From 3db6cec8b6300af6e147ac248b25451638c76109 Mon Sep 17 00:00:00 2001
From: bastien-mva <bastien.batardiere@gmail.com>
Date: Mon, 27 Mar 2023 22:25:17 +0200
Subject: [PATCH 01/15] add pylint to precommit
---
.pre-commit-config.yaml | 17 +++++++++++++++++
1 file changed, 17 insertions(+)
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index fe4c8217..d7189f77 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -8,3 +8,20 @@ repos:
rev: 22.3.0
hooks:
- id: black
+ - repo: local
+ hooks:
+ - id: pylint
+ name: pylint
+ entry: pylint
+ language: system
+ types: [python]
+ args:
+ [
+ "-rn",
+ "-sn",
+ "--load-plugins=pylint.extensions.docparams",
+ "--accept-no-yields-doc=no",
+ "--accept-no-return-doc=no",
+ "--accept-no-raise-doc=no",
+ "--accept-no-param-doc=no",
+ ]
--
GitLab
From 4527005a8a8f7c3a2964d7641230b9ab6e543baa Mon Sep 17 00:00:00 2001
From: bastien-mva <bastien.batardiere@gmail.com>
Date: Mon, 22 May 2023 15:24:41 +0200
Subject: [PATCH 02/15] updated toml file.
---
.gitlab-ci.yml | 16 ++++++++++++++--
1 file changed, 14 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index dbeb3877..c64dc913 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -20,12 +20,24 @@ tests:
- pip install -r requirements.txt
- pytest
+build_package:
+ stage: build
+ before_script:
+ - pip install build
+ script:
+ - rm -rf dist/
+ - python -m build
+ artifacts:
+ untracked: true
+ expire_in: 1 week
+ tags:
+ - docker
publish_package:
stage: publish
image: "python:3.9"
- script:
+ before_script:
- pip install twine
- - python setup.py bdist_wheel
+ script:
- TWINE_PASSWORD=${pypln_token} TWINE_USERNAME=__token__ python -m twine upload dist/*
tags:
- docker
--
GitLab
From 6e6881840ecbaf314e080d7268c73cf81eb4702c Mon Sep 17 00:00:00 2001
From: bastien-mva <bastien.batardiere@gmail.com>
Date: Mon, 22 May 2023 18:41:16 +0200
Subject: [PATCH 03/15] renaming PLNPCA to PlnPCAcollection and _PLNPCA to
PlnPCA. Now PlnPCA is public. PlnPCAcollection is a collection, I implement
all the required methods such as __getitem__ etc, and wrote tests for it.
---
pyPLNmodels/__init__.py | 12 +-
pyPLNmodels/_utils.py | 26 +--
pyPLNmodels/elbos.py | 8 +-
pyPLNmodels/models.py | 163 +++++++++---------
pyproject.toml | 9 +-
setup.py | 7 +-
tests/conftest.py | 28 +--
tests/test_common.py | 16 +-
tests/test_pln_full.py | 4 +-
...est_plnpca.py => test_plnpcacollection.py} | 30 ++--
tests/test_setters.py | 16 +-
11 files changed, 173 insertions(+), 146 deletions(-)
rename tests/{test_plnpca.py => test_plnpcacollection.py} (73%)
diff --git a/pyPLNmodels/__init__.py b/pyPLNmodels/__init__.py
index d895c7cd..e619625e 100644
--- a/pyPLNmodels/__init__.py
+++ b/pyPLNmodels/__init__.py
@@ -1,22 +1,24 @@
-from .models import PLNPCA, PLN # pylint:disable=[C0114]
+from .models import PlnPCAcollection, Pln, PlnPCA # pylint:disable=[C0114]
+from .oaks import load_oaks
from .elbos import profiled_elbo_pln, elbo_plnpca, elbo_pln
from ._utils import (
get_simulated_count_data,
get_real_count_data,
load_model,
- load_plnpca,
+ load_plnpcacollection,
load_pln,
)
__all__ = (
- "PLNPCA",
- "PLN",
+ "PlnPCAcollection",
+ "Pln",
+ "PlnPCA",
"profiled_elbo_pln",
"elbo_plnpca",
"elbo_pln",
"get_simulated_count_data",
"get_real_count_data",
"load_model",
- "load_plnpca",
+ "load_plnpcacollection",
"load_pln",
)
diff --git a/pyPLNmodels/_utils.py b/pyPLNmodels/_utils.py
index 4b977e0a..9dc16713 100644
--- a/pyPLNmodels/_utils.py
+++ b/pyPLNmodels/_utils.py
@@ -93,7 +93,7 @@ def _init_covariance(
counts: torch.Tensor, covariates: torch.Tensor, coef: torch.Tensor
) -> torch.Tensor:
"""
- Initialization for covariance for the PLN model. Take the log of counts
+ Initialization for covariance for the Pln model. Take the log of counts
(careful when counts=0), remove the covariates effects X@coef and
then do as a MLE for Gaussians samples.
@@ -124,7 +124,7 @@ def _init_components(
counts: torch.Tensor, covariates: torch.Tensor, coef: torch.Tensor, rank: int
) -> torch.Tensor:
"""
- Initialization for components for the PLN model. Get a first guess for covariance
+ Initialization for components for the Pln model. Get a first guess for covariance
that is easier to estimate and then takes the rank largest eigenvectors to get components.
Parameters
@@ -235,7 +235,7 @@ def sample_pln(
seed: int = None,
) -> tuple[torch.Tensor, torch.Tensor, torch.Tensor]:
"""
- Sample from the Poisson Log-Normal (PLN) model.
+ Sample from the Poisson Log-Normal (Pln) model.
Parameters
----------
@@ -273,7 +273,7 @@ def sample_pln(
parameter = torch.exp(offsets + gaussian)
if _coef_inflation is not None:
- print("ZIPLN is sampled")
+ print("ZIPln is sampled")
zero_inflated_mean = torch.matmul(covariates, _coef_inflation)
ksi = torch.bernoulli(1 / (1 + torch.exp(-zero_inflated_mean)))
else:
@@ -368,7 +368,7 @@ def log_posterior(
coef: torch.Tensor,
) -> torch.Tensor:
"""
- Compute the log posterior of the Poisson Log-Normal (PLN) model.
+ Compute the log posterior of the Poisson Log-Normal (Pln) model.
Parameters
----------
@@ -964,39 +964,39 @@ def load_model(path_of_directory: str) -> Dict[str, Any]:
def load_pln(path_of_directory: str) -> Dict[str, Any]:
"""
- Load PLN models from the given directory.
+ Load Pln models from the given directory.
Parameters
----------
path_of_directory : str
- The path to the directory containing the PLN models.
+ The path to the directory containing the Pln models.
Returns
-------
Dict[str, Any]
- A dictionary containing the loaded PLN models.
+ A dictionary containing the loaded Pln models.
"""
return load_model(path_of_directory)
-def load_plnpca(
+def load_plnpcacollection(
path_of_directory: str, ranks: Optional[list[int]] = None
) -> Dict[int, Dict[str, Any]]:
"""
- Load PLNPCA models from the given directory.
+ Load PlnPCAcollection models from the given directory.
Parameters
----------
path_of_directory : str
- The path to the directory containing the PLNPCA models.
+ The path to the directory containing the PlnPCAcollection models.
ranks : list[int], optional
A list of ranks specifying which models to load. If None, all models in the directory will be loaded.
Returns
-------
Dict[int, Dict[str, Any]]
- A dictionary containing the loaded PLNPCA models, with ranks as keys.
+ A dictionary containing the loaded PlnPCAcollection models, with ranks as keys.
Raises
------
@@ -1019,7 +1019,7 @@ def load_plnpca(
ranks.append(rank)
datas = {}
for rank in ranks:
- datas[rank] = load_model(f"_PLNPCA_rank_{rank}")
+ datas[rank] = load_model(f"PlnPCA_rank_{rank}")
os.chdir(working_dir)
return datas
diff --git a/pyPLNmodels/elbos.py b/pyPLNmodels/elbos.py
index c5f8927c..68b73247 100644
--- a/pyPLNmodels/elbos.py
+++ b/pyPLNmodels/elbos.py
@@ -16,7 +16,7 @@ def elbo_pln(
coef: torch.Tensor,
) -> torch.Tensor:
"""
- Compute the ELBO (Evidence Lower Bound) for the PLN model.
+ Compute the ELBO (Evidence Lower Bound) for the Pln model.
Parameters:
----------
@@ -75,7 +75,7 @@ def profiled_elbo_pln(
latent_var: torch.Tensor,
) -> torch.Tensor:
"""
- Compute the ELBO (Evidence Lower Bound) for the PLN model with profiled parameters.
+ Compute the ELBO (Evidence Lower Bound) for the Pln model with profiled parameters.
Parameters:
----------
@@ -122,7 +122,7 @@ def elbo_plnpca(
coef: torch.Tensor,
) -> torch.Tensor:
"""
- Compute the ELBO (Evidence Lower Bound) for the PLN model with PCA parametrization.
+ Compute the ELBO (Evidence Lower Bound) for the Pln model with PCA parametrization.
Parameters:
----------
@@ -186,7 +186,7 @@ def elbo_zi_pln(
_coef_inflation,
dirac,
):
- """Compute the ELBO (Evidence LOwer Bound) for the Zero Inflated PLN model.
+ """Compute the ELBO (Evidence LOwer Bound) for the Zero Inflated Pln model.
See the doc for more details on the computation.
Args:
diff --git a/pyPLNmodels/models.py b/pyPLNmodels/models.py
index c3849fb9..0c6c5c37 100644
--- a/pyPLNmodels/models.py
+++ b/pyPLNmodels/models.py
@@ -50,9 +50,9 @@ else:
NB_CHARACTERS_FOR_NICE_PLOT = 70
-class _PLN(ABC):
+class _Pln(ABC):
"""
- Virtual class for all the PLN models.
+ Virtual class for all the Pln models.
This class must be derivatived. The methods `get_covariance`, `compute_elbo`,
`_random_init_latent_parameters` and `_list_of_parameters_needing_gradient` must
@@ -195,7 +195,7 @@ class _PLN(ABC):
verbose=False,
):
"""
- Main function of the class. Fit a PLN to the data.
+ Main function of the class. Fit a Pln to the data.
Parameters
----------
counts : torch.tensor or ndarray or DataFrame.
@@ -559,8 +559,8 @@ class _PLN(ABC):
# need to do a good init for M and S
-class PLN(_PLN):
- _NAME = "PLN"
+class Pln(_Pln):
+ _NAME = "Pln"
coef: torch.Tensor
@property
@@ -634,7 +634,7 @@ class PLN(_PLN):
)
def _pring_beginning_message(self):
- print(f"Fitting a PLN model with {self._description}")
+ print(f"Fitting a Pln model with {self._description}")
@property
def latent_variables(self):
@@ -667,8 +667,9 @@ class PLN(_PLN):
pass
-class PLNPCA:
- _NAME = "PLNPCA"
+class PlnPCAcollection:
+ _NAME = "PlnPCAcollection"
+ _dict_models: dict
def __init__(
self,
@@ -680,6 +681,7 @@ class PLNPCA:
dict_of_dict_initialization=None,
take_log_offsets=False,
):
+ self._dict_models = {}
self._init_data(counts, covariates, offsets, offsets_formula, take_log_offsets)
self._init_models(ranks, dict_of_dict_initialization)
@@ -715,91 +717,87 @@ class PLNPCA:
@property
def covariates(self):
- return self.list_models[0].covariates
+ return self[self.ranks[0]].covariates
@property
def counts(self):
- return self.list_models[0].counts
+ return self[self.ranks[0]].counts
@property
def coef(self):
- return {model.rank: model.coef for model in self.list_models}
+ return {model.rank: model.coef for model in self.values()}
@property
def components(self):
- return {model.rank: model.components for model in self.list_models}
+ return {model.rank: model.components for model in self.values()}
@property
def latent_mean(self):
- return {model.rank: model.latent_mean for model in self.list_models}
+ return {model.rank: model.latent_mean for model in self.values()}
@property
def latent_var(self):
- return {model.rank: model.latent_var for model in self.list_models}
+ return {model.rank: model.latent_var for model in self.values()}
@counts.setter
@array2tensor
def counts(self, counts):
- for model in self.list_models:
+ for model in self.values():
model.counts = counts
@coef.setter
@array2tensor
def coef(self, coef):
- for model in self.list_models:
+ for model in self.values():
model.coef = coef
@covariates.setter
@array2tensor
def covariates(self, covariates):
- for model in self.list_models:
+ for model in self.values():
model.covariates = covariates
@property
def offsets(self):
- return self.list_models[0].offsets
+ return self[self.ranks[0]].offsets
@offsets.setter
@array2tensor
def offsets(self, offsets):
- for model in self.list_models:
+ for model in self.values():
model.offsets = offsets
def _init_models(self, ranks, dict_of_dict_initialization):
if isinstance(ranks, (Iterable, np.ndarray)):
- self.list_models = []
for rank in ranks:
if isinstance(rank, (int, np.integer)):
dict_initialization = _get_dict_initialization(
rank, dict_of_dict_initialization
)
- self.list_models.append(
- _PLNPCA(
- counts=self._counts,
- covariates=self._covariates,
- offsets=self._offsets,
- rank=rank,
- dict_initialization=dict_initialization,
- )
+ self._dict_models[rank] = PlnPCA(
+ counts=self._counts,
+ covariates=self._covariates,
+ offsets=self._offsets,
+ rank=rank,
+ dict_initialization=dict_initialization,
)
else:
raise TypeError(
- f"Please instantiate with either a list "
- f"of integers or an integer."
+ "Please instantiate with either a list "
+ "of integers or an integer."
)
elif isinstance(ranks, (int, np.integer)):
dict_initialization = _get_dict_initialization(
ranks, dict_of_dict_initialization
)
- self.list_models = [
- _PLNPCA(
- self._counts,
- self._covariates,
- self._offsets,
- ranks,
- dict_initialization,
- )
- ]
+ self._dict_models[rank] = PlnPCA(
+ self._counts,
+ self._covariates,
+ self._offsets,
+ ranks,
+ dict_initialization,
+ )
+
else:
raise TypeError(
f"Please instantiate with either a list " f"of integers or an integer."
@@ -807,14 +805,10 @@ class PLNPCA:
@property
def ranks(self):
- return [model.rank for model in self.list_models]
-
- @property
- def dict_models(self):
- return {model.rank: model for model in self.list_models}
+ return [model.rank for model in self.values()]
def _pring_beginning_message(self):
- return f"Adjusting {len(self.ranks)} PLN models for PCA analysis \n"
+ return f"Adjusting {len(self.ranks)} Pln models for PCA analysis \n"
@property
def dim(self):
@@ -825,7 +819,7 @@ class PLNPCA:
return self[self.ranks[0]].nb_cov
## should do something for this weird init. pb: if doing the init of self._counts etc
- ## only in PLNPCA, then we don't do it for each _PLNPCA but then PLN is not doing it.
+ ## only in PlnPCAcollection, then we don't do it for each PlnPCA but then Pln is not doing it.
def fit(
self,
nb_max_iteration=100000,
@@ -836,8 +830,8 @@ class PLNPCA:
verbose=False,
):
self._pring_beginning_message()
- for i in range(len(self.list_models)):
- model = self.list_models[i]
+ for i in range(len(self.values())):
+ model = self[self.ranks[i]]
model.fit(
nb_max_iteration,
lr,
@@ -846,8 +840,8 @@ class PLNPCA:
do_smart_init,
verbose,
)
- if i < len(self.list_models) - 1:
- next_model = self.list_models[i + 1]
+ if i < len(self.values()) - 1:
+ next_model = self[self.ranks[i + 1]]
self.init_next_model_with_previous_parameters(next_model, model)
self._print_ending_message()
@@ -869,26 +863,43 @@ class PLNPCA:
return self.best_model(criterion).rank
def __getitem__(self, rank):
- if (rank in self.ranks) is False:
- asked_rank = rank
- rank = _closest(self.ranks, asked_rank)
- warning_string = " \n No such a model in the collection."
- warning_string += "Returning model with _closest value.\n"
- warning_string += f"Requested: {asked_rank}, returned: {rank}"
- warnings.warn(message=warning_string)
- return self.dict_models[rank]
+ return self._dict_models[rank]
+
+ def __len__(self):
+ return len(self._dict_models)
+
+ def __iter__(self):
+ return iter(self._dict_models)
+
+ def __contains__(self, rank):
+ return rank in self._dict_models.keys()
+
+ def keys(self):
+ return self._dict_models.keys()
+
+ def get(self, key, default):
+ if key in self:
+ return self[key]
+ else:
+ return default
+
+ def values(self):
+ return self._dict_models.values()
+
+ def items(self):
+ return self._dict_models.items()
@property
def BIC(self):
- return {model.rank: int(model.BIC) for model in self.list_models}
+ return {model.rank: int(model.BIC) for model in self.values()}
@property
def AIC(self):
- return {model.rank: int(model.AIC) for model in self.list_models}
+ return {model.rank: int(model.AIC) for model in self.values()}
@property
def loglikes(self):
- return {model.rank: model.loglike for model in self.list_models}
+ return {model.rank: model.loglike for model in self.values()}
def show(self):
bic = self.BIC
@@ -932,7 +943,7 @@ class PLNPCA:
def save(self, path_of_directory="./", ranks=None):
if ranks is None:
ranks = self.ranks
- for model in self.list_models:
+ for model in self.values():
if model.rank in ranks:
model.save(path_of_directory)
@@ -942,21 +953,17 @@ class PLNPCA:
@property
def n_samples(self):
- return self.list_models[0].n_samples
+ return self[self.ranks[0]].n_samples
@property
def _p(self):
return self[self.ranks[0]].p
- @property
- def models(self):
- return self.dict_models.values()
-
- def __str__(self):
- nb_models = len(self.list_models)
+ def __repr__(self):
+ nb_models = len(self)
delimiter = "\n" + "-" * NB_CHARACTERS_FOR_NICE_PLOT + "\n"
to_print = delimiter
- to_print += f"Collection of {nb_models} PLNPCA models with \
+ to_print += f"Collection of {nb_models} PlnPCAcollection models with \
{self.dim} variables."
to_print += delimiter
to_print += f" - Ranks considered:{self.ranks}\n"
@@ -970,7 +977,7 @@ class PLNPCA:
to_print += f" Best model(lower AIC): \
{self.best_model(criterion = 'AIC')._rank}\n"
to_print += delimiter
- to_print += f"* Useful properties\n"
+ to_print += "* Useful properties\n"
to_print += f" {self._useful_properties_string}\n"
to_print += "* Useful methods \n"
to_print += f" {self._useful_methods_strings}"
@@ -987,8 +994,8 @@ class PLNPCA:
# Here, setting the value for each key in _dict_parameters
-class _PLNPCA(_PLN):
- _NAME = "_PLNPCA"
+class PlnPCA(_Pln):
+ _NAME = "PlnPCA"
_components: torch.Tensor
def __init__(
@@ -1059,7 +1066,7 @@ class _PLNPCA(_PLN):
@property
def directory_name(self):
return f"{self._NAME}_rank_{self._rank}"
- # return f"PLNPCA_nbcov_{self.nb_cov}_dim_{self.dim}/{self._NAME}_rank_{self._rank}"
+ # return f"PlnPCAcollection_nbcov_{self.nb_cov}_dim_{self.dim}/{self._NAME}_rank_{self._rank}"
@property
def covariates(self):
@@ -1075,7 +1082,7 @@ class _PLNPCA(_PLN):
@property
def path_to_directory(self):
- return f"PLNPCA_nbcov_{self.nb_cov}_dim_{self.dim}/"
+ return f"PlnPCAcollection_nbcov_{self.nb_cov}_dim_{self.dim}/"
@property
def rank(self):
@@ -1086,7 +1093,7 @@ class _PLNPCA(_PLN):
def _pring_beginning_message(self):
print("-" * NB_CHARACTERS_FOR_NICE_PLOT)
- print(f"Fitting a PLNPCA model with {self._rank} components")
+ print(f"Fitting a PlnPCAcollection model with {self._rank} components")
@property
def model_parameters(self):
@@ -1224,8 +1231,8 @@ class _PLNPCA(_PLN):
return self.latent_variables
-class ZIPLN(PLN):
- _NAME = "ZIPLN"
+class ZIPln(Pln):
+ _NAME = "ZIPln"
_pi: torch.Tensor
_coef_inflation: torch.Tensor
diff --git a/pyproject.toml b/pyproject.toml
index 94b2dc2a..fd481fbf 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -43,4 +43,11 @@ classifiers = [
# that you indicate whether you support Python 2, Python 3 or both.
"Programming Language :: Python :: 3 :: Only",
]
-dependencies = {file = ["requirements.txt"]}
+dependencies = [
+"matplotlib",
+"numpy",
+"pandas",
+"scipy",
+"seaborn",
+"torch"
+]
diff --git a/setup.py b/setup.py
index bdb83ce6..05753a23 100644
--- a/setup.py
+++ b/setup.py
@@ -1,17 +1,16 @@
# -*- coding: utf-8 -*-
from setuptools import setup, find_packages
-VERSION = "0.0.43"
+VERSION = "0.0.41"
with open("README.md", "r") as fh:
long_description = fh.read()
with open("requirements.txt", "r") as fh:
requirements = [line.strip() for line in fh]
-
setup(
name="pyPLNmodels",
version=VERSION,
- description="Package implementing PLN models",
+ description="Package implementing Pln models",
project_urls={
"Source": "https://forgemia.inra.fr/bbatardiere/pyplnmodels",
"Documentation": "https://bbatardiere.pages.mia.inra.fr/pyplnmodels/index.html",
@@ -28,7 +27,7 @@ setup(
"count data",
"high dimension",
"scRNAseq",
- "PLN",
+ "Pln",
],
install_requires=requirements,
py_modules=[
diff --git a/tests/conftest.py b/tests/conftest.py
index f4cdbbbd..f70e6aca 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -5,8 +5,8 @@ from functools import singledispatch
import pytest
import torch
from pytest_lazyfixture import lazy_fixture as lf
-from pyPLNmodels import load_model, load_plnpca
-from pyPLNmodels.models import PLN, _PLNPCA, PLNPCA
+from pyPLNmodels import load_model, load_plnpcacollection
+from pyPLNmodels.models import Pln, PlnPCA, PlnPCAcollection
sys.path.append("../")
@@ -58,40 +58,42 @@ instances = []
def convenient_plnpca(*args, **kwargs):
dict_init = kwargs.pop("dict_initialization", None)
if isinstance(args[0], str):
- return _PLNPCA.from_formula(
+ return PlnPCA.from_formula(
*args, **kwargs, dict_initialization=dict_init, rank=RANK
)
print("rank:", RANK)
- return _PLNPCA(*args, **kwargs, dict_initialization=dict_init, rank=RANK)
+ return PlnPCA(*args, **kwargs, dict_initialization=dict_init, rank=RANK)
def convenientplnpca(*args, **kwargs):
dict_init = kwargs.pop("dict_initialization", None)
if isinstance(args[0], str):
- return PLNPCA.from_formula(
+ return PlnPCAcollection.from_formula(
*args, **kwargs, dict_of_dict_initialization=dict_init, ranks=RANKS
)
- return PLNPCA(*args, **kwargs, dict_of_dict_initialization=dict_init, ranks=RANKS)
+ return PlnPCAcollection(
+ *args, **kwargs, dict_of_dict_initialization=dict_init, ranks=RANKS
+ )
def convenientpln(*args, **kwargs):
if isinstance(args[0], str):
- return PLN.from_formula(*args, **kwargs)
- return PLN(*args, **kwargs)
+ return Pln.from_formula(*args, **kwargs)
+ return Pln(*args, **kwargs)
def generate_new_model(model, *args, **kwargs):
name_dir = model.directory_name
name = model._NAME
- if name in ("PLN", "_PLNPCA"):
+ if name in ("Pln", "PlnPCA"):
path = model.path_to_directory + name_dir
init = load_model(path)
- if name == "PLN":
+ if name == "Pln":
new = convenientpln(*args, **kwargs, dict_initialization=init)
- if name == "_PLNPCA":
+ if name == "PlnPCA":
new = convenient_plnpca(*args, **kwargs, dict_initialization=init)
- if name == "PLNPCA":
- init = load_plnpca(name_dir)
+ if name == "PlnPCAcollection":
+ init = load_plnpcacollection(name_dir)
new = convenientplnpca(*args, **kwargs, dict_initialization=init)
return new
diff --git a/tests/test_common.py b/tests/test_common.py
index 4f539f0d..64cb6cae 100644
--- a/tests/test_common.py
+++ b/tests/test_common.py
@@ -10,7 +10,7 @@ from tests.import_data import true_sim_0cov, true_sim_2cov
@pytest.mark.parametrize("any_pln", dict_fixtures["fitted_pln"])
-@filter_models(["PLN", "_PLNPCA"])
+@filter_models(["Pln", "PlnPCA"])
def test_properties(any_pln):
assert hasattr(any_pln, "latent_parameters")
assert hasattr(any_pln, "latent_variables")
@@ -24,7 +24,7 @@ def test_print(any_pln):
@pytest.mark.parametrize("any_pln", dict_fixtures["fitted_pln"])
-@filter_models(["PLN", "_PLNPCA"])
+@filter_models(["Pln", "PlnPCA"])
def test_show_coef_transform_covariance_pcaprojected(any_pln):
any_pln.show()
any_pln._plotargs._show_loss()
@@ -39,7 +39,7 @@ def test_show_coef_transform_covariance_pcaprojected(any_pln):
@pytest.mark.parametrize("sim_pln", dict_fixtures["loaded_and_fitted_pln"])
-@filter_models(["PLN", "_PLNPCA"])
+@filter_models(["Pln", "PlnPCA"])
def test_predict_simulated(sim_pln):
if sim_pln.nb_cov == 0:
assert sim_pln.predict() is None
@@ -60,7 +60,7 @@ def test_verbose(any_instance_pln):
@pytest.mark.parametrize(
"simulated_fitted_any_pln", dict_fixtures["loaded_and_fitted_sim_pln"]
)
-@filter_models(["PLN", "_PLNPCA"])
+@filter_models(["Pln", "PlnPCA"])
def test_find_right_covariance(simulated_fitted_any_pln):
if simulated_fitted_any_pln.nb_cov == 0:
true_covariance = true_sim_0cov["Sigma"]
@@ -73,7 +73,7 @@ def test_find_right_covariance(simulated_fitted_any_pln):
@pytest.mark.parametrize(
"real_fitted_and_loaded_pln", dict_fixtures["loaded_and_fitted_real_pln"]
)
-@filter_models(["PLN", "_PLNPCA"])
+@filter_models(["Pln", "PlnPCA"])
def test_right_covariance_shape(real_fitted_and_loaded_pln):
assert real_fitted_and_loaded_pln.covariance.shape == (100, 100)
@@ -81,7 +81,7 @@ def test_right_covariance_shape(real_fitted_and_loaded_pln):
@pytest.mark.parametrize(
"simulated_fitted_any_pln", dict_fixtures["loaded_and_fitted_pln"]
)
-@filter_models(["PLN", "_PLNPCA"])
+@filter_models(["Pln", "PlnPCA"])
def test_find_right_coef(simulated_fitted_any_pln):
if simulated_fitted_any_pln.nb_cov == 2:
true_coef = true_sim_2cov["beta"]
@@ -92,7 +92,7 @@ def test_find_right_coef(simulated_fitted_any_pln):
@pytest.mark.parametrize("pln", dict_fixtures["loaded_and_fitted_pln"])
-@filter_models(["PLN", "_PLNPCA"])
+@filter_models(["Pln", "PlnPCA"])
def test_fail_count_setter(pln):
wrong_counts = torch.randint(size=(10, 5), low=0, high=10)
with pytest.raises(Exception):
@@ -110,7 +110,7 @@ def test__print_end_of_fitting_message(instance):
@pytest.mark.parametrize("pln", dict_fixtures["fitted_pln"])
-@filter_models(["PLN", "_PLNPCA"])
+@filter_models(["Pln", "PlnPCA"])
def test_fail_wrong_covariates_prediction(pln):
X = torch.randn(pln.n_samples, pln.nb_cov + 1)
with pytest.raises(Exception):
diff --git a/tests/test_pln_full.py b/tests/test_pln_full.py
index a9887353..0fa0e7ea 100644
--- a/tests/test_pln_full.py
+++ b/tests/test_pln_full.py
@@ -5,13 +5,13 @@ from tests.utils import filter_models
@pytest.mark.parametrize("fitted_pln", dict_fixtures["fitted_pln"])
-@filter_models(["PLN"])
+@filter_models(["Pln"])
def test_number_of_iterations_pln_full(fitted_pln):
nb_iterations = len(fitted_pln._elbos_list)
assert 50 < nb_iterations < 300
@pytest.mark.parametrize("pln", dict_fixtures["loaded_and_fitted_pln"])
-@filter_models(["PLN"])
+@filter_models(["Pln"])
def test_latent_var_full(pln):
assert pln.transform().shape == pln.counts.shape
diff --git a/tests/test_plnpca.py b/tests/test_plnpcacollection.py
similarity index 73%
rename from tests/test_plnpca.py
rename to tests/test_plnpcacollection.py
index 85f42885..ecb4a7ac 100644
--- a/tests/test_plnpca.py
+++ b/tests/test_plnpcacollection.py
@@ -9,14 +9,14 @@ from tests.utils import MSE, filter_models
@pytest.mark.parametrize("plnpca", dict_fixtures["loaded_and_fitted_pln"])
-@filter_models(["PLNPCA"])
+@filter_models(["PlnPCAcollection"])
def test_best_model(plnpca):
best_model = plnpca.best_model()
print(best_model)
@pytest.mark.parametrize("plnpca", dict_fixtures["loaded_and_fitted_pln"])
-@filter_models(["PLNPCA"])
+@filter_models(["PlnPCAcollection"])
def test_projected_variables(plnpca):
best_model = plnpca.best_model()
plv = best_model.projected_latent_variables
@@ -24,21 +24,21 @@ def test_projected_variables(plnpca):
@pytest.mark.parametrize("fitted_pln", dict_fixtures["fitted_pln"])
-@filter_models(["_PLNPCA"])
+@filter_models(["PlnPCA"])
def test_number_of_iterations_plnpca(fitted_pln):
nb_iterations = len(fitted_pln._elbos_list)
assert 100 < nb_iterations < 5000
@pytest.mark.parametrize("plnpca", dict_fixtures["loaded_and_fitted_pln"])
-@filter_models(["_PLNPCA"])
+@filter_models(["PlnPCA"])
def test_latent_var_pca(plnpca):
assert plnpca.transform(project=False).shape == plnpca.counts.shape
assert plnpca.transform().shape == (plnpca.n_samples, plnpca.rank)
@pytest.mark.parametrize("plnpca", dict_fixtures["loaded_and_fitted_pln"])
-@filter_models(["PLNPCA"])
+@filter_models(["PlnPCAcollection"])
def test_additional_methods_pca(plnpca):
plnpca.show()
plnpca.BIC
@@ -47,10 +47,9 @@ def test_additional_methods_pca(plnpca):
@pytest.mark.parametrize("plnpca", dict_fixtures["loaded_and_fitted_pln"])
-@filter_models(["PLNPCA"])
+@filter_models(["PlnPCAcollection"])
def test_viz_pca(plnpca):
- models = plnpca.models
- for model in models:
+ for model in plnpca.values():
_, ax = plt.subplots()
model.viz(ax=ax)
plt.show()
@@ -63,14 +62,25 @@ def test_viz_pca(plnpca):
@pytest.mark.parametrize("plnpca", dict_fixtures["loaded_and_fitted_pln"])
-@filter_models(["PLNPCA"])
+@filter_models(["PlnPCAcollection"])
def test__closest(plnpca):
with pytest.warns(UserWarning):
plnpca[9]
@pytest.mark.parametrize("plnpca", dict_fixtures["loaded_and_fitted_pln"])
-@filter_models(["PLNPCA"])
+@filter_models(["PlnPCAcollection"])
def test_wrong_criterion(plnpca):
with pytest.raises(ValueError):
plnpca.best_model("AIK")
+
+
+@pytest.mark.parametrize("collection", dict_fixtures["loaded_and_fitted_pln"])
+@filter_models(["PlnPCAcollection"])
+def test_item(collection):
+ print(collection[collection.ranks[0]])
+ with pytest.raises(KeyError):
+ collection[collection.ranks[0] + 50]
+ assert collection.ranks[0] in collection
+ assert collection.ranks[0] in list(collection.keys())
+ collection.get(collection.ranks[0], None)
diff --git a/tests/test_setters.py b/tests/test_setters.py
index 727c6ac6..14ad481a 100644
--- a/tests/test_setters.py
+++ b/tests/test_setters.py
@@ -15,12 +15,12 @@ def test_data_setter_with_torch(pln):
@pytest.mark.parametrize("pln", dict_fixtures["loaded_and_fitted_pln"])
-@filter_models(["PLN", "_PLNPCA"])
+@filter_models(["Pln", "PlnPCA"])
def test_parameters_setter_with_torch(pln):
pln.latent_mean = pln.latent_mean
pln.latent_var = pln.latent_var
pln.coef = pln.coef
- if pln._NAME == "_PLNPCA":
+ if pln._NAME == "PlnPCA":
pln.components = pln.components
pln.fit()
@@ -40,7 +40,7 @@ def test_data_setter_with_numpy(pln):
@pytest.mark.parametrize("pln", dict_fixtures["loaded_and_fitted_pln"])
-@filter_models(["PLN", "_PLNPCA"])
+@filter_models(["Pln", "PlnPCA"])
def test_parameters_setter_with_numpy(pln):
np_latent_mean = pln.latent_mean.numpy()
np_latent_var = pln.latent_var.numpy()
@@ -51,7 +51,7 @@ def test_parameters_setter_with_numpy(pln):
pln.latent_mean = np_latent_mean
pln.latent_var = np_latent_var
pln.coef = np_coef
- if pln._NAME == "_PLNPCA":
+ if pln._NAME == "PlnPCA":
pln.components = pln.components.numpy()
pln.fit()
@@ -71,7 +71,7 @@ def test_data_setter_with_pandas(pln):
@pytest.mark.parametrize("pln", dict_fixtures["loaded_and_fitted_pln"])
-@filter_models(["PLN", "_PLNPCA"])
+@filter_models(["Pln", "PlnPCA"])
def test_parameters_setter_with_pandas(pln):
pd_latent_mean = pd.DataFrame(pln.latent_mean.numpy())
pd_latent_var = pd.DataFrame(pln.latent_var.numpy())
@@ -82,7 +82,7 @@ def test_parameters_setter_with_pandas(pln):
pln.latent_mean = pd_latent_mean
pln.latent_var = pd_latent_var
pln.coef = pd_coef
- if pln._NAME == "_PLNPCA":
+ if pln._NAME == "PlnPCA":
pln.components = pd.DataFrame(pln.components.numpy())
pln.fit()
@@ -113,7 +113,7 @@ def test_fail_data_setter_with_torch(pln):
@pytest.mark.parametrize("pln", dict_fixtures["loaded_and_fitted_pln"])
-@filter_models(["PLN", "_PLNPCA"])
+@filter_models(["Pln", "PlnPCA"])
def test_fail_parameters_setter_with_torch(pln):
n, dim_latent = pln.latent_mean.shape
dim = pln.counts.shape[1]
@@ -130,7 +130,7 @@ def test_fail_parameters_setter_with_torch(pln):
with pytest.raises(ValueError):
pln.latent_var = torch.zeros(n, dim_latent + 1)
- if pln._NAME == "_PLNPCA":
+ if pln._NAME == "PlnPCA":
with pytest.raises(ValueError):
pln.components = torch.zeros(dim, dim_latent + 1)
--
GitLab
From 736806d24141acee41e5eba1f40f303c8cdc6ef2 Mon Sep 17 00:00:00 2001
From: bastien-mva <bastien.batardiere@gmail.com>
Date: Mon, 22 May 2023 18:45:00 +0200
Subject: [PATCH 04/15] forgot to add the stage in the ci.
---
.gitlab-ci.yml | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c64dc913..f60ae548 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,6 +1,7 @@
stages:
- checks
+ - build_package
- publish
black:
@@ -21,7 +22,7 @@ tests:
- pytest
build_package:
- stage: build
+ stage: build_package
before_script:
- pip install build
script:
@@ -32,6 +33,7 @@ build_package:
expire_in: 1 week
tags:
- docker
+
publish_package:
stage: publish
image: "python:3.9"
--
GitLab
From 9b3ccd72230ee375af2b37d150d5559eba302499 Mon Sep 17 00:00:00 2001
From: bastien-mva <bastien.batardiere@gmail.com>
Date: Mon, 22 May 2023 18:57:59 +0200
Subject: [PATCH 05/15] removed closest test and remove unused import in
models.
---
pyPLNmodels/models.py | 5 -----
tests/test_plnpcacollection.py | 7 -------
2 files changed, 12 deletions(-)
diff --git a/pyPLNmodels/models.py b/pyPLNmodels/models.py
index 0c6c5c37..a8cce1e7 100644
--- a/pyPLNmodels/models.py
+++ b/pyPLNmodels/models.py
@@ -1,9 +1,7 @@
import time
from abc import ABC, abstractmethod
-import pickle
import warnings
import os
-from functools import singledispatchmethod
from collections.abc import Iterable
import pandas as pd
@@ -12,7 +10,6 @@ import numpy as np
import seaborn as sns
import matplotlib.pyplot as plt
from sklearn.decomposition import PCA
-from patsy import dmatrices
from ._closed_forms import (
@@ -31,9 +28,7 @@ from ._utils import (
_format_model_param,
_nice_string_of_dict,
_plot_ellipse,
- _closest,
_check_data_shape,
- _check_right_rank,
_extract_data_from_formula,
_get_dict_initialization,
array2tensor,
diff --git a/tests/test_plnpcacollection.py b/tests/test_plnpcacollection.py
index ecb4a7ac..247335c4 100644
--- a/tests/test_plnpcacollection.py
+++ b/tests/test_plnpcacollection.py
@@ -61,13 +61,6 @@ def test_viz_pca(plnpca):
plt.show()
-@pytest.mark.parametrize("plnpca", dict_fixtures["loaded_and_fitted_pln"])
-@filter_models(["PlnPCAcollection"])
-def test__closest(plnpca):
- with pytest.warns(UserWarning):
- plnpca[9]
-
-
@pytest.mark.parametrize("plnpca", dict_fixtures["loaded_and_fitted_pln"])
@filter_models(["PlnPCAcollection"])
def test_wrong_criterion(plnpca):
--
GitLab
From 83673f6eabfdb14b7280cb08dc313b27d845dd19 Mon Sep 17 00:00:00 2001
From: bastien-mva <bastien.batardiere@gmail.com>
Date: Mon, 22 May 2023 19:24:08 +0200
Subject: [PATCH 06/15] forgot the image in the ci and remove docstrings so
that chatgpt can do it.
---
.gitlab-ci.yml | 1 +
pyPLNmodels/models.py | 52 +------------------------------------------
2 files changed, 2 insertions(+), 51 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index f60ae548..926a2fa8 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -23,6 +23,7 @@ tests:
build_package:
stage: build_package
+ image: "registry.forgemia.inra.fr/jbleger/docker-image-pandas-torch-sphinx:master"
before_script:
- pip install build
script:
diff --git a/pyPLNmodels/models.py b/pyPLNmodels/models.py
index a8cce1e7..4a021d94 100644
--- a/pyPLNmodels/models.py
+++ b/pyPLNmodels/models.py
@@ -46,14 +46,6 @@ NB_CHARACTERS_FOR_NICE_PLOT = 70
class _Pln(ABC):
- """
- Virtual class for all the Pln models.
-
- This class must be derivatived. The methods `get_covariance`, `compute_elbo`,
- `_random_init_latent_parameters` and `_list_of_parameters_needing_gradient` must
- be defined.
- """
-
_WINDOW = 15
n_samples: int
dim: int
@@ -75,10 +67,6 @@ class _Pln(ABC):
dict_initialization=None,
take_log_offsets=False,
):
- """
- Simple initialization method wors fine.
- """
-
self._counts, self._covariates, self._offsets = _format_model_param(
counts, covariates, offsets, offsets_formula, take_log_offsets
)
@@ -189,19 +177,6 @@ class _Pln(ABC):
do_smart_init=True,
verbose=False,
):
- """
- Main function of the class. Fit a Pln to the data.
- Parameters
- ----------
- counts : torch.tensor or ndarray or DataFrame.
- 2-d count data.
- covariates : torch.tensor or ndarray or DataFrame or
- None, default = None
- If not `None`, the first dimension should equal the first
- dimension of `counts`.
- offsets : torch.tensor or ndarray or DataFrame or None, default = None
- Model offset. If not `None`, size should be the same as `counts`.
- """
self._pring_beginning_message()
self._beginning_time = time.time()
@@ -223,9 +198,6 @@ class _Pln(ABC):
self._fitted = True
def _trainstep(self):
- """
- simple docstrings with black errors
- """
self.optim.zero_grad()
loss = -self.compute_elbo()
loss.backward()
@@ -291,23 +263,6 @@ class _Pln(ABC):
"""
def display_covariance(self, ax=None, savefig=False, name_file=""):
- """
- Display a heatmap of covariance to visualize correlations.
-
- If covariance is too big (size is > 400), will only display the
- first block of size (400,400).
-
- Parameters
- ----------
- ax : matplotlib Axes, optional
- Axes in which to draw the plot, otherwise use the
- currently-active Axes.
- savefig: bool, optional
- If True the figure will be saved. Default is False.
- name_file : str, optional
- The name of the file the graphic will be saved to if saved.
- Default is an empty string.
- """
if self.dim > 400:
warnings.warn("Only displaying the first 400 variables.")
sigma = sigma[:400, :400]
@@ -318,7 +273,7 @@ class _Pln(ABC):
plt.savefig(name_file + self._NAME)
plt.show() # to avoid displaying a blanck screen
- def __str__(self):
+ def __repr__(self):
delimiter = "=" * NB_CHARACTERS_FOR_NICE_PLOT
string = f"A multivariate Poisson Lognormal with {self._description} \n"
string += f"{delimiter}\n"
@@ -593,11 +548,6 @@ class Pln(_Pln):
return self.dim
def compute_elbo(self):
- """
- Compute the Evidence Lower BOund (ELBO) that will be
- maximized by pytorch. Here we use the profiled ELBO
- for the full covariance matrix.
- """
return profiled_elbo_pln(
self._counts,
self._covariates,
--
GitLab
From 53bf11fee748954c4fd46ff2bb2c371ab1dd2a8a Mon Sep 17 00:00:00 2001
From: bastien-mva <bastien.batardiere@gmail.com>
Date: Mon, 22 May 2023 20:14:02 +0200
Subject: [PATCH 07/15] remove setup as it was added not on purpose
---
setup.py | 58 --------------------------------------------------------
1 file changed, 58 deletions(-)
delete mode 100644 setup.py
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 05753a23..00000000
--- a/setup.py
+++ /dev/null
@@ -1,58 +0,0 @@
-# -*- coding: utf-8 -*-
-from setuptools import setup, find_packages
-
-VERSION = "0.0.41"
-
-with open("README.md", "r") as fh:
- long_description = fh.read()
-with open("requirements.txt", "r") as fh:
- requirements = [line.strip() for line in fh]
-setup(
- name="pyPLNmodels",
- version=VERSION,
- description="Package implementing Pln models",
- project_urls={
- "Source": "https://forgemia.inra.fr/bbatardiere/pyplnmodels",
- "Documentation": "https://bbatardiere.pages.mia.inra.fr/pyplnmodels/index.html",
- },
- author="Bastien Batardière, Julien Chiquet, Joon Kwon",
- author_email="bastien.batardiere@gmail.com, julien.chiquet@inrae.fr, joon.kwon@inrae.fr",
- long_description=long_description,
- packages=find_packages(),
- python_requires=">=3",
- keywords=[
- "python",
- "count",
- "data",
- "count data",
- "high dimension",
- "scRNAseq",
- "Pln",
- ],
- install_requires=requirements,
- py_modules=[
- "pyPLNmodels._utils",
- "pyPLNmodels.elbos",
- "pyPLNmodels.models",
- "pyPLNmodels._closed_forms",
- ],
- long_description_content_type="text/markdown",
- license="MIT",
- # See https://pypi.python.org/pypi?%3Aaction=list_classifiers
- classifiers=[
- # How mature is this project? Common values are
- # 3 - Alpha
- # 4 - Beta
- # 5 - Production/Stable
- "Development Status :: 3 - Alpha",
- # Indicate who your project is intended for
- "Intended Audience :: Science/Research",
- # Pick your license as you wish (should match "license" above)
- "License :: OSI Approved :: MIT License",
- # Specify the Python versions you support here. In particular, ensure
- # that you indicate whether you support Python 2, Python 3 or both.
- "Programming Language :: Python :: 3 :: Only",
- ],
- include_package_data=True,
- package_data={"": ["data/oaks/*.csv"]},
-)
--
GitLab
From 8a058b55dbbe3855dd4bc9141ae59f4fa7ffac6d Mon Sep 17 00:00:00 2001
From: bastien-mva <bastien.batardiere@gmail.com>
Date: Mon, 22 May 2023 20:39:29 +0200
Subject: [PATCH 08/15] docstrings for _PLN
---
pyPLNmodels/models.py | 595 +++++++++++++++++++++++++++++++++++++++---
1 file changed, 557 insertions(+), 38 deletions(-)
diff --git a/pyPLNmodels/models.py b/pyPLNmodels/models.py
index 4a021d94..6d28425c 100644
--- a/pyPLNmodels/models.py
+++ b/pyPLNmodels/models.py
@@ -3,6 +3,7 @@ from abc import ABC, abstractmethod
import warnings
import os
from collections.abc import Iterable
+from typing import Optional
import pandas as pd
import torch
@@ -60,13 +61,31 @@ class _Pln(ABC):
def __init__(
self,
- counts,
- covariates=None,
- offsets=None,
- offsets_formula="logsum",
- dict_initialization=None,
- take_log_offsets=False,
+ counts: torch.Tensor,
+ covariates: Optional[torch.Tensor] = None,
+ offsets: Optional[torch.Tensor] = None,
+ offsets_formula: str = "logsum",
+ dict_initialization: Optional[dict] = None,
+ take_log_offsets: bool = False,
):
+ """
+ Initializes the _Pln class.
+
+ Parameters
+ ----------
+ counts : torch.Tensor
+ The count data.
+ covariates : torch.Tensor, optional
+ The covariate data. Defaults to None.
+ offsets : torch.Tensor, optional
+ The offsets data. Defaults to None.
+ offsets_formula : str, optional
+ The formula for offsets. Defaults to "logsum".
+ dict_initialization : dict, optional
+ The initialization dictionary. Defaults to None.
+ take_log_offsets : bool, optional
+ Whether to take the log of offsets. Defaults to False.
+ """
self._counts, self._covariates, self._offsets = _format_model_param(
counts, covariates, offsets, offsets_formula, take_log_offsets
)
@@ -81,10 +100,31 @@ class _Pln(ABC):
cls,
formula: str,
data: dict,
- offsets_formula="logsum",
- dict_initialization=None,
- take_log_offsets=False,
+ offsets_formula: str = "logsum",
+ dict_initialization: Optional[dict] = None,
+ take_log_offsets: bool = False,
):
+ """
+ Create a _Pln instance from a formula and data.
+
+ Parameters
+ ----------
+ formula : str
+ The formula.
+ data : dict
+ The data dictionary.
+ offsets_formula : str, optional
+ The formula for offsets. Defaults to "logsum".
+ dict_initialization : dict, optional
+ The initialization dictionary. Defaults to None.
+ take_log_offsets : bool, optional
+ Whether to take the log of offsets. Defaults to False.
+
+ Returns
+ -------
+ _Pln
+ The initialized _Pln instance.
+ """
counts, covariates, offsets = _extract_data_from_formula(formula, data)
return cls(
counts,
@@ -95,7 +135,15 @@ class _Pln(ABC):
take_log_offsets,
)
- def _set_init_parameters(self, dict_initialization):
+ def _set_init_parameters(self, dict_initialization: dict):
+ """
+ Set initial parameters based on a dictionary.
+
+ Parameters
+ ----------
+ dict_initialization : dict
+ The initialization dictionary.
+ """
if "coef" not in dict_initialization.keys():
print("No coef is initialized.")
self.coef = None
@@ -104,51 +152,110 @@ class _Pln(ABC):
setattr(self, key, array)
@property
- def fitted(self):
+ def fitted(self) -> bool:
+ """
+ Whether the model is fitted.
+
+ Returns
+ -------
+ bool
+ True if the model is fitted, False otherwise.
+ """
return self._fitted
@property
- def nb_iteration_done(self):
+ def nb_iteration_done(self) -> int:
+ """
+ The number of iterations done.
+
+ Returns
+ -------
+ int
+ The number of iterations done.
+ """
return len(self._plotargs._elbos_list)
@property
- def n_samples(self):
+ def n_samples(self) -> int:
+ """
+ The number of samples.
+
+ Returns
+ -------
+ int
+ The number of samples.
+ """
return self._counts.shape[0]
@property
- def dim(self):
+ def dim(self) -> int:
+ """
+ The dimension.
+
+ Returns
+ -------
+ int
+ The dimension.
+ """
return self._counts.shape[1]
@property
- def nb_cov(self):
+ def nb_cov(self) -> int:
+ """
+ The number of covariates.
+
+ Returns
+ -------
+ int
+ The number of covariates.
+ """
if self.covariates is None:
return 0
return self.covariates.shape[1]
def _smart_init_coef(self):
+ """
+ Initialize coefficients smartly.
+ """
self._coef = _init_coef(self._counts, self._covariates, self._offsets)
def _random_init_coef(self):
+ """
+ Randomly initialize coefficients.
+ """
if self.nb_cov == 0:
self._coef = None
self._coef = torch.randn((self.nb_cov, self.dim), device=DEVICE)
@abstractmethod
def _random_init_model_parameters(self):
- pass
-
- @abstractmethod
- def _smart_init_model_parameters(self):
+ """
+ Abstract method to randomly initialize model parameters.
+ """
pass
@abstractmethod
def _random_init_latent_parameters(self):
+ """
+ Abstract method to randomly initialize latent parameters.
+ """
pass
def _smart_init_latent_parameters(self):
+ """
+ Initialize latent parameters smartly.
+ """
pass
- def _init_parameters(self, do_smart_init):
+ def _init_parameters(self, do_smart_init: bool):
+ """
+ Initialize model parameters.
+
+ Parameters
+ ----------
+ do_smart_init : bool
+ Whether to perform smart initialization.
+ """
print("Initialization ...")
if do_smart_init:
self._smart_init_model_parameters()
@@ -159,24 +266,51 @@ class _Pln(ABC):
print("Initialization finished")
def _put_parameters_to_device(self):
+ """
+ Move parameters to the device.
+ """
for parameter in self._list_of_parameters_needing_gradient:
parameter.requires_grad_(True)
@property
def _list_of_parameters_needing_gradient(self):
"""
- A list containing all the parameters that needs to be upgraded via a gradient step.
+ A list containing all the parameters that need to be upgraded via a gradient step.
+
+ Returns
+ -------
+ List[torch.Tensor]
+ List of parameters needing gradient.
"""
+ ...
def fit(
self,
- nb_max_iteration=50000,
- lr=0.01,
- class_optimizer=torch.optim.Rprop,
- tol=1e-3,
- do_smart_init=True,
- verbose=False,
+ nb_max_iteration: int = 50000,
+ lr: float = 0.01,
+ class_optimizer: torch.optim.Optimizer = torch.optim.Rprop,
+ tol: float = 1e-3,
+ do_smart_init: bool = True,
+ verbose: bool = False,
):
+ """
+ Fit the model.
+
+ Parameters
+ ----------
+ nb_max_iteration : int, optional
+ The maximum number of iterations. Defaults to 50000.
+ lr : float, optional
+ The learning rate. Defaults to 0.01.
+ class_optimizer : torch.optim.Optimizer, optional
+ The optimizer class. Defaults to torch.optim.Rprop.
+ tol : float, optional
+ The tolerance for convergence. Defaults to 1e-3.
+ do_smart_init : bool, optional
+ Whether to perform smart initialization. Defaults to True.
+ verbose : bool, optional
+ Whether to print training progress. Defaults to False.
+ """
self._pring_beginning_message()
self._beginning_time = time.time()
@@ -187,7 +321,7 @@ class _Pln(ABC):
self._put_parameters_to_device()
self.optim = class_optimizer(self._list_of_parameters_needing_gradient, lr=lr)
stop_condition = False
- while self.nb_iteration_done < nb_max_iteration and stop_condition == False:
+ while self.nb_iteration_done < nb_max_iteration and not stop_condition:
loss = self._trainstep()
criterion = self._compute_criterion_and_update_plotargs(loss, tol)
if abs(criterion) < tol:
@@ -198,6 +332,14 @@ class _Pln(ABC):
self._fitted = True
def _trainstep(self):
+ """
+ Perform a single training step.
+
+ Returns
+ -------
+ torch.Tensor
+ The loss value.
+ """
self.optim.zero_grad()
loss = -self.compute_elbo()
loss.backward()
@@ -205,7 +347,20 @@ class _Pln(ABC):
self._update_closed_forms()
return loss
- def pca_projected_latent_variables(self, n_components=None):
+ def pca_projected_latent_variables(self, n_components: Optional[int] = None):
+ """
+ Perform PCA on the latent variables and project them onto a lower-dimensional space.
+
+ Parameters
+ ----------
+ n_components : int, optional
+ The number of components to keep. If None, all components are kept. Defaults to None.
+
+ Returns
+ -------
+ numpy.ndarray
+ The projected latent variables.
+ """
if n_components is None:
n_components = self._get_max_components()
if n_components > self.dim:
@@ -218,9 +373,22 @@ class _Pln(ABC):
@property
@abstractmethod
def latent_variables(self):
+ """
+ Abstract property representing the latent variables.
+ """
pass
- def _print_end_of_fitting_message(self, stop_condition, tol):
+ def _print_end_of_fitting_message(self, stop_condition: bool, tol: float):
+ """
+ Print the end-of-fitting message.
+
+ Parameters
+ ----------
+ stop_condition : bool
+ Whether the stop condition was met.
+ tol : float
+ The tolerance for convergence.
+ """
if stop_condition is True:
print(
f"Tolerance {tol} reached "
@@ -235,12 +403,30 @@ class _Pln(ABC):
)
def print_stats(self):
+ """
+ Print the training statistics.
+ """
print("-------UPDATE-------")
print("Iteration number: ", self._plotargs.iteration_number)
print("Criterion: ", np.round(self._plotargs.criterions[-1], 8))
print("ELBO:", np.round(self._plotargs._elbos_list[-1], 6))
def _compute_criterion_and_update_plotargs(self, loss, tol):
+ """
+ Compute the convergence criterion and update the plot arguments.
+
+ Parameters
+ ----------
+ loss : torch.Tensor
+ The loss value.
+ tol : float
+ The tolerance for convergence.
+
+ Returns
+ -------
+ float
+ The computed criterion.
+ """
self._plotargs._elbos_list.append(-loss.item())
self._plotargs.running_times.append(time.time() - self._beginning_time)
if self._plotargs.iteration_number > self._WINDOW:
@@ -253,6 +439,9 @@ class _Pln(ABC):
return tol
def _update_closed_forms(self):
+ """
+ Update closed-form expressions.
+ """
pass
@abstractmethod
@@ -261,8 +450,21 @@ class _Pln(ABC):
Compute the Evidence Lower BOund (ELBO) that will be maximized
by pytorch.
"""
+ pass
def display_covariance(self, ax=None, savefig=False, name_file=""):
+ """
+ Display the covariance matrix.
+
+ Parameters
+ ----------
+ ax : matplotlib.axes.Axes, optional
+ The axes to plot on. If None, a new figure will be created. Defaults to None.
+ savefig : bool, optional
+ Whether to save the figure. Defaults to False.
+ name_file : str, optional
+ The name of the file to save. Defaults to "".
+ """
if self.dim > 400:
warnings.warn("Only displaying the first 400 variables.")
sigma = sigma[:400, :400]
@@ -271,9 +473,17 @@ class _Pln(ABC):
sns.heatmap(self.covariance, ax=ax)
if savefig:
plt.savefig(name_file + self._NAME)
- plt.show() # to avoid displaying a blanck screen
+ plt.show() # to avoid displaying a blank screen
def __repr__(self):
+ """
+ Generate the string representation of the object.
+
+ Returns
+ -------
+ str
+ The string representation of the object.
+ """
delimiter = "=" * NB_CHARACTERS_FOR_NICE_PLOT
string = f"A multivariate Poisson Lognormal with {self._description} \n"
string += f"{delimiter}\n"
@@ -285,19 +495,33 @@ class _Pln(ABC):
string += f" {self._useful_methods_strings}\n"
string += f"* Additional properties for {self._NAME}\n"
string += f" {self._additional_properties_string}\n"
- string += f"* Additionial methods for {self._NAME}\n"
+ string += f"* Additional methods for {self._NAME}\n"
string += f" {self._additional_methods_string}"
return string
@property
def _additional_methods_string(self):
+ """
+ Abstract property representing the additional methods string.
+ """
pass
@property
def _additional_properties_string(self):
+ """
+ Abstract property representing the additional properties string.
+ """
pass
def show(self, axes=None):
+ """
+ Show plots.
+
+ Parameters
+ ----------
+ axes : numpy.ndarray, optional
+ The axes to plot on. If None, a new figure will be created. Defaults to None.
+ """
print("Likelihood:", -self.loglike)
if self._fitted is False:
nb_axes = 1
@@ -315,10 +539,21 @@ class _Pln(ABC):
@property
def _elbos_list(self):
+ """
+ Property representing the list of ELBO values.
+ """
return self._plotargs._elbos_list
@property
def loglike(self):
+ """
+ Property representing the log-likelihood.
+
+ Returns
+ -------
+ float
+ The log-likelihood.
+ """
if self._fitted is False:
t0 = time.time()
self._plotargs._elbos_list.append(self.compute_elbo().item())
@@ -327,22 +562,62 @@ class _Pln(ABC):
@property
def BIC(self):
+ """
+ Property representing the Bayesian Information Criterion (BIC).
+
+ Returns
+ -------
+ float
+ The BIC value.
+ """
return -self.loglike + self.number_of_parameters / 2 * np.log(self.n_samples)
@property
def AIC(self):
+ """
+ Property representing the Akaike Information Criterion (AIC).
+
+ Returns
+ -------
+ float
+ The AIC value.
+ """
return -self.loglike + self.number_of_parameters
@property
def latent_parameters(self):
+ """
+ Property representing the latent parameters.
+
+ Returns
+ -------
+ dict
+ The dictionary of latent parameters.
+ """
return {"latent_var": self.latent_var, "latent_mean": self.latent_mean}
@property
def model_parameters(self):
+ """
+ Property representing the model parameters.
+
+ Returns
+ -------
+ dict
+ The dictionary of model parameters.
+ """
return {"coef": self.coef, "covariance": self.covariance}
@property
def dict_data(self):
+ """
+ Property representing the data dictionary.
+
+ Returns
+ -------
+ dict
+ The dictionary of data.
+ """
return {
"counts": self.counts,
"covariates": self.covariates,
@@ -351,27 +626,80 @@ class _Pln(ABC):
@property
def _model_in_a_dict(self):
+ """
+ Property representing the model in a dictionary.
+
+ Returns
+ -------
+ dict
+ The dictionary representing the model.
+ """
return self.dict_data | self._dict_parameters
@property
def _dict_parameters(self):
+ """
+ Property representing the dictionary of parameters.
+
+ Returns
+ -------
+ dict
+ The dictionary of parameters.
+ """
return self.model_parameters | self.latent_parameters
@property
def coef(self):
+ """
+ Property representing the coefficients.
+
+ Returns
+ -------
+ torch.Tensor or None
+ The coefficients or None.
+ """
return self._cpu_attribute_or_none("_coef")
@property
def latent_mean(self):
+ """
+ Property representing the latent mean.
+
+ Returns
+ -------
+ torch.Tensor or None
+ The latent mean or None.
+ """
return self._cpu_attribute_or_none("_latent_mean")
@property
def latent_var(self):
+ """
+ Property representing the latent variance.
+
+ Returns
+ -------
+ torch.Tensor or None
+ The latent variance or None.
+ """
return self._cpu_attribute_or_none("_latent_var")
@latent_mean.setter
@array2tensor
def latent_mean(self, latent_mean):
+ """
+ Setter for the latent mean property.
+
+ Parameters
+ ----------
+ latent_mean : torch.Tensor
+ The latent mean.
+
+ Raises
+ ------
+ ValueError
+ If the shape of the latent mean is incorrect.
+ """
if latent_mean.shape != (self.n_samples, self.dim):
raise ValueError(
f"Wrong shape. Expected {self.n_samples, self.dim}, got {latent_mean.shape}"
@@ -381,6 +709,19 @@ class _Pln(ABC):
@latent_var.setter
@array2tensor
def latent_var(self, latent_var):
+ """
+ Setter for the latent variance property.
+
+ Parameters
+ ----------
+ latent_var : torch.Tensor
+ The latent variance.
+
+ Raises
+ ------
+ ValueError
+ If the shape of the latent variance is incorrect.
+ """
if latent_var.shape != (self.n_samples, self.dim):
raise ValueError(
f"Wrong shape. Expected {self.n_samples, self.dim}, got {latent_var.shape}"
@@ -388,6 +729,19 @@ class _Pln(ABC):
self._latent_var = latent_var
def _cpu_attribute_or_none(self, attribute_name):
+ """
+ Get the CPU attribute or return None.
+
+ Parameters
+ ----------
+ attribute_name : str
+ The attribute name.
+
+ Returns
+ -------
+ torch.Tensor or None
+ The attribute value or None.
+ """
if hasattr(self, attribute_name):
attr = getattr(self, attribute_name)
if isinstance(attr, torch.Tensor):
@@ -395,7 +749,15 @@ class _Pln(ABC):
return attr
return None
- def save(self, path_of_directory="./"):
+ def save(self, path_of_directory: str = "./"):
+ """
+ Save the model parameters to disk.
+
+ Parameters
+ ----------
+ path_of_directory : str, optional
+ The path of the directory to save the parameters, by default "./".
+ """
path = f"{path_of_directory}/{self.path_to_directory}{self.directory_name}"
os.makedirs(path, exist_ok=True)
for key, value in self._dict_parameters.items():
@@ -411,19 +773,56 @@ class _Pln(ABC):
@property
def counts(self):
+ """
+ Property representing the counts.
+
+ Returns
+ -------
+ torch.Tensor or None
+ The counts or None.
+ """
return self._cpu_attribute_or_none("_counts")
@property
def offsets(self):
+ """
+ Property representing the offsets.
+
+ Returns
+ -------
+ torch.Tensor or None
+ The offsets or None.
+ """
return self._cpu_attribute_or_none("_offsets")
@property
def covariates(self):
+ """
+ Property representing the covariates.
+
+ Returns
+ -------
+ torch.Tensor or None
+ The covariates or None.
+ """
return self._cpu_attribute_or_none("_covariates")
@counts.setter
@array2tensor
def counts(self, counts):
+ """
+ Setter for the counts property.
+
+ Parameters
+ ----------
+ counts : torch.Tensor
+ The counts.
+
+ Raises
+ ------
+ ValueError
+ If the shape of the counts is incorrect or if the input is not integers.
+ """
if self.counts.shape != counts.shape:
raise ValueError(
f"Wrong shape for the counts. Expected {self.counts.shape}, got {counts.shape}"
@@ -435,6 +834,19 @@ class _Pln(ABC):
@offsets.setter
@array2tensor
def offsets(self, offsets):
+ """
+ Setter for the offsets property.
+
+ Parameters
+ ----------
+ offsets : torch.Tensor
+ The offsets.
+
+ Raises
+ ------
+ ValueError
+ If the shape of the offsets is incorrect.
+ """
if self.offsets.shape != offsets.shape:
raise ValueError(
f"Wrong shape for the offsets. Expected {self.offsets.shape}, got {offsets.shape}"
@@ -444,12 +856,38 @@ class _Pln(ABC):
@covariates.setter
@array2tensor
def covariates(self, covariates):
+ """
+ Setter for the covariates property.
+
+ Parameters
+ ----------
+ covariates : torch.Tensor
+ The covariates.
+
+ Raises
+ ------
+ ValueError
+ If the shape of the covariates or counts is incorrect.
+ """
_check_data_shape(self.counts, covariates, self.offsets)
self._covariates = covariates
@coef.setter
@array2tensor
def coef(self, coef):
+ """
+ Setter for the coef property.
+
+ Parameters
+ ----------
+ coef : torch.Tensor or None
+ The coefficients.
+
+ Raises
+ ------
+ ValueError
+ If the shape of the coef is incorrect.
+ """
if coef is None:
pass
elif coef.shape != (self.nb_cov, self.dim):
@@ -460,6 +898,14 @@ class _Pln(ABC):
@property
def dict_for_printing(self):
+ """
+ Property representing the dictionary for printing.
+
+ Returns
+ -------
+ dict
+ The dictionary for printing.
+ """
return {
"Loglike": np.round(self.loglike, 2),
"Dimension": self.dim,
@@ -470,22 +916,79 @@ class _Pln(ABC):
@property
def optim_parameters(self):
+ """
+ Property representing the optimization parameters.
+
+ Returns
+ -------
+ dict
+ The dictionary of optimization parameters.
+ """
return {"Number of iterations done": self.nb_iteration_done}
@property
def _useful_properties_string(self):
- return ".latent_variables, .model_parameters, .latent_parameters, \
-.optim_parameters"
+ """
+ Property representing the useful properties as a string.
+
+ Returns
+ -------
+ str
+ The string representation of the useful properties.
+ """
+ return ".latent_variables, .model_parameters, .latent_parameters, .optim_parameters"
@property
def _useful_methods_strings(self):
- return ".show(), .coef() .transform(), .sigma(), .predict(), \
-.pca_projected_latent_variables()"
+ """
+ Property representing the useful methods as a string.
+
+ Returns
+ -------
+ str
+ The string representation of the useful methods.
+ """
+ return ".show(), .coef() .transform(), .sigma(), .predict(), .pca_projected_latent_variables()"
def sigma(self):
+ """
+ Method returning the covariance matrix.
+
+ Returns
+ -------
+ torch.Tensor or None
+ The covariance matrix or None.
+ """
return self.covariance
def predict(self, covariates=None):
+ """
+ Method for making predictions.
+
+ Parameters
+ ----------
+ covariates : torch.Tensor, optional
+ The covariates, by default None.
+
+ Returns
+ -------
+ torch.Tensor or None
+ The predicted values or None.
+
+ Raises
+ ------
+ AttributeError
+ If there are no covariates in the model.
+ RuntimeError
+ If the shape of thecovariates is incorrect.
+
+ Notes
+ -----
+ - If `covariates` is not provided and there are no covariates in the model, None is returned.
+ - If `covariates` is provided, it should have the shape `(n_samples, nb_cov)`, where `n_samples` is the number of samples and `nb_cov` is the number of covariates.
+ - The predicted values are obtained by multiplying the covariates by the coefficients.
+
+ """
if covariates is not None and self.nb_cov == 0:
raise AttributeError("No covariates in the model, can't predict")
if covariates is None:
@@ -494,17 +997,33 @@ class _Pln(ABC):
return None
return self.covariates @ self.coef
if covariates.shape[-1] != self.nb_cov:
- error_string = f"X has wrong shape ({covariates.shape}).Should"
+ error_string = f"X has wrong shape ({covariates.shape}). Should"
error_string += f" be ({self.n_samples, self.nb_cov})."
raise RuntimeError(error_string)
return covariates @ self.coef
@property
def directory_name(self):
+ """
+ Property representing the directory name.
+
+ Returns
+ -------
+ str
+ The directory name.
+ """
return f"{self._NAME}_nbcov_{self.nb_cov}_dim_{self.dim}"
@property
def path_to_directory(self):
+ """
+ Property representing the path to the directory.
+
+ Returns
+ -------
+ str
+ The path to the directory.
+ """
return ""
--
GitLab
From e414c54818dd66518e31fd470c60429b1f6396d6 Mon Sep 17 00:00:00 2001
From: bastien-mva <bastien.batardiere@gmail.com>
Date: Mon, 22 May 2023 21:34:38 +0200
Subject: [PATCH 09/15] import data with pkg_resource.
---
pyPLNmodels/_utils.py | 35 +++----------
pyPLNmodels/models.py | 119 ++++++++++++++++++++++++++++++++++++++++++
2 files changed, 125 insertions(+), 29 deletions(-)
diff --git a/pyPLNmodels/_utils.py b/pyPLNmodels/_utils.py
index 9dc16713..0206b3b4 100644
--- a/pyPLNmodels/_utils.py
+++ b/pyPLNmodels/_utils.py
@@ -10,6 +10,7 @@ from matplotlib.patches import Ellipse
import matplotlib.pyplot as plt
from patsy import dmatrices
from typing import Optional, Dict, Any, Union
+import pkg_resources
torch.set_default_dtype(torch.float64)
@@ -646,32 +647,6 @@ def _format_model_param(
return counts, covariates, offsets
-def _remove_useless_intercepts(covariates: torch.Tensor) -> torch.Tensor:
- """
- Remove useless intercepts from covariates.
-
- Parameters
- ----------
- covariates : torch.Tensor, shape (n, d)
- Covariate data.
-
- Returns
- -------
- torch.Tensor
- Covariate data with useless intercepts removed.
- """
- covariates = _format_data(covariates)
- if covariates.shape[1] < 2:
- return covariates
- first_column = covariates[:, 0]
- second_column = covariates[:, 1]
- diff = first_column - second_column
- if torch.sum(torch.abs(diff - diff[0])) == 0:
- print("removing one")
- return covariates[:, 1:]
- return covariates
-
-
def _check_data_shape(
counts: torch.Tensor, covariates: torch.Tensor, offsets: torch.Tensor
) -> None:
@@ -902,9 +877,11 @@ def get_real_count_data(n_samples: int = 270, dim: int = 100) -> np.ndarray:
f"\nTaking the whole 100 variables. Requested:dim={dim}, returned:100"
)
dim = 100
- counts = pd.read_csv("../example_data/real_data/Y_mark.csv").values[
- :n_samples, :dim
- ]
+ counts_stream = pkg_resources.resource_stream(__name__, "data/scRT/Y_mark.csv")
+ counts = pd.read_csv(counts_stream).values[:n_samples, :dim]
+ # counts = pd.read_csv("./pyPLNmodels/data/scRT/Y_mark.csv").values[
+ # :n_samples, :dim
+ # ]
print(f"Returning dataset of size {counts.shape}")
return counts
diff --git a/pyPLNmodels/models.py b/pyPLNmodels/models.py
index 6d28425c..e73b5fd4 100644
--- a/pyPLNmodels/models.py
+++ b/pyPLNmodels/models.py
@@ -1034,10 +1034,26 @@ class Pln(_Pln):
@property
def _description(self):
+ """
+ Property representing the description of the model.
+
+ Returns
+ -------
+ str
+ The description of the model.
+ """
return "full covariance model."
@property
def coef(self):
+ """
+ Property representing the coefficients.
+
+ Returns
+ -------
+ torch.Tensor or None
+ The coefficients or None.
+ """
if (
hasattr(self, "_latent_mean")
and hasattr(self, "_covariates")
@@ -1048,12 +1064,26 @@ class Pln(_Pln):
@coef.setter
def coef(self, coef):
+ """
+ Setter for the coef property.
+
+ Parameters
+ ----------
+ coef : torch.Tensor
+ The coefficients.
+ """
pass
def _smart_init_latent_parameters(self):
+ """
+ Method for smartly initializing the latent parameters.
+ """
self._random_init_latent_parameters()
def _random_init_latent_parameters(self):
+ """
+ Method for randomly initializing the latent parameters.
+ """
if not hasattr(self, "_latent_var"):
self._latent_var = 1 / 2 * torch.ones((self.n_samples, self.dim)).to(DEVICE)
if not hasattr(self, "_latent_mean"):
@@ -1061,12 +1091,36 @@ class Pln(_Pln):
@property
def _list_of_parameters_needing_gradient(self):
+ """
+ Property representing the list of parameters needing gradient.
+
+ Returns
+ -------
+ list
+ The list of parameters needing gradient.
+ """
return [self._latent_mean, self._latent_var]
def _get_max_components(self):
+ """
+ Method for getting the maximum number of components.
+
+ Returns
+ -------
+ int
+ The maximum number of components.
+ """
return self.dim
def compute_elbo(self):
+ """
+ Method for computing the evidence lower bound (ELBO).
+
+ Returns
+ -------
+ torch.Tensor
+ The computed ELBO.
+ """
return profiled_elbo_pln(
self._counts,
self._covariates,
@@ -1076,19 +1130,41 @@ class Pln(_Pln):
)
def _smart_init_model_parameters(self):
+ """
+ Method for smartly initializing the model parameters.
+ """
# no model parameters since we are doing a profiled ELBO
pass
def _random_init_model_parameters(self):
+ """
+ Method for randomly initializing the model parameters.
+ """
# no model parameters since we are doing a profiled ELBO
pass
@property
def _coef(self):
+ """
+ Property representing the coefficients.
+
+ Returns
+ -------
+ torch.Tensor
+ The coefficients.
+ """
return _closed_formula_coef(self._covariates, self._latent_mean)
@property
def _covariance(self):
+ """
+ Property representing the covariance matrix.
+
+ Returns
+ -------
+ torch.Tensor or None
+ The covariance matrix or None.
+ """
return _closed_formula_covariance(
self._covariates,
self._latent_mean,
@@ -1098,21 +1174,56 @@ class Pln(_Pln):
)
def _pring_beginning_message(self):
+ """
+ Method for printing the beginning message.
+ """
print(f"Fitting a Pln model with {self._description}")
@property
def latent_variables(self):
+ """
+ Property representing the latent variables.
+
+ Returns
+ -------
+ torch.Tensor
+ The latent variables.
+ """
return self.latent_mean
@property
def number_of_parameters(self):
+ """
+ Property representing the number of parameters.
+
+ Returns
+ -------
+ int
+ The number of parameters.
+ """
return self.dim * (self.dim + self.nb_cov)
def transform(self):
+ """
+ Method for transforming the model.
+
+ Returns
+ -------
+ torch.Tensor
+ The transformed model.
+ """
return self.latent_variables
@property
def covariance(self):
+ """
+ Property representing the covariance matrix.
+
+ Returns
+ -------
+ torch.Tensor or None
+ The covariance matrix or None.
+ """
if all(
hasattr(self, attr)
for attr in [
@@ -1128,6 +1239,14 @@ class Pln(_Pln):
@covariance.setter
def covariance(self, covariance):
+ """
+ Setter for the covariance property.
+
+ Parameters
+ ----------
+ covariance : torch.Tensor
+ The covariance matrix.
+ """
pass
--
GitLab
From e3ab04f6c9fb450a1fffcec70a198d6892191756 Mon Sep 17 00:00:00 2001
From: bastien-mva <bastien.batardiere@gmail.com>
Date: Mon, 22 May 2023 21:35:11 +0200
Subject: [PATCH 10/15] move data from example_data to data inside the
module.py
---
pyPLNmodels/data/scRT/Y_mark.csv | 271 ++++++++++++++++++
pyPLNmodels/data/test_data/O_test.csv | 201 +++++++++++++
pyPLNmodels/data/test_data/Y_test.csv | 201 +++++++++++++
pyPLNmodels/data/test_data/cov_test.csv | 201 +++++++++++++
.../true_parameters/true_Sigma_test.csv | 51 ++++
.../true_parameters/true_beta_test.csv | 3 +
6 files changed, 928 insertions(+)
create mode 100644 pyPLNmodels/data/scRT/Y_mark.csv
create mode 100644 pyPLNmodels/data/test_data/O_test.csv
create mode 100644 pyPLNmodels/data/test_data/Y_test.csv
create mode 100644 pyPLNmodels/data/test_data/cov_test.csv
create mode 100644 pyPLNmodels/data/test_data/true_parameters/true_Sigma_test.csv
create mode 100644 pyPLNmodels/data/test_data/true_parameters/true_beta_test.csv
diff --git a/pyPLNmodels/data/scRT/Y_mark.csv b/pyPLNmodels/data/scRT/Y_mark.csv
new file mode 100644
index 00000000..43c88887
--- /dev/null
+++ b/pyPLNmodels/data/scRT/Y_mark.csv
@@ -0,0 +1,271 @@
+0.0,0.0,0.0,0.0,1.0,3.0,1.0,0.0,2.0,1.0,0.0,1.0,0.0,2.0,0.0,2.0,2.0,0.0,0.0,0.0,0.0,1.0,12.0,2.0,1.0,0.0,0.0,0.0,0.0,1.0,0.0,2.0,2.0,0.0,0.0,0.0,4.0,0.0,0.0,1.0,1.0,0.0,1.0,5.0,0.0,1.0,0.0,0.0,3.0,2.0,2.0,1.0,2.0,2.0,3.0,0.0,0.0,0.0,0.0,0.0,3.0,0.0,6.0,4.0,0.0,0.0,0.0,3.0,1.0,0.0,0.0,1.0,0.0,6.0,5.0,0.0,12.0,0.0,3.0,1.0,1.0,0.0,10.0,2.0,2.0,9.0,2.0,15.0,14.0,0.0,6.0,0.0,8.0,9.0,0.0,0.0,17.0,1.0,0.0,1.0
+4.0,0.0,0.0,0.0,2.0,2.0,0.0,4.0,1.0,1.0,1.0,0.0,0.0,1.0,3.0,2.0,1.0,0.0,1.0,1.0,1.0,0.0,0.0,4.0,3.0,0.0,0.0,0.0,0.0,2.0,0.0,7.0,0.0,0.0,0.0,3.0,2.0,0.0,7.0,3.0,1.0,0.0,1.0,5.0,0.0,3.0,0.0,0.0,3.0,0.0,2.0,0.0,2.0,1.0,1.0,0.0,3.0,1.0,2.0,0.0,5.0,0.0,10.0,3.0,3.0,0.0,1.0,3.0,4.0,0.0,4.0,3.0,3.0,7.0,7.0,0.0,7.0,1.0,3.0,1.0,0.0,0.0,8.0,0.0,7.0,16.0,8.0,10.0,18.0,1.0,5.0,0.0,7.0,5.0,9.0,0.0,33.0,11.0,0.0,12.0
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diff --git a/pyPLNmodels/data/test_data/O_test.csv b/pyPLNmodels/data/test_data/O_test.csv
new file mode 100644
index 00000000..e7dc0f58
--- /dev/null
+++ b/pyPLNmodels/data/test_data/O_test.csv
@@ -0,0 +1,201 @@
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diff --git a/pyPLNmodels/data/test_data/Y_test.csv b/pyPLNmodels/data/test_data/Y_test.csv
new file mode 100644
index 00000000..8cb44706
--- /dev/null
+++ b/pyPLNmodels/data/test_data/Y_test.csv
@@ -0,0 +1,201 @@
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diff --git a/pyPLNmodels/data/test_data/true_parameters/true_beta_test.csv b/pyPLNmodels/data/test_data/true_parameters/true_beta_test.csv
new file mode 100644
index 00000000..71739e47
--- /dev/null
+++ b/pyPLNmodels/data/test_data/true_parameters/true_beta_test.csv
@@ -0,0 +1,3 @@
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--
GitLab
From 3fa827d1bf5a3a5346dc57c93d61dac38644e0c8 Mon Sep 17 00:00:00 2001
From: bastien-mva <bastien.batardiere@gmail.com>
Date: Mon, 22 May 2023 21:35:34 +0200
Subject: [PATCH 11/15] removed data since in module/data
---
example_data/real_data/Y_mark.csv | 271 ------------------
example_data/test_data/O_test.csv | 201 -------------
example_data/test_data/Y_test.csv | 201 -------------
example_data/test_data/cov_test.csv | 201 -------------
.../true_parameters/true_Sigma_test.csv | 51 ----
.../true_parameters/true_beta_test.csv | 3 -
6 files changed, 928 deletions(-)
delete mode 100644 example_data/real_data/Y_mark.csv
delete mode 100644 example_data/test_data/O_test.csv
delete mode 100644 example_data/test_data/Y_test.csv
delete mode 100644 example_data/test_data/cov_test.csv
delete mode 100644 example_data/test_data/true_parameters/true_Sigma_test.csv
delete mode 100644 example_data/test_data/true_parameters/true_beta_test.csv
diff --git a/example_data/real_data/Y_mark.csv b/example_data/real_data/Y_mark.csv
deleted file mode 100644
index 43c88887..00000000
--- a/example_data/real_data/Y_mark.csv
+++ /dev/null
@@ -1,271 +0,0 @@
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diff --git a/example_data/test_data/O_test.csv b/example_data/test_data/O_test.csv
deleted file mode 100644
index e7dc0f58..00000000
--- a/example_data/test_data/O_test.csv
+++ /dev/null
@@ -1,201 +0,0 @@
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diff --git a/example_data/test_data/Y_test.csv b/example_data/test_data/Y_test.csv
deleted file mode 100644
index 8cb44706..00000000
--- a/example_data/test_data/Y_test.csv
+++ /dev/null
@@ -1,201 +0,0 @@
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diff --git a/example_data/test_data/cov_test.csv b/example_data/test_data/cov_test.csv
deleted file mode 100644
index 73d4b377..00000000
--- a/example_data/test_data/cov_test.csv
+++ /dev/null
@@ -1,201 +0,0 @@
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diff --git a/example_data/test_data/true_parameters/true_Sigma_test.csv b/example_data/test_data/true_parameters/true_Sigma_test.csv
deleted file mode 100644
index b75812e2..00000000
--- a/example_data/test_data/true_parameters/true_Sigma_test.csv
+++ /dev/null
@@ -1,51 +0,0 @@
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diff --git a/example_data/test_data/true_parameters/true_beta_test.csv b/example_data/test_data/true_parameters/true_beta_test.csv
deleted file mode 100644
index 71739e47..00000000
--- a/example_data/test_data/true_parameters/true_beta_test.csv
+++ /dev/null
@@ -1,3 +0,0 @@
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--0.1825361663498224,0.6561939377574013,-0.08713411783498594,0.37454658245767186,-0.8184755538842826,-0.811027847003693,0.14656398925870345,0.04634181999477537,-0.6945838730937708,-0.652368414546377,-0.5221643907075153,-0.7442440386062351,0.44537092310581317,-0.3313532930496876,-0.32150797273271986,0.26471361464855475,-0.12039304605334028,0.00885922337520712,-0.13544930358628202,0.022114138228844782,-0.7168062568036008,-1.3011860490924494,0.32559372712736606,-0.37074161440200565,-0.45881981367381414,-0.8178683088030576,-0.3518502660928557,0.2703246278743951,-0.19015000160710324,0.3856590426505826,0.24727271848728993,-0.2273218003212685,-0.5394712689482709,0.6681922368751265,-0.7066869994200711,0.12939891327495456,0.31531280270453,-0.6596119036906076,-0.08138855553916928,-0.5194537340157103,0.5575768569103515,0.6685327721070952,0.11280316160105659,0.5035441552702621,-0.8434094543016583,1.4619847301845788,0.36087975766917896,-0.48538159749890714,0.38075430757133794,0.36949237120558087
--
GitLab
From 23e8314d810fce75436ca983d724b282b52e6f25 Mon Sep 17 00:00:00 2001
From: bastien-mva <bastien.batardiere@gmail.com>
Date: Mon, 22 May 2023 22:23:35 +0200
Subject: [PATCH 12/15] docstring with chatgpt for all models
---
pyPLNmodels/models.py | 898 +++++++++++++++++++++++++++++++++++++-----
1 file changed, 805 insertions(+), 93 deletions(-)
diff --git a/pyPLNmodels/models.py b/pyPLNmodels/models.py
index e73b5fd4..9997d705 100644
--- a/pyPLNmodels/models.py
+++ b/pyPLNmodels/models.py
@@ -3,7 +3,7 @@ from abc import ABC, abstractmethod
import warnings
import os
from collections.abc import Iterable
-from typing import Optional
+from typing import Optional, Dict, List, Type, Any
import pandas as pd
import torch
@@ -1256,21 +1256,62 @@ class PlnPCAcollection:
def __init__(
self,
- counts,
- covariates=None,
- offsets=None,
- offsets_formula="logsum",
- ranks=range(3, 5),
- dict_of_dict_initialization=None,
- take_log_offsets=False,
+ counts: torch.Tensor,
+ covariates: Optional[torch.Tensor] = None,
+ offsets: Optional[torch.Tensor] = None,
+ offsets_formula: str = "logsum",
+ ranks: Iterable[int] = range(3, 5),
+ dict_of_dict_initialization: Optional[dict] = None,
+ take_log_offsets: bool = False,
):
+ """
+ Constructor for PlnPCAcollection.
+
+ Parameters
+ ----------
+ counts : torch.Tensor
+ The counts.
+ covariates : torch.Tensor, optional
+ The covariates, by default None.
+ offsets : torch.Tensor, optional
+ The offsets, by default None.
+ offsets_formula : str, optional
+ The formula for offsets, by default "logsum".
+ ranks : Iterable[int], optional
+ The range of ranks, by default range(3, 5).
+ dict_of_dict_initialization : dict, optional
+ The dictionary of initialization, by default None.
+ take_log_offsets : bool, optional
+ Whether to take the logarithm of offsets, by default False.
+ """
self._dict_models = {}
self._init_data(counts, covariates, offsets, offsets_formula, take_log_offsets)
self._init_models(ranks, dict_of_dict_initialization)
def _init_data(
- self, counts, covariates, offsets, offsets_formula, take_log_offsets
+ self,
+ counts: torch.Tensor,
+ covariates: Optional[torch.Tensor],
+ offsets: Optional[torch.Tensor],
+ offsets_formula: str,
+ take_log_offsets: bool,
):
+ """
+ Method for initializing the data.
+
+ Parameters
+ ----------
+ counts : torch.Tensor
+ The counts.
+ covariates : torch.Tensor, optional
+ The covariates, by default None.
+ offsets : torch.Tensor, optional
+ The offsets, by default None.
+ offsets_formula : str
+ The formula for offsets.
+ take_log_offsets : bool
+ Whether to take the logarithm of offsets.
+ """
self._counts, self._covariates, self._offsets = _format_model_param(
counts, covariates, offsets, offsets_formula, take_log_offsets
)
@@ -1282,11 +1323,34 @@ class PlnPCAcollection:
cls,
formula: str,
data: dict,
- offsets_formula="logsum",
- ranks=range(3, 5),
- dict_of_dict_initialization=None,
- take_log_offsets=False,
- ):
+ offsets_formula: str = "logsum",
+ ranks: Iterable[int] = range(3, 5),
+ dict_of_dict_initialization: Optional[dict] = None,
+ take_log_offsets: bool = False,
+ ) -> "PlnPCAcollection":
+ """
+ Create an instance of PlnPCAcollection from a formula.
+
+ Parameters
+ ----------
+ formula : str
+ The formula.
+ data : dict
+ The data dictionary.
+ offsets_formula : str, optional
+ The formula for offsets, by default "logsum".
+ ranks : Iterable[int], optional
+ The range of ranks, by default range(3, 5).
+ dict_of_dict_initialization : dict, optional
+ The dictionary of initialization, by default None.
+ take_log_offsets : bool, optional
+ Whether to take the logarithm of offsets, by default False.
+
+ Returns
+ -------
+ PlnPCAcollection
+ The created PlnPCAcollection instance.
+ """
counts, covariates, offsets = _extract_data_from_formula(formula, data)
return cls(
counts,
@@ -1299,58 +1363,158 @@ class PlnPCAcollection:
)
@property
- def covariates(self):
+ def covariates(self) -> torch.Tensor:
+ """
+ Property representing the covariates.
+
+ Returns
+ -------
+ torch.Tensor
+ The covariates.
+ """
return self[self.ranks[0]].covariates
@property
- def counts(self):
+ def counts(self) -> torch.Tensor:
+ """
+ Property representing the counts.
+
+ Returns
+ -------
+ torch.Tensor
+ The counts.
+ """
return self[self.ranks[0]].counts
@property
- def coef(self):
+ def coef(self) -> Dict[int, torch.Tensor]:
+ """
+ Property representing the coefficients.
+
+ Returns
+ -------
+ Dict[int, torch.Tensor]
+ The coefficients.
+ """
return {model.rank: model.coef for model in self.values()}
@property
- def components(self):
+ def components(self) -> Dict[int, torch.Tensor]:
+ """
+ Property representing the components.
+
+ Returns
+ -------
+ Dict[int, torch.Tensor]
+ The components.
+ """
return {model.rank: model.components for model in self.values()}
@property
- def latent_mean(self):
+ def latent_mean(self) -> Dict[int, torch.Tensor]:
+ """
+ Property representing the latent means.
+
+ Returns
+ -------
+ Dict[int, torch.Tensor]
+ The latent means.
+ """
return {model.rank: model.latent_mean for model in self.values()}
@property
- def latent_var(self):
+ def latent_var(self) -> Dict[int, torch.Tensor]:
+ """
+ Property representing the latent variances.
+
+ Returns
+ -------
+ Dict[int, torch.Tensor]
+ The latent variances.
+ """
return {model.rank: model.latent_var for model in self.values()}
@counts.setter
@array2tensor
- def counts(self, counts):
+ def counts(self, counts: torch.Tensor):
+ """
+ Setter for the counts property.
+
+ Parameters
+ ----------
+ counts : torch.Tensor
+ The counts.
+ """
for model in self.values():
model.counts = counts
@coef.setter
@array2tensor
- def coef(self, coef):
+ def coef(self, coef: torch.Tensor):
+ """
+ Setter for the coef property.
+
+ Parameters
+ ----------
+ coef : torch.Tensor
+ The coefficients.
+ """
for model in self.values():
model.coef = coef
@covariates.setter
@array2tensor
- def covariates(self, covariates):
+ def covariates(self, covariates: torch.Tensor):
+ """
+ Setter for the covariates property.
+
+ Parameters
+ ----------
+ covariates : torch.Tensor
+ The covariates.
+ """
for model in self.values():
model.covariates = covariates
@property
- def offsets(self):
+ def offsets(self) -> torch.Tensor:
+ """
+ Property representing the offsets.
+
+ Returns
+ -------
+ torch.Tensor
+ The offsets.
+ """
return self[self.ranks[0]].offsets
@offsets.setter
@array2tensor
- def offsets(self, offsets):
+ def offsets(self, offsets: torch.Tensor):
+ """
+ Setter for the offsets property.
+
+ Parameters
+ ----------
+ offsets : torch.Tensor
+ The offsets.
+ """
for model in self.values():
model.offsets = offsets
- def _init_models(self, ranks, dict_of_dict_initialization):
+ def _init_models(
+ self, ranks: Iterable[int], dict_of_dict_initialization: Optional[dict]
+ ):
+ """
+ Method for initializing the models.
+
+ Parameters
+ ----------
+ ranks : Iterable[int]
+ The range of ranks.
+ dict_of_dict_initialization : dict, optional
+ The dictionary of initialization.
+ """
if isinstance(ranks, (Iterable, np.ndarray)):
for rank in ranks:
if isinstance(rank, (int, np.integer)):
@@ -1387,31 +1551,79 @@ class PlnPCAcollection:
)
@property
- def ranks(self):
+ def ranks(self) -> List[int]:
+ """
+ Property representing the ranks.
+
+ Returns
+ -------
+ List[int]
+ The ranks.
+ """
return [model.rank for model in self.values()]
- def _pring_beginning_message(self):
+ def _pring_beginning_message(self) -> str:
+ """
+ Method for printing the beginning message.
+
+ Returns
+ -------
+ str
+ The beginning message.
+ """
return f"Adjusting {len(self.ranks)} Pln models for PCA analysis \n"
@property
- def dim(self):
+ def dim(self) -> int:
+ """
+ Property representing the dimension.
+
+ Returns
+ -------
+ int
+ The dimension.
+ """
return self[self.ranks[0]].dim
@property
- def nb_cov(self):
+ def nb_cov(self) -> int:
+ """
+ Property representing the number of covariates.
+
+ Returns
+ -------
+ int
+ The number of covariates.
+ """
return self[self.ranks[0]].nb_cov
- ## should do something for this weird init. pb: if doing the init of self._counts etc
- ## only in PlnPCAcollection, then we don't do it for each PlnPCA but then Pln is not doing it.
def fit(
self,
- nb_max_iteration=100000,
- lr=0.01,
- class_optimizer=torch.optim.Rprop,
- tol=1e-3,
- do_smart_init=True,
- verbose=False,
+ nb_max_iteration: int = 100000,
+ lr: float = 0.01,
+ class_optimizer: Type[torch.optim.Optimizer] = torch.optim.Rprop,
+ tol: float = 1e-3,
+ do_smart_init: bool = True,
+ verbose: bool = False,
):
+ """
+ Fit the PlnPCAcollection.
+
+ Parameters
+ ----------
+ nb_max_iteration : int, optional
+ The maximum number of iterations, by default 100000.
+ lr : float, optional
+ The learning rate, by default 0.01.
+ class_optimizer : Type[torch.optim.Optimizer], optional
+ The optimizer class, by default torch.optim.Rprop.
+ tol : float, optional
+ The tolerance, by default 1e-3.
+ do_smart_init : bool, optional
+ Whether to do smart initialization, by default True.
+ verbose : bool, optional
+ Whether to print verbose output, by default False.
+ """
self._pring_beginning_message()
for i in range(len(self.values())):
model = self[self.ranks[i]]
@@ -1428,13 +1640,28 @@ class PlnPCAcollection:
self.init_next_model_with_previous_parameters(next_model, model)
self._print_ending_message()
- def init_next_model_with_previous_parameters(self, next_model, current_model):
+ def init_next_model_with_previous_parameters(
+ self, next_model: Any, current_model: Any
+ ):
+ """
+ Initialize the next model with the parameters of the current model.
+
+ Parameters
+ ----------
+ next_model : Any
+ The next model to initialize.
+ current_model : Any
+ The current model.
+ """
next_model.coef = current_model.coef
next_model.components = torch.zeros(self.dim, next_model.rank)
with torch.no_grad():
next_model._components[:, : current_model.rank] = current_model._components
def _print_ending_message(self):
+ """
+ Method for printing the ending message.
+ """
delimiter = "=" * NB_CHARACTERS_FOR_NICE_PLOT
print(f"{delimiter}\n")
print("DONE!")
@@ -1442,49 +1669,170 @@ class PlnPCAcollection:
print(f" Best model(lower AIC): {self._criterion_dict('AIC')}\n ")
print(f"{delimiter}\n")
- def _criterion_dict(self, criterion="AIC"):
+ def _criterion_dict(self, criterion: str = "AIC") -> int:
+ """
+ Return the rank of the best model according to the specified criterion.
+
+ Parameters
+ ----------
+ criterion : str, optional
+ The criterion to use ('AIC' or 'BIC'), by default 'AIC'.
+
+ Returns
+ -------
+ int
+ The rank of the best model.
+ """
return self.best_model(criterion).rank
- def __getitem__(self, rank):
+ def __getitem__(self, rank: int) -> Any:
+ """
+ Get the model with the specified rank.
+
+ Parameters
+ ----------
+ rank : int
+ The rank of the model.
+
+ Returns
+ -------
+ Any
+ The model with the specified rank.
+ """
return self._dict_models[rank]
- def __len__(self):
+ def __len__(self) -> int:
+ """
+ Get the number of models in the collection.
+
+ Returns
+ -------
+ int
+ The number of models in the collection.
+ """
return len(self._dict_models)
def __iter__(self):
+ """
+ Iterate over the models in the collection.
+
+ Returns
+ -------
+ Iterator
+ Iterator over the models.
+ """
return iter(self._dict_models)
- def __contains__(self, rank):
+ def __contains__(self, rank: int) -> bool:
+ """
+ Check if a model with the specified rank exists in the collection.
+
+ Parameters
+ ----------
+ rank : int
+ The rank to check.
+
+ Returns
+ -------
+ bool
+ True if a model with the specified rank exists, False otherwise.
+ """
return rank in self._dict_models.keys()
def keys(self):
+ """
+ Get the ranks of the models in the collection.
+
+ Returns
+ -------
+ KeysView
+ The ranks of the models.
+ """
return self._dict_models.keys()
- def get(self, key, default):
+ def get(self, key: Any, default: Any) -> Any:
+ """
+ Get the model with the specified key, or return a default value if the key does not exist.
+
+ Parameters
+ ----------
+ key : Any
+ The key to search for.
+ default : Any
+ The default value to return if the key does not exist.
+
+ Returns
+ -------
+ Any
+ The model with the specified key, or the default value if the key does not exist.
+ """
if key in self:
return self[key]
else:
return default
def values(self):
+ """
+ Get the models in the collection.
+
+ Returns
+ -------
+ ValuesView
+ The models in the collection.
+ """
return self._dict_models.values()
def items(self):
+ """
+ Get the key-value pairs of the models in the collection.
+
+ Returns
+ -------
+ ItemsView
+ The key-value pairs of the models.
+ """
return self._dict_models.items()
@property
- def BIC(self):
+ def BIC(self) -> Dict[int, int]:
+ """
+ Property representing the BIC scores of the models in the collection.
+
+ Returns
+ -------
+ Dict[int, int]
+ The BIC scores of the models.
+ """
return {model.rank: int(model.BIC) for model in self.values()}
@property
- def AIC(self):
+ def AIC(self) -> Dict[int, int]:
+ """
+ Property representing the AIC scores of the models in the collection.
+
+ Returns
+ -------
+ Dict[int, int]
+ The AIC scores of the models.
+ """
return {model.rank: int(model.AIC) for model in self.values()}
@property
- def loglikes(self):
+ def loglikes(self) -> Dict[int, Any]:
+ """
+ Property representing the log-likelihoods of the models in the collection.
+
+ Returns
+ -------
+ Dict[int, Any]
+ The log-likelihoods of the models.
+ """
return {model.rank: model.loglike for model in self.values()}
def show(self):
+ """
+ Show a plot with BIC scores, AIC scores, and negative log-likelihoods of the models.
+ """
bic = self.BIC
aic = self.AIC
loglikes = self.loglikes
@@ -1509,21 +1857,60 @@ class PlnPCAcollection:
plt.show()
@property
- def best_BIC_model_rank(self):
+ def best_BIC_model_rank(self) -> int:
+ """
+ Property representing the rank of the best model according to the BIC criterion.
+
+ Returns
+ -------
+ int
+ The rank of the best model.
+ """
return self.ranks[np.argmin(list(self.BIC.values()))]
@property
- def best_AIC_model_rank(self):
+ def best_AIC_model_rank(self) -> int:
+ """
+ Property representing the rank of the best model according to the AIC criterion.
+
+ Returns
+ -------
+ int
+ The rank of the best model.
+ """
return self.ranks[np.argmin(list(self.AIC.values()))]
- def best_model(self, criterion="AIC"):
+ def best_model(self, criterion: str = "AIC") -> Any:
+ """
+ Get the best model according to the specified criterion.
+
+ Parameters
+ ----------
+ criterion : str, optional
+ The criterion to use ('AIC' or 'BIC'), by default 'AIC'.
+
+ Returns
+ -------
+ Any
+ The best model.
+ """
if criterion == "BIC":
return self[self.best_BIC_model_rank]
if criterion == "AIC":
return self[self.best_AIC_model_rank]
raise ValueError(f"Unknown criterion {criterion}")
- def save(self, path_of_directory="./", ranks=None):
+ def save(self, path_of_directory: str = "./", ranks: Optional[List[int]] = None):
+ """
+ Save the models in the specified directory.
+
+ Parameters
+ ----------
+ path_of_directory : str, optional
+ The path of the directory to save the models, by default "./".
+ ranks : Optional[List[int]], optional
+ The ranks of the models to save, by default None.
+ """
if ranks is None:
ranks = self.ranks
for model in self.values():
@@ -1531,18 +1918,38 @@ class PlnPCAcollection:
model.save(path_of_directory)
@property
- def directory_name(self):
+ def directory_name(self) -> str:
+ """
+ Property representing the directory name.
+
+ Returns
+ -------
+ str
+ The directory name.
+ """
return f"{self._NAME}_nbcov_{self.nb_cov}_dim_{self.dim}"
@property
- def n_samples(self):
+ def n_samples(self) -> int:
+ """
+ Property representing the number of samples.
+
+ Returns
+ -------
+ int
+ The number of samples.
+ """
return self[self.ranks[0]].n_samples
- @property
- def _p(self):
- return self[self.ranks[0]].p
+ def __repr__(self) -> str:
+ """
+ Return a string representation of the PlnPCAcollection object.
- def __repr__(self):
+ Returns
+ -------
+ str
+ The string representation of the PlnPCAcollection object.
+ """
nb_models = len(self)
delimiter = "\n" + "-" * NB_CHARACTERS_FOR_NICE_PLOT + "\n"
to_print = delimiter
@@ -1552,13 +1959,12 @@ class PlnPCAcollection:
to_print += f" - Ranks considered:{self.ranks}\n"
dict_bic = {"rank": "criterion"} | self.BIC
to_print += f" - BIC metric:\n{_nice_string_of_dict(dict_bic)}\n"
-
dict_to_print = self.best_model(criterion="BIC")._rank
to_print += f" Best model(lower BIC): {dict_to_print}\n \n"
dict_aic = {"rank": "criterion"} | self.AIC
to_print += f" - AIC metric:\n{_nice_string_of_dict(dict_aic)}\n"
to_print += f" Best model(lower AIC): \
- {self.best_model(criterion = 'AIC')._rank}\n"
+ {self.best_model(criterion='AIC')._rank}\n"
to_print += delimiter
to_print += "* Useful properties\n"
to_print += f" {self._useful_properties_string}\n"
@@ -1568,28 +1974,62 @@ class PlnPCAcollection:
return to_print
@property
- def _useful_methods_strings(self):
+ def _useful_methods_strings(self) -> str:
+ """
+ Property representing the useful methods.
+
+ Returns
+ -------
+ str
+ The string representation of the useful methods.
+ """
return ".show(), .best_model()"
@property
- def _useful_properties_string(self):
+ def _useful_properties_string(self) -> str:
+ """
+ Property representing the useful properties.
+
+ Returns
+ -------
+ str
+ The string representation of the useful properties.
+ """
return ".BIC, .AIC, .loglikes"
# Here, setting the value for each key in _dict_parameters
class PlnPCA(_Pln):
- _NAME = "PlnPCA"
+ _NAME: str = "PlnPCA"
_components: torch.Tensor
def __init__(
self,
- counts,
- covariates=None,
- offsets=None,
- offsets_formula="logsum",
- rank=5,
- dict_initialization=None,
+ counts: torch.Tensor,
+ covariates: Optional[torch.Tensor] = None,
+ offsets: Optional[torch.Tensor] = None,
+ offsets_formula: str = "logsum",
+ rank: int = 5,
+ dict_initialization: Optional[Dict[str, torch.Tensor]] = None,
):
+ """
+ Initialize the PlnPCA object.
+
+ Parameters
+ ----------
+ counts : torch.Tensor
+ The counts tensor.
+ covariates : torch.Tensor, optional
+ The covariates tensor, by default None.
+ offsets : torch.Tensor, optional
+ The offsets tensor, by default None.
+ offsets_formula : str, optional
+ The offsets formula, by default "logsum".
+ rank : int, optional
+ The rank of the approximation, by default 5.
+ dict_initialization : Dict[str, torch.Tensor], optional
+ The dictionary for initialization, by default None.
+ """
self._rank = rank
self._counts, self._covariates, self._offsets = _format_model_param(
counts, covariates, offsets, None, take_log_offsets=False
@@ -1603,14 +2043,43 @@ class PlnPCA(_Pln):
@classmethod
def from_formula(
- cls, formula, data, rank=5, offsets_formula="logsum", dict_initialization=None
+ cls,
+ formula: str,
+ data: Any,
+ rank: int = 5,
+ offsets_formula: str = "logsum",
+ dict_initialization: Optional[Dict[str, torch.Tensor]] = None,
):
+ """
+ Create a PlnPCA object from a formula.
+
+ Parameters
+ ----------
+ formula : str
+ The formula.
+ data : Any
+ The data.
+ rank : int, optional
+ The rank of the approximation, by default 5.
+ offsets_formula : str, optional
+ The offsets formula, by default "logsum".
+ dict_initialization : Dict[str, torch.Tensor], optional
+ The dictionary for initialization, by default None.
+
+ Returns
+ -------
+ PlnPCA
+ The created PlnPCA object.
+ """
counts, covariates, offsets = _extract_data_from_formula(formula, data)
return cls(
counts, covariates, offsets, offsets_formula, rank, dict_initialization
)
def _check_if_rank_is_too_high(self):
+ """
+ Check if the rank is too high and issue a warning if necessary.
+ """
if self.dim < self.rank:
warning_string = (
f"\nThe requested rank of approximation {self.rank} "
@@ -1621,16 +2090,40 @@ class PlnPCA(_Pln):
self._rank = self.dim
@property
- def latent_mean(self):
+ def latent_mean(self) -> torch.Tensor:
+ """
+ Property representing the latent mean.
+
+ Returns
+ -------
+ torch.Tensor
+ The latent mean tensor.
+ """
return self._cpu_attribute_or_none("_latent_mean")
@property
- def latent_var(self):
+ def latent_var(self) -> torch.Tensor:
+ """
+ Property representing the latent variance.
+
+ Returns
+ -------
+ torch.Tensor
+ The latent variance tensor.
+ """
return self._cpu_attribute_or_none("_latent_var")
@latent_mean.setter
@array2tensor
- def latent_mean(self, latent_mean):
+ def latent_mean(self, latent_mean: torch.Tensor):
+ """
+ Setter for the latent mean.
+
+ Parameters
+ ----------
+ latent_mean : torch.Tensor
+ The latent mean tensor.
+ """
if latent_mean.shape != (self.n_samples, self.rank):
raise ValueError(
f"Wrong shape. Expected {self.n_samples, self.rank}, got {latent_mean.shape}"
@@ -1639,7 +2132,15 @@ class PlnPCA(_Pln):
@latent_var.setter
@array2tensor
- def latent_var(self, latent_var):
+ def latent_var(self, latent_var: torch.Tensor):
+ """
+ Setter for the latent variance.
+
+ Parameters
+ ----------
+ latent_var : torch.Tensor
+ The latent variance tensor.
+ """
if latent_var.shape != (self.n_samples, self.rank):
raise ValueError(
f"Wrong shape. Expected {self.n_samples, self.rank}, got {latent_var.shape}"
@@ -1647,42 +2148,103 @@ class PlnPCA(_Pln):
self._latent_var = latent_var
@property
- def directory_name(self):
+ def directory_name(self) -> str:
+ """
+ Property representing the directory name.
+
+ Returns
+ -------
+ str
+ The directory name.
+ """
return f"{self._NAME}_rank_{self._rank}"
- # return f"PlnPCAcollection_nbcov_{self.nb_cov}_dim_{self.dim}/{self._NAME}_rank_{self._rank}"
@property
- def covariates(self):
+ def covariates(self) -> torch.Tensor:
+ """
+ Property representing the covariates.
+
+ Returns
+ -------
+ torch.Tensor
+ The covariates tensor.
+ """
return self._cpu_attribute_or_none("_covariates")
@covariates.setter
@array2tensor
- def covariates(self, covariates):
+ def covariates(self, covariates: torch.Tensor):
+ """
+ Setter for the covariates.
+
+ Parameters
+ ----------
+ covariates : torch.Tensor
+ The covariates tensor.
+ """
_check_data_shape(self.counts, covariates, self.offsets)
self._covariates = covariates
print("Setting coef to initialization")
self._smart_init_coef()
@property
- def path_to_directory(self):
+ def path_to_directory(self) -> str:
+ """
+ Property representing the path to the directory.
+
+ Returns
+ -------
+ str
+ The path to the directory.
+ """
return f"PlnPCAcollection_nbcov_{self.nb_cov}_dim_{self.dim}/"
@property
- def rank(self):
+ def rank(self) -> int:
+ """
+ Property representing the rank.
+
+ Returns
+ -------
+ int
+ The rank.
+ """
return self._rank
- def _get_max_components(self):
+ def _get_max_components(self) -> int:
+ """
+ Get the maximum number of components.
+
+ Returns
+ -------
+ int
+ The maximum number of components.
+ """
return self._rank
def _pring_beginning_message(self):
+ """
+ Print the beginning message.
+ """
print("-" * NB_CHARACTERS_FOR_NICE_PLOT)
print(f"Fitting a PlnPCAcollection model with {self._rank} components")
@property
- def model_parameters(self):
+ def model_parameters(self) -> Dict[str, torch.Tensor]:
+ """
+ Property representing the model parameters.
+
+ Returns
+ -------
+ Dict[str, torch.Tensor]
+ The model parameters.
+ """
return {"coef": self.coef, "components": self.components}
def _smart_init_model_parameters(self):
+ """
+ Initialize the model parameters smartly.
+ """
if not hasattr(self, "_coef"):
super()._smart_init_coef()
if not hasattr(self, "_components"):
@@ -1691,14 +2253,23 @@ class PlnPCA(_Pln):
)
def _random_init_model_parameters(self):
+ """
+ Randomly initialize the model parameters.
+ """
super()._random_init_coef()
self._components = torch.randn((self.dim, self._rank)).to(DEVICE)
def _random_init_latent_parameters(self):
+ """
+ Randomly initialize the latent parameters.
+ """
self._latent_var = 1 / 2 * torch.ones((self.n_samples, self._rank)).to(DEVICE)
self._latent_mean = torch.ones((self.n_samples, self._rank)).to(DEVICE)
def _smart_init_latent_parameters(self):
+ """
+ Initialize the latent parameters smartly.
+ """
if not hasattr(self, "_latent_mean"):
self._latent_mean = (
_init_latent_mean(
@@ -1718,11 +2289,27 @@ class PlnPCA(_Pln):
@property
def _list_of_parameters_needing_gradient(self):
+ """
+ Property representing the list of parameters needing gradient.
+
+ Returns
+ -------
+ List[torch.Tensor]
+ The list of parameters needing gradient.
+ """
if self._coef is None:
return [self._components, self._latent_mean, self._latent_var]
return [self._components, self._coef, self._latent_mean, self._latent_var]
- def compute_elbo(self):
+ def compute_elbo(self) -> torch.Tensor:
+ """
+ Compute the evidence lower bound (ELBO).
+
+ Returns
+ -------
+ torch.Tensor
+ The ELBO value.
+ """
return elbo_plnpca(
self._counts,
self._covariates,
@@ -1734,20 +2321,52 @@ class PlnPCA(_Pln):
)
@property
- def number_of_parameters(self):
+ def number_of_parameters(self) -> int:
+ """
+ Property representing the number of parameters.
+
+ Returns
+ -------
+ int
+ The number of parameters.
+ """
return self.dim * (self.nb_cov + self._rank) - self._rank * (self._rank - 1) / 2
@property
- def _additional_properties_string(self):
+ def _additional_properties_string(self) -> str:
+ """
+ Property representing the additional properties string.
+
+ Returns
+ -------
+ str
+ The additional properties string.
+ """
return ".projected_latent_variables"
@property
- def _additional_methods_string(self):
+ def _additional_methods_string(self) -> str:
+ """
+ Property representing the additional methods string.
+
+ Returns
+ -------
+ str
+ The additional methods string.
+ """
string = " only for rank=2: .viz()"
return string
@property
- def covariance(self):
+ def covariance(self) -> Optional[torch.Tensor]:
+ """
+ Property representing the covariance.
+
+ Returns
+ -------
+ Optional[torch.Tensor]
+ The covariance tensor or None if components are not present.
+ """
if hasattr(self, "_components"):
cov_latent = self._latent_mean.T @ self._latent_mean
cov_latent += torch.diag(torch.sum(torch.square(self._latent_var), dim=0))
@@ -1756,19 +2375,58 @@ class PlnPCA(_Pln):
return None
@property
- def _description(self):
+ def _description(self) -> str:
+ """
+ Property representing the description.
+
+ Returns
+ -------
+ str
+ The description string.
+ """
return f" {self.rank} principal component."
@property
- def latent_variables(self):
+ def latent_variables(self) -> torch.Tensor:
+ """
+ Property representing the latent variables.
+
+ Returns
+ -------
+ torch.Tensor
+ The latent variables.
+ """
return torch.matmul(self._latent_mean, self._components.T)
@property
- def projected_latent_variables(self):
+ def projected_latent_variables(self) -> torch.Tensor:
+ """
+ Property representing the projected latent variables.
+
+ Returns
+ -------
+ torch.Tensor
+ The projected latent variables.
+ """
ortho_components = torch.linalg.qr(self._components, "reduced")[0]
return torch.mm(self.latent_variables, ortho_components).detach().cpu()
- def pca_projected_latent_variables(self, n_components=None):
+ def pca_projected_latent_variables(
+ self, n_components: Optional[int] = None
+ ) -> np.ndarray:
+ """
+ Perform PCA on projected latent variables.
+
+ Parameters
+ ----------
+ n_components : Optional[int]
+ Number of components to keep. Defaults to None.
+
+ Returns
+ -------
+ np.ndarray
+ The transformed projected latent variables.
+ """
if n_components is None:
n_components = self._get_max_components()
if n_components > self.dim:
@@ -1779,12 +2437,33 @@ class PlnPCA(_Pln):
return pca.fit_transform(self.projected_latent_variables.detach().cpu())
@property
- def components(self):
+ def components(self) -> torch.Tensor:
+ """
+ Property representing the components.
+
+ Returns
+ -------
+ torch.Tensor
+ The components.
+ """
return self._cpu_attribute_or_none("_components")
@components.setter
@array2tensor
- def components(self, components):
+ def components(self, components: torch.Tensor):
+ """
+ Setter for the components.
+
+ Parameters
+ ----------
+ components : torch.Tensor
+ The components to set.
+
+ Raises
+ ------
+ ValueError
+ If the components have an invalid shape.
+ """
if components.shape != (self.dim, self.rank):
raise ValueError(
f"Wrong shape. Expected {self.dim, self.rank}, got {components.shape}"
@@ -1792,6 +2471,26 @@ class PlnPCA(_Pln):
self._components = components
def viz(self, ax=None, colors=None):
+ """
+ Visualize the PlnPCA model.
+
+ Parameters
+ ----------
+ ax : Optional[Any], optional
+ The matplotlib axis to use. If None, the current axis is used, by default None.
+ colors : Optional[Any], optional
+ The colors to use for plotting, by default None.
+
+ Raises
+ ------
+ RuntimeError
+ If the rank is less than 2.
+
+ Returns
+ -------
+ Any
+ The matplotlib axis.
+ """
if ax is None:
ax = plt.gca()
if self._rank < 2:
@@ -1808,7 +2507,20 @@ class PlnPCA(_Pln):
_plot_ellipse(x[i], y[i], cov=covariances[i], ax=ax)
return ax
- def transform(self, project=True):
+ def transform(self, project: bool = True) -> torch.Tensor:
+ """
+ Transform the model.
+
+ Parameters
+ ----------
+ project : bool, optional
+ Whether to project the latent variables, by default True.
+
+ Returns
+ -------
+ torch.Tensor
+ The transformed model.
+ """
if project is True:
return self.projected_latent_variables
return self.latent_variables
--
GitLab
From 6488d8fa10cdbd96cbb9562f925b10d07deeea07 Mon Sep 17 00:00:00 2001
From: bastien-mva <bastien.batardiere@gmail.com>
Date: Mon, 22 May 2023 22:24:12 +0200
Subject: [PATCH 13/15] link to all the classes documentation
---
docs/source/index.rst | 1 +
docs/source/module.rst | 14 +++++++++++---
2 files changed, 12 insertions(+), 3 deletions(-)
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 71513b20..8bfed1a8 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -12,6 +12,7 @@ Welcome to pyPLNmodels's documentation!
./module.rst
+
Indices and tables working once again
=====================================
diff --git a/docs/source/module.rst b/docs/source/module.rst
index 7c22fce6..de0c03d0 100644
--- a/docs/source/module.rst
+++ b/docs/source/module.rst
@@ -1,15 +1,23 @@
API documentation
=================
-.. autoclass:: pyPLNmodels.PLN
+.. autoclass:: pyPLNmodels.PlnPCAcollection
+ :members:
+ :show-inheritance:
+ :special-members: __init__
+ :undoc-members:
+
+
+.. autoclass:: pyPLNmodels.PlnPCA
:members:
:inherited-members:
:special-members: __init__
:undoc-members:
:show-inheritance:
-.. autoclass:: pyPLNmodels.PLNPCA
+.. autoclass:: pyPLNmodels.Pln
:members:
- :show-inheritance:
+ :inherited-members:
:special-members: __init__
:undoc-members:
+ :show-inheritance:
--
GitLab
From 035fe8ff51a57e35696cb184cf5e19feebd08e04 Mon Sep 17 00:00:00 2001
From: bastien-mva <bastien.batardiere@gmail.com>
Date: Mon, 22 May 2023 22:51:15 +0200
Subject: [PATCH 14/15] update readme with from_formula
---
README.md | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/README.md b/README.md
index e98669f6..991dbec1 100644
--- a/README.md
+++ b/README.md
@@ -28,7 +28,7 @@ pip install pyPLNmodels
The package comes with an ecological data set to present the functionality
```
import pyPLNmodels
-from pyPLNmodels.models import PLNPCA, PLN
+from pyPLNmodels.models import PlnPCAcollection, Pln
from pyPLNmodels.oaks import load_oaks
oaks = load_oaks()
```
@@ -36,16 +36,16 @@ oaks = load_oaks()
### Unpenalized Poisson lognormal model (aka PLN)
```
-pln = PLN("counts ~ 1 + tree + dist2ground + orientation ", data = oaks, take_log_offsets = True)
+pln = Pln.from_formula("counts ~ 1 + tree + dist2ground + orientation ", data = oaks, take_log_offsets = True)
pln.fit()
print(pln)
```
-### Rank Constrained Poisson lognormal for Poisson Principal Component Analysis (aka PLNPCA)
+### Rank Constrained Poisson lognormal for Poisson Principal Component Analysis (aka PlnPCACollection)
```
-pca = PLNPCA("counts ~ 1 + tree + dist2ground + orientation ", data = oaks, take_log_offsets = True, ranks = [3,4,5])
+pca = PlnPCACollection.from_formula("counts ~ 1 + tree + dist2ground + orientation ", data = oaks, take_log_offsets = True, ranks = [3,4,5])
pca.fit()
print(pca)
```
--
GitLab
From 2f08fa59d1d856e3dbc1f2b8d82832243b9bfc63 Mon Sep 17 00:00:00 2001
From: bastien-mva <bastien.batardiere@gmail.com>
Date: Mon, 22 May 2023 23:09:50 +0200
Subject: [PATCH 15/15] error in the README
---
README.md | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/README.md b/README.md
index 991dbec1..212b1ce9 100644
--- a/README.md
+++ b/README.md
@@ -45,7 +45,7 @@ print(pln)
### Rank Constrained Poisson lognormal for Poisson Principal Component Analysis (aka PlnPCACollection)
```
-pca = PlnPCACollection.from_formula("counts ~ 1 + tree + dist2ground + orientation ", data = oaks, take_log_offsets = True, ranks = [3,4,5])
+pca = PlnPCAcollection.from_formula("counts ~ 1 + tree + dist2ground + orientation ", data = oaks, take_log_offsets = True, ranks = [3,4,5])
pca.fit()
print(pca)
```
--
GitLab