junipertcy/bipartiteSBM
Quick start
Why should I use bipartiteSBM?
Installation
Example Kernighan-Lin inference
Example MCMC inference
More MCMC inference
Explore the consistency of results
Generate synthetic networks
Make plots
Run codes in parallel
How to interpret entropy?
Dataset
Graph input format
Node type ordering
Southern women network
Malaria gene-substring network
Ancient metabolic network
Module documentation
biSBM package
engines package
Frequently Asked Questions (FAQ)
Local minima
Choosing parameters
Detectability limit
Additional resources
Useful slides
junipertcy/bipartiteSBM
Docs
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Index
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Index
A
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B
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C
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D
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E
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G
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I
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K
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L
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M
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N
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O
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P
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S
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V
A
accept_mb_merge (in module biSBM.utils)
adjacency_entropy() (in module biSBM.utils)
assemble_e_rs_from_mb() (in module biSBM.utils)
assemble_edgelist_old2new() (in module biSBM.utils)
assemble_eta_rk_from_edgelist_and_mb (in module biSBM.utils)
assemble_mb_new2old (in module biSBM.utils)
assemble_n_k_from_edgelist (in module biSBM.utils)
assemble_n_r_from_mb (in module biSBM.utils)
assemble_old2new_mapping() (in module biSBM.utils)
B
biSBM (module)
biSBM.int_part (module)
biSBM.ioutils (module)
biSBM.optimalks (module)
biSBM.painter (module)
biSBM.utils (module)
C
compute_and_update() (biSBM.OptimalKs method)
(biSBM.optimalks.OptimalKs method)
compute_dl() (biSBM.OptimalKs method)
(biSBM.optimalks.OptimalKs method)
compute_profile_likelihood() (in module biSBM.utils)
compute_profile_likelihood_from_e_rs (in module biSBM.utils)
D
db_factorial_ln() (in module biSBM.utils)
degree_entropy() (in module biSBM.utils)
E
engine() (engines.KL method)
(engines.MCMC method)
(engines.kl.KL method)
(engines.mcmc.MCMC method)
engines (module)
engines.kl (module)
engines.mcmc (module)
G
gen_bicliques_edgelist (in module biSBM.utils)
gen_e_rs() (in module biSBM.utils)
gen_e_rs_hard() (in module biSBM.utils)
gen_e_rs_harder() (in module biSBM.utils)
gen_equal_bipartite_partition() (in module biSBM.utils)
gen_equal_partition() (in module biSBM.utils)
gen_types() (engines.KL static method)
(engines.MCMC static method)
(engines.kl.KL static method)
(engines.mcmc.MCMC static method)
gen_unequal_partition() (in module biSBM.utils)
get__q_cache() (biSBM.OptimalKs method)
(biSBM.optimalks.OptimalKs method)
get_desc_len_from_data() (in module biSBM.utils)
get_desc_len_from_data_uni() (in module biSBM.utils)
get_edgelist() (in module biSBM.ioutils)
get_f_edgelist_name() (biSBM.OptimalKs method)
(biSBM.optimalks.OptimalKs method)
get_flat_entropies() (in module biSBM.utils)
get_nested_entropies() (in module biSBM.utils)
get_types() (in module biSBM.ioutils)
get_v() (in module biSBM.int_part)
I
init_q_cache() (in module biSBM.int_part)
K
KL (class in engines)
(class in engines.kl)
L
lbinom() (in module biSBM.int_part)
log_q() (in module biSBM.int_part)
log_q_approx() (in module biSBM.int_part)
log_q_approx_small() (in module biSBM.int_part)
log_sum (in module biSBM.int_part)
loky_executor() (in module biSBM.utils)
M
MCMC (class in engines)
(class in engines.mcmc)
minimize_bisbm_dl() (biSBM.OptimalKs method)
(biSBM.optimalks.OptimalKs method)
model_entropy() (in module biSBM.utils)
N
natural_merge() (biSBM.OptimalKs method)
(biSBM.optimalks.OptimalKs method)
O
OptimalKs (class in biSBM)
(class in biSBM.optimalks)
P
paint_block_mat() (in module biSBM.painter)
paint_block_mat_from_e_rs() (in module biSBM.painter)
paint_dl_trace() (in module biSBM.painter)
paint_landscape() (in module biSBM.painter)
paint_mds() (in module biSBM.painter)
paint_similarity_trace() (in module biSBM.painter)
paint_sorted_adj_mat() (in module biSBM.painter)
paint_trace() (in module biSBM.painter)
partition_entropy() (in module biSBM.utils)
prepare_engine() (engines.KL method)
(engines.MCMC method)
(engines.kl.KL method)
(engines.mcmc.MCMC method)
S
save_mb_to_file() (in module biSBM.ioutils)
set_adaptive_ratio() (biSBM.OptimalKs method)
(biSBM.optimalks.OptimalKs method)
set_await_steps() (engines.MCMC method)
(engines.mcmc.MCMC method)
set_c() (biSBM.OptimalKs method)
(biSBM.optimalks.OptimalKs method)
set_cooling() (engines.MCMC method)
(engines.mcmc.MCMC method)
set_cooling_param_1() (engines.MCMC method)
(engines.mcmc.MCMC method)
set_cooling_param_2() (engines.MCMC method)
(engines.mcmc.MCMC method)
set_epsilon() (engines.MCMC method)
(engines.mcmc.MCMC method)
set_k_th_neighbor_to_search() (biSBM.OptimalKs method)
(biSBM.optimalks.OptimalKs method)
set_nm() (biSBM.OptimalKs method)
(biSBM.optimalks.OptimalKs method)
set_params() (biSBM.OptimalKs method)
(biSBM.optimalks.OptimalKs method)
set_steps() (engines.MCMC method)
(engines.mcmc.MCMC method)
summary() (biSBM.OptimalKs method)
(biSBM.optimalks.OptimalKs method)
summary_dl() (biSBM.OptimalKs method)
(biSBM.optimalks.OptimalKs method)
V
virtual_moves_ds() (in module biSBM.utils)