Index

_

__init__() (att.benchmarks.CouplingBenchmark method) (att.binding.BindingDetector method) (att.cone.ConeDetector method) (att.embedding.JointEmbedder method) (att.embedding.TakensEmbedder method) (att.neuro.EEGLoader method) (att.topology.PersistenceAnalyzer method) (att.transitions.TransitionDetector method)

A

aizawa_system() (in module att.synthetic) (in module att.synthetic.generators) att.benchmarks module att.benchmarks.methods module att.binding module att.cli module att.cli.main module att.cone module att.config module att.config.experiment module att.config.seed module att.embedding module att.embedding.delay module att.embedding.dimension module att.embedding.validation module

att.llm module att.neuro module att.neuro.eeg_params module att.neuro.embedding module att.surrogates module att.surrogates.core module att.synthetic module att.synthetic.generators module att.topology module att.transitions module att.viz module att.viz.plotting module attention_to_distance() (att.llm.AttentionHiddenBinding static method), [1] AttentionHiddenBinding (class in att.llm), [1] availability_profile() (att.cone.ConeDetector method), [1]

B

betti_matrices (att.llm.CROCKERMatrix property), [1] binding_features() (att.binding.BindingDetector method), [1] binding_image() (att.binding.BindingDetector method), [1]

binding_profile() (att.llm.AttentionHiddenBinding method), [1] binding_score() (att.binding.BindingDetector method), [1] BindingDetector (class in att.binding), [1] bottleneck_profile() (att.llm.LayerwiseAnalyzer method), [1]

C

compute_binding() (att.llm.AttentionHiddenBinding method), [1] compute_binding_from_diagrams() (att.llm.AttentionHiddenBinding method), [1] ConeDetector (class in att.cone), [1] confidence_interval() (att.binding.BindingDetector method), [1] coupled_lorenz() (in module att.synthetic) (in module att.synthetic.generators) coupled_oscillators() (in module att.synthetic) (in module att.synthetic.generators)

coupled_rossler_lorenz() (in module att.synthetic) (in module att.synthetic.generators) coupling_influence_subspace() (att.cone.ConeDetector method), [1] CouplingBenchmark (class in att.benchmarks), [1] CROCKERMatrix (class in att.llm), [1] crqa() (in module att.benchmarks) (in module att.benchmarks.methods)

D

depth_asymmetry() (att.cone.ConeDetector method), [1]

detect_changepoints() (att.transitions.TransitionDetector method), [1] distance() (att.topology.PersistenceAnalyzer method), [1]

E

EEGLoader (class in att.neuro), [1] embed_channel() (in module att.neuro) (in module att.neuro.embedding) embedding_quality() (att.binding.BindingDetector method), [1] EmbeddingDegeneracyWarning, [1] (class in att.embedding.validation) ensemble_scores (att.binding.BindingDetector property), [1] entropy_profile() (att.llm.LayerwiseAnalyzer method), [1] estimate_delay() (in module att.embedding) (in module att.embedding.delay)

estimate_dimension() (in module att.embedding) (in module att.embedding.dimension) estimate_projection_axis() (att.cone.ConeDetector method), [1] export_to_json() (in module att.viz) (in module att.viz.plotting) extract_batch() (att.llm.TopologicalFeatureExtractor method), [1] extract_per_problem() (att.llm.TopologicalFeatureExtractor method), [1] extract_single() (att.llm.TopologicalFeatureExtractor method), [1]

F

feature_names (att.llm.TopologicalFeatureExtractor property), [1] filtration_range (att.llm.CROCKERMatrix property), [1] fit() (att.binding.BindingDetector method), [1] (att.cone.ConeDetector method), [1] (att.embedding.JointEmbedder method), [1] (att.embedding.TakensEmbedder method), [1] (att.llm.LayerwiseAnalyzer method), [1] (att.llm.ZigzagLayerAnalyzer method), [1]

fit_by_difficulty() (att.llm.CROCKERMatrix method), [1] fit_by_layer() (att.llm.CROCKERMatrix method), [1] fit_transform() (att.embedding.JointEmbedder method), [1] (att.embedding.TakensEmbedder method), [1] (att.topology.PersistenceAnalyzer method), [1] (att.transitions.TransitionDetector method), [1] full_chain_emergence() (att.cone.ConeDetector method), [1]

G

get_channel_groups() (att.neuro.EEGLoader static method), [1] get_events() (att.neuro.EEGLoader method), [1] get_fallback_params() (att.neuro.EEGLoader static method), [1] (in module att.neuro) (in module att.neuro.eeg_params) get_layer_cloud() (att.llm.HiddenStateLoader method), [1]

get_level_cloud() (att.llm.HiddenStateLoader method), [1] get_level_mask() (att.llm.HiddenStateLoader method), [1] get_rng() (in module att.config) (in module att.config.seed) get_seed() (in module att.config.seed) get_sfreq() (att.neuro.EEGLoader method), [1]

H

hidden_dim (att.llm.HiddenStateLoader property), [1]

HiddenStateLoader (class in att.llm), [1]

I

id_profile() (in module att.llm), [1]

J

JointEmbedder (class in att.embedding), [1]

K

knn_graph_laplacian() (in module att.topology)

kuramoto_oscillators() (in module att.synthetic) (in module att.synthetic.generators)

L

last_hidden (att.llm.HiddenStateLoader property), [1] layer_hidden (att.llm.HiddenStateLoader property), [1] LayerwiseAnalyzer (class in att.llm), [1] level_counts() (att.llm.HiddenStateLoader method), [1] levels (att.llm.HiddenStateLoader property), [1] load() (att.neuro.EEGLoader method), [1]

load_config() (in module att.config) (in module att.config.experiment) load_from_json() (in module att.viz) (in module att.viz.plotting) lorenz_system() (in module att.synthetic) (in module att.synthetic.generators)

M

main() (in module att.cli) (in module att.cli.main) model_name (att.llm.HiddenStateLoader property), [1] module att.benchmarks att.benchmarks.methods att.binding att.cli att.cli.main att.cone att.config att.config.experiment att.config.seed att.embedding att.embedding.delay att.embedding.dimension att.embedding.validation att.llm att.neuro att.neuro.eeg_params att.neuro.embedding att.surrogates att.surrogates.core att.synthetic att.synthetic.generators att.topology att.transitions att.viz att.viz.plotting

N

n_features (att.llm.TopologicalFeatureExtractor property), [1]

n_problems (att.llm.HiddenStateLoader property), [1] num_layers (att.llm.HiddenStateLoader property), [1]

P

pac() (in module att.benchmarks) (in module att.benchmarks.methods) pairwise_l1_distances() (att.llm.CROCKERMatrix method), [1] parameter_labels (att.llm.CROCKERMatrix property), [1] partition() (att.llm.TokenPartitioner method), [1] partition_batch() (att.llm.TokenPartitioner method), [1] PersistenceAnalyzer (class in att.topology), [1] phase_randomize() (in module att.surrogates) (in module att.surrogates.core) phd_dimension() (in module att.llm), [1] plot() (att.topology.PersistenceAnalyzer method), [1] plot_attention_binding_heatmap() (in module att.viz.plotting) plot_attractor_3d() (in module att.viz) (in module att.viz.plotting) plot_barcode() (in module att.viz) (in module att.viz.plotting) plot_benchmark_sweep() (in module att.viz) (in module att.viz.plotting) plot_betti_curve() (in module att.viz) (in module att.viz.plotting) plot_binding_comparison() (in module att.viz) (in module att.viz.plotting) plot_binding_image() (att.binding.BindingDetector method), [1] (in module att.viz) (in module att.viz.plotting)

plot_comparison() (att.binding.BindingDetector method), [1] plot_compression_decomposition() (in module att.viz.plotting) plot_crocker() (in module att.viz.plotting) plot_cross_model_zscore() (in module att.viz.plotting) plot_id_profile() (in module att.viz.plotting) plot_persistence_diagram() (in module att.viz) (in module att.viz.plotting) plot_persistence_image() (in module att.viz) (in module att.viz.plotting) plot_roc_curves() (in module att.viz.plotting) plot_spectral_comparison() (in module att.viz.plotting) plot_surrogate_distribution() (in module att.viz) (in module att.viz.plotting) plot_timeline() (att.transitions.TransitionDetector method), [1] plot_token_partition_topology() (in module att.viz.plotting) plot_transition_timeline() (in module att.viz) (in module att.viz.plotting) plot_zigzag_barcode() (in module att.viz.plotting) plot_zigzag_comparison() (in module att.viz.plotting) plot_zscore_profile() (in module att.viz.plotting) preprocess() (att.neuro.EEGLoader method), [1]

R

register_method() (att.benchmarks.CouplingBenchmark method), [1] results_per_layer (att.llm.LayerwiseAnalyzer property), [1]

rossler_system() (in module att.synthetic) (in module att.synthetic.generators) run() (att.benchmarks.CouplingBenchmark method), [1]

S

save_config() (in module att.config) (in module att.config.experiment) seq_lengths (att.llm.HiddenStateLoader property), [1] set_seed() (in module att.config) (in module att.config.seed) slice_at_depth() (att.cone.ConeDetector method), [1]

spectral_distance_matrix() (in module att.topology) svd_embedding() (in module att.embedding) (in module att.embedding.validation) sweep() (att.benchmarks.CouplingBenchmark method), [1] switching_rossler() (in module att.synthetic) (in module att.synthetic.generators)

T

TakensEmbedder (class in att.embedding), [1] test_significance() (att.binding.BindingDetector method), [1] (att.llm.AttentionHiddenBinding method), [1] time_shuffle() (in module att.surrogates) (in module att.surrogates.core) to_image() (att.topology.PersistenceAnalyzer method), [1] to_landscape() (att.topology.PersistenceAnalyzer method), [1] to_timeseries() (att.neuro.EEGLoader method), [1] token_trajectories (att.llm.HiddenStateLoader property), [1] TokenPartitioner (class in att.llm), [1]

TopologicalFeatureExtractor (class in att.llm), [1] TopologyDimensionalityWarning transfer_entropy() (in module att.benchmarks) (in module att.benchmarks.methods) transform() (att.embedding.JointEmbedder method), [1] (att.embedding.TakensEmbedder method), [1] transform_marginals() (att.embedding.JointEmbedder method), [1] TransitionDetector (class in att.transitions), [1] twin_surrogate() (in module att.surrogates) (in module att.surrogates.core) twonn_dimension() (in module att.llm), [1]

U

unique_levels (att.llm.HiddenStateLoader property), [1]

V

validate_embedding() (in module att.embedding) (in module att.embedding.validation)

validate_partition() (att.llm.TokenPartitioner static method), [1]

Z

ZigzagLayerAnalyzer (class in att.llm), [1]

zscore_profile() (att.llm.LayerwiseAnalyzer method), [1]