| algorithms |
Names of the experiment’s algorithms (keys in experiment | | [amplitude](slots/amplitude.qmd) | | | [analysis](slots/analysis.qmd) | Marks this observation as an analysis observable that operates on the solve/l... | | [anatomicalAxesOrientation](slots/anatomicalAxesOrientation.qmd) | Add the axes orientation in standard anatomical terms (XYZ) | | [application_category](slots/application_category.qmd) | High-level category (e | | [apply_every](slots/apply_every.qmd) | Apply update every N iterations | | [apply_on_dimension](slots/apply_on_dimension.qmd) | Which dimension to apply the transformation on | | [args](slots/args.qmd) | Ordered parameter names passed to the callable | | [arguments](slots/arguments.qmd) | Variables consumed by the function (referenced in the equation), keyed by arg... | | [atlas](slots/atlas.qmd) | | | [author](slots/author.qmd) | Original author(s) or creating organization(s) | | [authors](slots/authors.qmd) | Author display strings (full detail in references | | [autonomous](slots/autonomous.qmd) | Whether the system is autonomous (equations do not depend explicitly on time ... | | [aux_data](slots/aux_data.qmd) | Ordered list of auxiliary inputs the observation pipeline consumes | | [average](slots/average.qmd) | Averaging mode across trials | | [axesOrigin](slots/axesOrigin.qmd) | Enter the origin (central point where all axes intersect) | | [axis](slots/axis.qmd) | Dimension along which the distribution is sampled | | [baseline_value](slots/baseline_value.qmd) | Preoperative baseline value of the score | | [batch_size](slots/batch_size.qmd) | Batch size for vectorized operations (None = auto) | | [bc_type](slots/bc_type.qmd) | | | [bids](slots/bids.qmd) | BIDS filename entities for this dataset | | [bids_dir](slots/bids_dir.qmd) | Path to BEP017-compliant BIDS directory for loading connectivity matrices | | [bids_root](slots/bids_root.qmd) | Path to BIDS dataset root directory | | [bindings](slots/bindings.qmd) | Per-backend construction bindings, keyed by backend id (e | | [bothside](slots/bothside.qmd) | Continue branch in both directions | | [boundary_conditions](slots/boundary_conditions.qmd) | | | [bounds](slots/bounds.qmd) | Constraints on parameter values after update | | [branches](slots/branches.qmd) | Child branches to continue from detected bifurcation points (PO from Hopf, fo... | | [build_hash](slots/build_hash.qmd) | Deterministic hash of the resolved dependency set | | [builder](slots/builder.qmd) | Optional Python callable that builds the network at YAML load time | | [call_args](slots/call_args.qmd) | Arguments passed when calling the instance (__call__) | | [callable](slots/callable.qmd) | Name of the constructor function in the library | | [cases](slots/cases.qmd) | | | [category](slots/category.qmd) | Coarse classification of the phenotype bundle, used for filtering in larger s... | | [center](slots/center.qmd) | Add the center coordinate of this entity | | [checkpoint_interval](slots/checkpoint_interval.qmd) | Gradient-checkpointing interval in milliseconds (backward-pass memory/time tr... | | [citation](slots/citation.qmd) | Additional citation strings or DOIs | | [citekey](slots/citekey.qmd) | BibTeX citation key; the join key into references | | [class_call](slots/class_call.qmd) | Class instantiation and call (alternative to callable/function) | | [class_reference](slots/class_reference.qmd) | Direct class reference (alternative to pipeline) | | [clinical_improvement](slots/clinical_improvement.qmd) | Observed improvement relative to baseline based on a defined score | | [clinical_scores](slots/clinical_scores.qmd) | | | [coefficient](slots/coefficient.qmd) | | | [cohort](slots/cohort.qmd) | Cohort label (e | | [color](slots/color.qmd) | Add the color code used for visual representation of this entity | | [comment](slots/comment.qmd) | | | [compile](slots/compile.qmd) | Code-generation hint (opt-in, backend-independent): request that the generate... | | [concept_iri](slots/concept_iri.qmd) | Cognitive Atlas IRI of the cognitive construct measured (e | | [condition](slots/condition.qmd) | Experimental condition label (e | | [condition_parameters](slots/condition_parameters.qmd) | Parameter symbols accessible in the condition function | | [condition_states](slots/condition_states.qmd) | State variable symbols accessible in the condition function | | [conditional](slots/conditional.qmd) | | | [conditionals](slots/conditionals.qmd) | Conditional logic for piecewise equations | | [conditions](slots/conditions.qmd) | Global condition labels applied across all subjects (e | | [connectivity](slots/connectivity.qmd) | | | [connectivity_ref](slots/connectivity_ref.qmd) | Reference to connectivity data (_conndata-network_connectivity | | [constructor_args](slots/constructor_args.qmd) | Arguments passed to __init__ when instantiating the class | | [contact_id](slots/contact_id.qmd) | Identifier (e | | [contacts](slots/contacts.qmd) | List of physical contacts along the electrode | | [container_image](slots/container_image.qmd) | Container image reference (e | | [continuation](slots/continuation.qmd) | Override solver settings for this branch | | [continuations](slots/continuations.qmd) | Numerical continuation and bifurcation analysis specifications | | [coordinate](slots/coordinate.qmd) | 3D coordinate of the contact center in the defined coordinate space | | [coordinate_space](slots/coordinate_space.qmd) | | | [coordinates](slots/coordinates.qmd) | Node coordinates (x,y,z) in the given coordinate space | | [correlated](slots/correlated.qmd) | | | [correlation](slots/correlation.qmd) | | | [coupling](slots/coupling.qmd) | Reusable coupling configurations referenced by edges (e | | [coupling_function](slots/coupling_function.qmd) | Mathematical function defining the coupling | | [coupling_inputs](slots/coupling_inputs.qmd) | | | [coupling_terms](slots/coupling_terms.qmd) | | | [coupling_variable](slots/coupling_variable.qmd) | Whether this state variable is transmitted to connected nodes through the cou... | | [cse](slots/cse.qmd) | Code-generation hint (opt-in, backend-independent): eliminate common subexpre... | | [curvature](slots/curvature.qmd) | Optional path to per-vertex curvature (N,) float | | [data](slots/data.qmd) | | | [data_file](slots/data_file.qmd) | Path to the h5 companion (relative to the yaml) | | [data_source](slots/data_source.qmd) | | | [dataLocation](slots/dataLocation.qmd) | | | [dataset](slots/dataset.qmd) | Multi-subject dataset for workflow rendering | | [dataset_id](slots/dataset_id.qmd) | Unique identifier for this phenotype bundle | | [dataset_path](slots/dataset_path.qmd) | Dataset path for array-valued parameters | | [datatype](slots/datatype.qmd) | Declared value type of this parameter, given as a schema range name — a primi... | | [date_created](slots/date_created.qmd) | Date the software was first released (YYYY-MM-DD) | | [date_modified](slots/date_modified.qmd) | Date of the most recent release or significant update | | [default](slots/default.qmd) | | | [defaultImage](slots/defaultImage.qmd) | Add all image files used as visual representation of this common coordinate s... | | [definition](slots/definition.qmd) | | | [degree](slots/degree.qmd) | Polynomial degree per mesh interval for collocation | | [delay](slots/delay.qmd) | Conduction delay (explicit edges, ms) | | [delayed](slots/delayed.qmd) | | | [delta_p](slots/delta_p.qmd) | Initial parameter offset from the bifurcation point | | [depends_on](slots/depends_on.qmd) | Upstream task whose result seeds this optimization | | [derivative_initial_value](slots/derivative_initial_value.qmd) | Initial value for the first time derivative, used when equation_order > 1 | | [derived_from](slots/derived_from.qmd) | | | [derived_from_model](slots/derived_from_model.qmd) | | | [derived_parameters](slots/derived_parameters.qmd) | | | [derived_variables](slots/derived_variables.qmd) | | | [description](slots/description.qmd) | | | [descriptor](slots/descriptor.qmd) | Short alphanumeric identifier for the BIDS desc- filename entity (e | | [detect_bifurcation](slots/detect_bifurcation.qmd) | Bifurcation detection level | | [detect_fold](slots/detect_fold.qmd) | Enable fold (limit point) detection | | [development_status](slots/development_status.qmd) | Development status (repostatus | | [diagnosis](slots/diagnosis.qmd) | | | [differentiation](slots/differentiation.qmd) | Backend-neutral strategy for propagating gradients through the temporal integ... | | [dimension](slots/dimension.qmd) | Dimensionality of the coupling input (number of coupled values) | | [dimension_labels](slots/dimension_labels.qmd) | Ordered labels for the matrix columns (dim-1) when the matrix is non-square | | [directed](slots/directed.qmd) | Whether to generate a directed graph | | [discretization](slots/discretization.qmd) | Discretization method for the branch solution | | [distance](slots/distance.qmd) | Edge length / tract distance (explicit edges, mm) | | [distance_unit](slots/distance_unit.qmd) | Unit for distances/lengths in the network | | [distribution](slots/distribution.qmd) | Distribution for sampling initial conditions per node | | [doi](slots/doi.qmd) | Digital Object Identifier for the software or its reference publication | | [domain](slots/domain.qmd) | | | [downsample_period](slots/downsample_period.qmd) | Intermediate downsampling period (ms) | | [ds](slots/ds.qmd) | Initial arc-length step size | | [ds_max](slots/ds_max.qmd) | Maximum adaptive step size | | [ds_min](slots/ds_min.qmd) | Minimum adaptive step size | | [dt](slots/dt.qmd) | Time step (s) | | [dtype](slots/dtype.qmd) | Data type for matrix values | | [duration](slots/duration.qmd) | | | [dynamics](slots/dynamics.qmd) | Dictionary of dynamics models keyed by name | | [ecosystem](slots/ecosystem.qmd) | Package ecosystem(s) through which the software is distributed | | [edge_matrix_files](slots/edge_matrix_files.qmd) | | | [edge_template](slots/edge_template.qmd) | Default Edge attributes applied to every Edge in this Network | | [edges](slots/edges.qmd) | List of directed edges with coupling references (optional, for explicit edge ... | | [efield](slots/efield.qmd) | Metadata about the E-field result for this setting | | [electrode_id](slots/electrode_id.qmd) | Unique identifier for this electrode | | [electrode_reference](slots/electrode_reference.qmd) | | | [electrodes](slots/electrodes.qmd) | | | [element](slots/element.qmd) | Element/node index this range applies to | | [element_domains](slots/element_domains.qmd) | Per-element domain overrides for heterogeneous parameters | | [element_type](slots/element_type.qmd) | | | [elements](slots/elements.qmd) | Topology indices: either a file reference, or (when inlined on a Network) a d... | | [empirical_data](slots/empirical_data.qmd) | Paths to empirical recordings for this session (e | | [enforce](slots/enforce.qmd) | For a state-variable ``domain``: whether/how to enforce the range during inte... | | [engine](slots/engine.qmd) | Primary engine (must appear in environment | | [entities](slots/entities.qmd) | | | [environment](slots/environment.qmd) | | | [environment_type](slots/environment_type.qmd) | Category: conda, venv, docker, etc | | [equation](slots/equation.qmd) | | | [equation_order](slots/equation_order.qmd) | Order of the time derivative on the LHS | | [equation_type](slots/equation_type.qmd) | Type of equation: 'differential' (default) means dx/dt = rhs, 'algebraic' mea... | | [evaluator](slots/evaluator.qmd) | Who performed the rating (e | | [event_type](slots/event_type.qmd) | Type of event trigger mechanism | | [events](slots/events.qmd) | Events attached to this node (e | | [execution](slots/execution.qmd) | Per-optimization execution configuration (overrides experiment-level defaults... | | [experiment_yaml_hash](slots/experiment_yaml_hash.qmd) | SHA-256 hex digest of the normalised experiment YAML that produced this artif... | | [explorations](slots/explorations.qmd) | Parameter exploration/grid search specifications | | [explored_values](slots/explored_values.qmd) | Explicit explored values for this element | | [expression](slots/expression.qmd) | The equation to apply when the condition is met | | [extension](slots/extension.qmd) | | | [field](slots/field.qmd) | Dotted-path subkey within the referenced entity (optional) | | [field_dynamics](slots/field_dynamics.qmd) | | | [file](slots/file.qmd) | | | [find_fixpoint](slots/find_fixpoint.qmd) | Whether to find a fixed point (steady state) before time integration | | [format](slots/format.qmd) | Storage format in binary companion (dense, csr, coo) | | [free](slots/free.qmd) | | | [free_parameters](slots/free_parameters.qmd) | Parameters to optimize in this stage | | [freeze_parameters](slots/freeze_parameters.qmd) | Parameters from previous stages to freeze (keep at optimized value but not up... | | [frequency](slots/frequency.qmd) | | | [function](slots/function.qmd) | Custom distribution function (PDF or sampling callable) | | [functions](slots/functions.qmd) | | | [funder](slots/funder.qmd) | Funding bodies or grants (e | | [gaussian](slots/gaussian.qmd) | Indicates whether the noise is Gaussian | | [generated_at](slots/generated_at.qmd) | Timestamp when this TimeSeries was generated | | [generated_by](slots/generated_by.qmd) | Software/agent identifier (prov:wasGeneratedBy) | | [geometry](slots/geometry.qmd) | Optional file for geometry/ROI mask (e | | [graph_generator](slots/graph_generator.qmd) | Graph generator specification | | [grounding](slots/grounding.qmd) | External ontology IRIs (typically GO, ChEBI, UBERON, CL, MeSH) that this enti... | | [group](slots/group.qmd) | Group assignment (e | | [groups](slots/groups.qmd) | | | [handedness](slots/handedness.qmd) | | | [has_reference](slots/has_reference.qmd) | | | [hash](slots/hash.qmd) | Build or artifact hash for exact reproducibility | | [head](slots/head.qmd) | | | [hemi](slots/hemi.qmd) | BIDS hemi- entity (L or R) for hemisphere-specific surface/volume data | | [hemisphere](slots/hemisphere.qmd) | Add the hemisphere of this entity | | [heterogeneous](slots/heterogeneous.qmd) | | | [hi](slots/hi.qmd) | Upper bound or stopping value | | [history](slots/history.qmd) | | | [homepage](slots/homepage.qmd) | Project homepage URL | | [hyperparameters](slots/hyperparameters.qmd) | Stage-specific hyperparameters (e | | [id](slots/id.qmd) | Unique node identifier | | [imaging_modality](slots/imaging_modality.qmd) | Type of imaging modality (BOLD, EEG, MEG, etc | | [includes](slots/includes.qmd) | Include update rules from other algorithms with optional argument overrides | | [incoming_states](slots/incoming_states.qmd) | References to state variables from connected (source) nodes | | [inferences](slots/inferences.qmd) | Bayesian inference configurations (posterior over parameters given an observa... | | [initial_expression](slots/initial_expression.qmd) | Analytic initial condition for the field | | [initial_state](slots/initial_state.qmd) | How to obtain the initial equilibrium | | [initial_value](slots/initial_value.qmd) | | | [inner_coupling](slots/inner_coupling.qmd) | For hierarchical coupling: inner coupling applied at regional level | | [inner_iterations](slots/inner_iterations.qmd) | For mode=nested only: number of inner-loop iterations to run per outer iterat... | | [input](slots/input.qmd) | Simple input reference: name of previous function's output in pipeline | | [inputs](slots/inputs.qmd) | Per-input fingerprints for cache invalidation | | [integration](slots/integration.qmd) | Integration settings for optimization simulations (overrides experiment defau... | | [intensity](slots/intensity.qmd) | Optional scalar or vector intensity parameter for noise | | [intermediate_expressions](slots/intermediate_expressions.qmd) | | | [interoperates_with](slots/interoperates_with.qmd) | Tools this tool can exchange data with or delegate to | | [interpolate_delays](slots/interpolate_delays.qmd) | For delayed coupling: read delayed states by linear interpolation between the... | | [interpolation](slots/interpolation.qmd) | Interpolation for a data-driven stimulus: 'linear' or 'cubic' | | [iri](slots/iri.qmd) | Optional stable IRI (or compact URI) for this entity in an external ontology ... | | [is_accessible_for_free](slots/is_accessible_for_free.qmd) | Whether the tool is free/open-source | | [issue_tracker](slots/issue_tracker.qmd) | URL of the bug tracker or issue board | | [key](slots/key.qmd) | Key/variable name within the file (for | | [keys](slots/keys.qmd) | Named keys for multi-dimensional coupling | | [keywords](slots/keywords.qmd) | Tags for topic-based discovery and clustering | | [label](slots/label.qmd) | | | [labels_dimensions](slots/labels_dimensions.qmd) | Mapping of dimension names to their labels (JSON-encoded dict) | | [labels_ordering](slots/labels_ordering.qmd) | Ordering of dimensions: Time, State Variable, Space, Mode | | [latex](slots/latex.qmd) | | | [learning_rate](slots/learning_rate.qmd) | | | [learning_rate_schedule](slots/learning_rate_schedule.qmd) | Learning rate schedule: 'constant', 'linear', 'exponential' | | [learning_rate_warmup](slots/learning_rate_warmup.qmd) | Linear warmup of learning rate from 0 to learning_rate over n_iterations | | [lhs](slots/lhs.qmd) | | | [library](slots/library.qmd) | Native library/module providing the callable | | [license](slots/license.qmd) | SPDX license identifier (e | | [likelihood](slots/likelihood.qmd) | Observation model p(data | sim(theta)) | | [linear_solver](slots/linear_solver.qmd) | Linear solver for the Newton bordered system | | [lo](slots/lo.qmd) | Lower bound or starting value | | [loader](slots/loader.qmd) | Callable that loads the data (e | | [local](slots/local.qmd) | Marks this as a LOCAL (surface/local-connectivity) coupling term rather than ... | | [local_coupling_term](slots/local_coupling_term.qmd) | | | [local_states](slots/local_states.qmd) | References to state variables from the local (target) node | | [log_scale](slots/log_scale.qmd) | Whether to use logarithmic spacing | | [loss](slots/loss.qmd) | Loss function call | | [maintainer](slots/maintainer.qmd) | Current maintainer(s) or responsible organization(s) | | [manufacturer](slots/manufacturer.qmd) | | | [max_bisection_steps](slots/max_bisection_steps.qmd) | Maximum bisection steps for bifurcation point localization | | [max_iterations](slots/max_iterations.qmd) | | | [max_steps](slots/max_steps.qmd) | Maximum continuation steps | | [measure](slots/measure.qmd) | Selector into the source | | [measure_specs](slots/measure_specs.qmd) | Optional per-measure metadata (Cognitive Atlas IRIs, units, description) | | [measure_type](slots/measure_type.qmd) | Sub-type within the phenotype (e | | [measures](slots/measures.qmd) | Names of the measures present in the h5 companion (one ``measures/<name>`` da... | | [mesh](slots/mesh.qmd) | Optional triangle mesh geometry | | [mesh_file](slots/mesh_file.qmd) | Path to external mesh file (GIFTI, VTK, MSH, FreeSurfer, etc | | [mesh_format](slots/mesh_format.qmd) | Explicit format override (gifti, freesurfer, meshio, vtk, gmsh) | | [mesh_intervals](slots/mesh_intervals.qmd) | Number of mesh intervals (time slices) for collocation or trapezoid methods | | [metadata](slots/metadata.qmd) | Additional subject metadata as key-value pairs or path to a sidecar JSON file | | [method](slots/method.qmd) | Discretization method | | [metric](slots/metric.qmd) | Metric equation for matching (e | | [modality](slots/modality.qmd) | Imaging modality or simulation output type | | [mode](slots/mode.qmd) | | | [model](slots/model.qmd) | | | [model_equation_ref](slots/model_equation_ref.qmd) | BIDS ModelEq reference: path to _eq | | [model_paradigm](slots/model_paradigm.qmd) | Computational paradigms supported | | [model_param_ref](slots/model_param_ref.qmd) | BIDS ModelParam reference: path to _param | | [model_type](slots/model_type.qmd) | Coarse classification of this model (mean_field, neural_mass, phase_oscillato... | | [modes](slots/modes.qmd) | | | [modified](slots/modified.qmd) | | | [module](slots/module.qmd) | | | [modules](slots/modules.qmd) | (Deprecated) Use environment | | [mtime](slots/mtime.qmd) | File modification time at fingerprinting (POSIX timestamp) | | [n](slots/n.qmd) | Number of points (alternative to step for grid exploration) | | [n_inversion](slots/n_inversion.qmd) | Number of eigenvalue sign inversions to flag a bifurcation | | [n_iterations](slots/n_iterations.qmd) | Number of outer iterations to run in this stage | | [n_parallel](slots/n_parallel.qmd) | Parallel evaluations | | [n_regions](slots/n_regions.qmd) | Total number of regions | | [n_sections](slots/n_sections.qmd) | Number of shooting sections for shooting or Poincaré methods | | [n_threads](slots/n_threads.qmd) | Number of CPU threads per worker (-1 = auto-detect) | | [n_trials](slots/n_trials.qmd) | Number of independent trials per grid point | | [n_vertices](slots/n_vertices.qmd) | Total number of vertices | | [n_workers](slots/n_workers.qmd) | Number of parallel workers (maps to pmap devices in JAX, processes in multipr... | | [name](slots/name.qmd) | Full name of the scale (e | | [nativeUnit](slots/nativeUnit.qmd) | Add the native unit that is used for this common coordinate space version | | [network](slots/network.qmd) | Path to subject-specific connectome (when not session-dependent) | | [nev](slots/nev.qmd) | Number of eigenvalues to compute | | [newton_max_iterations](slots/newton_max_iterations.qmd) | Maximum Newton corrector iterations per step | | [newton_tol](slots/newton_tol.qmd) | Absolute tolerance for Newton corrector convergence | | [node_mapping](slots/node_mapping.qmd) | HDF5 dataset path for node-to-parent mapping | | [node_template](slots/node_template.qmd) | Default Node attributes applied to every Node in this Network | | [nodes](slots/nodes.qmd) | Network nodes a stimulus-type event is applied to (node ids / indices) | | [noise](slots/noise.qmd) | Optional stochastic contribution to the stimulus | | [noise_type](slots/noise_type.qmd) | | | [non_negative](slots/non_negative.qmd) | All values >= 0 | | [normals](slots/normals.qmd) | Optional path inside the parent Network's h5 (or an external file) to per-ver... | | [notes](slots/notes.qmd) | | | [num_chains](slots/num_chains.qmd) | Independent MCMC chains | | [num_samples](slots/num_samples.qmd) | Posterior samples to draw | | [num_warmup](slots/num_warmup.qmd) | Warmup/adaptation steps before sampling | | [number_of_elements](slots/number_of_elements.qmd) | Number of elements (triangles, quads, tetrahedra, etc | | [number_of_modes](slots/number_of_modes.qmd) | | | [number_of_nodes](slots/number_of_nodes.qmd) | Number of nodes in the network (derived from nodes if not set) | | [number_of_stages](slots/number_of_stages.qmd) | | | [number_of_subjects](slots/number_of_subjects.qmd) | Number of subjects in the tractography dataset | | [number_of_vertices](slots/number_of_vertices.qmd) | Number of vertices in the mesh | | [objective](slots/objective.qmd) | What the algorithm optimizes for | | [objectives](slots/objectives.qmd) | Names of observations minimised by an adaptivestrategy(e | | [observable](slots/observable.qmd) | Observable to compute at each point | | [observational_measures](slots/observational_measures.qmd) | BEP017 measure names for observational targets (e | | [observations](slots/observations.qmd) | References to observations defined in the observations section | | [observed](slots/observed.qmd) | Observable functions computed from states, inputs, and parameters after simul... | | [ode_solver](slots/ode_solver.qmd) | ODE solver for flow-based methods (shooting, poincaré) | | [on_region](slots/on_region.qmd) | Mesh/atlas subset where BC applies | | [operating_system](slots/operating_system.qmd) | Supported operating systems (e | | [operator_type](slots/operator_type.qmd) | | | [operators](slots/operators.qmd) | | | [optimizations](slots/optimizations.qmd) | Parameter optimization configurations | | [optional](slots/optional.qmd) | | | [options](slots/options.qmd) | Toolkit-specific string options (jacobian type, etc | | [originalLookupLabel](slots/originalLookupLabel.qmd) | Add the original label of this entity as defined in the parcellation terminol... | | [output](slots/output.qmd) | Named outputs (keyed by name), e | | [output_equation](slots/output_equation.qmd) | Output transformation equation (if equation-based) | | [outsym](slots/outsym.qmd) | Output symbol names for the edge model | | [over](slots/over.qmd) | Dimension to aggregate over (e | | [package](slots/package.qmd) | Reference to the software package identity | | [parallel_batch_size](slots/parallel_batch_size.qmd) | Chunk size for ``lax_map`` and chunked-``vmap`` modes | | [parallel_mode](slots/parallel_mode.qmd) | How trial-axis parallelism is realised at codegen time | | [parameter](slots/parameter.qmd) | Dotted reference to the Parameter being swept | | [parameters](slots/parameters.qmd) | | | [parcel_map_field](slots/parcel_map_field.qmd) | When the mesh is inlined on a Network with a parcellation, the dotted path in... | | [parcellation](slots/parcellation.qmd) | Brain parcellation/atlas reference | | [parent_network](slots/parent_network.qmd) | Path/URI to parent (coarser) Network | | [parent_score](slots/parent_score.qmd) | If this score is a subscore of a broader composite | | [path](slots/path.qmd) | | | [percent_change](slots/percent_change.qmd) | Percent change compared to preoperative baseline (positive = improvement) | | [period](slots/period.qmd) | Sampling period for monitors (ms) | | [pipeline](slots/pipeline.qmd) | Ordered sequence of Functions | | [platform](slots/platform.qmd) | OS / architecture (e | | [position](slots/position.qmd) | Spatial coordinates (x, y, z) of the node | | [post_expression](slots/post_expression.qmd) | Post-processing expression applied after coupling | | [pre_expression](slots/pre_expression.qmd) | Pre-processing expression applied before coupling | | [precision](slots/precision.qmd) | Floating point precision: 'float32' or 'float64' | | [preconditioner](slots/preconditioner.qmd) | | | [preprocessing](slots/preprocessing.qmd) | Optional preprocessing to apply after loading | | [primary_weight](slots/primary_weight.qmd) | Name of the edge group that should serve as the canonical weights matrix when... | | [priors](slots/priors.qmd) | Priors over the inferred parameters, keyed by each parameter's dotted name (e | | [procedure](slots/procedure.qmd) | Optional symbolic procedure for derived generators (e | | [processing_pipeline](slots/processing_pipeline.qmd) | Processing pipeline used to generate the tractography | | [programming_language](slots/programming_language.qmd) | Implementation languages | | [protocols](slots/protocols.qmd) | All DBS protocols assigned to this subject | | [provenance](slots/provenance.qmd) | W3C PROV-O metadata for the source of these scores | | [pulse_width](slots/pulse_width.qmd) | | | [pycode](slots/pycode.qmd) | Python code for the equation | | [quantity_kind](slots/quantity_kind.qmd) | Scalar, vector, or tensor | | [random_seed](slots/random_seed.qmd) | Base random seed for reproducibility | | [random_state](slots/random_state.qmd) | | | [recon_path](slots/recon_path.qmd) | | | [reconstruction](slots/reconstruction.qmd) | BIDS rec- entity (e | | [record](slots/record.qmd) | Whether to include this element in simulation output files | | [reference](slots/reference.qmd) | DOI or citation for this dataset | | [reference_publication](slots/reference_publication.qmd) | DOI of the primary reference publication for this tool | | [references](slots/references.qmd) | | | [region](slots/region.qmd) | Brain region or anatomical label | | [region_mapping](slots/region_mapping.qmd) | For hierarchical coupling: vertex-to-region mapping for aggregation | | [regional_connectivity](slots/regional_connectivity.qmd) | For hierarchical coupling: region-to-region connectivity with weights and del... | | [regions](slots/regions.qmd) | | | [rel_tol](slots/rel_tol.qmd) | Relative tolerance for ODE integration | | [relatedUBERONTerm](slots/relatedUBERONTerm.qmd) | Add the related anatomical entity as defined by the UBERON ontology | | [reported_optimum](slots/reported_optimum.qmd) | | | [repository](slots/repository.qmd) | Source code repository URL | | [required](slots/required.qmd) | Whether a value for this parameter must be supplied | | [requirements](slots/requirements.qmd) | | | [requires](slots/requires.qmd) | Observables required by this update rule | | [rhs](slots/rhs.qmd) | | | [role](slots/role.qmd) | | | [run_id](slots/run_id.qmd) | BIDS run number | | [runtime_platform](slots/runtime_platform.qmd) | Execution backends or platforms (e | | [same_as](slots/same_as.qmd) | URIs that unambiguously identify this tool (Wikidata, bio | | [sample](slots/sample.qmd) | | | [sampler](slots/sampler.qmd) | MCMC sampler ('nuts') | | [sampling_period](slots/sampling_period.qmd) | Time between samples (inverse of sampling_rate) | | [sampling_period_unit](slots/sampling_period_unit.qmd) | Unit of the sampling period (e | | [sampling_rate](slots/sampling_rate.qmd) | Sample rate of thedataLocationwaveform in samples per millisecond (e | | [scale](slots/scale.qmd) | The scale this score belongs to, if applicable | | [scipy_ode_base](slots/scipy_ode_base.qmd) | | | [score](slots/score.qmd) | | | [seed](slots/seed.qmd) | Random seed for reproducible graph generation | | [segmentation](slots/segmentation.qmd) | BIDS seg- entity (e | | [session_id](slots/session_id.qmd) | BIDS session identifier | | [sessions](slots/sessions.qmd) | Data collection sessions for this subject | | [settings](slots/settings.qmd) | | | [sex](slots/sex.qmd) | Biological sex | | [shape](slots/shape.qmd) | Matrix dimensions [N, M] | | [sigma](slots/sigma.qmd) | Observation-noise scale of the likelihood | | [simulation_experiments](slots/simulation_experiments.qmd) | | | [simulation_period](slots/simulation_period.qmd) | Duration of each simulation step (e | | [size](slots/size.qmd) | File size in bytes at fingerprinting | | [skip_t](slots/skip_t.qmd) | Number of samples to skip at the start (transient removal) | | [software](slots/software.qmd) | | | [software_environment](slots/software_environment.qmd) | Software environment used to generate this data | | [solver](slots/solver.qmd) | ODE solver for time_integration method | | [source](slots/source.qmd) | | | [source_branch](slots/source_branch.qmd) | Name of a previously computed branch (for from_branch method) | | [source_code](slots/source_code.qmd) | | | [source_experiment](slots/source_experiment.qmd) | Reference to the SimulationExperiment that generated this TimeSeries | | [source_network](slots/source_network.qmd) | Path or name of the Network whose nodes define the source endpoints of this E... | | [source_point](slots/source_point.qmd) | Which point on the source branch: 'endpoint', 'hopf:1', 'fold:2', a step numb... | | [source_url](slots/source_url.qmd) | Canonical source or repository URL | | [source_var](slots/source_var.qmd) | Output variable from source node to use (e | | [sources](slots/sources.qmd) | | | [space](slots/space.qmd) | Ordered list of exploration axes spanning the search space | | [sparse](slots/sparse.qmd) | Whether the coupling uses sparse representations | | [stages](slots/stages.qmd) | Ordered list of optimization stages | | [state](slots/state.qmd) | Per-node initial state variable values, keyed by state variable name | | [state_variables](slots/state_variables.qmd) | | | [state_wise_sigma](slots/state_wise_sigma.qmd) | | | [step](slots/step.qmd) | Step size | | [step_size](slots/step_size.qmd) | | | [steps](slots/steps.qmd) | Ordered intermediate steps | | [stimulation](slots/stimulation.qmd) | | | [stimulation_variable](slots/stimulation_variable.qmd) | | | [stimulus](slots/stimulus.qmd) | | | [strategy](slots/strategy.qmd) | Search strategy over the decision space (thespaceaxes) | | [structural_measures](slots/structural_measures.qmd) | BEP017 measure names for structural connectivity (e | | [subject_id](slots/subject_id.qmd) | BIDS subject identifier | | [subjects](slots/subjects.qmd) | Ordered list of subject IDs (e | | [subnetwork](slots/subnetwork.qmd) | Optional finer-scale Network that "lives inside" this Node (network-of-networ... | | [symbol](slots/symbol.qmd) | | | [symmetry](slots/symmetry.qmd) | Edge symmetry type for NetworkDynamics | | [system_type](slots/system_type.qmd) | | | [tail](slots/tail.qmd) | | | [tail_samples](slots/tail_samples.qmd) | Number of samples from the end to use | | [target](slots/target.qmd) | Target node ID (set for explicit edges, absent for template edges) | | [target_component](slots/target_component.qmd) | Component to attach this event to | | [target_data](slots/target_data.qmd) | Reference to empirical data observation for matching objectives | | [target_network](slots/target_network.qmd) | Path or name of the Network whose nodes define the target endpoints (e | | [target_parameter](slots/target_parameter.qmd) | The parameter to update (e | | [target_regions](slots/target_regions.qmd) | Regions a stimulus-type event targets: 'all' (broadcast to every node) or exp... | | [target_structure](slots/target_structure.qmd) | Anatomical target structure from a brain atlas | | [target_value](slots/target_value.qmd) | Target value for activity objectives | | [target_var](slots/target_var.qmd) | Input variable on target node to connect to (e | | [target_variable](slots/target_variable.qmd) | State variable that a stimulus-type event drives — the variable its signal is... | | [targets](slots/targets.qmd) | State variables this noise applies to; if omitted, applies globally | | [task_iri](slots/task_iri.qmd) | Cognitive Atlas (``cogat:``) IRI of the assessment instrument / task that pro... | | [task_name](slots/task_name.qmd) | BIDS task name for the simulation (e | | [template](slots/template.qmd) | BIDS tpl- entity (e | | [tensor_coefficient](slots/tensor_coefficient.qmd) | Optional anisotropic tensor (e | | [terminology](slots/terminology.qmd) | Add the parcellation terminology version used for this brain atlas version | | [threshold_applied](slots/threshold_applied.qmd) | Threshold value applied to the E-field simulation | | [time](slots/time.qmd) | | | [time_dependent](slots/time_dependent.qmd) | | | [time_integrator](slots/time_integrator.qmd) | e | | [time_post_surgery](slots/time_post_surgery.qmd) | Timepoint of assessment in days or months after implantation | | [time_range](slots/time_range.qmd) | Time range for generated TimeSeries (for kernel generators) | | [time_scale](slots/time_scale.qmd) | Time unit for the integration / simulation | | [time_unit](slots/time_unit.qmd) | Default time unit for the network | | [timepoint](slots/timepoint.qmd) | Timepoint of assessment (e | | [timing_info](slots/timing_info.qmd) | | | [title](slots/title.qmd) | | | [tol_stability](slots/tol_stability.qmd) | Tolerance on real part of eigenvalue for stability boundary | | [tolerances](slots/tolerances.qmd) | Abs/rel tolerances | | [tool_role](slots/tool_role.qmd) | Primary function(s) in a simulation workflow | | [tractogram](slots/tractogram.qmd) | Reference to tractography data | | [trajectory](slots/trajectory.qmd) | The planned trajectory for electrode implantation | | [transform](slots/transform.qmd) | Optional decode applied to this axis's value before it is bound to the refere... | | [transforms](slots/transforms.qmd) | Ordered list of transforms applied to edge property matrices | | [transient_time](slots/transient_time.qmd) | | | [trigger_times](slots/trigger_times.qmd) | Predetermined trigger times for preset_time events | | [truncation_window](slots/truncation_window.qmd) | Truncated-BPTT window in milliseconds of simulated time: gradients flow back ... | | [type](slots/type.qmd) | Optional graph family name | | [unit](slots/unit.qmd) | Physical unit of measurement | | [update_expression](slots/update_expression.qmd) | | | [update_rules](slots/update_rules.qmd) | How parameters are updated each iteration | | [url](slots/url.qmd) | (Deprecated) Use source_url | | [valid_diagonal](slots/valid_diagonal.qmd) | Self-connections are meaningful | | [value](slots/value.qmd) | Numeric, string, or boolean value, OR an array (nested list) for array-valued... | | [values](slots/values.qmd) | | | [variable_of_interest](slots/variable_of_interest.qmd) | | | [vectorized](slots/vectorized.qmd) | Opt in to the vectorized matmul fast path for a source-only coupling — one wh... | | [version](slots/version.qmd) | Version of the instrument (e | | [version_spec](slots/version_spec.qmd) | Version or constraint specifier (e | | [vertex_to_region](slots/vertex_to_region.qmd) | Array mapping each vertex index to its parent region index | | [vertices_field](slots/vertices_field.qmd) | When the mesh is inlined on a Network, the dotted path inside the parent's h5... | | [voi](slots/voi.qmd) | Variable of interest index (which state variable to monitor) | | [volume_data](slots/volume_data.qmd) | Reference to raw or thresholded volume | | [warmup](slots/warmup.qmd) | Whether to apply learning rate warmup to this update rule | | [warmup_from](slots/warmup_from.qmd) | Previous stage to initialize from | | [warmup_source](slots/warmup_source.qmd) | Reference to transient simulation result for history initialization (e | | [weight](slots/weight.qmd) | Connection weight (explicit edges) | | [weight_distribution](slots/weight_distribution.qmd) | Distribution to sample per-region stimulus weights from, as an alternative to... | | [weighted](slots/weighted.qmd) | Matrix entries carry weights (not just 0/1) | | [weighting](slots/weighting.qmd) | | | [weights](slots/weights.qmd) | Per-node stimulus weighting, aligned withnodes` |