def test_simple_smoke(num_leaves, num_steps, batch_shape, sample_shape):
leaf_times = torch.rand(batch_shape + (num_leaves, )).pow(0.5) * num_steps
d = CoalescentTimes(leaf_times)
coal_times = d.sample(sample_shape)
assert coal_times.shape == sample_shape + batch_shape + (num_leaves - 1, )
actual = d.log_prob(coal_times)
assert actual.shape == sample_shape + batch_shape
def test_log_prob_unit_rate(num_leaves, num_steps, batch_shape, sample_shape):
leaf_times = torch.rand(batch_shape + (num_leaves, )).pow(0.5) * num_steps
d1 = CoalescentTimes(leaf_times)
rate_grid = torch.ones(batch_shape + (num_steps, ))
d2 = CoalescentTimesWithRate(leaf_times, rate_grid)
coal_times = d1.sample(sample_shape)
assert_close(d1.log_prob(coal_times), d2.log_prob(coal_times))
def test_log_prob_constant_rate_2(num_leaves, num_steps, batch_shape, sample_shape):
rate = torch.randn(batch_shape).exp()
rate_grid = rate.unsqueeze(-1).expand(batch_shape + (num_steps,))
leaf_times = torch.rand(batch_shape + (num_leaves,)).pow(0.5) * num_steps
d1 = CoalescentTimes(leaf_times, rate)
coal_times = d1.sample(sample_shape)
log_prob_1 = d1.log_prob(coal_times)
d2 = CoalescentTimesWithRate(leaf_times, rate_grid)
log_prob_2 = d2.log_prob(coal_times)
assert_close(log_prob_1, log_prob_2)
def test_log_prob_constant_rate(num_leaves, num_steps, batch_shape, sample_shape):
rate = torch.randn(batch_shape).exp()
rate_grid = rate.unsqueeze(-1).expand(batch_shape + (num_steps,))
leaf_times_2 = torch.rand(batch_shape + (num_leaves,)).pow(0.5) * num_steps
leaf_times_1 = leaf_times_2 * rate.unsqueeze(-1)
d1 = CoalescentTimes(leaf_times_1)
coal_times_1 = d1.sample(sample_shape)
log_prob_1 = d1.log_prob(coal_times_1)
d2 = CoalescentTimesWithRate(leaf_times_2, rate_grid)
coal_times_2 = coal_times_1 / rate.unsqueeze(-1)
log_prob_2 = d2.log_prob(coal_times_2)
log_abs_det_jacobian = -coal_times_2.size(-1) * rate.log()
assert_close(log_prob_1 - log_abs_det_jacobian, log_prob_2)
def test_likelihood_vectorized(num_leaves, num_steps, batch_shape, clamped):
if clamped:
leaf_times = torch.rand(batch_shape + (num_leaves,)).pow(0.5) * num_steps
coal_times = CoalescentTimes(leaf_times).sample().clamp(min=0)
else:
leaf_times = torch.randn(batch_shape + (num_leaves,))
leaf_times.mul_(0.25).add_(0.75).mul_(num_steps)
coal_times = CoalescentTimes(leaf_times).sample()
rate_grid = torch.rand(batch_shape + (num_steps,)) + 0.5
d = CoalescentTimesWithRate(leaf_times, rate_grid)
expected = d.log_prob(coal_times)
likelihood = CoalescentRateLikelihood(leaf_times, coal_times, num_steps)
actual = likelihood(rate_grid).sum(-1)
assert_close(actual, expected)