Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Z _ __init__() (fishy.analysis.biomarker.AutomatedBiomarkerDiscovery method) (fishy.analysis.xai.ExplainerConfig method) (fishy.analysis.xai.GradCAM method) (fishy.analysis.xai.ModelWrapper method) (fishy.data.augmentation.AugmentationConfig method) (fishy.data.augmentation.DataAugmenter method) (fishy.data.datasets.BalancedBatchSampler method) (fishy.data.datasets.BaseDataset method) (fishy.data.datasets.SiameseDataset method) (fishy.data.module.DataModule method) (fishy.data.module.DataProcessor method) (fishy.engine.muon.Muon method) (fishy.engine.trainer.EMA method) (fishy.engine.trainer.Trainer method) (fishy.experiments.classic_training.SklearnTrainer method) (fishy.experiments.contrastive.ContrastiveConfig method) (fishy.experiments.contrastive.ContrastiveTrainer method) (fishy.experiments.deep_training.MixedOptimizer method) (fishy.experiments.deep_training.ModelTrainer method) (fishy.experiments.pre_training.PreTrainer method) (fishy.experiments.pre_training.PreTrainingConfig method) (fishy.experiments.pre_training.PreTrainingOrchestrator method) (fishy.experiments.unified_trainer.UnifiedTrainer method) (fishy.models.classic.opls_da.OPLS_DA method) (fishy.models.contrastive.barlow_twins.BarlowTwinsLoss method) (fishy.models.contrastive.barlow_twins.BarlowTwinsModel method) (fishy.models.contrastive.byol.BYOLLoss method) (fishy.models.contrastive.byol.BYOLModel method) (fishy.models.contrastive.moco.MoCoLoss method) (fishy.models.contrastive.moco.MoCoModel method) (fishy.models.contrastive.simclr.ProjectionHead method) (fishy.models.contrastive.simclr.SimCLRLoss method) (fishy.models.contrastive.simclr.SimCLRModel method) (fishy.models.contrastive.simsiam.SimSiamLoss method) (fishy.models.contrastive.simsiam.SimSiamModel method) (fishy.models.deep.augformer.AugFormer method) (fishy.models.deep.augformer.EngramMemory method) (fishy.models.deep.augformer.ManifoldProjection method) (fishy.models.deep.augformer.MultiHeadAttention method) (fishy.models.deep.augformer.MultiHeadLatentAttention method) (fishy.models.deep.augformer.RMSNorm method) (fishy.models.deep.augformer.SpectralGating method) (fishy.models.deep.augformer.TransformerBlock method) (fishy.models.deep.augformer_v2.AugFormerV2 method) (fishy.models.deep.augformer_v2.LeakyReluSq method) (fishy.models.deep.augformer_v2.MultiHeadAttentionV2 method) (fishy.models.deep.augformer_v2.TransformerBlockV2 method) (fishy.models.deep.cnn.CNN method) (fishy.models.deep.dense.Dense method) (fishy.models.deep.ensemble.MultiScaleTransformerEnsemble method) (fishy.models.deep.gatedmlp.GatedMLP method) (fishy.models.deep.gatedmlp.GatedMLPBlock method) (fishy.models.deep.gatedmlp.RMSNorm method) (fishy.models.deep.gmoe.SparselyGatedMoE method) (fishy.models.deep.hybrid.Hybrid method) (fishy.models.deep.kan.KAN method) (fishy.models.deep.kan.KANLayer method) (fishy.models.deep.lewm.GatedEncoderBlock method) (fishy.models.deep.lewm.LEWM method) (fishy.models.deep.lewm.SIGReg method) (fishy.models.deep.lstm.LSTM method) (fishy.models.deep.mamba.Mamba method) (fishy.models.deep.mamba.MambaBlock method) (fishy.models.deep.mamba.SiameseMamba method) (fishy.models.deep.moe.MixtureOfExperts method) (fishy.models.deep.nextformer.GroupedQueryAttention method) (fishy.models.deep.nextformer.NextFormer method) (fishy.models.deep.nextformer.NextFormerBlock method) (fishy.models.deep.nextformer.RMSNorm method) (fishy.models.deep.nextformer.SwiGLU method) (fishy.models.deep.ode.ODE method) (fishy.models.deep.ode.ODEFunc method) (fishy.models.deep.ordinal.EarlyStopping method) (fishy.models.deep.ordinal.PositionalEncoding method) (fishy.models.deep.ordinal.TransformerOrdinal method) (fishy.models.deep.performer.FastAttention method) (fishy.models.deep.performer.Performer method) (fishy.models.deep.performer.PerformerLayer method) (fishy.models.deep.rcnn.RCNN method) (fishy.models.deep.rcnn.ResidualBlock method) (fishy.models.deep.rwkv.RWKV method) (fishy.models.deep.rwkv.RWKVBlock method) (fishy.models.deep.rwkv.RWKVParallel method) (fishy.models.deep.srmlp.GatedMLPBlock method) (fishy.models.deep.srmlp.SRMLP method) (fishy.models.deep.srmlp.SRNorm method) (fishy.models.deep.tcn.Chomp1d method) (fishy.models.deep.tcn.TCN method) (fishy.models.deep.tcn.TemporalBlock method) (fishy.models.deep.transformer.MultiHeadAttention method) (fishy.models.deep.transformer.Transformer method) (fishy.models.deep.vae.SiameseVAE method) (fishy.models.deep.vae.VAE method) (fishy.models.deep.wavenet.CausalConv1d method) (fishy.models.deep.wavenet.ResidualBlock method) (fishy.models.deep.wavenet.WaveNet method) (fishy.models.evolutionary.eda.EDA method) (fishy.models.evolutionary.es.ES method) (fishy.models.evolutionary.ga.GA method) (fishy.models.evolutionary.gp.GP method) (fishy.models.evolutionary.pso.PSO method) (fishy.models.probabilistic.gp.GaussianProcess method) (fishy.models.probabilistic.laplace_logistic.BayesianLogisticRegression method) (fishy.models.probabilistic.probabilistic_svc.ProbabilisticSVC method) A adapt_for_finetuning() (fishy.experiments.pre_training.PreTrainingOrchestrator method) apply_shadow() (fishy.engine.trainer.EMA method) ask_numbered_choice() (in module fishy.cli.wizard) attention (fishy.models.deep.nextformer.NextFormerBlock attribute) attention_layers (fishy.models.deep.transformer.Transformer attribute) attention_norm (fishy.models.deep.nextformer.NextFormerBlock attribute) AugFormer (class in fishy.models.deep.augformer) AugFormerV2 (class in fishy.models.deep.augformer_v2) augment() (fishy.data.augmentation.DataAugmenter method) AugmentationConfig (class in fishy.data.augmentation) AutomatedBiomarkerDiscovery (class in fishy.analysis.biomarker) B b_splines() (fishy.models.deep.kan.KANLayer method) BalancedBatchSampler (class in fishy.data.datasets) barlow_lambda (fishy.experiments.contrastive.ContrastiveConfig attribute) BarlowTwinsLoss (class in fishy.models.contrastive.barlow_twins) BarlowTwinsModel (class in fishy.models.contrastive.barlow_twins) BaseDataset (class in fishy.data.datasets) batch_size (fishy.experiments.contrastive.ContrastiveConfig attribute) BayesianLogisticRegression (class in fishy.models.probabilistic.laplace_logistic) blocks (fishy.models.deep.nextformer.NextFormer attribute) byol_m (fishy.experiments.contrastive.ContrastiveConfig attribute) BYOLLoss (class in fishy.models.contrastive.byol) BYOLModel (class in fishy.models.contrastive.byol) C CausalConv1d (class in fishy.models.deep.wavenet) Chomp1d (class in fishy.models.deep.tcn) chunk_size (fishy.experiments.pre_training.PreTrainingConfig attribute), [1] classifier (fishy.models.deep.ensemble.MultiScaleTransformerEnsemble attribute) CNN (class in fishy.models.deep.cnn) compileMultiTree() (in module fishy.models.evolutionary.gp) config (fishy.experiments.pre_training.PreTrainingOrchestrator attribute) contrastive_method (fishy.experiments.contrastive.ContrastiveConfig attribute) ContrastiveConfig (class in fishy.experiments.contrastive) ContrastiveTrainer (class in fishy.experiments.contrastive) convert_class_labels_to_integers() (in module fishy.models.deep.ordinal) coral_logits_to_prediction() (in module fishy.models.deep.ordinal) coral_loss() (in module fishy.engine.losses) create_data_module() (in module fishy.data.module) create_optimizer() (fishy.experiments.deep_training.ModelTrainer method) create_scheduler() (fishy.experiments.deep_training.ModelTrainer method) crop_enabled (fishy.data.augmentation.AugmentationConfig attribute) (fishy.experiments.pre_training.PreTrainingConfig attribute), [1] crop_size (fishy.data.augmentation.AugmentationConfig attribute) (fishy.experiments.pre_training.PreTrainingConfig attribute), [1] ctx (fishy.experiments.pre_training.PreTrainingOrchestrator attribute) cumulative_link_loss() (in module fishy.engine.losses) CumulativeLinkLoss (class in fishy.models.deep.ordinal) CustomDataset (class in fishy.data.datasets) D DataAugmenter (class in fishy.data.augmentation) DataModule (class in fishy.data.module) DataProcessor (class in fishy.data.module) dataset (fishy.experiments.contrastive.ContrastiveConfig attribute) DeepEngine (class in fishy.engine.trainer) Dense (class in fishy.models.deep.dense) device (fishy.analysis.xai.ExplainerConfig attribute) (fishy.experiments.pre_training.PreTrainingConfig attribute), [1] (fishy.experiments.pre_training.PreTrainingOrchestrator attribute) display_final_summary() (in module fishy.cli.main) display_statistical_summary() (in module fishy.analysis.statistical) dropout (fishy.models.deep.dense.Dense attribute) (fishy.models.deep.nextformer.NextFormerBlock attribute) (fishy.models.deep.transformer.Transformer attribute) (fishy.models.deep.vae.VAE attribute) E EarlyStopping (class in fishy.models.deep.ordinal) EDA (class in fishy.models.evolutionary.eda) EMA (class in fishy.engine.trainer) embedding_dim (fishy.experiments.contrastive.ContrastiveConfig attribute) enabled (fishy.data.augmentation.AugmentationConfig attribute) encode() (fishy.models.deep.vae.VAE method) encode_labels() (fishy.data.module.DataProcessor method) encoder_type (fishy.experiments.contrastive.ContrastiveConfig attribute) EngramMemory (class in fishy.models.deep.augformer) ensure_conv_input() (in module fishy.models.utils) ensure_seq_input() (in module fishy.models.utils) eps (fishy.models.deep.nextformer.RMSNorm attribute) ES (class in fishy.models.evolutionary.es) evaluate() (fishy.engine.trainer.Trainer method) (in module fishy.models.deep.ordinal) evaluate_model() (fishy.engine.trainer.DeepEngine static method) evaluate_pairwise_performance() (fishy.experiments.contrastive.ContrastiveTrainer method) experts (fishy.models.deep.ensemble.MultiScaleTransformerEnsemble attribute) (fishy.models.deep.gmoe.SparselyGatedMoE attribute) (fishy.models.deep.moe.MixtureOfExperts attribute) ExplainerConfig (class in fishy.analysis.xai) extract_groups() (fishy.data.module.DataProcessor method) F FastAttention (class in fishy.models.deep.performer) fc_out (fishy.models.deep.nextformer.NextFormer attribute) (fishy.models.deep.transformer.MultiHeadAttention attribute) (fishy.models.deep.transformer.Transformer attribute) feed_forward (fishy.models.deep.nextformer.NextFormerBlock attribute) (fishy.models.deep.transformer.Transformer attribute) ffn_norm (fishy.models.deep.nextformer.NextFormerBlock attribute) file_path (fishy.experiments.contrastive.ContrastiveConfig attribute) (fishy.experiments.pre_training.PreTrainingConfig attribute), [1] filter_data() (fishy.data.module.DataProcessor method) filter_data_for_oil() (in module fishy.models.deep.ordinal) fishy module fishy.analysis module fishy.analysis.benchmark module fishy.analysis.biomarker module fishy.analysis.statistical module fishy.analysis.xai module fishy.cli module fishy.cli.main module fishy.cli.wizard module fishy.data module fishy.data.assets module fishy.data.augmentation module fishy.data.datasets module fishy.data.module module fishy.engine module fishy.engine.losses module fishy.engine.muon module fishy.engine.trainer module fishy.experiments module fishy.experiments.classic_training module fishy.experiments.contrastive module fishy.experiments.deep_training module fishy.experiments.pre_training module fishy.experiments.transfer module fishy.experiments.unified_trainer module fishy.models module fishy.models.classic module fishy.models.classic.opls_da module fishy.models.contrastive module fishy.models.contrastive.barlow_twins module fishy.models.contrastive.byol module fishy.models.contrastive.moco module fishy.models.contrastive.simclr module fishy.models.contrastive.simsiam module fishy.models.deep module fishy.models.deep.augformer module fishy.models.deep.augformer_v2 module fishy.models.deep.cnn module fishy.models.deep.dense module fishy.models.deep.ensemble module fishy.models.deep.gatedmlp module fishy.models.deep.gmoe module fishy.models.deep.hybrid module fishy.models.deep.kan module fishy.models.deep.lewm module fishy.models.deep.lstm module fishy.models.deep.mamba module fishy.models.deep.moe module fishy.models.deep.nextformer module fishy.models.deep.ode module fishy.models.deep.ordinal module fishy.models.deep.performer module fishy.models.deep.rcnn module fishy.models.deep.rwkv module fishy.models.deep.srmlp module fishy.models.deep.tcn module fishy.models.deep.transformer module fishy.models.deep.ttt_mixin module fishy.models.deep.vae module fishy.models.deep.wavenet module fishy.models.evolutionary module fishy.models.evolutionary.eda module fishy.models.evolutionary.es module fishy.models.evolutionary.ga module fishy.models.evolutionary.gp module fishy.models.evolutionary.pso module fishy.models.probabilistic module fishy.models.probabilistic.gp module fishy.models.probabilistic.laplace_logistic module fishy.models.probabilistic.probabilistic_svc module fishy.models.utils module fit() (fishy.models.classic.opls_da.OPLS_DA method) (fishy.models.evolutionary.eda.EDA method) (fishy.models.evolutionary.es.ES method) (fishy.models.evolutionary.ga.GA method) (fishy.models.evolutionary.gp.GP method) (fishy.models.evolutionary.pso.PSO method) (fishy.models.probabilistic.gp.GaussianProcess method) (fishy.models.probabilistic.laplace_logistic.BayesianLogisticRegression method) (fishy.models.probabilistic.probabilistic_svc.ProbabilisticSVC method) flip_enabled (fishy.data.augmentation.AugmentationConfig attribute) (fishy.experiments.pre_training.PreTrainingConfig attribute), [1] forward() (fishy.models.contrastive.barlow_twins.BarlowTwinsLoss method) (fishy.models.contrastive.barlow_twins.BarlowTwinsModel method) (fishy.models.contrastive.byol.BYOLLoss method) (fishy.models.contrastive.byol.BYOLModel method) (fishy.models.contrastive.moco.MoCoLoss method) (fishy.models.contrastive.moco.MoCoModel method) (fishy.models.contrastive.simclr.ProjectionHead method) (fishy.models.contrastive.simclr.SimCLRLoss method) (fishy.models.contrastive.simclr.SimCLRModel method) (fishy.models.contrastive.simsiam.SimSiamLoss method) (fishy.models.contrastive.simsiam.SimSiamModel method) (fishy.models.deep.augformer.AugFormer method) (fishy.models.deep.augformer.EngramMemory method) (fishy.models.deep.augformer.ManifoldProjection method) (fishy.models.deep.augformer.MultiHeadAttention method) (fishy.models.deep.augformer.MultiHeadLatentAttention method) (fishy.models.deep.augformer.RMSNorm method) (fishy.models.deep.augformer.SpectralGating method) (fishy.models.deep.augformer.TransformerBlock method) (fishy.models.deep.augformer_v2.AugFormerV2 method) (fishy.models.deep.augformer_v2.LeakyReluSq method) (fishy.models.deep.augformer_v2.MultiHeadAttentionV2 method) (fishy.models.deep.augformer_v2.TransformerBlockV2 method) (fishy.models.deep.cnn.CNN method) (fishy.models.deep.dense.Dense method) (fishy.models.deep.ensemble.MultiScaleTransformerEnsemble method) (fishy.models.deep.gatedmlp.GatedMLP method) (fishy.models.deep.gatedmlp.GatedMLPBlock method) (fishy.models.deep.gatedmlp.RMSNorm method) (fishy.models.deep.gmoe.SparselyGatedMoE method) (fishy.models.deep.hybrid.Hybrid method) (fishy.models.deep.kan.KAN method) (fishy.models.deep.kan.KANLayer method) (fishy.models.deep.lewm.GatedEncoderBlock method) (fishy.models.deep.lewm.LEWM method) (fishy.models.deep.lewm.SIGReg method) (fishy.models.deep.lstm.LSTM method) (fishy.models.deep.mamba.Mamba method) (fishy.models.deep.mamba.MambaBlock method) (fishy.models.deep.mamba.SiameseMamba method) (fishy.models.deep.moe.MixtureOfExperts method) (fishy.models.deep.nextformer.GroupedQueryAttention method) (fishy.models.deep.nextformer.NextFormer method) (fishy.models.deep.nextformer.NextFormerBlock method) (fishy.models.deep.nextformer.RMSNorm method) (fishy.models.deep.nextformer.SwiGLU method) (fishy.models.deep.ode.ODE method) (fishy.models.deep.ode.ODEFunc method) (fishy.models.deep.ordinal.CumulativeLinkLoss method) (fishy.models.deep.ordinal.PositionalEncoding method) (fishy.models.deep.ordinal.TransformerOrdinal method) (fishy.models.deep.performer.FastAttention method) (fishy.models.deep.performer.Performer method) (fishy.models.deep.performer.PerformerLayer method) (fishy.models.deep.rcnn.RCNN method) (fishy.models.deep.rcnn.ResidualBlock method) (fishy.models.deep.rwkv.RWKV method) (fishy.models.deep.rwkv.RWKVBlock method) (fishy.models.deep.rwkv.RWKVParallel method) (fishy.models.deep.srmlp.GatedMLPBlock method) (fishy.models.deep.srmlp.SRMLP method) (fishy.models.deep.srmlp.SRNorm method) (fishy.models.deep.tcn.Chomp1d method) (fishy.models.deep.tcn.TCN method) (fishy.models.deep.tcn.TemporalBlock method) (fishy.models.deep.transformer.MultiHeadAttention method) (fishy.models.deep.transformer.Transformer method) (fishy.models.deep.vae.SiameseVAE method) (fishy.models.deep.vae.VAE method) (fishy.models.deep.wavenet.CausalConv1d method) (fishy.models.deep.wavenet.ResidualBlock method) (fishy.models.deep.wavenet.WaveNet method) forward_one() (fishy.models.contrastive.simclr.SimCLRModel method) (fishy.models.deep.mamba.SiameseMamba method) (fishy.models.deep.vae.SiameseVAE method) forward_ttt() (fishy.models.deep.ttt_mixin.TTTMixin method) G GA (class in fishy.models.evolutionary.ga) gate (fishy.models.deep.gmoe.SparselyGatedMoE attribute) (fishy.models.deep.moe.MixtureOfExperts attribute) GatedEncoderBlock (class in fishy.models.deep.lewm) GatedMLP (class in fishy.models.deep.gatedmlp) GatedMLPBlock (class in fishy.models.deep.gatedmlp) (class in fishy.models.deep.srmlp) GaussianProcess (class in fishy.models.probabilistic.gp) generate_cam() (fishy.analysis.xai.GradCAM method) generate_report() (fishy.analysis.biomarker.AutomatedBiomarkerDiscovery method) get_all_datasets() (in module fishy.cli.main) get_all_models() (in module fishy.cli.main) get_class_names() (fishy.data.module.DataModule method) get_data_path() (in module fishy) get_dataloader() (in module fishy.models.deep.ordinal) get_dataset() (fishy.data.module.DataModule method) get_filtered_dataframe() (fishy.data.module.DataModule method) get_groups() (fishy.data.module.DataModule method) get_input_dim() (fishy.data.module.DataModule method) get_num_classes() (fishy.data.module.DataModule method) get_numpy_data() (fishy.data.module.DataModule method) get_peak_vram() (in module fishy.analysis.benchmark) get_train_dataframe() (fishy.data.module.DataModule method) get_train_dataloader() (fishy.data.module.DataModule method) get_uncertainty() (fishy.models.probabilistic.gp.GaussianProcess method) (fishy.models.probabilistic.laplace_logistic.BayesianLogisticRegression method) GP (class in fishy.models.evolutionary.gp) (in module fishy.models.probabilistic.gp) GradCAM (class in fishy.analysis.xai) GroupedQueryAttention (class in fishy.models.deep.nextformer) H head_dim (fishy.models.deep.nextformer.GroupedQueryAttention attribute) (fishy.models.deep.transformer.MultiHeadAttention attribute) hidden_dim (fishy.models.deep.dense.Dense attribute) (fishy.models.deep.vae.VAE attribute) Hybrid (class in fishy.models.deep.hybrid) I identify_top_peaks() (fishy.analysis.biomarker.AutomatedBiomarkerDiscovery method) input_dim (fishy.experiments.pre_training.PreTrainingOrchestrator attribute) (fishy.models.deep.dense.Dense attribute) (fishy.models.deep.transformer.MultiHeadAttention attribute) (fishy.models.deep.vae.VAE attribute) input_embedding (fishy.models.deep.ordinal.TransformerOrdinal attribute) K k (fishy.models.deep.gmoe.SparselyGatedMoE attribute) KAN (class in fishy.models.deep.kan) KANLayer (class in fishy.models.deep.kan) L label_to_coral_levels() (in module fishy.models.deep.ordinal) layer_norm1 (fishy.models.deep.transformer.Transformer attribute) layer_norm2 (fishy.models.deep.transformer.Transformer attribute) lda (fishy.models.classic.opls_da.OPLS_DA attribute) LeakyReluSq (class in fishy.models.deep.augformer_v2) learning_rate (fishy.experiments.contrastive.ContrastiveConfig attribute) (fishy.experiments.pre_training.PreTrainingConfig attribute), [1] levels_from_labelbatch() (in module fishy.engine.losses) LEWM (class in fishy.models.deep.lewm) load_data() (fishy.data.module.DataProcessor method) log_contrastive_visualizations() (fishy.experiments.contrastive.ContrastiveTrainer method) log_transform (fishy.experiments.contrastive.ContrastiveConfig attribute) logger (fishy.experiments.pre_training.PreTrainingOrchestrator attribute) LSTM (class in fishy.models.deep.lstm) M main() (in module fishy.cli.main) make_pairwise_test_split() (in module fishy.data.module) Mamba (class in fishy.models.deep.mamba) MambaBlock (class in fishy.models.deep.mamba) ManifoldProjection (class in fishy.models.deep.augformer) mask_spectra_side() (in module fishy.experiments.pre_training) measure_inference_performance() (in module fishy.analysis.benchmark) measure_model_size() (in module fishy.analysis.benchmark) method (fishy.models.deep.ordinal.TransformerOrdinal attribute) minmax (fishy.experiments.contrastive.ContrastiveConfig attribute) MixedOptimizer (class in fishy.experiments.deep_training) MixtureOfExperts (class in fishy.models.deep.moe) moco_k (fishy.experiments.contrastive.ContrastiveConfig attribute) moco_m (fishy.experiments.contrastive.ContrastiveConfig attribute) moco_t (fishy.experiments.contrastive.ContrastiveConfig attribute) MoCoLoss (class in fishy.models.contrastive.moco) MoCoModel (class in fishy.models.contrastive.moco) ModelTrainer (class in fishy.experiments.deep_training) ModelWrapper (class in fishy.analysis.xai) module fishy fishy.analysis fishy.analysis.benchmark fishy.analysis.biomarker fishy.analysis.statistical fishy.analysis.xai fishy.cli fishy.cli.main fishy.cli.wizard fishy.data fishy.data.assets fishy.data.augmentation fishy.data.datasets fishy.data.module fishy.engine fishy.engine.losses fishy.engine.muon fishy.engine.trainer fishy.experiments fishy.experiments.classic_training fishy.experiments.contrastive fishy.experiments.deep_training fishy.experiments.pre_training fishy.experiments.transfer fishy.experiments.unified_trainer fishy.models fishy.models.classic fishy.models.classic.opls_da fishy.models.contrastive fishy.models.contrastive.barlow_twins fishy.models.contrastive.byol fishy.models.contrastive.moco fishy.models.contrastive.simclr fishy.models.contrastive.simsiam fishy.models.deep fishy.models.deep.augformer fishy.models.deep.augformer_v2 fishy.models.deep.cnn fishy.models.deep.dense fishy.models.deep.ensemble fishy.models.deep.gatedmlp fishy.models.deep.gmoe fishy.models.deep.hybrid fishy.models.deep.kan fishy.models.deep.lewm fishy.models.deep.lstm fishy.models.deep.mamba fishy.models.deep.moe fishy.models.deep.nextformer fishy.models.deep.ode fishy.models.deep.ordinal fishy.models.deep.performer fishy.models.deep.rcnn fishy.models.deep.rwkv fishy.models.deep.srmlp fishy.models.deep.tcn fishy.models.deep.transformer fishy.models.deep.ttt_mixin fishy.models.deep.vae fishy.models.deep.wavenet fishy.models.evolutionary fishy.models.evolutionary.eda fishy.models.evolutionary.es fishy.models.evolutionary.ga fishy.models.evolutionary.gp fishy.models.evolutionary.pso fishy.models.probabilistic fishy.models.probabilistic.gp fishy.models.probabilistic.laplace_logistic fishy.models.probabilistic.probabilistic_svc fishy.models.utils MultiHeadAttention (class in fishy.models.deep.augformer) (class in fishy.models.deep.transformer) MultiHeadAttentionV2 (class in fishy.models.deep.augformer_v2) MultiHeadLatentAttention (class in fishy.models.deep.augformer) MultiScaleTransformerEnsemble (class in fishy.models.deep.ensemble) Muon (class in fishy.engine.muon) N n_components (fishy.models.classic.opls_da.OPLS_DA attribute) n_features (fishy.experiments.pre_training.PreTrainingConfig attribute), [1] n_heads (fishy.models.deep.nextformer.GroupedQueryAttention attribute) n_kv_heads (fishy.models.deep.nextformer.GroupedQueryAttention attribute) n_rep (fishy.models.deep.nextformer.GroupedQueryAttention attribute) NextFormer (class in fishy.models.deep.nextformer) NextFormerBlock (class in fishy.models.deep.nextformer) noise_enabled (fishy.data.augmentation.AugmentationConfig attribute) (fishy.experiments.pre_training.PreTrainingConfig attribute), [1] noise_level (fishy.data.augmentation.AugmentationConfig attribute) norm (fishy.models.deep.nextformer.NextFormer attribute) normalize (fishy.experiments.contrastive.ContrastiveConfig attribute) normalize_intensities() (fishy.analysis.xai.ModelWrapper method) normalized_distances() (in module fishy.models.evolutionary.gp) num_augmentations (fishy.data.augmentation.AugmentationConfig attribute) num_epochs (fishy.experiments.contrastive.ContrastiveConfig attribute) (fishy.experiments.pre_training.PreTrainingConfig attribute), [1] num_features (fishy.analysis.xai.ExplainerConfig attribute) num_heads (fishy.models.deep.transformer.MultiHeadAttention attribute) num_samples (fishy.analysis.xai.ExplainerConfig attribute) O ODE (class in fishy.models.deep.ode) ODEFunc (class in fishy.models.deep.ode) opls (fishy.models.classic.opls_da.OPLS_DA attribute) OPLS_DA (class in fishy.models.classic.opls_da) output_dim (fishy.models.deep.dense.Dense attribute) (fishy.models.deep.gmoe.SparselyGatedMoE attribute) (fishy.models.deep.vae.VAE attribute) output_dir (fishy.analysis.xai.ExplainerConfig attribute) output_layer (fishy.models.deep.ordinal.TransformerOrdinal attribute) P perform_significance_test() (in module fishy.analysis.statistical) Performer (class in fishy.models.deep.performer) PerformerLayer (class in fishy.models.deep.performer) permutation_enabled (fishy.data.augmentation.AugmentationConfig attribute) (fishy.experiments.pre_training.PreTrainingConfig attribute), [1] polar (fishy.experiments.contrastive.ContrastiveConfig attribute) pos_encoder (fishy.models.deep.ordinal.TransformerOrdinal attribute) PositionalEncoding (class in fishy.models.deep.ordinal) pre_train() (fishy.experiments.deep_training.ModelTrainer method) pre_train_contrastive_invariance() (fishy.experiments.pre_training.PreTrainer method) pre_train_denoising_autoencoder() (fishy.experiments.pre_training.PreTrainer method) pre_train_masked_spectra() (fishy.experiments.pre_training.PreTrainer method) pre_train_next_spectra() (fishy.experiments.pre_training.PreTrainer method) pre_train_peak_prediction() (fishy.experiments.pre_training.PreTrainer method) predict() (fishy.models.classic.opls_da.OPLS_DA method) (fishy.models.evolutionary.eda.EDA method) (fishy.models.evolutionary.es.ES method) (fishy.models.evolutionary.ga.GA method) (fishy.models.evolutionary.gp.GP method) (fishy.models.evolutionary.pso.PSO method) (fishy.models.probabilistic.gp.GaussianProcess method) (fishy.models.probabilistic.laplace_logistic.BayesianLogisticRegression method) (fishy.models.probabilistic.probabilistic_svc.ProbabilisticSVC method) predict_proba() (fishy.analysis.xai.ModelWrapper method) (fishy.models.classic.opls_da.OPLS_DA method) (fishy.models.evolutionary.eda.EDA method) (fishy.models.evolutionary.es.ES method) (fishy.models.evolutionary.ga.GA method) (fishy.models.evolutionary.gp.GP method) (fishy.models.evolutionary.pso.PSO method) (fishy.models.probabilistic.gp.GaussianProcess method) (fishy.models.probabilistic.laplace_logistic.BayesianLogisticRegression method) (fishy.models.probabilistic.probabilistic_svc.ProbabilisticSVC method) preprocess_data_pipeline() (in module fishy.data.module) PreTrainer (class in fishy.experiments.pre_training) PreTrainingConfig (class in fishy.experiments.pre_training) PreTrainingOrchestrator (class in fishy.experiments.pre_training) ProbabilisticSVC (class in fishy.models.probabilistic.probabilistic_svc) projection_dim (fishy.experiments.contrastive.ContrastiveConfig attribute) ProjectionHead (class in fishy.models.contrastive.simclr) PSO (class in fishy.models.evolutionary.pso) Q qkv (fishy.models.deep.transformer.MultiHeadAttention attribute) quantize (fishy.experiments.contrastive.ContrastiveConfig attribute) query_lipidmaps() (fishy.analysis.biomarker.AutomatedBiomarkerDiscovery method) quick_evaluate() (in module fishy.models.evolutionary.gp) R random_projection (fishy.experiments.contrastive.ContrastiveConfig attribute) random_seed (fishy.analysis.xai.ExplainerConfig attribute) RCNN (class in fishy.models.deep.rcnn) read_reims_excel_file() (in module fishy.models.deep.ordinal) register() (fishy.engine.trainer.EMA method) remove_first_two_characters() (in module fishy.models.deep.ordinal) remove_hooks() (fishy.analysis.xai.GradCAM method) reparameterize() (fishy.models.deep.vae.VAE method) repeat_kv() (in module fishy.models.deep.nextformer) reset_parameters() (fishy.models.deep.kan.KANLayer method) ResidualBlock (class in fishy.models.deep.rcnn) (class in fishy.models.deep.wavenet) restore() (fishy.engine.trainer.EMA method) RMSNorm (class in fishy.models.deep.augformer) (class in fishy.models.deep.gatedmlp) (class in fishy.models.deep.nextformer) run (fishy.experiments.contrastive.ContrastiveConfig attribute) run() (fishy.experiments.classic_training.SklearnTrainer method) (fishy.experiments.unified_trainer.UnifiedTrainer method) run_all() (fishy.experiments.pre_training.PreTrainingOrchestrator method) run_all_benchmarks() (in module fishy.experiments.unified_trainer) run_benchmark() (in module fishy.analysis.benchmark) run_biomarker_pipeline() (in module fishy.analysis.biomarker) run_contrastive_experiment() (in module fishy.experiments.contrastive) run_gradcam_analysis() (in module fishy.analysis.xai) run_lime_explanation() (in module fishy.analysis.xai) run_sequential_transfer_learning() (in module fishy.experiments.transfer) run_sklearn_experiment() (in module fishy.experiments.classic_training) run_training_pipeline() (in module fishy.experiments.deep_training) run_unified_training() (in module fishy.experiments.unified_trainer) run_wizard() (in module fishy.cli.wizard) RWKV (class in fishy.models.deep.rwkv) RWKVBlock (class in fishy.models.deep.rwkv) RWKVParallel (class in fishy.models.deep.rwkv) S save_activation() (fishy.analysis.xai.GradCAM method) save_checkpoint() (fishy.models.deep.ordinal.EarlyStopping method) save_gradient() (fishy.analysis.xai.GradCAM method) savgol (fishy.experiments.contrastive.ContrastiveConfig attribute) scale (fishy.models.deep.transformer.MultiHeadAttention attribute) scale_enabled (fishy.data.augmentation.AugmentationConfig attribute) (fishy.experiments.pre_training.PreTrainingConfig attribute), [1] scale_range (fishy.data.augmentation.AugmentationConfig attribute) scaler (fishy.models.classic.opls_da.OPLS_DA attribute) selective_scan() (fishy.models.deep.mamba.MambaBlock method) set_score_request() (fishy.models.classic.opls_da.OPLS_DA method) (fishy.models.evolutionary.eda.EDA method) (fishy.models.evolutionary.es.ES method) (fishy.models.evolutionary.ga.GA method) (fishy.models.evolutionary.gp.GP method) (fishy.models.evolutionary.pso.PSO method) (fishy.models.probabilistic.gp.GaussianProcess method) (fishy.models.probabilistic.laplace_logistic.BayesianLogisticRegression method) (fishy.models.probabilistic.probabilistic_svc.ProbabilisticSVC method) setup() (fishy.data.module.DataModule method) (fishy.experiments.contrastive.ContrastiveTrainer method) setup_parser() (in module fishy.cli.main) shift_enabled (fishy.data.augmentation.AugmentationConfig attribute) (fishy.experiments.pre_training.PreTrainingConfig attribute), [1] shift_range (fishy.data.augmentation.AugmentationConfig attribute) SiameseDataset (class in fishy.data.datasets) SiameseMamba (class in fishy.models.deep.mamba) SiameseVAE (class in fishy.models.deep.vae) SIGReg (class in fishy.models.deep.lewm) SimCLRLoss (class in fishy.models.contrastive.simclr) SimCLRModel (class in fishy.models.contrastive.simclr) SimSiamLoss (class in fishy.models.contrastive.simsiam) SimSiamModel (class in fishy.models.contrastive.simsiam) SklearnTrainer (class in fishy.experiments.classic_training) snv (fishy.experiments.contrastive.ContrastiveConfig attribute) softmax_kernel() (in module fishy.models.deep.performer) SparselyGatedMoE (class in fishy.models.deep.gmoe) SpectralGating (class in fishy.models.deep.augformer) SRMLP (class in fishy.models.deep.srmlp) SRNorm (class in fishy.models.deep.srmlp) staticLimit() (in module fishy.models.evolutionary.gp) step() (fishy.engine.muon.Muon method) (fishy.experiments.deep_training.MixedOptimizer method) summarize_results() (in module fishy.analysis.statistical) SwiGLU (class in fishy.models.deep.nextformer) T task_configs (fishy.experiments.pre_training.PreTrainingOrchestrator attribute) TCN (class in fishy.models.deep.tcn) temperature (fishy.experiments.contrastive.ContrastiveConfig attribute) TemporalBlock (class in fishy.models.deep.tcn) train() (fishy.engine.trainer.Trainer method) (fishy.experiments.contrastive.ContrastiveTrainer method) (fishy.experiments.deep_training.ModelTrainer method) (in module fishy.models.deep.ordinal) train_model() (fishy.engine.trainer.DeepEngine static method) Trainer (class in fishy.engine.trainer) transfer_learning() (fishy.engine.trainer.DeepEngine static method) transform() (fishy.models.classic.opls_da.OPLS_DA method) (fishy.models.evolutionary.eda.EDA method) (fishy.models.evolutionary.es.ES method) (fishy.models.evolutionary.ga.GA method) (fishy.models.evolutionary.pso.PSO method) Transformer (class in fishy.models.deep.transformer) transformer_encoder (fishy.models.deep.ordinal.TransformerOrdinal attribute) TransformerBlock (class in fishy.models.deep.augformer) TransformerBlockV2 (class in fishy.models.deep.augformer_v2) TransformerOrdinal (class in fishy.models.deep.ordinal) TTTMixin (class in fishy.models.deep.ttt_mixin) turbo_quant (fishy.experiments.contrastive.ContrastiveConfig attribute) U UnifiedTrainer (class in fishy.experiments.unified_trainer) update() (fishy.engine.trainer.EMA method) V VAE (class in fishy.models.deep.vae) W w1 (fishy.models.deep.nextformer.SwiGLU attribute) w2 (fishy.models.deep.nextformer.SwiGLU attribute) w3 (fishy.models.deep.nextformer.SwiGLU attribute) wandb_entity (fishy.experiments.contrastive.ContrastiveConfig attribute) wandb_log (fishy.experiments.contrastive.ContrastiveConfig attribute) wandb_project (fishy.experiments.contrastive.ContrastiveConfig attribute) WaveNet (class in fishy.models.deep.wavenet) weight (fishy.models.deep.nextformer.RMSNorm attribute) weight_decay (fishy.experiments.contrastive.ContrastiveConfig attribute) wk (fishy.models.deep.nextformer.GroupedQueryAttention attribute) wo (fishy.models.deep.nextformer.GroupedQueryAttention attribute) wq (fishy.models.deep.nextformer.GroupedQueryAttention attribute) wrapper_fitness() (in module fishy.models.evolutionary.gp) wv (fishy.models.deep.nextformer.GroupedQueryAttention attribute) X xmate() (in module fishy.models.evolutionary.gp) xmut() (in module fishy.models.evolutionary.gp) Z zero_grad() (fishy.experiments.deep_training.MixedOptimizer method) zeropower_via_newtonschulz5() (in module fishy.engine.muon)