Search code examples
pythontensorflowtensorflow2.0tensorflow-probability

Optimise function for many pseudodata realisations in TensorFlow 2

My end goal is to simulate likelihood ratio test statistics, however, the core problem I am having is that I do not understand how to get TensorFlow 2 to perform many optimizations for different data inputs. Here is my attempt, hopefully, it gives you the idea of what I am trying:

import tensorflow as tf
import tensorflow_probability as tfp
from tensorflow_probability import distributions as tfd
import numpy as np

# Bunch of independent Poisson distributions that we want to combine
poises0 = [tfp.distributions.Poisson(rate = 10) for i in range(5)]

# Construct joint distributions
joint0 = tfd.JointDistributionSequential(poises0)

# Generate samples
N = int(1e3)
samples0 = joint0.sample(N)

# Now we need the same distributions but with floating parameters,
# and need to define the function to be minimised
mus = [tf.Variable(np.random.randn(), name='mu{0}'.format(i)) for i in range(5)]

#@tf.function
def loss():
    poises_free = [tfp.distributions.Poisson(rate = mus[i]) for i in range(5)]
    joint_free = tfd.JointDistributionSequential(poises_free)
    # Construct (half of) test statistic
    return -2*(joint_free.log_prob(samples0))

# Minimise (for all samples? Apparently not?)
opt = tf.optimizers.SGD(0.1).minimize(loss,var_list=mus)

print(mus)
print(loss())
print(opt)
quit()

Output:

[<tf.Variable 'mu0:0' shape=() dtype=float32, numpy=53387.016>, <tf.Variable 'mu1:0' shape=() dtype=float32, numpy=2540.568>, <tf.Variable 'mu2:0' shape=() dtype=float32, numpy=-5136.6226>, <tf.Variable 'mu3:0' shape=() dtype=float32, numpy=-3714.5227>, <tf.Variable 'mu4:0' shape=() dtype=float32, numpy=1062.9396>]
tf.Tensor(
[nan nan nan nan ... nan nan nan], shape=(1000,), dtype=float32)
<tf.Variable 'UnreadVariable' shape=() dtype=int64, numpy=1>

In the end I want to compute the test statistic

q = -2*joint0.log_prob(samples0) - loss()

and show that it has a chi-squared distribution with 5 degrees of freedom.

I am new to TensorFlow so perhaps I am doing this entirely wrong, but I hope you get the idea of what I want.

Edit:

So I played around a bit more, and I suppose that TensorFlow simply doesn't perform optimizations over the input tensors in parallel like I assumed. Or perhaps it can, but I need to set things up differently, i.e. perhaps give it a tensor of input parameters and a gigantic joint loss function for all the minimizations at once?

I also tried doing things with a simple loop just to see what happens. As predicted it is pathetically slow, but I also don't even get the right answer:

poises0 = [tfp.distributions.Poisson(rate = 10) for i in range(5)]
joint0 = tfd.JointDistributionSequential(poises0)

N = int(5e2)
samples0 = joint0.sample(N)

mus = [tf.Variable(10., name='mu{0}'.format(i)) for i in range(5)]

#@tf.function
def loss(xi):
    def loss_inner():
        poises_free = [tfp.distributions.Poisson(rate = mus[i]) for i in range(5)]
        joint_free = tfd.JointDistributionSequential(poises_free)
        # Construct (half of) test statistic
        return -2*(joint_free.log_prob(xi))
    return loss_inner

# Minimise
# I think I have to loop over the samples... bit lame. Can perhaps parallelise though.
q = []
for i in range(N):
   xi = [x[i] for x in samples0]
   opt = tf.optimizers.SGD(0.1).minimize(loss=loss(xi),var_list=mus)
   q += [-2*joint0.log_prob(xi) - loss(xi)()]

fig = plt.figure()
ax = fig.add_subplot(111)
sns.distplot(q, kde=False, ax=ax, norm_hist=True)
qx = np.linspace(np.min(q),np.max(q),1000)
qy = np.exp(tfd.Chi2(df=5).log_prob(qx))
sns.lineplot(qx,qy)
plt.show()

The output is not a chi-squared distribution with DOF=5. Indeed the test statistic often has negative values, which means that the optimized result is often a worse fit than the null hypothesis, which should be impossible.

Not a chi-squared distribution with DOF=5

Edit 2:

Here is an attempt at the "monster" solution where I minimize a giant network of different input variables for each pseudodata realization all at once. This feels more like something that TensorFlow might be good at doing, though I feel like I will run out of RAM once I go to large sets of pseudo-data. Still, I can probably loop over batches of pseudo-data.

poises0 = [tfp.distributions.Poisson(rate = 10) for i in range(5)]
joint0 = tfd.JointDistributionSequential(poises0)

N = int(5e3)
samples0 = joint0.sample(N)

mus = [tf.Variable(10*np.ones(N, dtype='float32'), name='mu{0}'.format(i)) for i in range(5)]

poises_free = [tfp.distributions.Poisson(rate = mus[i]) for i in range(5)]
joint_free = tfd.JointDistributionSequential(poises_free)
qM = -2*(joint_free.log_prob(samples0))

@tf.function
def loss():
    return tf.math.reduce_sum(qM,axis=0)

# Minimise
opt = tf.optimizers.SGD(0.1).minimize(loss,var_list=mus)
print("parameters:", mus)
print("loss:", loss())
q0 =-2*joint0.log_prob(samples0)
print("q0:", q0)
print("qM:", qM)
q = q0 - qM

fig = plt.figure()
ax = fig.add_subplot(111)
sns.distplot(q, kde=False, ax=ax, norm_hist=True)
qx = np.linspace(np.min(q),np.max(q),1000)
qy = np.exp(tfd.Chi2(df=5).log_prob(qx))
sns.lineplot(qx,qy)
plt.show()

Unfortunately I now get the error:

Traceback (most recent call last):
  File "testing3.py", line 35, in <module>
    opt = tf.optimizers.SGD(0.1).minimize(loss,var_list=mus)   
  File "/home/farmer/anaconda3/envs/general/lib/python3.6/site-packages/tensorflow/python/keras/optimizer_v2/optimizer_v2.py", line 298, in minimize
    return self.apply_gradients(grads_and_vars, name=name)
  File "/home/farmer/anaconda3/envs/general/lib/python3.6/site-packages/tensorflow/python/keras/optimizer_v2/optimizer_v2.py", line 396, in apply_gradients
    grads_and_vars = _filter_grads(grads_and_vars)
  File "/home/farmer/anaconda3/envs/general/lib/python3.6/site-packages/tensorflow/python/keras/optimizer_v2/optimizer_v2.py", line 924, in _filter_grads
    ([v.name for _, v in grads_and_vars],))
ValueError: No gradients provided for any variable: ['mu0:0', 'mu1:0', 'mu2:0', 'mu3:0', 'mu4:0'].

which I suppose is a basic sort of error. I think I just don't understand how TensorFlow keeps track of the derivatives it needs to compute. It seems like things work if I define variables inside the loss function rather than outside, but I need them outside in order to access their values later. So I guess I don't understand something here.

Solution

  • Ok so here is what I came up with. The keys things I was missing were:

    1. Define input variables as giant tensors so that all minimisations can occur at once.
    2. Construct a single combined loss function for all minimisations at once
    3. Construct intermediate variables for loss computation inside the loss function definition, so that TensorFlow can track the gradients (I think the minimize function wraps the loss function in a gradient tape or some such).
    4. Define the loss function as part of a class so that intermediate variables can be stored.
    5. minimize only does one step of the minimisation, so we need to loop over it lots of times until it converges according to some criterion.
    6. I was running into some NaNs due to the invalid-ness of means less than zero for Poisson distributions. So I needed to add a constraint to the input variables.

    With this, I can now do the equivalent of a million minimisations in like 10 seconds on my laptop, which is pretty nice!

    import tensorflow as tf
import tensorflow_probability as tfp
from tensorflow_probability import distributions as tfd
import seaborn as sns
import numpy as np
import matplotlib.pyplot as plt

# Bunch of independent Poisson distributions that we want to combine
poises0 = [tfd.Poisson(rate = 10) for i in range(5)]

# Construct joint distributions
joint0 = tfd.JointDistributionSequential(poises0)

N = int(1e6)
samples0 = joint0.sample(N)

class Model(object):
  def __init__(self):
     self.mus = [tf.Variable(10*np.ones(N, dtype='float32'), name='mu{0}'.format(i),
                    constraint=lambda x: tf.clip_by_value(x, 0.000001, np.infty)) for i in range(5)]

  def loss(self):
     poises_free = [tfd.Poisson(rate = self.mus[i]) for i in range(5)]
     joint_free = tfd.JointDistributionSequential(poises_free)
     # Construct (half of) test statistic
     self.qM = -2*(joint_free.log_prob(samples0))
     self.last_loss = tf.math.reduce_sum(self.qM,axis=0)
     return self.last_loss

model = Model()

# Minimise
tol = 0.01 * N
delta_loss = 1e99
prev_loss = 1e99
i = 0
print("tol:", tol)
while delta_loss > tol:
    opt = tf.optimizers.SGD(0.1).minimize(model.loss,var_list=model.mus)
    delta_loss = np.abs(prev_loss - model.last_loss)
    print("i:", i," delta_loss:", delta_loss)
    i+=1
    prev_loss = model.last_loss

q0 =-2*joint0.log_prob(samples0)
q = q0 - model.qM

print("parameters:", model.mus)
print("loss:", model.last_loss)
print("q0:", q0)
print("qM:", model.qM)

fig = plt.figure()
ax = fig.add_subplot(111)
sns.distplot(q, kde=False, ax=ax, norm_hist=True)
qx = np.linspace(np.min(q),np.max(q),1000)
qy = np.exp(tfd.Chi2(df=5).log_prob(qx))
sns.lineplot(qx,qy)
plt.show()

    Output:

    tol: 10000.0
i: 0  delta_loss: inf
i: 1  delta_loss: 197840.0
i: 2  delta_loss: 189366.0
i: 3  delta_loss: 181456.0
i: 4  delta_loss: 174040.0
i: 5  delta_loss: 167042.0
i: 6  delta_loss: 160448.0
i: 7  delta_loss: 154216.0
i: 8  delta_loss: 148310.0
i: 9  delta_loss: 142696.0
i: 10  delta_loss: 137352.0
i: 11  delta_loss: 132268.0
i: 12  delta_loss: 127404.0
...
i: 69  delta_loss: 11894.0
i: 70  delta_loss: 11344.0
i: 71  delta_loss: 10824.0
i: 72  delta_loss: 10318.0
i: 73  delta_loss: 9860.0
parameters: [<tf.Variable 'mu0:0' shape=(1000000,) dtype=float32, numpy=
array([ 6.5849004, 14.81182  ,  7.506216 , ..., 10.       , 11.491933 ,
       10.760278 ], dtype=float32)>, <tf.Variable 'mu1:0' shape=(1000000,) dtype=float32, numpy=
array([12.881036,  7.506216, 12.881036, ...,  7.506216, 14.186232,
       10.760278], dtype=float32)>, <tf.Variable 'mu2:0' shape=(1000000,) dtype=float32, numpy=
array([16.01586  ,  8.378036 , 12.198007 , ...,  6.5849004, 12.198007 ,
        8.378036 ], dtype=float32)>, <tf.Variable 'mu3:0' shape=(1000000,) dtype=float32, numpy=
array([10.      ,  7.506216, 12.198007, ...,  9.207426, 10.760278,
       11.491933], dtype=float32)>, <tf.Variable 'mu4:0' shape=(1000000,) dtype=float32, numpy=
array([ 8.378036 , 14.81182  , 10.       , ...,  6.5849004, 12.198007 ,
       10.760278 ], dtype=float32)>]
loss: tf.Tensor(20760090.0, shape=(), dtype=float32)
q0: tf.Tensor([31.144037 31.440613 25.355555 ... 24.183338 27.195362 22.123463], shape=(1000000,), dtype=float32)
qM: tf.Tensor([21.74377  21.64162  21.526024 ... 19.488544 22.40428  21.08519 ], shape=(1000000,), dtype=float32)

    Result is now chi-squared DOF=5! Or at least pretty close. enter image description here