
| [priors](../slots/priors.qmd) | * <br/> [Prior](../classes/Prior.qmd) | Priors over the inferred parameters, keyed by each parameter's dotted name (e | direct |
| [likelihood](../slots/likelihood.qmd) | 1 <br/> [Likelihood](../classes/Likelihood.qmd) | Observation model p(data | sim(theta)) | direct |
| [sampler](../slots/sampler.qmd) | 0..1 <br/> [xsd:string](http://www.w3.org/2001/XMLSchema#string) | MCMC sampler ('nuts') | direct |
| [num_samples](../slots/num_samples.qmd) | 0..1 <br/> [xsd:integer](http://www.w3.org/2001/XMLSchema#integer) | Posterior samples to draw | direct |
| [num_warmup](../slots/num_warmup.qmd) | 0..1 <br/> [xsd:integer](http://www.w3.org/2001/XMLSchema#integer) | Warmup/adaptation steps before sampling | direct |
| [num_chains](../slots/num_chains.qmd) | 0..1 <br/> [xsd:integer](http://www.w3.org/2001/XMLSchema#integer) | Independent MCMC chains | direct |
| [seed](../slots/seed.qmd) | 0..1 <br/> [xsd:integer](http://www.w3.org/2001/XMLSchema#integer) | PRNG seed for reproducible sampling | direct |
| [execution](../slots/execution.qmd) | 0..1 <br/> [ExecutionConfig](../classes/ExecutionConfig.qmd) | Per-inference execution config (overrides experiment defaults) | direct |
| [integration](../slots/integration.qmd) | 0..1 <br/> [Integrator](../classes/Integrator.qmd) | Forward-model integration settings (overrides experiment defaults) | direct |
| [depends_on](../slots/depends_on.qmd) | 0..1 <br/> [Algorithm](../classes/Algorithm.qmd) | Optional algorithm whose result state seeds the inference | direct |





## Usages

| used by | used in | type | used |
| ---  | --- | --- | --- |
| [SimulationExperiment](../classes/SimulationExperiment.qmd) | [inferences](../slots/inferences.qmd) | range | [Inference](../classes/Inference.qmd) |












## Identifier and Mapping Information





### Schema Source


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




## Mappings

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






## LinkML Source

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

### Direct

<details>
```yaml
name: Inference
description: 'Bayesian inference of model parameters from an observation, via MCMC.
  A standalone, first-class concept (NOT an Optimization): it produces a POSTERIOR,
  not a point estimate, using priors + a likelihood + a sampler instead of a loss
  + optimizer. It runs the SAME differentiable forward model, wrapped in a probabilistic
  model (sample priors -> forward -> likelihood).'
from_schema: https://w3id.org/tvbo
slots:
- name
- label
- description
attributes:
  priors:
    name: priors
    description: Priors over the inferred parameters, keyed by each parameter's dotted
      name (e.g. "Generic2dOscillator.eta" or "PulseInput.amplitude"). The KEYS are
      the inferred parameters — there is no separate free-parameter list.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Inference
    range: Prior
    multivalued: true
    inlined: true
  likelihood:
    name: likelihood
    description: Observation model p(data | sim(theta)).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    domain_of:
    - Inference
    range: Likelihood
    required: true
    inlined: true
  sampler:
    name: sampler
    description: MCMC sampler ('nuts'). Each backend maps its own way.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(nuts)
    domain_of:
    - Inference
    range: string
  num_samples:
    name: num_samples
    description: Posterior samples to draw.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: integer(1000)
    domain_of:
    - Inference
    range: integer
  num_warmup:
    name: num_warmup
    description: Warmup/adaptation steps before sampling.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: integer(1000)
    domain_of:
    - Inference
    range: integer
  num_chains:
    name: num_chains
    description: Independent MCMC chains.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: integer(1)
    domain_of:
    - Inference
    range: integer
  seed:
    name: seed
    description: PRNG seed for reproducible sampling.
    from_schema: https://w3id.org/tvbo
    ifabsent: integer(0)
    domain_of:
    - GraphGenerator
    - Distribution
    - Noise
    - Inference
    range: integer
  execution:
    name: execution
    description: Per-inference execution config (overrides experiment defaults).
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Analysis
    - Optimization
    - Exploration
    - Inference
    - Algorithm
    - Continuation
    - SimulationExperiment
    range: ExecutionConfig
    inlined: true
  integration:
    name: integration
    description: Forward-model integration settings (overrides experiment defaults).
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Network
    - Optimization
    - Inference
    - SimulationExperiment
    range: Integrator
    inlined: true
  depends_on:
    name: depends_on
    description: Optional algorithm whose result state seeds the inference.
    from_schema: https://w3id.org/tvbo
    domain_of:
    - Optimization
    - Inference
    - Algorithm
    range: Algorithm
    inlined: false
class_uri: tvbo:Inference

```
</details>

### Induced

<details>
```yaml
name: Inference
description: 'Bayesian inference of model parameters from an observation, via MCMC.
  A standalone, first-class concept (NOT an Optimization): it produces a POSTERIOR,
  not a point estimate, using priors + a likelihood + a sampler instead of a loss
  + optimizer. It runs the SAME differentiable forward model, wrapped in a probabilistic
  model (sample priors -> forward -> likelihood).'
from_schema: https://w3id.org/tvbo
attributes:
  priors:
    name: priors
    description: Priors over the inferred parameters, keyed by each parameter's dotted
      name (e.g. "Generic2dOscillator.eta" or "PulseInput.amplitude"). The KEYS are
      the inferred parameters — there is no separate free-parameter list.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Inference
    domain_of:
    - Inference
    range: Prior
    multivalued: true
    inlined: true
  likelihood:
    name: likelihood
    description: Observation model p(data | sim(theta)).
    from_schema: https://w3id.org/tvbo
    rank: 1000
    owner: Inference
    domain_of:
    - Inference
    range: Likelihood
    required: true
    inlined: true
  sampler:
    name: sampler
    description: MCMC sampler ('nuts'). Each backend maps its own way.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: string(nuts)
    owner: Inference
    domain_of:
    - Inference
    range: string
  num_samples:
    name: num_samples
    description: Posterior samples to draw.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: integer(1000)
    owner: Inference
    domain_of:
    - Inference
    range: integer
  num_warmup:
    name: num_warmup
    description: Warmup/adaptation steps before sampling.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: integer(1000)
    owner: Inference
    domain_of:
    - Inference
    range: integer
  num_chains:
    name: num_chains
    description: Independent MCMC chains.
    from_schema: https://w3id.org/tvbo
    rank: 1000
    ifabsent: integer(1)
    owner: Inference
    domain_of:
    - Inference
    range: integer
  seed:
    name: seed
    description: PRNG seed for reproducible sampling.
    from_schema: https://w3id.org/tvbo
    ifabsent: integer(0)
    owner: Inference
    domain_of:
    - GraphGenerator
    - Distribution
    - Noise
    - Inference
    range: integer
  execution:
    name: execution
    description: Per-inference execution config (overrides experiment defaults).
    from_schema: https://w3id.org/tvbo
    owner: Inference
    domain_of:
    - Analysis
    - Optimization
    - Exploration
    - Inference
    - Algorithm
    - Continuation
    - SimulationExperiment
    range: ExecutionConfig
    inlined: true
  integration:
    name: integration
    description: Forward-model integration settings (overrides experiment defaults).
    from_schema: https://w3id.org/tvbo
    owner: Inference
    domain_of:
    - Network
    - Optimization
    - Inference
    - SimulationExperiment
    range: Integrator
    inlined: true
  depends_on:
    name: depends_on
    description: Optional algorithm whose result state seeds the inference.
    from_schema: https://w3id.org/tvbo
    owner: Inference
    domain_of:
    - Optimization
    - Inference
    - Algorithm
    range: Algorithm
    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: Inference
    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: Inference
    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: Inference
    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:Inference

```
</details></div>