Earlier than we leap into the technicalities: This put up is, after all, devoted to McElreath who wrote certainly one of most intriguing books on Bayesian (or ought to we simply say – scientific?) modeling we’re conscious of. In the event you haven’t learn Statistical Rethinking, and are keen on modeling, you would possibly undoubtedly wish to test it out. On this put up, we’re not going to attempt to re-tell the story: Our clear focus will, as a substitute, be an indication of find out how to do MCMC with tfprobability.

Concretely, this put up has two components. The primary is a fast overview of find out how to use tfd_joint_sequential_distribution to assemble a mannequin, after which pattern from it utilizing Hamiltonian Monte Carlo. This half could be consulted for fast code look-up, or as a frugal template of the entire course of.

The second half then walks by means of a multi-level mannequin in additional element, displaying find out how to extract, post-process and visualize sampling in addition to diagnostic outputs.

## Reedfrogs

The info comes with the `rethinking`

bundle.

```
'knowledge.body': 48 obs. of 5 variables:
$ density : int 10 10 10 10 10 10 10 10 10 10 ...
$ pred : Issue w/ 2 ranges "no","pred": 1 1 1 1 1 1 1 1 2 2 ...
$ measurement : Issue w/ 2 ranges "huge","small": 1 1 1 1 2 2 2 2 1 1 ...
$ surv : int 9 10 7 10 9 9 10 9 4 9 ...
$ propsurv: num 0.9 1 0.7 1 0.9 0.9 1 0.9 0.4 0.9 ...
```

The duty is modeling survivor counts amongst tadpoles, the place tadpoles are held in tanks of various sizes (equivalently, totally different numbers of inhabitants). Every row within the dataset describes one tank, with its preliminary rely of inhabitants (`density`

) and variety of survivors (`surv`

).

Within the technical overview half, we construct a easy unpooled mannequin that describes each tank in isolation. Then, within the detailed walk-through, we’ll see find out how to assemble a *various intercepts* mannequin that permits for info sharing between tanks.

## Setting up fashions with `tfd_joint_distribution_sequential`

`tfd_joint_distribution_sequential`

represents a mannequin as an inventory of conditional distributions.

That is best to see on an actual instance, so we’ll leap proper in, creating an unpooled mannequin of the tadpole knowledge.

That is the how the mannequin specification would look in *Stan*:

```
mannequin{
vector[48] p;
a ~ regular( 0 , 1.5 );
for ( i in 1:48 ) {
p[i] = a[tank[i]];
p[i] = inv_logit(p[i]);
}
S ~ binomial( N , p );
}
```

And right here is `tfd_joint_distribution_sequential`

:

```
library(tensorflow)
# be sure you have at the least model 0.7 of TensorFlow Likelihood
# as of this writing, it's required of set up the grasp department:
# install_tensorflow(model = "nightly")
library(tfprobability)
n_tadpole_tanks <- nrow(d)
n_surviving <- d$surv
n_start <- d$density
m1 <- tfd_joint_distribution_sequential(
list(
# regular prior of per-tank logits
tfd_multivariate_normal_diag(
loc = rep(0, n_tadpole_tanks),
scale_identity_multiplier = 1.5),
# binomial distribution of survival counts
operate(l)
tfd_independent(
tfd_binomial(total_count = n_start, logits = l),
reinterpreted_batch_ndims = 1
)
)
)
```

The mannequin consists of two distributions: Prior means and variances for the 48 tadpole tanks are specified by `tfd_multivariate_normal_diag`

; then `tfd_binomial`

generates survival counts for every tank.

Be aware how the primary distribution is unconditional, whereas the second depends upon the primary. Be aware too how the second needs to be wrapped in `tfd_independent`

to keep away from mistaken broadcasting. (That is a facet of `tfd_joint_distribution_sequential`

utilization that deserves to be documented extra systematically, which is definitely going to occur. Simply suppose that this performance was added to TFP `grasp`

solely three weeks in the past!)

As an apart, the mannequin specification right here finally ends up shorter than in *Stan* as `tfd_binomial`

optionally takes logits as parameters.

As with each TFP distribution, you are able to do a fast performance test by sampling from the mannequin:

```
# pattern a batch of two values
# we get samples for each distribution within the mannequin
s <- m1 %>% tfd_sample(2)
```

```
[[1]]
Tensor("MultivariateNormalDiag/pattern/affine_linear_operator/ahead/add:0",
form=(2, 48), dtype=float32)
[[2]]
Tensor("IndependentJointDistributionSequential/pattern/Beta/pattern/Reshape:0",
form=(2, 48), dtype=float32)
```

and computing log possibilities:

```
# we must always get solely the general log likelihood of the mannequin
m1 %>% tfd_log_prob(s)
```

```
t[[1]]
Tensor("MultivariateNormalDiag/pattern/affine_linear_operator/ahead/add:0",
form=(2, 48), dtype=float32)
[[2]]
Tensor("IndependentJointDistributionSequential/pattern/Beta/pattern/Reshape:0",
form=(2, 48), dtype=float32)
```

Now, let’s see how we are able to pattern from this mannequin utilizing Hamiltonian Monte Carlo.

## Working Hamiltonian Monte Carlo in TFP

We outline a Hamiltonian Monte Carlo kernel with dynamic step measurement adaptation primarily based on a desired acceptance likelihood.

```
# variety of steps to run burnin
n_burnin <- 500
# optimization goal is the chance of the logits given the information
logprob <- operate(l)
m1 %>% tfd_log_prob(list(l, n_surviving))
hmc <- mcmc_hamiltonian_monte_carlo(
target_log_prob_fn = logprob,
num_leapfrog_steps = 3,
step_size = 0.1,
) %>%
mcmc_simple_step_size_adaptation(
target_accept_prob = 0.8,
num_adaptation_steps = n_burnin
)
```

We then run the sampler, passing in an preliminary state. If we wish to run (n) chains, that state needs to be of size (n), for each parameter within the mannequin (right here we’ve only one).

The sampling operate, mcmc_sample_chain, might optionally be handed a `trace_fn`

that tells TFP which sorts of meta info to avoid wasting. Right here we save acceptance ratios and step sizes.

```
# variety of steps after burnin
n_steps <- 500
# variety of chains
n_chain <- 4
# get beginning values for the parameters
# their form implicitly determines the variety of chains we'll run
# see current_state parameter handed to mcmc_sample_chain beneath
c(initial_logits, .) %<-% (m1 %>% tfd_sample(n_chain))
# inform TFP to maintain observe of acceptance ratio and step measurement
trace_fn <- operate(state, pkr) {
list(pkr$inner_results$is_accepted,
pkr$inner_results$accepted_results$step_size)
}
res <- hmc %>% mcmc_sample_chain(
num_results = n_steps,
num_burnin_steps = n_burnin,
current_state = initial_logits,
trace_fn = trace_fn
)
```

When sampling is completed, we are able to entry the samples as `res$all_states`

:

```
mcmc_trace <- res$all_states
mcmc_trace
```

```
Tensor("mcmc_sample_chain/trace_scan/TensorArrayStack/TensorArrayGatherV3:0",
form=(500, 4, 48), dtype=float32)
```

That is the form of the samples for `l`

, the 48 per-tank logits: 500 samples occasions 4 chains occasions 48 parameters.

From these samples, we are able to compute efficient pattern measurement and (rhat) (alias `mcmc_potential_scale_reduction`

):

```
# Tensor("Imply:0", form=(48,), dtype=float32)
ess <- mcmc_effective_sample_size(mcmc_trace) %>% tf$reduce_mean(axis = 0L)
# Tensor("potential_scale_reduction/potential_scale_reduction_single_state/sub_1:0", form=(48,), dtype=float32)
rhat <- mcmc_potential_scale_reduction(mcmc_trace)
```

Whereas diagnostic info is accessible in `res$hint`

:

```
# Tensor("mcmc_sample_chain/trace_scan/TensorArrayStack_1/TensorArrayGatherV3:0",
# form=(500, 4), dtype=bool)
is_accepted <- res$hint[[1]]
# Tensor("mcmc_sample_chain/trace_scan/TensorArrayStack_2/TensorArrayGatherV3:0",
# form=(500,), dtype=float32)
step_size <- res$hint[[2]]
```

After this fast define, let’s transfer on to the subject promised within the title: multi-level modeling, or partial pooling. This time, we’ll additionally take a better have a look at sampling outcomes and diagnostic outputs.

## Multi-level tadpoles

The multi-level mannequin – or *various intercepts mannequin*, on this case: we’ll get to *various slopes* in a later put up – provides a *hyperprior* to the mannequin. As an alternative of deciding on a imply and variance of the traditional prior the logits are drawn from, we let the mannequin study means and variances for particular person tanks.

These per-tank means, whereas being priors for the binomial logits, are assumed to be usually distributed, and are themselves regularized by a traditional prior for the imply and an exponential prior for the variance.

For the Stan-savvy, right here is the Stan formulation of this mannequin.

```
list(
# a_bar, the prior for the imply of the traditional distribution of per-tank logits
tfd_normal(loc = 0, scale = 1.5),
# sigma, the prior for the variance of the traditional distribution of per-tank logits
tfd_exponential(price = 1),
# regular distribution of per-tank logits
# parameters sigma and a_bar check with the outputs of the above two distributions
operate(sigma, a_bar)
tfd_sample_distribution(
tfd_normal(loc = a_bar, scale = sigma),
sample_shape = list(n_tadpole_tanks)
),
# binomial distribution of survival counts
# parameter l refers back to the output of the traditional distribution instantly above
operate(l)
tfd_independent(
tfd_binomial(total_count = n_start, logits = l),
reinterpreted_batch_ndims = 1
)
)
)
```

Technically, dependencies in `tfd_joint_distribution_sequential`

are outlined through spatial proximity within the checklist: Within the realized prior for the logits

```
operate(sigma, a_bar)
tfd_sample_distribution(
tfd_normal(loc = a_bar, scale = sigma),
sample_shape = list(n_tadpole_tanks)
)
```

`sigma`

refers back to the distribution instantly above, and `a_bar`

to the one above that.

Analogously, within the distribution of survival counts

```
operate(l)
tfd_independent(
tfd_binomial(total_count = n_start, logits = l),
reinterpreted_batch_ndims = 1
)
```

`l`

refers back to the distribution instantly previous its personal definition.

Once more, let’s pattern from this mannequin to see if shapes are appropriate.

```
s <- m2 %>% tfd_sample(2)
s
```

They’re.

```
[[1]]
Tensor("Regular/sample_1/Reshape:0", form=(2,), dtype=float32)
[[2]]
Tensor("Exponential/sample_1/Reshape:0", form=(2,), dtype=float32)
[[3]]
Tensor("SampleJointDistributionSequential/sample_1/Regular/pattern/Reshape:0",
form=(2, 48), dtype=float32)
[[4]]
Tensor("IndependentJointDistributionSequential/sample_1/Beta/pattern/Reshape:0",
form=(2, 48), dtype=float32)
```

And to ensure we get one total `log_prob`

per batch:

`Tensor("JointDistributionSequential/log_prob/add_3:0", form=(2,), dtype=float32)`

Coaching this mannequin works like earlier than, besides that now the preliminary state includes three parameters, *a_bar*, *sigma* and *l*:

`c(initial_a, initial_s, initial_logits, .) %<-% (m2 %>% tfd_sample(n_chain))`

Right here is the sampling routine:

```
# the joint log likelihood now's primarily based on three parameters
logprob <- operate(a, s, l)
m2 %>% tfd_log_prob(list(a, s, l, n_surviving))
hmc <- mcmc_hamiltonian_monte_carlo(
target_log_prob_fn = logprob,
num_leapfrog_steps = 3,
# one step measurement for every parameter
step_size = list(0.1, 0.1, 0.1),
) %>%
mcmc_simple_step_size_adaptation(target_accept_prob = 0.8,
num_adaptation_steps = n_burnin)
run_mcmc <- operate(kernel) {
kernel %>% mcmc_sample_chain(
num_results = n_steps,
num_burnin_steps = n_burnin,
current_state = list(initial_a, tf$ones_like(initial_s), initial_logits),
trace_fn = trace_fn
)
}
res <- hmc %>% run_mcmc()
mcmc_trace <- res$all_states
```

This time, `mcmc_trace`

is an inventory of three: We’ve got

```
[[1]]
Tensor("mcmc_sample_chain/trace_scan/TensorArrayStack/TensorArrayGatherV3:0",
form=(500, 4), dtype=float32)
[[2]]
Tensor("mcmc_sample_chain/trace_scan/TensorArrayStack_1/TensorArrayGatherV3:0",
form=(500, 4), dtype=float32)
[[3]]
Tensor("mcmc_sample_chain/trace_scan/TensorArrayStack_2/TensorArrayGatherV3:0",
form=(500, 4, 48), dtype=float32)
```

Now let’s create graph nodes for the outcomes and knowledge we’re keen on.

```
# as above, that is the uncooked end result
mcmc_trace_ <- res$all_states
# we carry out some reshaping operations immediately in tensorflow
all_samples_ <-
tf$concat(
list(
mcmc_trace_[[1]] %>% tf$expand_dims(axis = -1L),
mcmc_trace_[[2]] %>% tf$expand_dims(axis = -1L),
mcmc_trace_[[3]]
),
axis = -1L
) %>%
tf$reshape(list(2000L, 50L))
# diagnostics, additionally as above
is_accepted_ <- res$hint[[1]]
step_size_ <- res$hint[[2]]
# efficient pattern measurement
# once more we use tensorflow to get conveniently formed outputs
ess_ <- mcmc_effective_sample_size(mcmc_trace)
ess_ <- tf$concat(
list(
ess_[[1]] %>% tf$expand_dims(axis = -1L),
ess_[[2]] %>% tf$expand_dims(axis = -1L),
ess_[[3]]
),
axis = -1L
)
# rhat, conveniently post-processed
rhat_ <- mcmc_potential_scale_reduction(mcmc_trace)
rhat_ <- tf$concat(
list(
rhat_[[1]] %>% tf$expand_dims(axis = -1L),
rhat_[[2]] %>% tf$expand_dims(axis = -1L),
rhat_[[3]]
),
axis = -1L
)
```

And we’re prepared to truly run the chains.

```
# to this point, no sampling has been performed!
# the precise sampling occurs after we create a Session
# and run the above-defined nodes
sess <- tf$Session()
eval <- operate(...) sess$run(list(...))
c(mcmc_trace, all_samples, is_accepted, step_size, ess, rhat) %<-%
eval(mcmc_trace_, all_samples_, is_accepted_, step_size_, ess_, rhat_)
```

This time, let’s truly examine these outcomes.

## Multi-level tadpoles: Outcomes

First, how do the chains behave?

### Hint plots

Extract the samples for `a_bar`

and `sigma`

, in addition to one of many realized priors for the logits:

Right here’s a hint plot for `a_bar`

:

```
prep_tibble <- operate(samples) {
as_tibble(samples, .name_repair = ~ c("chain_1", "chain_2", "chain_3", "chain_4")) %>%
add_column(pattern = 1:500) %>%
collect(key = "chain", worth = "worth", -pattern)
}
plot_trace <- operate(samples, param_name) {
prep_tibble(samples) %>%
ggplot(aes(x = pattern, y = worth, coloration = chain)) +
geom_line() +
ggtitle(param_name)
}
plot_trace(a_bar, "a_bar")
```

And right here for `sigma`

and `a_1`

:

How in regards to the posterior distributions of the parameters, before everything, the various intercepts `a_1`

… `a_48`

?

### Posterior distributions

```
plot_posterior <- operate(samples) {
prep_tibble(samples) %>%
ggplot(aes(x = worth, coloration = chain)) +
geom_density() +
theme_classic() +
theme(legend.place = "none",
axis.title = element_blank(),
axis.textual content = element_blank(),
axis.ticks = element_blank())
}
plot_posteriors <- operate(sample_array, num_params) {
plots <- purrr::map(1:num_params, ~ plot_posterior(sample_array[ , , .x] %>% as.matrix()))
do.call(grid.organize, plots)
}
plot_posteriors(mcmc_trace[[3]], dim(mcmc_trace[[3]])[3])
```

Now let’s see the corresponding posterior means and highest posterior density intervals.

(The beneath code consists of the hyperpriors in `abstract`

as we’ll wish to show a whole *summary*-like output quickly.)

### Posterior means and HPDIs

```
all_samples <- all_samples %>%
as_tibble(.name_repair = ~ c("a_bar", "sigma", paste0("a_", 1:48)))
means <- all_samples %>%
summarise_all(list (~ imply)) %>%
collect(key = "key", worth = "imply")
sds <- all_samples %>%
summarise_all(list (~ sd)) %>%
collect(key = "key", worth = "sd")
hpdis <-
all_samples %>%
summarise_all(list(~ list(hdi(.) %>% t() %>% as_tibble()))) %>%
unnest()
hpdis_lower <- hpdis %>% choose(-accommodates("higher")) %>%
rename(lower0 = decrease) %>%
collect(key = "key", worth = "decrease") %>%
organize(as.integer(str_sub(key, 6))) %>%
mutate(key = c("a_bar", "sigma", paste0("a_", 1:48)))
hpdis_upper <- hpdis %>% choose(-accommodates("decrease")) %>%
rename(upper0 = higher) %>%
collect(key = "key", worth = "higher") %>%
organize(as.integer(str_sub(key, 6))) %>%
mutate(key = c("a_bar", "sigma", paste0("a_", 1:48)))
abstract <- means %>%
inner_join(sds, by = "key") %>%
inner_join(hpdis_lower, by = "key") %>%
inner_join(hpdis_upper, by = "key")
abstract %>%
filter(!key %in% c("a_bar", "sigma")) %>%
mutate(key_fct = factor(key, ranges = unique(key))) %>%
ggplot(aes(x = key_fct, y = imply, ymin = decrease, ymax = higher)) +
geom_pointrange() +
coord_flip() +
xlab("") + ylab("put up. imply and HPDI") +
theme_minimal()
```

Now for an equal to *summary*. We already computed means, customary deviations and the HPDI interval.

Let’s add *n_eff*, the efficient variety of samples, and *rhat*, the Gelman-Rubin statistic.

### Complete abstract (a.okay.a. “summary”)

```
is_accepted <- is_accepted %>% as.integer() %>% mean()
step_size <- purrr::map(step_size, imply)
ess <- apply(ess, 2, imply)
summary_with_diag <- abstract %>% add_column(ess = ess, rhat = rhat)
summary_with_diag
```

```
# A tibble: 50 x 7
key imply sd decrease higher ess rhat
<chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 a_bar 1.35 0.266 0.792 1.87 405. 1.00
2 sigma 1.64 0.218 1.23 2.05 83.6 1.00
3 a_1 2.14 0.887 0.451 3.92 33.5 1.04
4 a_2 3.16 1.13 1.09 5.48 23.7 1.03
5 a_3 1.01 0.698 -0.333 2.31 65.2 1.02
6 a_4 3.02 1.04 1.06 5.05 31.1 1.03
7 a_5 2.11 0.843 0.625 3.88 49.0 1.05
8 a_6 2.06 0.904 0.496 3.87 39.8 1.03
9 a_7 3.20 1.27 1.11 6.12 14.2 1.02
10 a_8 2.21 0.894 0.623 4.18 44.7 1.04
# ... with 40 extra rows
```

For the various intercepts, efficient pattern sizes are fairly low, indicating we’d wish to examine doable causes.

Let’s additionally show posterior survival possibilities, analogously to determine 13.2 within the ebook.

### Posterior survival possibilities

```
sim_tanks <- rnorm(8000, a_bar, sigma)
tibble(x = sim_tanks) %>% ggplot(aes(x = x)) + geom_density() + xlab("distribution of per-tank logits")
```

```
# our common sigmoid by one other title (undo the logit)
logistic <- operate(x) 1/(1 + exp(-x))
probs <- map_dbl(sim_tanks, logistic)
tibble(x = probs) %>% ggplot(aes(x = x)) + geom_density() + xlab("likelihood of survival")
```

Lastly, we wish to be sure that we see the shrinkage conduct displayed in determine 13.1 within the ebook.

### Shrinkage

```
abstract %>%
filter(!key %in% c("a_bar", "sigma")) %>%
choose(key, imply) %>%
mutate(est_survival = logistic(imply)) %>%
add_column(act_survival = d$propsurv) %>%
choose(-imply) %>%
collect(key = "kind", worth = "worth", -key) %>%
ggplot(aes(x = key, y = worth, coloration = kind)) +
geom_point() +
geom_hline(yintercept = mean(d$propsurv), measurement = 0.5, coloration = "cyan" ) +
xlab("") +
ylab("") +
theme_minimal() +
theme(axis.textual content.x = element_blank())
```

We see outcomes comparable in spirit to McElreath’s: estimates are shrunken to the imply (the cyan-colored line). Additionally, shrinkage appears to be extra lively in smaller tanks, that are the lower-numbered ones on the left of the plot.

## Outlook

On this put up, we noticed find out how to assemble a *various intercepts* mannequin with `tfprobability`

, in addition to find out how to extract sampling outcomes and related diagnostics. In an upcoming put up, we’ll transfer on to *various slopes*.

With non-negligible likelihood, our instance will construct on certainly one of Mc Elreath’s once more…

Thanks for studying!