Merge branch 'ig/full_branch' into ig/update_api

Author: ilan-gold

batchglm/models/__init__.py

@@ -1 +1 @@
-from . import base_glm, glm_beta, glm_nb, glm_norm
+from . import base_glm, glm_beta, glm_nb, glm_norm, glm_poisson

batchglm/models/base_glm/model.py

@@ -54,7 +54,7 @@ def __init__(
         input_data: Optional[InputDataGLM] = None,
     ):
         """
-        Create a new _ModelGLM object.
+        Create a new ModelGLM object.
 
         :param input_data: Input data for the model
 

batchglm/models/glm_poisson/__init__.py

@@ -0,0 +1 @@
+from .model import Model

batchglm/models/glm_poisson/external.py

@@ -0,0 +1,4 @@
+import batchglm.utils.data as data_utils
+from batchglm import pkg_constants
+from batchglm.models.base_glm import ModelGLM, closedform_glm_mean, closedform_glm_scale
+from batchglm.utils.linalg import groupwise_solve_lm

batchglm/models/glm_poisson/model.py

@@ -0,0 +1,102 @@
+import abc
+from typing import Any, Callable, Dict, Optional, Tuple, Union
+
+import dask.array
+import numpy as np
+
+from .external import ModelGLM
+
+
+class Model(ModelGLM, metaclass=abc.ABCMeta):
+    """
+    Generalized Linear Model (GLM) with Poisson noise.
+    """
+
+    def link_loc(self, data) -> Union[np.ndarray, dask.array.core.Array]:
+        return np.log(data)
+
+    def inverse_link_loc(self, data) -> Union[np.ndarray, dask.array.core.Array]:
+        return np.exp(data)
+
+    def link_scale(self, data) -> Union[np.ndarray, dask.array.core.Array]:
+        return np.log(data)
+
+    def inverse_link_scale(self, data) -> Union[np.ndarray, dask.array.core.Array]:
+        return np.exp(data)
+
+    @property
+    def eta_loc(self) -> Union[np.ndarray, dask.array.core.Array]:
+        eta = np.matmul(self.design_loc, self.theta_location_constrained)
+        if self.size_factors is not None:
+            eta += self.size_factors
+        eta = self.np_clip_param(eta, "eta_loc")
+        return eta
+
+    def eta_loc_j(self, j) -> Union[np.ndarray, dask.array.core.Array]:
+        # Make sure that dimensionality of sliced array is kept:
+        if isinstance(j, int) or isinstance(j, np.int32) or isinstance(j, np.int64):
+            j = [j]
+        eta = np.matmul(self.design_loc, self.theta_location_constrained[:, j])
+        if self.size_factors is not None:
+            eta += self.size_factors
+        eta = self.np_clip_param(eta, "eta_loc")
+        return eta
+
+    # Re-parameterizations:
+
+    @property
+    def lam(self) -> Union[np.ndarray, dask.array.core.Array]:
+        return self.location
+
+    # param constraints:
+
+    def bounds(self, sf, dmax, dtype) -> Tuple[Dict[str, Any], Dict[str, Any]]:
+
+        bounds_min = {
+            "theta_location": np.log(np.nextafter(0, np.inf, dtype=dtype)) / sf,
+            "eta_loc": np.log(np.nextafter(0, np.inf, dtype=dtype)) / sf,
+            "loc": np.nextafter(0, np.inf, dtype=dtype),
+            "scale": np.nextafter(0, np.inf, dtype=dtype),
+            "likelihood": dtype(0),
+            "ll": np.log(np.nextafter(0, np.inf, dtype=dtype)),
+            # Not used and should be removed: https://github.com/theislab/batchglm/issues/148
+            "theta_scale": np.log(np.nextafter(0, np.inf, dtype=dtype)) / sf,
+            "eta_scale": np.log(np.nextafter(0, np.inf, dtype=dtype)) / sf,
+        }
+        bounds_max = {
+            "theta_location": np.nextafter(np.log(dmax), -np.inf, dtype=dtype) / sf,
+            "eta_loc": np.nextafter(np.log(dmax), -np.inf, dtype=dtype) / sf,
+            "loc": np.nextafter(dmax, -np.inf, dtype=dtype) / sf,
+            "scale": np.nextafter(dmax, -np.inf, dtype=dtype) / sf,
+            "likelihood": dtype(1),
+            "ll": dtype(0),
+            # Not used and should be removed: https://github.com/theislab/batchglm/issues/148
+            "theta_scale": np.log(dmax) / sf,
+            "eta_scale": np.log(dmax) / sf,
+
+        }
+        return bounds_min, bounds_max
+
+    # simulator:
+
+    @property
+    def rand_fn_ave(self) -> Optional[Callable]:
+        return lambda shape: np.random.poisson(500, shape) + 1
+
+    @property
+    def rand_fn(self) -> Optional[Callable]:
+        return lambda shape: np.abs(np.random.uniform(0.5, 2, shape))
+
+    @property
+    def rand_fn_loc(self) -> Optional[Callable]:
+        return None
+
+    @property
+    def rand_fn_scale(self) -> Optional[Callable]:
+        return None
+
+    def generate_data(self) -> np.ndarray:
+        """
+        Sample random data based on poisson distribution and parameters.
+        """
+        return np.random.poisson(lam=self.lam)

batchglm/models/glm_poisson/utils.py

@@ -0,0 +1,115 @@
+import logging
+from typing import Callable, Optional, Tuple, Union
+
+import dask
+import numpy as np
+import scipy.sparse
+
+from .external import closedform_glm_mean
+
+logger = logging.getLogger("batchglm")
+
+
+def closedform_poisson_glm_loglam(
+    x: Union[np.ndarray, scipy.sparse.csr_matrix, dask.array.core.Array],
+    design_loc: Union[np.ndarray, dask.array.core.Array],
+    constraints_loc: Union[np.ndarray, dask.array.core.Array],
+    size_factors: Optional[np.ndarray] = None,
+    link_fn: Callable = np.log,
+    inv_link_fn: Callable = np.exp,
+):
+    r"""
+    Calculates a closed-form solution for the `lam` parameters of poisson GLMs.
+
+    :param x: The sample data
+    :param design_loc: design matrix for location
+    :param constraints_loc: tensor (all parameters x dependent parameters)
+        Tensor that encodes how complete parameter set which includes dependent
+        parameters arises from indepedent parameters: all = <constraints, indep>.
+        This form of constraints is used in vector generalized linear models (VGLMs).
+    :param size_factors: size factors for X
+    :return: tuple: (groupwise_means, mu, rmsd)
+    """
+    return closedform_glm_mean(
+        x=x,
+        dmat=design_loc,
+        constraints=constraints_loc,
+        size_factors=size_factors,
+        link_fn=link_fn,
+        inv_link_fn=inv_link_fn,
+    )
+
+
+def init_par(model, init_location: str) -> Tuple[np.ndarray, np.ndarray, bool, bool]:
+    r"""
+    standard:
+    Only initialise intercept and keep other coefficients as zero.
+
+    closed-form:
+    Initialize with Maximum Likelihood / Maximum of Momentum estimators
+
+    Idea:
+    $$
+        \theta &= f(x) \\
+        \Rightarrow f^{-1}(\theta) &= x \\
+            &= (D \cdot D^{+}) \cdot x \\
+            &= D \cdot (D^{+} \cdot x) \\
+            &= D \cdot x' = f^{-1}(\theta)
+    $$
+    """
+    train_loc = False
+
+    def auto_loc(dmat: Union[np.ndarray, dask.array.core.Array]) -> str:
+        """
+        Checks if dmat is one-hot encoded and returns 'closed_form' if so, else 'standard'
+
+        :param dmat The design matrix to check.
+        """
+        unique_params = np.unique(dmat)
+        if isinstance(unique_params, dask.array.core.Array):
+            unique_params = unique_params.compute()
+        if len(unique_params) == 2 and unique_params[0] == 0.0 and unique_params[1] == 1.0:
+            return "closed_form"
+        logger.warning(
+            (
+                "Cannot use 'closed_form' init for loc model: "
+                "design_loc is not one-hot encoded. Falling back to standard initialization."
+            )
+        )
+        return "standard"
+
+    groupwise_means = None
+
+    init_location_str = init_location.lower()
+    # Chose option if auto was chosen
+    if init_location_str == "auto":
+
+        init_location_str = auto_loc(model.design_loc)
+
+    if init_location_str == "closed_form":
+        groupwise_means, init_theta_location, rmsd_a = closedform_poisson_glm_loglam(
+            x=model.x,
+            design_loc=model.design_loc,
+            constraints_loc=model.constraints_loc,
+            size_factors=model.size_factors,
+            link_fn=lambda lam: np.log(lam + np.nextafter(0, 1, dtype=lam.dtype)),
+        )
+        # train mu, if the closed-form solution is inaccurate
+        train_loc = not (np.all(np.abs(rmsd_a) < 1e-20) or rmsd_a.size == 0)
+        if model.size_factors is not None:
+            if np.any(model.size_factors != 1):
+                train_loc = True
+
+    elif init_location_str == "standard":
+        overall_means = np.mean(model.x, axis=0)  # directly calculate the mean
+        init_theta_location = np.zeros([model.num_loc_params, model.num_features])
+        init_theta_location[0, :] = np.log(overall_means)
+        train_loc = True
+    elif init_location_str == "all_zero":
+        init_theta_location = np.zeros([model.num_loc_params, model.num_features])
+        train_loc = True
+    else:
+        raise ValueError("init_location string %s not recognized" % init_location)
+
+    # Scale is not used so just return init_theta_location for what would be init_theta_scale
+    return init_theta_location, init_theta_location, train_loc, True

batchglm/train/numpy/__init__.py

@@ -1 +1 @@
-from . import glm_nb as nb
+from . import glm_nb, glm_poisson

batchglm/train/numpy/glm_poisson/__init__.py

@@ -0,0 +1,2 @@
+from .estimator import Estimator
+from .model_container import ModelContainer

batchglm/train/numpy/glm_poisson/estimator.py

@@ -0,0 +1,58 @@
+import sys
+from typing import Optional, Tuple, Union
+
+import numpy as np
+
+from .external import EstimatorGlm, Model, init_par
+from .model_container import ModelContainer
+
+
+class Estimator(EstimatorGlm):
+    """
+    Estimator for Generalized Linear Models (GLMs) with negative binomial noise.
+    Uses the natural logarithm as linker function.
+
+    Attributes
+    ----------
+    model_vars : ModelVars
+        model variables
+    """
+
+    def __init__(
+        self,
+        model: Model,
+        init_location: str = "AUTO",
+        init_scale: str = "AUTO",
+        # batch_size: Optional[Union[Tuple[int, int], int]] = None,
+        quick_scale: bool = False,
+        dtype: str = "float64",
+    ):
+        """
+        Performs initialisation and creates a new estimator.
+
+        :param init_location: (Optional)
+            Low-level initial values for a. Can be:
+
+            - str:
+                * "auto": automatically choose best initialization
+                * "standard": initialize intercept with observed mean
+                * "init_model": initialize with another model (see `ìnit_model` parameter)
+                * "closed_form": try to initialize with closed form
+            - np.ndarray: direct initialization of 'a'
+        :param dtype: Numerical precision.
+        """
+        init_theta_location, _, train_loc, _ = init_par(model=model, init_location=init_location)
+        self._train_loc = train_loc
+        # no need to train the scale parameter for the poisson model since it only has one parameter
+        self._train_scale = False
+        sys.stdout.write("training location model: %s\n" % str(self._train_loc))
+        init_theta_location = init_theta_location.astype(dtype)
+
+        _model_container = ModelContainer(
+            model=model,
+            init_theta_location=init_theta_location,
+            init_theta_scale=init_theta_location,  # Not used.
+            chunk_size_genes=model.chunk_size_genes,
+            dtype=dtype,
+        )
+        super(Estimator, self).__init__(model_container=_model_container, dtype=dtype)

batchglm/train/numpy/glm_poisson/exceptions.py

@@ -0,0 +1,8 @@
+class NoScaleError(Exception):
+    """
+    Exception raised for attempting to access the scale parameter (or one of its derived methods) of a poisson model.
+    """
+
+    def __init__(self, method):
+        self.message = f"Attempted to access {method}. No scale parameter is fit for poisson - please use location."
+        super().__init__(self.message)