Sampling functions for the MuE/missing data discrete HMM.

examples/contrib/mue/FactorMuE.py

@@ -23,8 +23,8 @@
 
 Reference:
 [1] E. N. Weinstein, D. S. Marks (2021)
-"Generative probabilistic biological sequence models that account for
-mutational variability"
+"A structured observation distribution for generative biological sequence
+prediction and forecasting"
 https://www.biorxiv.org/content/10.1101/2020.07.31.231381v2.full.pdf
 """
 
@@ -62,10 +62,10 @@ def generate_data(small_test, include_stop, device):
 def main(args):
 
     # Load dataset.
-    if args.cpu_data and args.cuda:
+    if args.cpu_data or not args.cuda:
         device = torch.device("cpu")
     else:
-        device = None
+        device = torch.device("cuda")
     if args.test:
         dataset = generate_data(args.small, args.include_stop, device)
     else:
@@ -84,7 +84,7 @@ def main(args):
         # Specific data split seed, for comparability across models and
         # parameter initializations.
         pyro.set_rng_seed(args.rng_data_seed)
-        indices = torch.randperm(sum(data_lengths)).tolist()
+        indices = torch.randperm(sum(data_lengths), device=device).tolist()
         dataset_train, dataset_test = [
             torch.utils.data.Subset(dataset, indices[(offset - length) : offset])
             for offset, length in zip(
@@ -131,7 +131,12 @@ def main(args):
     )
     n_epochs = args.n_epochs
     losses = model.fit_svi(
-        dataset_train, n_epochs, args.anneal, args.batch_size, scheduler, args.jit
+        dataset_train,
+        n_epochs,
+        args.anneal,
+        args.batch_size,
+        scheduler,
+        args.jit,
     )
 
     # Evaluate.
@@ -233,13 +238,18 @@ def main(args):
         )
         with open(
             os.path.join(
-                args.out_folder, "FactorMuE_results.input_{}.txt".format(time_stamp)
+                args.out_folder,
+                "FactorMuE_results.input_{}.txt".format(time_stamp),
             ),
             "w",
         ) as ow:
             ow.write("[args]\n")
+            args.latent_seq_length = model.latent_seq_length
+            args.latent_alphabet = model.latent_alphabet_length
             for elem in list(args.__dict__.keys()):
                 ow.write("{} = {}\n".format(elem, args.__getattribute__(elem)))
+            ow.write("alphabet_str = {}\n".format("".join(dataset.alphabet)))
+            ow.write("max_length = {}\n".format(dataset.max_length))
 
 
 if __name__ == "__main__":

examples/contrib/mue/ProfileHMM.py

@@ -27,8 +27,8 @@
 Cambridge university press
 
 [2] E. N. Weinstein, D. S. Marks (2021)
-"Generative probabilistic biological sequence models that account for
-mutational variability"
+"A structured observation distribution for generative biological sequence
+prediction and forecasting"
 https://www.biorxiv.org/content/10.1101/2020.07.31.231381v2.full.pdf
 """
 
@@ -68,10 +68,10 @@ def main(args):
     pyro.set_rng_seed(args.rng_seed)
 
     # Load dataset.
-    if args.cpu_data and args.cuda:
+    if args.cpu_data or not args.cuda:
         device = torch.device("cpu")
     else:
-        device = None
+        device = torch.device("cuda")
     if args.test:
         dataset = generate_data(args.small, args.include_stop, device)
     else:
@@ -90,7 +90,7 @@ def main(args):
         # Specific data split seed, for comparability across models and
         # parameter initializations.
         pyro.set_rng_seed(args.rng_data_seed)
-        indices = torch.randperm(sum(data_lengths)).tolist()
+        indices = torch.randperm(sum(data_lengths), device=device).tolist()
         dataset_train, dataset_test = [
             torch.utils.data.Subset(dataset, indices[(offset - length) : offset])
             for offset, length in zip(
@@ -200,8 +200,11 @@ def main(args):
             "w",
         ) as ow:
             ow.write("[args]\n")
+            args.latent_seq_length = model.latent_seq_length
             for elem in list(args.__dict__.keys()):
                 ow.write("{} = {}\n".format(elem, args.__getattribute__(elem)))
+            ow.write("alphabet_str = {}\n".format("".join(dataset.alphabet)))
+            ow.write("max_length = {}\n".format(dataset.max_length))
 
 
 if __name__ == "__main__":

pyro/contrib/mue/dataloaders.py

@@ -141,3 +141,60 @@ def __len__(self):
     def __getitem__(self, ind):
 
         return (self.seq_data[ind], self.L_data[ind])
+
+
+def write(x, alphabet, file, truncate_stop=False, append=False, scores=None):
+    """
+    Write sequence samples to file.
+
+    :param ~torch.Tensor x: One-hot encoded sequences, with size
+        ``(data_size, seq_length, alphabet_length)``. May be padded with
+        zeros for variable length sequences.
+    :param ~np.array alphabet: Alphabet.
+    :param str file: Output file, where sequences will be written
+        in fasta format.
+    :param bool truncate_stop: If True, sequences will be truncated at the
+        first stop symbol (i.e. the stop symbol and everything after will not
+        be written). If False, the whole sequence will be written, including
+        any internal stop symbols.
+    :param bool append: If True, sequences are appended to the end of the
+        output file. If False, the file is first erased.
+    """
+    print_alphabet = np.array(list(alphabet) + [""])
+    x = torch.cat([x, torch.zeros(list(x.shape[:2]) + [1])], -1)
+    if truncate_stop:
+        mask = (
+            torch.cumsum(
+                torch.matmul(
+                    x, torch.tensor(print_alphabet == "*", dtype=torch.double)
+                ),
+                -1,
+            )
+            > 0
+        ).to(torch.double)
+        x = x * (1 - mask).unsqueeze(-1)
+        x[:, :, -1] = mask
+    else:
+        x[:, :, -1] = (torch.sum(x, -1) < 0.5).to(torch.double)
+    index = (
+        torch.matmul(x, torch.arange(x.shape[-1], dtype=torch.double))
+        .to(torch.long)
+        .cpu()
+        .numpy()
+    )
+    if scores is None:
+        seqs = [
+            ">{}\n".format(j) + "".join(elem) + "\n"
+            for j, elem in enumerate(print_alphabet[index])
+        ]
+    else:
+        seqs = [
+            ">{}\n".format(j) + "".join(elem) + "\n"
+            for j, elem in zip(scores, print_alphabet[index])
+        ]
+    if append:
+        open_flag = "a"
+    else:
+        open_flag = "w"
+    with open(file, open_flag) as fw:
+        fw.write("".join(seqs))

pyro/contrib/mue/missingdatahmm.py

@@ -2,6 +2,7 @@
 # SPDX-License-Identifier: Apache-2.0
 
 import torch
+from torch.distributions import Categorical, OneHotCategorical
 
 from pyro.distributions import constraints
 from pyro.distributions.hmm import _sequential_logmatmulexp
@@ -110,3 +111,207 @@ def log_prob(self, value):
         # Marginalize out final state.
         result = result.logsumexp(-1)
         return result
+
+    def sample(self, sample_shape=torch.Size([])):
+        """
+        :param ~torch.Size sample_shape: Sample shape, last dimension must be
+            ``num_steps`` and must be broadcastable to
+            ``(batch_size, num_steps)``. batch_size must be int not tuple.
+        """
+        # shape: batch_size x num_steps x categorical_size
+        shape = broadcast_shape(
+            torch.Size(list(self.batch_shape) + [1, 1]),
+            torch.Size(list(sample_shape) + [1]),
+            torch.Size((1, 1, self.event_shape[-1])),
+        )
+        # state: batch_size x state_dim
+        state = OneHotCategorical(logits=self.initial_logits).sample()
+        # sample: batch_size x num_steps x categorical_size
+        sample = torch.zeros(shape)
+        for i in range(shape[-2]):
+            # batch_size x 1 x state_dim @
+            # batch_size x state_dim x categorical_size
+            obs_logits = torch.matmul(
+                state.unsqueeze(-2), self.observation_logits
+            ).squeeze(-2)
+            sample[:, i, :] = OneHotCategorical(logits=obs_logits).sample()
+            # batch_size x 1 x state_dim @
+            # batch_size x state_dim x state_dim
+            trans_logits = torch.matmul(
+                state.unsqueeze(-2), self.transition_logits
+            ).squeeze(-2)
+            state = OneHotCategorical(logits=trans_logits).sample()
+
+        return sample
+
+    def filter(self, value):
+        """
+        Compute the marginal probability of the state variable at each
+        step conditional on the previous observations.
+
+        :param ~torch.Tensor value: One-hot encoded observation.
+            Must be real-valued (float) and broadcastable to
+            ``(batch_size, num_steps, categorical_size)`` where
+            ``categorical_size`` is the dimension of the categorical output.
+        """
+        # batch_size x num_steps x state_dim
+        shape = broadcast_shape(
+            torch.Size(list(self.batch_shape) + [1, 1]),
+            torch.Size(list(value.shape[:-1]) + [1]),
+            torch.Size((1, 1, self.initial_logits.shape[-1])),
+        )
+        filter = torch.zeros(shape)
+
+        # Combine observation and transition factors.
+        # batch_size x num_steps x state_dim
+        value_logits = torch.matmul(
+            value, torch.transpose(self.observation_logits, -2, -1)
+        )
+        # batch_size x num_steps-1 x state_dim x state_dim
+        result = self.transition_logits.unsqueeze(-3) + value_logits[..., 1:, None, :]
+
+        # Forward pass. (This could be parallelized using the
+        # Sarkka & Garcia-Fernandez method.)
+        filter[..., 0, :] = self.initial_logits + value_logits[..., 0, :]
+        filter[..., 0, :] = filter[..., 0, :] - torch.logsumexp(
+            filter[..., 0, :], -1, True
+        )
+        for i in range(1, shape[-2]):
+            filter[..., i, :] = torch.logsumexp(
+                filter[..., i - 1, :, None] + result[..., i - 1, :, :], -2
+            )
+            filter[..., i, :] = filter[..., i, :] - torch.logsumexp(
+                filter[..., i, :], -1, True
+            )
+        return filter
+
+    def smooth(self, value):
+        """
+        Compute posterior expected value of state at each position (smoothing).
+
+        :param ~torch.Tensor value: One-hot encoded observation.
+            Must be real-valued (float) and broadcastable to
+            ``(batch_size, num_steps, categorical_size)`` where
+            ``categorical_size`` is the dimension of the categorical output.
+        """
+        # Compute filter and initialize.
+        filter = self.filter(value)
+        shape = filter.shape
+        backfilter = torch.zeros(shape)
+
+        # Combine observation and transition factors.
+        # batch_size x num_steps x state_dim
+        value_logits = torch.matmul(
+            value, torch.transpose(self.observation_logits, -2, -1)
+        )
+        # batch_size x num_steps-1 x state_dim x state_dim
+        result = self.transition_logits.unsqueeze(-3) + value_logits[..., 1:, None, :]
+        # Construct backwards filter.
+        for i in range(shape[-2] - 1, 0, -1):
+            backfilter[..., i - 1, :] = torch.logsumexp(
+                backfilter[..., i, None, :] + result[..., i - 1, :, :], -1
+            )
+
+        # Compute smoothed version.
+        smooth = filter + backfilter
+        smooth = smooth - torch.logsumexp(smooth, -1, True)
+        return smooth
+
+    def sample_states(self, value):
+        """
+        Sample states with forward filtering-backward sampling algorithm.
+
+        :param ~torch.Tensor value: One-hot encoded observation.
+            Must be real-valued (float) and broadcastable to
+            ``(batch_size, num_steps, categorical_size)`` where
+            ``categorical_size`` is the dimension of the categorical output.
+        """
+        filter = self.filter(value)
+        shape = filter.shape
+        joint = filter.unsqueeze(-1) + self.transition_logits.unsqueeze(-3)
+        states = torch.zeros(shape[:-1], dtype=torch.long)
+        states[..., -1] = Categorical(logits=filter[..., -1, :]).sample()
+        for i in range(shape[-2] - 1, 0, -1):
+            logits = torch.gather(
+                joint[..., i - 1, :, :],
+                -1,
+                states[..., i, None, None]
+                * torch.ones([shape[-1], 1], dtype=torch.long),
+            ).squeeze(-1)
+            states[..., i - 1] = Categorical(logits=logits).sample()
+        return states
+
+    def map_states(self, value):
+        """
+        Compute maximum a posteriori (MAP) estimate of state variable with
+        Viterbi algorithm.
+
+        :param ~torch.Tensor value: One-hot encoded observation.
+            Must be real-valued (float) and broadcastable to
+            ``(batch_size, num_steps, categorical_size)`` where
+            ``categorical_size`` is the dimension of the categorical output.
+        """
+        # Setup for Viterbi.
+        # batch_size x num_steps x state_dim
+        shape = broadcast_shape(
+            torch.Size(list(self.batch_shape) + [1, 1]),
+            torch.Size(list(value.shape[:-1]) + [1]),
+            torch.Size((1, 1, self.initial_logits.shape[-1])),
+        )
+        state_logits = torch.zeros(shape)
+        state_traceback = torch.zeros(shape, dtype=torch.long)
+
+        # Combine observation and transition factors.
+        # batch_size x num_steps x state_dim
+        value_logits = torch.matmul(
+            value, torch.transpose(self.observation_logits, -2, -1)
+        )
+        # batch_size x num_steps-1 x state_dim x state_dim
+        result = self.transition_logits.unsqueeze(-3) + value_logits[..., 1:, None, :]
+
+        # Forward pass.
+        state_logits[..., 0, :] = self.initial_logits + value_logits[..., 0, :]
+        for i in range(1, shape[-2]):
+            transit_weights = (
+                state_logits[..., i - 1, :, None] + result[..., i - 1, :, :]
+            )
+            state_logits[..., i, :], state_traceback[..., i, :] = torch.max(
+                transit_weights, -2
+            )
+        # Traceback.
+        map_states = torch.zeros(shape[:-1], dtype=torch.long)
+        map_states[..., -1] = torch.argmax(state_logits[..., -1, :], -1)
+        for i in range(shape[-2] - 1, 0, -1):
+            map_states[..., i - 1] = torch.gather(
+                state_traceback[..., i, :], -1, map_states[..., i].unsqueeze(-1)
+            ).squeeze(-1)
+        return map_states
+
+    def given_states(self, states):
+        """
+        Distribution conditional on the state variable.
+
+        :param ~torch.Tensor map_states: State trajectory. Must be
+            integer-valued (long) and broadcastable to
+            ``(batch_size, num_steps)``.
+        """
+        shape = broadcast_shape(
+            list(self.batch_shape) + [1, 1],
+            list(states.shape[:-1]) + [1, 1],
+            [1, 1, self.observation_logits.shape[-1]],
+        )
+        states_index = states.unsqueeze(-1) * torch.ones(shape, dtype=torch.long)
+        obs_logits = self.observation_logits * torch.ones(shape)
+        logits = torch.gather(obs_logits, -2, states_index)
+        return OneHotCategorical(logits=logits)
+
+    def sample_given_states(self, states):
+        """
+        Sample an observation conditional on the state variable.
+
+        :param ~torch.Tensor map_states: State trajectory. Must be
+            integer-valued (long) and broadcastable to
+            ``(batch_size, num_steps)``.
+        """
+        conditional = self.given_states(states)
+        return conditional.sample()