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Contents:

  • Installation
  • Technical overview
  • Framework
  • API reference
    • engine: Differentiable engine
    • functional: Functions and functionals
      • activation: Activation functions
        • amplitude_tanh
        • amplitude_atanh
        • corrnorm
        • isochor: PSD normalisation
      • cmass: Centre of mass
        • cmass_coor: Centre of mass, any coordinates
        • cmass: Centre of mass, array coordinates
        • diffuse: Diffuseness around centre of mass
        • Displacement from a reference centre of mass
      • connectopy: Connectopic manifolds
        • laplacian_eigenmaps
        • diffusion_mapping
      • cov: Covariances and correlations
        • cov: Covariance
        • corr: Pearson correlation
        • partialcov: Partial covariance
        • partialcorr: Partial correlation
        • pairedcov: Paired covariance
        • pairedcorr: Paired correlation
        • conditionalcov: Conditional covariance
        • conditionalcorr: Conditional correlation
        • precision: Inverse covariance (precision)
      • fourier: Frequency-domain filter
        • product_filter
        • product_filtfilt: Zero-phase filter
        • unwrap: Unwrap phase
        • analytic_signal
        • hilbert_transform
        • envelope
        • instantaneous_phase
        • instantaneous_frequency
        • env_inst
      • graph: Graphs and networks
        • girvan_newman_null
        • modularity_matrix
        • coaffiliation: Community coaffiliation
        • relaxed_modularity
        • graph_laplacian: Graph Laplacian
      • interpolate: Interpolation and imputation
        • hybrid_interpolate: Linear + spectral interpolation
        • linear_interpolate: Linear interpolation
        • weighted_interpolate
        • spectral_interpolate
      • kernel: Parameterised kernels
        • linear_kernel
        • param_norm
        • linear_distance
        • polynomial_kernel
        • sigmoid_kernel
        • gaussian_kernel
        • rbf_kernel
        • cosine_kernel
        • cov_kernel
        • corr_kernel
      • matrix: Matrix operations
        • cholesky_invert
        • symmetric
        • spd
        • expand_outer
        • recondition_eigenspaces
        • delete_diagonal
        • diag_embed
        • fill_diagonal
        • toeplitz_2d
        • toeplitz
        • sym2vec
        • vec2sym
        • squareform
      • residualise
      • semidefinite: Positive semidefinite cone
        • tangent_project_spd
        • cone_project_spd
        • mean_euc_spd
        • mean_harm_spd
        • mean_logeuc_spd
        • mean_geom_spd
      • sparse: Sparse matrix operations
        • random_sparse
        • spdiagmm
        • dspdmm
        • spspmm_full
        • topk
        • as_topk
        • full_as_topk
        • sparse_astype
        • trace_spspmm
        • spspmm
        • spsp_pairdiff
        • select_indices
        • topkx
        • sp_block_serialise
        • splr_hadamard
        • spsp_innerpaired
        • topk_to_bcoo
        • topk_diagzero
        • topk_diagreplace
        • block_serialise
      • sphere: Spherical coordinates
        • spherical_geodesic
        • sphere_to_normals
        • sphere_to_latlong
        • spatial_conv
        • spherical_conv
        • euclidean_conv
      • sylo: Sylo function
      • symmap: Symmetric matrix maps
        • symmap
        • symexp
        • symlog
        • symsqrt
      • tsconv: Time series convolution
        • conv
        • tsconv2d
        • basischan
        • basisconv2d
        • polychan
        • polyconv2d
      • utils: Miscellaneous
        • conform_mask
        • apply_mask
        • mask_tensor
        • complex_decompose
        • complex_recompose
        • amplitude_apply
      • window: Random windowing
        • sample_windows
        • sample_nonoverlapping_windows_existing_ax
        • sample_nonoverlapping_windows_new_ax
        • sample_overlapping_windows_new_ax
        • sample_overlapping_windows_existing_ax
    • init: Initialisation schemes
      • atlas: Atlas initialisation
        • BaseAtlas
        • DirichletInitBaseAtlas
        • DiscreteVolumetricAtlas
        • MultiVolumetricAtlas
        • MultifileVolumetricAtlas
        • CortexSubcortexCIfTIAtlas
        • DirichletInitVolumetricAtlas
        • DirichletInitSurfaceAtlas
        • AtlasInitialiser
      • atlasmixins: Atlas mixins
      • base: Base initialisations
        • from_distr_init
        • constant_init
        • identity_init
        • MappedInitialiser
        • DistributionInitialiser
        • IdentityInitialiser
      • deltaplus
      • dirichlet
      • freqfilter: Frequency band init
        • FreqFilterSpec
      • iirfilter: IIR filter init
      • laplace
      • mapparam: Mapped parameters and parameter maps
        • MappedParameter
        • DomainMappedParameter
        • IdentityMappedParameter
        • AffineMappedParameter
        • TanhMappedParameter
        • AmplitudeTanhMappedParameter
        • MappedLogits
        • NormSphereParameter
        • ProbabilitySimplexParameter
        • AmplitudeProbabilitySimplexParameter
        • OrthogonalParameter
        • IsochoricParameter
        • Clip
        • Renormalise
        • ForcePositiveDefinite
        • PhaseAmplitudeMixin
      • mpbl
      • semidefinite
        • TangencyInitialiser
        • SemidefiniteMean
      • sylo
      • toeplitz
    • loss: Loss and regularisation
      • Loss: Base class for scalar-valued losses
      • ParameterisedLoss: Extensible class for custom parameterised losses
      • MSELoss: Mean squared error
      • NormedLoss: Normed parameter regularisation
      • identity: Identity function
      • zero: Zero function
      • difference: Elementwise difference
      • constraint_violation: Soft constraints
      • unilateral_loss: Unilateral penalties
      • hinge_loss: SVM hinge loss
      • smoothness: Backwards differences
      • bimodal_symmetric: Minimal distance from 2 modes
      • det_gram: Gramian determinant
      • log_det_gram: Gram log-determinant loss
      • entropy: Categorical entropy
      • kl_divergence: Kullback-Leibler divergence
      • js_divergence: Jensen-Shannon divergence
      • bregman_divergence: Bregman divergences
      • equilibrium: Equilibrium loss
      • second_moment: Second moments
      • auto_tol: Significance tolerance
      • batch_corr: Batch-axis correlation
      • qcfc: QC-FC measures and loss
      • reference_tether: Spatial tether to reference points
      • interhemispheric_tether: Inter-hemispheric tethering loss
      • compactness: Compactness
      • dispersion: Vector dispersion
      • multivariate_kurtosis: Time series stationarity
      • connectopy: Generalised connectopy
      • modularity: Relaxed modularity
      • sum_scalarise: Sum scalarisation
      • mean_scalarise: Mean scalarisation
      • meansq_scalarise: Squared mean scalarisation
      • max_scalarise: Maximum-value scalarisation
      • norm_scalarise: Norm scalarisation
      • vnorm_scalarise: Vector norm scalarisation
      • wmean_scalarise: Weighted mean scalarisation
      • selfwmean_scalarise: Self-weighted mean scalarisation
      • LossApply: Selectively apply loss to parameters
      • LossScheme: Scheme for multiple losses
    • neuro: Neuroscience data utilities
      • synth: Data synthesis
        • match_spectra
        • match_covariance
        • match_reference
        • match_cov_and_spectrum
        • synthesise_matched
        • synthesise_from_cov_and_spectrum
    • nn: Neural network modules
      • activation: Activation functions as modules
        • CorrelationNorm: Correlation normalisation
        • Isochor: Isochoric normalisation
      • atlas: Atlas layers
        • AtlasLinear: Linear atlas layer
      • cov: Covariance modules
        • BaseCovariance: Covariance base class
        • UnaryCovariance
        • UnaryCovarianceTW
        • UnaryCovarianceUW
        • BinaryCovariance
        • BinaryCovarianceTW
        • BinaryCovarianceUW
      • freqfilter: Frequency-domain filter layer
      • iirfilter: IIR filter layer
      • interpolate: Interpolation layers
        • SpectralInterpolate
        • LinearInterpolate
        • HybridInterpolate
      • recombinator
        • Recombinator
      • Residualise
      • semidefinite
        • TangentProject
        • BatchTangentProject
      • SPDNoise
      • SVM
      • sylo
        • Sylo
        • SyloResNet
      • vertcom: Vertex compression
        • VerticalCompression
      • WindowAmplifier
  • Examples
  • hypercoil
  • functional: Functions and functionals

matrix: Matrix operations#

Special matrix functions.

  • cholesky_invert
  • symmetric
  • spd
  • expand_outer
  • recondition_eigenspaces
  • delete_diagonal
  • diag_embed
  • fill_diagonal
  • toeplitz_2d
  • toeplitz
  • sym2vec
  • vec2sym
  • squareform
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