Index

_

__init__() (fennomix_mhc.mhc_binding_model.HlaDataSet method) (fennomix_mhc.mhc_binding_model.ModelHlaEncoder method) (fennomix_mhc.mhc_binding_model.ModelSeqEncoder method) (fennomix_mhc.mhc_binding_retriever.MHCBindingRetriever method) (fennomix_mhc.mhc_utils.NonSpecificDigest method) (fennomix_mhc.pipeline_api.PretrainedModels method) (fennomix_mhc.tda_fmm.DecoyModel method) (fennomix_mhc.tda_fmm.TDA_fmm method)

_use_pseudo (fennomix_mhc.pipeline_api.PretrainedModels attribute)

A

adjust_axes() (in module fennomix_mhc.plotting_utils)

B

background_protein_df (fennomix_mhc.pipeline_api.PretrainedModels attribute)

batch_converter (fennomix_mhc.pipeline_api.PretrainedModels attribute) batchify_hla_esm_list() (in module fennomix_mhc.mhc_binding_model)

C

count_motif_bits() (in module fennomix_mhc.plotting_utils)

D

d_model (fennomix_mhc.mhc_binding_retriever.MHCBindingRetriever attribute) dataset (fennomix_mhc.mhc_binding_retriever.MHCBindingRetriever attribute) deconvolute_and_predict_peptides() (in module fennomix_mhc.pipeline_api) deconvolute_peptides() (fennomix_mhc.pipeline_api.PretrainedModels method) (in module fennomix_mhc.pipeline_api)

decoy_rnd_seed (fennomix_mhc.mhc_binding_retriever.MHCBindingRetriever attribute) DecoyModel (class in fennomix_mhc.tda_fmm) device (fennomix_mhc.mhc_binding_retriever.MHCBindingRetriever attribute) (fennomix_mhc.pipeline_api.PretrainedModels attribute)

E

embed_hla_esm_list() (in module fennomix_mhc.mhc_binding_model) embed_peptides() (in module fennomix_mhc.mhc_binding_model) embed_peptides_from_fasta() (fennomix_mhc.pipeline_api.PretrainedModels method) embed_peptides_from_file() (in module fennomix_mhc.pipeline_api) embed_peptides_tsv() (fennomix_mhc.pipeline_api.PretrainedModels method)

embed_proteins() (fennomix_mhc.pipeline_api.PretrainedModels method) (in module fennomix_mhc.pipeline_api) esm2_alphabet (fennomix_mhc.pipeline_api.PretrainedModels attribute) esm2_model (fennomix_mhc.pipeline_api.PretrainedModels attribute) external_model (fennomix_mhc.tda_fmm.TDA_fmm attribute)

F

fennomix_mhc module fennomix_mhc.mhc_binding_model module fennomix_mhc.mhc_binding_retriever module fennomix_mhc.mhc_utils module fennomix_mhc.pipeline_api module

fennomix_mhc.plotting_utils module fennomix_mhc.tda_fmm module fit() (fennomix_mhc.tda_fmm.DecoyModel method) (fennomix_mhc.tda_fmm.TDA_fmm method) fit_hla_umap_reducer() (in module fennomix_mhc.plotting_utils) forward() (fennomix_mhc.mhc_binding_model.ModelHlaEncoder method) (fennomix_mhc.mhc_binding_model.ModelSeqEncoder method)

G

gamma_pdf() (in module fennomix_mhc.tda_fmm) gauss_pdf() (in module fennomix_mhc.tda_fmm) get_allele_embed() (fennomix_mhc.mhc_binding_model.HlaDataSet method) get_ascii_indices() (in module fennomix_mhc.mhc_binding_model) get_binding_distances() (fennomix_mhc.mhc_binding_retriever.MHCBindingRetriever method) get_binding_fdr_for_best_allele() (in module fennomix_mhc.mhc_binding_retriever) get_binding_fdrs() (in module fennomix_mhc.mhc_binding_retriever) get_binding_metrics_for_embeds() (fennomix_mhc.mhc_binding_retriever.MHCBindingRetriever method) get_binding_metrics_for_peptides() (fennomix_mhc.mhc_binding_retriever.MHCBindingRetriever method) get_binding_metrics_for_self_proteins() (fennomix_mhc.mhc_binding_retriever.MHCBindingRetriever method)

get_binding_ranks() (in module fennomix_mhc.mhc_binding_retriever) get_cosine_schedule_with_warmup() (in module fennomix_mhc.mhc_binding_model) get_embedding_distances() (fennomix_mhc.mhc_binding_retriever.MHCBindingRetriever method) get_fdrs() (in module fennomix_mhc.mhc_binding_retriever) get_hla_dataloader() (in module fennomix_mhc.mhc_binding_model) get_loss() (fennomix_mhc.mhc_binding_model.SiameseCELoss method) get_neg_pept() (fennomix_mhc.mhc_binding_model.HlaDataSet method) get_peptide_seqs_from_idxes() (fennomix_mhc.mhc_utils.NonSpecificDigest method) get_pi0() (fennomix_mhc.tda_fmm.TDA_fmm method) get_q_values() (in module fennomix_mhc.mhc_binding_retriever) get_random_pept_df() (fennomix_mhc.mhc_utils.NonSpecificDigest method)

H

helper_pdf (fennomix_mhc.tda_fmm.TDA_fmm attribute) hla_df (fennomix_mhc.pipeline_api.PretrainedModels attribute) hla_embeddings (fennomix_mhc.pipeline_api.PretrainedModels attribute)

hla_embeds (fennomix_mhc.mhc_binding_retriever.MHCBindingRetriever attribute) hla_encoder (fennomix_mhc.mhc_binding_retriever.MHCBindingRetriever attribute) (fennomix_mhc.pipeline_api.PretrainedModels attribute) HlaDataSet (class in fennomix_mhc.mhc_binding_model)

L

load_peptide_df_from_mixmhcpred() (in module fennomix_mhc.mhc_utils)

load_peptide_embedding_pkl() (in module fennomix_mhc.pipeline_api) loglik_BIC() (fennomix_mhc.tda_fmm.TDA_fmm method)

M

main_pdf (fennomix_mhc.tda_fmm.TDA_fmm attribute) margin (fennomix_mhc.mhc_binding_model.SiameseCELoss attribute) max_iter (fennomix_mhc.tda_fmm.TDA_fmm attribute) MHCBindingRetriever (class in fennomix_mhc.mhc_binding_retriever) ModelHlaEncoder (class in fennomix_mhc.mhc_binding_model) ModelSeqEncoder (class in fennomix_mhc.mhc_binding_model) module fennomix_mhc fennomix_mhc.mhc_binding_model fennomix_mhc.mhc_binding_retriever fennomix_mhc.mhc_utils fennomix_mhc.pipeline_api fennomix_mhc.plotting_utils fennomix_mhc.tda_fmm

mu (fennomix_mhc.tda_fmm.TDA_fmm attribute)

N

n_components (fennomix_mhc.tda_fmm.TDA_fmm attribute)

n_decoy_samples (fennomix_mhc.mhc_binding_retriever.MHCBindingRetriever attribute) NonSpecificDigest (class in fennomix_mhc.mhc_utils)

O

outlier_threshold (fennomix_mhc.mhc_binding_retriever.MHCBindingRetriever attribute)

P

pdf() (fennomix_mhc.tda_fmm.DecoyModel method) (fennomix_mhc.tda_fmm.TDA_fmm method) pdf_mix() (fennomix_mhc.tda_fmm.TDA_fmm method) pep() (fennomix_mhc.tda_fmm.TDA_fmm method) pept_encoder (fennomix_mhc.mhc_binding_retriever.MHCBindingRetriever attribute) (fennomix_mhc.pipeline_api.PretrainedModels attribute) pept_hla_collate() (in module fennomix_mhc.mhc_binding_model) plot() (fennomix_mhc.tda_fmm.TDA_fmm method)

plot_motif() (in module fennomix_mhc.plotting_utils) plot_motif_multi_mer() (in module fennomix_mhc.plotting_utils) plot_umap_df() (in module fennomix_mhc.plotting_utils) predict_epitopes_for_mhc() (fennomix_mhc.pipeline_api.PretrainedModels method) (in module fennomix_mhc.pipeline_api) predict_mhc_binders_for_epitopes() (fennomix_mhc.pipeline_api.PretrainedModels method) (in module fennomix_mhc.pipeline_api) PretrainedModels (class in fennomix_mhc.pipeline_api)

S

select_best_fmm() (in module fennomix_mhc.tda_fmm) select_optimal_a_cover() (in module fennomix_mhc.plotting_utils)

SiameseCELoss (class in fennomix_mhc.mhc_binding_model) sigma (fennomix_mhc.tda_fmm.TDA_fmm attribute)

T

TDA_fmm (class in fennomix_mhc.tda_fmm) test() (in module fennomix_mhc.mhc_binding_model) train() (in module fennomix_mhc.mhc_binding_model)

transform_embeds_to_tSNE_df() (in module fennomix_mhc.plotting_utils) transform_embeds_to_umap_df() (in module fennomix_mhc.plotting_utils) transform_matrix_to_mds_df() (in module fennomix_mhc.plotting_utils)

U

use_fmm_fdr (fennomix_mhc.mhc_binding_retriever.MHCBindingRetriever attribute)

V

verbose (fennomix_mhc.mhc_binding_retriever.MHCBindingRetriever attribute)

W

weights (fennomix_mhc.tda_fmm.TDA_fmm attribute)