# Faster sampling with unused parameters included in model

Hi,

So I have been working with estimation of a linear time varying parameter system (details not necessary for following question). The test case I am exploring is a relatively simple hidden markov model. The really odd thing is that when I include two additional parameters that are completely unused by the model sampling happens about 5 times faster (or more). I discovered this by accident when I was updating how I was defining the noise and accidentally left in these parameters.

The model without the extra parameters:

``````functions{
real matrix_normal_lpdf(matrix y, matrix mu, matrix LSigma){
int pdims = dims(y);
matrix[pdims,pdims] error_sc = mdivide_left_tri_low(LSigma, y - mu);
real p1 = -0.5*pdims*(pdims*log(2*pi()) + 2*sum(log(diagonal(LSigma))));
real p2 = -0.5*sum(error_sc .* error_sc);
return p1+p2;

}
}

data {
int<lower=0> N;
row_vector[N] u;
row_vector[N] y;
real x0;
real<lower=1e-8> P0_diag;
matrix[2, N] p;
matrix[2, N] q;
}

parameters {
row_vector[N+1] x;
row_vector A;
row_vector B;
row_vector C;
row_vector D;
cholesky_factor_cov LPI;

}

transformed parameters {
row_vector[N] mu;
row_vector[N] mu_y;
matrix[2, N] mu_c;
// TODO: Actually implement a kronecker product in stan
mu = (A * p) .* x[1:N] + (B * q) .* u;
mu_y = (C * p) .* x[1:N] + (D * q) .* u;

// combine
mu_c[1, :] = mu;
mu_c[2, :] = mu_y;
}

model {
// initial state prior
x ~ normal(x0, P0_diag);      //

// combined distribution
target += matrix_normal_lpdf(append_row(x[2:N+1],y) | mu_c, LPI);
}
generated quantities {
cov_matrix PI;
row_vector[N] yhat;
PI = LPI * LPI';
yhat = mu_y + normal_rng(0, sqrt(PI[2,2]));
}

``````

The model with the two additional unused parameters

``````functions{
real matrix_normal_lpdf(matrix y, matrix mu, matrix LSigma){
int pdims = dims(y);
matrix[pdims,pdims] error_sc = mdivide_left_tri_low(LSigma, y - mu);
real p1 = -0.5*pdims*(pdims*log(2*pi()) + 2*sum(log(diagonal(LSigma))));
real p2 = -0.5*sum(error_sc .* error_sc);
return p1+p2;

}
}

data {
int<lower=0> N;
row_vector[N] u;
row_vector[N] y;
real x0;
real<lower=1e-8> P0_diag;
matrix[2, N] p;
matrix[2, N] q;
}

parameters {
row_vector[N+1] x;
row_vector A;
row_vector B;
row_vector C;
row_vector D;
real<lower=1e-8> sigma_v;
real<lower=1e-8> sigma_w;
cholesky_factor_cov LPI;

}

transformed parameters {
row_vector[N] mu;
row_vector[N] mu_y;
matrix[2, N] mu_c;
// TODO: Actually implement a kronecker product in stan
mu = (A * p) .* x[1:N] + (B * q) .* u;
mu_y = (C * p) .* x[1:N] + (D * q) .* u;

// combine
mu_c[1, :] = mu;
mu_c[2, :] = mu_y;
}

model {
// initial state prior
x ~ normal(x0, P0_diag);      //

// combined distribution
target += matrix_normal_lpdf(append_row(x[2:N+1],y) | mu_c, LPI);
}
generated quantities {
cov_matrix PI;
row_vector[N] yhat;
PI = LPI * LPI';
yhat = mu_y + normal_rng(0, sqrt(PI[2,2]));
}

``````

I have been using the same data as well as initializing all chains to the true values to keep results as consistent as possible. I have also experimented with placing various priors on the covariance matrix (including transforming it and using the LKJ prior) with the same result in all cases. In all cases the resulting estimates look good.

Since I’m not sure how to upload my data (saving it using json as a .data file) I will include a short python script below that generates the data and the initial values.

``````import numpy as np
import matplotlib.pyplot as plt
import scipy.linalg as linalg
import json
import pandas as pd

N = 100    # Number of data samples

nx = 1      # state dim
nu = 1      # input dim
ny = 1      # output dim
nv = 2      # time varying signal size??

# true system
A1 = 0.9
B1 = 1
C1 = 0.5
D1 = 0

A2 = 0.6
B2 = 1
C2 = 0.7
D2 = 0

A = np.hstack([A1, A2])
B = np.hstack([B1, B2])
C = np.hstack([C1, C2])
D = np.hstack([D1, D2])
# Q = np.eye(nx) / 10
# R = np.eye(ny) / 10
Q = np.eye(nx) / 10
R = np.eye(ny) / 10

# exo signals
u = np.random.randn(nu,N)
p = (np.sin(2*np.pi*np.linspace(0,3,N))+1)/2
p = np.vstack([p, 1-p])
q = p

w = linalg.sqrtm(Q)*np.random.randn(nx,N)
v = linalg.sqrtm(R)*np.random.randn(ny,N)

x = np.zeros((nx, N+1))
y = np.zeros((ny, N))
y_test = np.zeros((ny, N))

for k in range(N):
x[:, k+1] = A @ np.kron(p[:, k], x[:, k]) + B @ np.kron(q[:, k], u[:, k]) + w[:, k]
y[:, k] = C @ np.kron(p[:, k], x[:, k]) + D @ np.kron(q[:, k], u[:, k]) + v[:, k]

PI = np.array([[Q[0,0], 0],[0, R[0,0]]])
# uncomment below stuff to include initialisation
stan_init = {
'x':x.flatten().tolist(),
'A':A.tolist(),
'B':B.tolist(),
'D':D.tolist(),
'C':C.tolist(),
'LPI': linalg.cholesky(PI).tolist()
}

with open('models/lpv_init.json', 'w') as outfile:
json.dump(stan_init, outfile)

# save data for inference in stan
stan_data = {
'N': int(N),
'u': u.flatten().tolist(),
'y': y.flatten().tolist(),
'x0': 0.0,
'P0_diag':0.01,
'p':p.tolist(),
'q':q.tolist(),
}

with open('models/lpv_v01.data.json', 'w') as outfile:
json.dump(stan_data, outfile)
``````

This behavior seems somewhat confusing, my only guess is that the extra parameters somehow regulate the manifold that it is sampling from.

2 Likes

I haven’t looked into the details of your model, but one possibility is that your additional parameters are triggering the no-U-turn criterion before the rest of the parameters would otherwise trigger it. If that’s what’s happening, then you should see two things:

1. Even if the model finishes faster, it should yield lower effective sample sizes for some of the parameters that are common to both models. Perhaps much lower, such that the ESS per second is similar or even worse in the model that appears to sample faster.
2. Larger treedepths in the slower model.

Edit: You might also see a lower energy fraction of missing information in the model that seems to go faster.

Edit2: These same observations could also result if the new parameters are affecting the warmup routine such that it lands on a larger adapted step-size. You can check the step-size directly to see whether this might be contributing.

Edit3: Wait, I just realized these additional parameters aren’t even given a prior. Whatever is happening, it can’t be good. The posterior is improper.

1 Like

I was a bit intrigued by this, so I just played around a bit.

Using `cmdstan` via `cmdstanr`, I started with the following model:

``````parameters {
real y;
real z;
}
model {
y ~ std_normal();
}
``````

This is relatively slow and produced a bunch of treedepth warnings. But then I tried:

``````parameters {
real y;
real<lower = 0> z;
}

model {
y ~ std_normal();
}
``````

This is very “fast” but only because most iterations yield divergences. So I think that’s the answer. The “fast” sampling is an illusion caused by most of your Hamiltonian trajectories terminating prematurely in divergences. Thinking about the Jacobian term and why it leads to divergences for the lower-bounded case is a useful exercise :)

3 Likes

Thank you very much for this helpful insight. I have only recently changed from using PyStan 2 to cmdstan (I didn’t like pystan 3). I was used to getting a handy little warning about divergent chains from pystan 2 and had forgot to check it in cmdstan.

2 Likes