From da2395f25c895af96b0b52f0887a930f21eb4783 Mon Sep 17 00:00:00 2001
From: gileshd <gileshd@googlemail.com>
Date: Mon, 23 Sep 2024 12:58:32 +0100
Subject: [PATCH] Add further type annotations to poisson hmm

---
 .../hidden_markov_model/models/poisson_hmm.py | 51 +++++++++++++------
 1 file changed, 35 insertions(+), 16 deletions(-)

diff --git a/dynamax/hidden_markov_model/models/poisson_hmm.py b/dynamax/hidden_markov_model/models/poisson_hmm.py
index 6dc77090..b5c79203 100644
--- a/dynamax/hidden_markov_model/models/poisson_hmm.py
+++ b/dynamax/hidden_markov_model/models/poisson_hmm.py
@@ -1,4 +1,4 @@
-from typing import NamedTuple, Optional, Tuple, Union
+from typing import Any, Dict, NamedTuple, Optional, Tuple, Union
 
 import jax.numpy as jnp
 import jax.random as jr
@@ -6,13 +6,14 @@
 import tensorflow_probability.substrates.jax.distributions as tfd
 from jaxtyping import Array, Float
 
+from dynamax.hidden_markov_model.inference import HMMPosterior
 from dynamax.hidden_markov_model.models.abstractions import HMM, HMMEmissions
 from dynamax.hidden_markov_model.models.initial import ParamsStandardHMMInitialState
 from dynamax.hidden_markov_model.models.initial import StandardHMMInitialState
 from dynamax.hidden_markov_model.models.transitions import ParamsStandardHMMTransitions
 from dynamax.hidden_markov_model.models.transitions import StandardHMMTransitions
 from dynamax.parameters import ParameterProperties, ParameterSet, PropertySet
-from dynamax.types import Scalar
+from dynamax.types import IntScalar, Scalar
 from dynamax.utils.utils import pytree_sum
 
 
@@ -23,10 +24,10 @@ class ParamsPoissonHMMEmissions(NamedTuple):
 class PoissonHMMEmissions(HMMEmissions):
 
     def __init__(self,
-                 num_states,
-                 emission_dim,
-                 emission_prior_concentration=1.1,
-                 emission_prior_rate=0.1):
+                 num_states: int,
+                 emission_dim: int,
+                 emission_prior_concentration: Scalar = 1.1,
+                 emission_prior_rate: Scalar = 0.1):
         """_summary_
 
         Args:
@@ -40,12 +41,13 @@ def __init__(self,
         self.emission_prior_rate = emission_prior_rate
 
     @property
-    def emission_shape(self):
+    def emission_shape(self) -> Tuple[int]:
         return (self.emission_dim,)
 
-    def initialize(self, key=jr.PRNGKey(0),
-                   method="prior",
-                   emission_rates=None):
+    def initialize(self, key: Array=jr.PRNGKey(0),
+                   method: str = "prior",
+                   emission_rates: Optional[Float[Array, "num_states emission_dim"]] = None
+    ) -> Tuple[ParamsPoissonHMMEmissions, ParamsPoissonHMMEmissions]:
         # Initialize the emission probabilities
         if emission_rates is None:
             if method.lower() == "prior":
@@ -64,24 +66,41 @@ def initialize(self, key=jr.PRNGKey(0),
         props = ParamsPoissonHMMEmissions(rates=ParameterProperties(constrainer=tfb.Softplus()))
         return params, props
 
-    def distribution(self, params, state, inputs=None):
+    def distribution(
+            self,
+            params: ParamsPoissonHMMEmissions,
+            state: IntScalar,
+            inputs: Optional[Array] = None
+            ) -> tfd.Distribution:
         return tfd.Independent(tfd.Poisson(rate=params.rates[state]),
                                reinterpreted_batch_ndims=1)
 
-    def log_prior(self, params):
+    def log_prior(self, params: ParamsPoissonHMMEmissions) -> Float[Array, ""]:
         prior = tfd.Gamma(self.emission_prior_concentration, self.emission_prior_rate)
         return prior.log_prob(params.rates).sum()
 
-    def collect_suff_stats(self, params, posterior, emissions, inputs=None):
+    def collect_suff_stats(
+            self,
+            params: ParamsPoissonHMMEmissions,
+            posterior: HMMPosterior,
+            emissions: Float[Array, "num_timesteps emission_dim"],
+            inputs: Optional[Array] = None
+            ) -> Dict[str, Float[Array, "..."]]:
         expected_states = posterior.smoothed_probs
         sum_w = jnp.einsum("tk->k", expected_states)[:, None]
         sum_x = jnp.einsum("tk, ti->ki", expected_states, emissions)
         return dict(sum_w=sum_w, sum_x=sum_x)
 
-    def initialize_m_step_state(self, params, props):
+    def initialize_m_step_state(self, params: ParamsPoissonHMMEmissions, props: ParamsPoissonHMMEmissions) -> None:
         return None
 
-    def m_step(self, params, props, batch_stats, m_step_state):
+    def m_step(
+            self,
+            params: ParamsPoissonHMMEmissions,
+            props: ParamsPoissonHMMEmissions,
+            batch_stats: Dict[str, Float[Array, "..."]],
+            m_step_state: Any
+            ) -> Tuple[ParamsPoissonHMMEmissions, Any]:
         if props.rates.trainable:
             emission_stats = pytree_sum(batch_stats, axis=0)
             post_concentration = self.emission_prior_concentration + emission_stats['sum_x']
@@ -132,7 +151,7 @@ def __init__(self,
         emission_component = PoissonHMMEmissions(num_states, emission_dim, emission_prior_concentration=emission_prior_concentration, emission_prior_rate=emission_prior_rate)
         super().__init__(num_states, initial_component, transition_component, emission_component)
 
-    def initialize(self, key=jr.PRNGKey(0),
+    def initialize(self, key: Array=jr.PRNGKey(0),
                    method="prior",
                    initial_probs: Optional[Float[Array, " num_states"]]=None,
                    transition_matrix: Optional[Float[Array, "num_states num_states"]]=None,