Add helper to convert Bio.Phylo trees to PyTorch

docs/source/conf.py

@@ -192,6 +192,7 @@
     'funsor': ('http://funsor.pyro.ai/en/stable/', None),
     'opt_einsum': ('https://optimized-einsum.readthedocs.io/en/stable/', None),
     'scipy': ('https://docs.scipy.org/doc/scipy/reference/', None),
+    'Bio': ('https://biopython.readthedocs.io/en/latest/', None),
 }
 
 # document class constructors (__init__ methods):

docs/source/contrib.epidemiology.rst

@@ -39,3 +39,5 @@ Distributions
     :show-inheritance:
     :member-order: bysource
     :special-members: __call__
+
+.. autofunction:: pyro.distributions.coalescent.bio_phylo_to_times

pyro/contrib/epidemiology/__init__.py

@@ -1,12 +1,15 @@
 # Copyright Contributors to the Pyro project.
 # SPDX-License-Identifier: Apache-2.0
 
+from pyro.distributions.coalescent import bio_phylo_to_times
+
 from .compartmental import CompartmentalModel
 from .distributions import beta_binomial_dist, binomial_dist, infection_dist
 
 __all__ = [
     "CompartmentalModel",
     "beta_binomial_dist",
     "binomial_dist",
+    "bio_phylo_to_times",
     "infection_dist",
 ]

pyro/distributions/coalescent.py

@@ -302,6 +302,53 @@ def __call__(self, rate_grid, t=slice(None)):
         return const + linear + log
 
 
+def bio_phylo_to_times(tree, *, get_time=None):
+    """
+    Extracts coalescent summary statistics from a phylogeny, suitable for use
+    with :class:`~pyro.distributions.CoalescentRateLikelihood`.
+
+    :param Bio.Phylo.BaseTree.Clade tree: A phylogenetic tree.
+    :param callable get_time: Optional function to extract the time point of
+        each sub-:class:`~Bio.Phylo.BaseTree.Clade`. If absent, times will be
+        computed by cumulative `.branch_length`.
+    :returns: A pair of :class:`~torch.Tensor` s ``(leaf_times, coal_times)``
+        where ``leaf_times`` are times of sampling events (leaf nodes in the
+        phylogenetic tree) and ``coal_times`` are times of coalescences (leaf
+        nodes in the phylogenetic binary tree).
+    :rtype: tuple
+    """
+    if get_time is None:
+        # Compute time as cumulative branch length.
+        def get_branch_length(clade):
+            branch_length = clade.branch_length
+            return 1.0 if branch_length is None else branch_length
+        times = {tree.root: get_branch_length(tree.root)}
+
+    leaf_times = []
+    coal_times = []
+    for clade in tree.find_clades():
+        if get_time is None:
+            time = times[clade]
+            for child in clade:
+                times[child] = time + get_branch_length(child)
+        else:
+            time = get_time(clade)
+
+        num_children = len(clade)
+        if num_children == 0:
+            leaf_times.append(time)
+        else:
+            # Pyro expects binary coalescent events, so we split n-ary events
+            # into n-1 separate binary events.
+            for _ in range(num_children - 1):
+                coal_times.append(time)
+    assert len(leaf_times) == 1 + len(coal_times)
+
+    leaf_times = torch.tensor(leaf_times)
+    coal_times = torch.tensor(coal_times)
+    return leaf_times, coal_times
+
+
 def _gather(tensor, dim, index):
     """
     Like :func:`torch.gather` but broadcasts.

scripts/update_headers.py

@@ -7,7 +7,7 @@
 import sys
 
 root = os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
-blacklist = ["/build/", "/dist/"]
+blacklist = ["/build/", "/dist/", "/pyro/_version.py"]
 file_types = [
     ("*.py", "# {}"),
     ("*.cpp", "// {}"),

setup.py

@@ -62,6 +62,7 @@
     'matplotlib>=1.3',
     'torchvision>=0.6.0',
     'visdom>=0.1.4',
+    # 'biopython>=1.54',  # requires Python 3.6
     'pandas',
     'seaborn',
     'wget',

tests/distributions/test_coalescent.py

@@ -1,12 +1,16 @@
 # Copyright Contributors to the Pyro project.
 # SPDX-License-Identifier: Apache-2.0
 
+import io
+import re
+
 import pytest
 import torch
 
 import pyro
 from pyro.distributions import CoalescentTimes, CoalescentTimesWithRate
-from pyro.distributions.coalescent import CoalescentRateLikelihood, CoalescentTimesConstraint, _sample_coalescent_times
+from pyro.distributions.coalescent import (CoalescentRateLikelihood, CoalescentTimesConstraint,
+                                           _sample_coalescent_times, bio_phylo_to_times)
 from pyro.distributions.util import broadcast_shape
 from tests.common import assert_close
 
@@ -144,3 +148,84 @@ def test_likelihood_sequential(num_leaves, num_steps, batch_shape, clamped):
                  for t in range(num_steps))
 
     assert_close(actual, expected)
+
+
+TREE_NEXUS = """
+#NEXUS
+Begin Trees;
+ Tree tree1=((EPI_ISL_408009:0.00000[&date=2020.08],
+ EPI_ISL_408008:0.00000[&date=2020.08]) NODE_0000004:0.17430[&date=2020.08],
+ (EPI_ISL_417931:0.28554[&date=2020.21],
+ (EPI_ISL_417332:0.11102[&date=2020.20], EPI_ISL_413931:0.08643[&date=2020.18])
+ NODE_0000005:0.16360[&date=2020.09], ((EPI_ISL_413558:0.11909[&date=2020.16],
+     (EPI_ISL_413559:0.07179[&date=2020.16],
+         (EPI_ISL_412862:0.00000[&date=2020.15],
+             EPI_ISL_413561:0.01093[&date=2020.16])
+         NODE_0000011:0.06086[&date=2020.15])
+     NODE_0000012:0.04730[&date=2020.09]) NODE_0000007:0.06603[&date=2020.04],
+     (EPI_ISL_411955:0.09393[&date=2020.11],
+         (EPI_ISL_417325:0.08372[&date=2020.17],
+             (EPI_ISL_417318:0.02411[&date=2020.16],
+                 EPI_ISL_417320:0.03504[&date=2020.17])
+             NODE_0000009:0.05141[&date=2020.14])
+         NODE_0000006:0.07032[&date=2020.09])
+     NODE_0000014:0.04474[&date=2020.02]) NODE_0000010:0.04578[&date=2019.97],
+ (EPI_ISL_417933:0.15496[&date=2020.21], EPI_ISL_414648:0.13583[&date=2020.19],
+         (EPI_ISL_417932:0.09490[&date=2020.21],
+             (EPI_ISL_417937:0.05785[&date=2020.21],
+                 EPI_ISL_417331:0.04419[&date=2020.20])
+             NODE_0000001:0.03705[&date=2020.15],
+             (EPI_ISL_417938:0.06860[&date=2020.21],
+                 (EPI_ISL_417939:0.04394[&date=2020.21],
+                     (EPI_ISL_417330:0.00314[&date=2020.20],
+                         (EPI_ISL_416457:0.00000[&date=2020.21],
+                             EPI_ISL_417935:0.00000[&date=2020.21])
+                         NODE_0000018:0.01680[&date=2020.21])
+                     NODE_0000017:0.02714[&date=2020.19])
+                 NODE_0000016:0.02466[&date=2020.17])
+                 NODE_0000015:0.02630[&date=2020.14])
+                 NODE_0000000:0.06006[&date=2020.12])
+         NODE_0000002:0.13059[&date=2020.06])
+ NODE_0000003:0.02264[&date=2019.93]) NODE_0000008:0.10000[&date=2019.90];
+End;
+"""
+
+
+@pytest.fixture
+def tree():
+    Phylo = pytest.importorskip("Bio.Phylo")
+    tree_file = io.StringIO(TREE_NEXUS)
+    trees = list(Phylo.parse(tree_file, "nexus"))
+    assert len(trees) == 1
+    return trees[0]
+
+
+def test_bio_phylo_to_times(tree):
+    leaf_times, coal_times = bio_phylo_to_times(tree)
+    assert len(coal_times) + 1 == len(leaf_times)
+
+    # Check positivity.
+    times = torch.cat([coal_times, leaf_times])
+    signs = torch.cat([-torch.ones_like(coal_times), torch.ones_like(leaf_times)])
+    times, index = times.sort(0)
+    signs = signs[index]
+    lineages = signs.flip([0]).cumsum(0).flip([0])
+    assert (lineages >= 0).all()
+
+
+def test_bio_phylo_to_times_custom(tree):
+    # Test a custom time parser.
+    def get_time(clade):
+        date_string = re.search(r"date=(\d\d\d\d\.\d\d)", clade.comment).group(1)
+        return (float(date_string) - 2020) * 365.25
+
+    leaf_times, coal_times = bio_phylo_to_times(tree, get_time=get_time)
+    assert len(coal_times) + 1 == len(leaf_times)
+
+    # Check positivity.
+    times = torch.cat([coal_times, leaf_times])
+    signs = torch.cat([-torch.ones_like(coal_times), torch.ones_like(leaf_times)])
+    times, index = times.sort(0)
+    signs = signs[index]
+    lineages = signs.flip([0]).cumsum(0).flip([0])
+    assert (lineages >= 0).all()