Introduction to Turing

Introduction

This is the first of a series of tutorials on the universal probabilistic programming language Turing.

Turing is a probabilistic programming system written entirely in Julia. It has an intuitive modelling syntax and supports a wide range of sampling-based inference algorithms.

Familiarity with Julia is assumed throughout this tutorial. If you are new to Julia, Learning Julia is a good starting point.

For users new to Bayesian machine learning, please consider more thorough introductions to the field such as Pattern Recognition and Machine Learning. This tutorial tries to provide an intuition for Bayesian inference and gives a simple example on how to use Turing. Note that this is not a comprehensive introduction to Bayesian machine learning.

Coin Flipping Without Turing

The following example illustrates the effect of updating our beliefs with every piece of new evidence we observe.

Assume that we are unsure about the probability of heads in a coin flip. To get an intuitive understanding of what "updating our beliefs" is, we will visualize the probability of heads in a coin flip after each observed evidence.

First, let us load some packages that we need to simulate a coin flip

using Distributions

using Random
Random.seed!(12); # Set seed for reproducibility

and to visualize our results.

using StatsPlots

Note that Turing is not loaded here — we do not use it in this example. If you are already familiar with posterior updates, you can proceed to the next step.

Next, we configure the data generating model. Let us set the true probability that a coin flip turns up heads

p_true = 0.5;

and set the number of coin flips we will show our model.

N = 100;

We simulate N coin flips by drawing N random samples from the Bernoulli distribution with success probability p_true. The draws are collected in a variable called data:

data = rand(Bernoulli(p_true), N);

Here is what the first five coin flips look like:

data[1:5]

5-element Vector{Bool}:
 1
 0
 0
 1
 1

Next, we specify a prior belief about the distribution of heads and tails in a coin toss. Here we choose a Beta distribution as prior distribution for the probability of heads. Before any coin flip is observed, we assume a uniform distribution $\operatorname{U}(0, 1) = \operatorname{Beta}(1, 1)$ of the probability of heads. I.e., every probability is equally likely initially.

prior_belief = Beta(1, 1);

With our priors set and our data at hand, we can perform Bayesian inference.

This is a fairly simple process. We expose one additional coin flip to our model every iteration, such that the first run only sees the first coin flip, while the last iteration sees all the coin flips. In each iteration we update our belief to an updated version of the original Beta distribution that accounts for the new proportion of heads and tails. The update is particularly simple since our prior distribution is a conjugate prior. Note that a closed-form expression for the posterior (implemented in the updated_belief expression below) is not accessible in general and usually does not exist for more interesting models.

function updated_belief(prior_belief::Beta, data::AbstractArray{Bool})
    # Count the number of heads and tails.
    heads = sum(data)
    tails = length(data) - heads

    # Update our prior belief in closed form (this is possible because we use a conjugate prior).
    return Beta(prior_belief.α + heads, prior_belief.β + tails)
end

# Show updated belief for increasing number of observations
@gif for n in 0:N
    plot(
        updated_belief(prior_belief, data[1:n]);
        size=(500, 250),
        title="Updated belief after $n observations",
        xlabel="probability of heads",
        ylabel="",
        legend=nothing,
        xlim=(0, 1),
        fill=0,
        α=0.3,
        w=3,
    )
    vline!([p_true])
end

The animation above shows that with increasing evidence our belief about the probability of heads in a coin flip slowly adjusts towards the true value. The orange line in the animation represents the true probability of seeing heads on a single coin flip, while the mode of the distribution shows what the model believes the probability of a heads is given the evidence it has seen.

For the mathematically inclined, the $\operatorname{Beta}$ distribution is updated by adding each coin flip to the parameters $\alpha$ and $\beta$ of the distribution. Initially, the parameters are defined as $\alpha = 1$ and $\beta = 1$. Over time, with more and more coin flips, $\alpha$ and $\beta$ will be approximately equal to each other as we are equally likely to flip a heads or a tails.

The mean of the $\operatorname{Beta}(\alpha, \beta)$ distribution is

$$\operatorname{E}[X] = \dfrac{\alpha}{\alpha+\beta}.$$

This implies that the plot of the distribution will become centered around 0.5 for a large enough number of coin flips, as we expect $\alpha \approx \beta$.

The variance of the $\operatorname{Beta}(\alpha, \beta)$ distribution is

$$\operatorname{var}[X] = \dfrac{\alpha\beta}{(\alpha + \beta)^2 (\alpha + \beta + 1)}.$$

Thus the variance of the distribution will approach 0 with more and more samples, as the denominator will grow faster than will the numerator. More samples means less variance. This implies that the distribution will reflect less uncertainty about the probability of receiving a heads and the plot will become more tightly centered around 0.5 for a large enough number of coin flips.

Coin Flipping With Turing

We now move away from the closed-form expression above. We use Turing to specify the same model and to approximate the posterior distribution with samples. To do so, we first need to load Turing.

using Turing

Additionally, we load MCMCChains, a library for analyzing and visualizing the samples with which we approximate the posterior distribution.

using MCMCChains

First, we define the coin-flip model using Turing.

# Unconditioned coinflip model with `N` observations.
@model function coinflip(; N::Int)
    # Our prior belief about the probability of heads in a coin toss.
    p ~ Beta(1, 1)

    # Heads or tails of a coin are drawn from `N` independent and identically
    # distributed Bernoulli distributions with success rate `p`.
    y ~ filldist(Bernoulli(p), N)

    return y
end;

In the Turing model the prior distribution of the variable p, the probability of heads in a coin toss, and the distribution of the observations y are specified on the right-hand side of the ~ expressions. The @model macro modifies the body of the Julia function coinflip and, e.g., replaces the ~ statements with internal function calls that are used for sampling.

Here we defined a model that is not conditioned on any specific observations as this allows us to easily obtain samples of both p and y with

rand(coinflip(; N))

(p = 0.6010770913516256, y = Bool[1, 1, 1, 0, 0, 1, 0, 0, 0, 0  …  1, 1, 1,
 0, 1, 0, 1, 1, 1, 1])

The model can be conditioned on some observations with |. See the documentation of the condition syntax in DynamicPPL.jl for more details. In the conditioned model the observations y are fixed to data.

coinflip(y::AbstractVector{<:Real}) = coinflip(; N=length(y)) | (; y)

model = coinflip(data);

After defining the model, we can approximate the posterior distribution by drawing samples from the distribution. In this example, we use a Hamiltonian Monte Carlo sampler to draw these samples. Other tutorials give more information on the samplers available in Turing and discuss their use for different models.

sampler = NUTS();

We approximate the posterior distribution with 1000 samples:

chain = sample(model, sampler, 1_000; progress=false);

The sample function and common keyword arguments are explained more extensively in the documentation of AbstractMCMC.jl.

After finishing the sampling process, we can visually compare the closed-form posterior distribution with the approximation obtained with Turing.

histogram(chain)

Now we can build our plot:

# Visualize a blue density plot of the approximate posterior distribution using HMC (see Chain 1 in the legend).
density(chain; xlim=(0, 1), legend=:best, w=2, c=:blue)

# Visualize a green density plot of the posterior distribution in closed-form.
plot!(
    0:0.01:1,
    pdf.(updated_belief(prior_belief, data), 0:0.01:1);
    xlabel="probability of heads",
    ylabel="",
    title="",
    xlim=(0, 1),
    label="Closed-form",
    fill=0,
    α=0.3,
    w=3,
    c=:lightgreen,
)

# Visualize the true probability of heads in red.
vline!([p_true]; label="True probability", c=:red)

As we can see, the samples obtained with Turing closely approximate the true posterior distribution. Hopefully this tutorial has provided an easy-to-follow, yet informative introduction to Turing's simpler applications. More advanced usage is demonstrated in other tutorials.

Appendix

These tutorials are a part of the TuringTutorials repository, found at: https://github.com/TuringLang/TuringTutorials.

To locally run this tutorial, do the following commands:

using TuringTutorials
TuringTutorials.weave("00-introduction", "00_introduction.jmd")

Computer Information:

Julia Version 1.9.3
Commit bed2cd540a1 (2023-08-24 14:43 UTC)
Build Info:
  Official https://julialang.org/ release
Platform Info:
  OS: Linux (x86_64-linux-gnu)
  CPU: 128 × AMD EPYC 7502 32-Core Processor
  WORD_SIZE: 64
  LIBM: libopenlibm
  LLVM: libLLVM-14.0.6 (ORCJIT, znver2)
  Threads: 1 on 16 virtual cores
Environment:
  JULIA_CPU_THREADS = 16
  JULIA_DEPOT_PATH = /cache/julia-buildkite-plugin/depots/7aa0085e-79a4-45f3-a5bd-9743c91cf3da

Package Information:

Status `/cache/build/default-amdci4-1/julialang/turingtutorials/tutorials/00-introduction/Project.toml`
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  [0ac62f75] libass_jll v0.15.1+0
  [2db6ffa8] libevdev_jll v1.11.0+0
  [f638f0a6] libfdk_aac_jll v2.0.2+0
  [36db933b] libinput_jll v1.18.0+0
  [b53b4c65] libpng_jll v1.6.38+0
  [f27f6e37] libvorbis_jll v1.3.7+1
  [009596ad] mtdev_jll v1.1.6+0
  [1270edf5] x264_jll v2021.5.5+0
  [dfaa095f] x265_jll v3.5.0+0
  [d8fb68d0] xkbcommon_jll v1.4.1+1
  [0dad84c5] ArgTools v1.1.1
  [56f22d72] Artifacts
  [2a0f44e3] Base64
  [ade2ca70] Dates
  [8ba89e20] Distributed
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching
  [9fa8497b] Future
  [b77e0a4c] InteractiveUtils
  [4af54fe1] LazyArtifacts
  [b27032c2] LibCURL v0.6.3
  [76f85450] LibGit2
  [8f399da3] Libdl
  [37e2e46d] LinearAlgebra
  [56ddb016] Logging
  [d6f4376e] Markdown
  [a63ad114] Mmap
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.9.2
  [de0858da] Printf
  [3fa0cd96] REPL
  [9a3f8284] Random
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization
  [1a1011a3] SharedArrays
  [6462fe0b] Sockets
  [2f01184e] SparseArrays
  [10745b16] Statistics v1.9.0
  [4607b0f0] SuiteSparse
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test
  [cf7118a7] UUIDs
  [4ec0a83e] Unicode
  [e66e0078] CompilerSupportLibraries_jll v1.0.5+0
  [deac9b47] LibCURL_jll v7.84.0+0
  [29816b5a] LibSSH2_jll v1.10.2+0
  [c8ffd9c3] MbedTLS_jll v2.28.2+0
  [14a3606d] MozillaCACerts_jll v2022.10.11
  [4536629a] OpenBLAS_jll v0.3.21+4
  [05823500] OpenLibm_jll v0.8.1+0
  [efcefdf7] PCRE2_jll v10.42.0+0
  [bea87d4a] SuiteSparse_jll v5.10.1+6
  [83775a58] Zlib_jll v1.2.13+0
  [8e850b90] libblastrampoline_jll v5.8.0+0
  [8e850ede] nghttp2_jll v1.48.0+0
  [3f19e933] p7zip_jll v17.4.0+0
Info Packages marked with ⌃ and ⌅ have new versions available, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`