Schemas

Language-independent JSON Schema definitions for rtemis. The same config drives rtemis (R), rtemis-py and rtemislive — these documents are the contract between them.

160 schemasschema.rtemis.org index.json

Machine learning

117

Start here — configs you author

ClassificationMetricsResclassificationmetricsres

Classification metrics aggregated across resamples: each resample's metrics, the aggregate confusion matrix in long form, and the mean and standard deviation of the overall metrics.

ClusterConfigcluster

Language-independent config for an rtemis clustering pipeline: a data reference, a `ClusteringConfig`, and an output directory.

ClusterConfigcluster

Language-independent config for an rtemis clustering pipeline: a data reference, a `ClusteringConfig`, and an output directory.

DecomposeConfigdecompose

Language-independent config for an rtemis decomposition pipeline: a data reference, a `DecompositionConfig`, and an output directory.

DecomposeConfigdecompose

Language-independent config for an rtemis decomposition pipeline: a data reference, a `DecompositionConfig`, and an output directory.

RegressionMetricsResregressionmetricsres

Regression metrics aggregated across resamples: each resample's metrics, plus their mean and standard deviation.

SuperConfigsupervised

Language-independent config for an rtemis supervised-learning run. Mirrors the `SuperConfig` object: data references, optional preprocessing / decomposition, an algorithm with hyperparameters, optional tuning and outer resampling, and execution settings. The same config drives rtemis (R), rtemis CLI/shell, and rtemislive.

SuperConfigsupervised

Components — composed into the configs above

ClassificationMetricsclassificationmetrics

Classification metrics for one sample: the confusion matrix in long form (one row per cell), overall metrics, and per-class metrics. Which overall columns are present depends on the task, so only the invariant ones are required.

ClusteringConfigclustering

Language-independent config for an rtemis clustering run. Mirrors the `ClusteringConfig` object: an algorithm name and an algorithm-specific `config`. The same config drives rtemis (R), rtemis CLI/shell, and rtemislive to identical output.

selected by algorithm

cmeansdbscanhardclkmeansneuralgas

ClusteringConfigclustering

selected by algorithm

cmeansdbscanhardclkmeansneuralgas

DataFingerprintdatafingerprint

Identity of one dataset: a content hash plus the structural facts that make a mismatch diagnosable rather than merely detectable.

DecompositionConfigdecomposition

Language-independent config for an rtemis decomposition (dimensionality reduction). Mirrors the `DecompositionConfig` object: an algorithm name, an algorithm-specific `config`, and an optional feature subset. The same config drives rtemis (R), rtemis CLI/shell, and rtemislive to identical output.

selected by algorithm

icaisomapnmfpcatsneumap

DecompositionConfigdecomposition

selected by algorithm

icaisomapnmfpcatsneumap

DecompositionMetricsdecompositionmetrics

Decomposition metrics: a single-row table of reconstruction quality, component redundancy and effective dimensionality. Which cells are populated follows from the algorithm's traits -- a metric its algorithm cannot support is null -- so every column is declared for every algorithm and every cell is nullable. Unprefixed columns describe the data the decomposition was fitted on; `oos_` columns describe data the fit never saw.

ExecutionConfigexecution

Language-independent config for rtemis execution: sequential, parallel, or distributed. Mirrors the `ExecutionConfig` object / `setup_ExecutionConfig` arguments.

ExecutionConfigexecution

Language-independent config for rtemis execution: sequential, parallel, or distributed. Mirrors the `ExecutionConfig` object / `setup_ExecutionConfig` arguments.

PreprocessorConfigpreprocessor

Language-independent config for rtemis preprocessing. Mirrors the `PreprocessorConfig` object / `setup_Preprocessor` arguments. The same config drives rtemis (R), rtemis CLI/shell, and rtemislive to identical output.

PreprocessorConfigpreprocessor

Provenanceprovenance

What produced a run record: package and language versions, platform, timing, how the run ended, and a fingerprint of each dataset used. Referenced by every `<family>/v1/record.json`.

RegressionMetricsregressionmetrics

Regression metrics for one sample: a single-row table of mean absolute error, mean squared error, root mean squared error and R-squared. Every cell is nullable, a metric being genuinely undefined for some samples.

ResamplerConfigresampler

Language-independent config for an rtemis resampler. Mirrors the `ResamplerConfig` object: a resampler type plus its type-specific settings. The same config drives rtemis (R), rtemis CLI/shell, and rtemislive to identical resamples.

selected by type

bootstrapcustomkfoldloocvstratbootstratsub

ResamplerConfigresampler

selected by type

bootstrapcustomkfoldloocvstratbootstratsub

TunerConfigtuner

Language-independent config for rtemis hyperparameter tuning. Mirrors the `TunerConfig` object: a tuner type and a type-specific `config`.

selected by type

gridsearch

TunerConfigtuner

Language-independent config for rtemis hyperparameter tuning. Mirrors the `TunerConfig` object: a tuner type and a type-specific `config`.

selected by type

gridsearch

Composition

How the schemas above assemble — every reference is a link

SuperConfigsupervised/v1/record.json

dat_training_pathstring | null

dat_validation_pathstring | null

dat_test_pathstring | null

weightsstring | null

positive_classstring | null

preprocessor_config

PreprocessorConfig

decomposition_config

DecompositionConfig

algorithm:PCA·ICA·NMF·UMAP·tSNE·Isomap

hyperparameters

Hyperparameters

algorithm:GLM·GAM·GLMNET·GLMTree·SPLS·MARS·LinearSVM·RadialSVM·CART·Ranger·LightCART·LightRF·LightGBM·LightRuleFit·BART·Isotonic·MLP·TabNet·KNN·HAL·MonotonicHAL·LINAD·LINADForest·NNLS·SuperLearner·ModalityStacking·ConditionalSuperLearner

tuner_config

TunerConfig

type:GridSearch

outer_resampling_config

ResamplerConfig

type:KFold·StratSub·StratBoot·Bootstrap·LOOCV·Custom

execution_config

ExecutionConfig

questionstring | null

outdirstring | null

verbosityinteger

originobject

foldsobject[]

metricsobject

metrics_sdobject

provenance

Provenance

SuperConfigsupervised/v1

dat_training_pathstring | null

dat_validation_pathstring | null

dat_test_pathstring | null

weightsstring | null

positive_classstring | null

preprocessor_config

PreprocessorConfig

decomposition_config

DecompositionConfig

algorithm:PCA·ICA·NMF·UMAP·tSNE·Isomap

hyperparameters

Hyperparameters

tuner_config

TunerConfig

type:GridSearch

outer_resampling_config

ResamplerConfig

type:KFold·StratSub·StratBoot·Bootstrap·LOOCV·Custom

execution_config

ExecutionConfig

questionstring | null

outdirstring | null

verbosityinteger

DecomposeConfigdecompose/v1/record.json

dat_pathstring | null

algorithmstring | null

decomposition_config

DecompositionConfig

algorithm:PCA·ICA·NMF·UMAP·tSNE·Isomap

outdirstring

verbosityinteger

originobject

metrics

DecompositionMetrics

provenance

Provenance

ClusterConfigcluster/v1/record.json

dat_pathstring | null

algorithmstring | null

clustering_config

ClusteringConfig

algorithm:KMeans·HardCL·NeuralGas·CMeans·DBSCAN

outdirstring

verbosityinteger

originobject

provenance

Provenance

ClassificationMetricsResclassificationmetricsres/v1

samplestring | null

confusion_longarray | null

res_metricsClassificationMetrics[]

mean_metricsarray | null

sd_metricsarray | null

ClusterConfigcluster/v1

dat_pathstring | null

algorithmstring | null

clustering_config

ClusteringConfig

algorithm:KMeans·HardCL·NeuralGas·CMeans·DBSCAN

outdirstring

verbosityinteger

DecomposeConfigdecompose/v1

dat_pathstring | null

algorithmstring | null

decomposition_config

DecompositionConfig

algorithm:PCA·ICA·NMF·UMAP·tSNE·Isomap

outdirstring

verbosityinteger

RegressionMetricsResregressionmetricsres/v1

samplestring | null

res_metricsRegressionMetrics[]

mean_metricsarray | null

sd_metricsarray | null

Domain formats

Formats

A3a3

Amino Acid Annotation (A3) format — structured annotation of amino acid sequences.

chartchart

Language-independent config for an rtemis chart. A chart type plus its type-specific data binding, semantics and appearance. The same config drives rtemis.draw (R) and rtemislive (TypeScript) to the same chart.

chartchart

ConformalConfigconformal

Language-independent config for an rtemis conformal prediction region. Mirrors the `ConformalConfig` object: a construction plus its construction-specific settings. The construction is tagged rather than inferred, since which of them a run may use depends on the model it is applied to, not on the document.

ConformalConfigconformal

ExplanationConfigexplanation

Language-independent config for a per-case rtemis explanation. Mirrors the `ExplanationConfig` object: a kind of explanation plus its kind-specific settings. The kind is tagged rather than inferred, so a second kind of explanation can be added without changing how the first is read.

ExplanationConfigexplanation