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# Bijectors.jl

This package implements a set of functions for transforming constrained random variables (e.g. simplexes, intervals) to Euclidean space. The 3 main functions implemented in this package are the `link`julia-observer-quote-cut-paste-269_work`julia-observer-quote-cut-paste-1work`julia-observer-quote-cut-paste-255work`julia-observer-quote-cut-paste-2_work` for a number of distributions. The distributions supported are:

1. `RealDistribution`: `Union{Cauchy, Gumbel, Laplace, Logistic, NoncentralT, Normal, NormalCanon, TDist}`,
2. `PositiveDistribution`: `Union{BetaPrime, Chi, Chisq, Erlang, Exponential, FDist, Frechet, Gamma, InverseGamma, InverseGaussian, Kolmogorov, LogNormal, NoncentralChisq, NoncentralF, Rayleigh, Weibull}`,
3. `UnitDistribution`: `Union{Beta, KSOneSided, NoncentralBeta}`,
4. `SimplexDistribution`: `Union{Dirichlet}`,
5. `PDMatDistribution`: `Union{InverseWishart, Wishart}`, and
6. `TransformDistribution`: `Union{T, Truncated{T}} where T<:ContinuousUnivariateDistribution`.

All exported names from the Distributions.jl package are reexported from `Bijectors`.

Bijectors.jl also provides a nice interface for working with these maps: composition, inversion, etc. The following table lists mathematical operations for a bijector and the corresponding code in Bijectors.jl.

Operation Method Automatic
`b ↦ b⁻¹` `inv(b)`
`(b₁, b₂) ↦ (b₁ ∘ b₂)` `b₁ ∘ b₂`
`(b₁, b₂) ↦ [b₁, b₂]` `stack(b₁, b₂)`
`x ↦ b(x)` `b(x)` ×
`y ↦ b⁻¹(y)` `inv(b)(y)` ×
`x ↦ log｜det J(b, x)｜` `logabsdetjac(b, x)` AD
`x ↦ b(x), log｜det J(b, x)｜` `forward(b, x)`
`p ↦ q := b_* p` `q = transformed(p, b)`
`y ∼ q` `y = rand(q)`
`p ↦ b` such that `support(b_* p) = ℝᵈ` `bijector(p)`
`(x ∼ p, b(x), log｜det J(b, x)｜, log q(y))` `forward(q)`

In this table, `b` denotes a `Bijector`julia-observer-quote-cut-paste-270_work`julia-observer-quote-cut-paste-41work`denotes the jacobian of`julia-observer-quote-cut-paste-42work`evaluated at`julia-observer-quote-cut-paste-43work`julia-observer-quote-cut-paste-287work`julia-observer-quote-cut-paste-44work`denotes the [push-forward](https://www.wikiwand.com/en/Pushforward_measure) of`julia-observer-quote-cut-paste-45work`by`julia-observer-quote-cut-paste-46work`, and`julia-observer-quote-cut-paste-47work`denotes`julia-observer-quote-cut-paste-48work`sampled from the distribution with density`julia-observer-quote-cut-paste-49_work`.

The "Automatic" column in the table refers to whether or not you are required to implement the feature for a custom `Bijector`. "AD" refers to the fact that it can be implemented "automatically" using automatic differentiation, i.e. `ADBijector`.

## Functions

1. `link`: maps a sample of a random distribution `dist` from its support to a value in R^n. Example: ``` julia> using Bijectors

julia> dist = Beta(2, 2) Beta{Float64}(α=2.0, β=2.0)

julia> x = rand(dist) 0.7472542331020509

julia> y = link(dist, x) 1.084021356473311

``````
``````

julia> z = invlink(dist, y) 0.7472542331020509

julia> x ≈ z true

``````
3. `logpdf_with_trans`: finds `log` of the (transformed) probability density function of a distribution `dist` at a sample `x`. Example:
``````

julia> using Bijectors

julia> dist = Dirichlet(2, 3) Dirichlet{Float64}(alpha=[3.0, 3.0])

julia> x = rand(dist) 2-element Array{Float64,1}: 0.46094823621110165 0.5390517637888984

julia> logpdf_with_trans(dist, x, false) # ignoring the transformation 0.6163709733893024

julia> logpdf_with_trans(dist, x, true) # considering the transformation -0.7760422307471244

``````
## `Bijector` interface
A `Bijector` is a differentiable bijection with a differentiable inverse. That's basically it.

The primary application of `Bijector`s is the (very profitable) business of transforming (usually continuous) probability densities. If we transfrom a random variable `x ~ p(x)` to `y = b(x)` where `b` is a `Bijector`, we also get a canonical density `q(y) = p(b⁻¹(y)) |det J(b⁻¹, y)|` for `y`. Here `J(b⁻¹, y)` is the jacobian of the inverse transform evaluated at `y`. `q` is also known as the _push-forward_ of `p` by `b` in measure theory.

There's plenty of different reasons why one would want to do something like this. It can be because your `p` has non-zero probability (support) on a closed interval `[a, b]` and you want to use AD without having to worry about reaching the boundary. E.g. `Beta` has support `[0, 1]` so if we could transform `p = Beta` into a density `q` with support on ℝ, we could instead compute the derivative of `logpdf(q, y)` wrt. `y`, and then transform back `x = b⁻¹(y)`. This is very useful for certain inference methods, e.g. Hamiltonian Monte-Carlo, where we need to take the derivative of the logpdf-computation wrt. input.

Another use-case is constructing a _parameterized_ `Bijector` and consider transforming a "simple" density, e.g. `MvNormal`, to match a more complex density. One class of such bijectors is _Normalizing Flows (NFs)_ which are compositions of differentiable and invertible neural networks, i.e. composition of a particular family of parameterized bijectors.[1] We'll see an example of this later on.

### Basic usage
Other than the `logpdf_with_trans` methods, the package also provides a more composable interface through the `Bijector` types. Consider for example the one from above with `Beta(2, 2)`.
``````

julia> using Random; Random.seed!(42);

julia> using Bijectors; using Bijectors: Logit

julia> dist = Beta(2, 2) Beta{Float64}(α=2.0, β=2.0)

julia> x = rand(dist) 0.36888689965963756

julia> b = bijector(dist) # bijection (0, 1) → ℝ Logit{Float64}(0.0, 1.0)

julia> y = b(x) -0.5369949942509267

``````
In this case we see that `bijector(d::Distribution)` returns the corresponding constrained-to-unconstrained bijection for `Beta`, which indeed is a `Logit` with `a = 0.0` and `b = 1.0`. The resulting `Logit <: Bijector` has a method `(b::Logit)(x)` defined, allowing us to call it just like any other function. Comparing with the above example, `b(x) ≈ link(dist, x)`. Just to convince ourselves:
``````

julia> b(x) ≈ link(dist, x) true

``````
#### Inversion

``````

julia> b⁻¹ = inv(b) Inverse{Logit{Float64},0}(Logit{Float64}(0.0, 1.0))

julia> b⁻¹(y) 0.3688868996596376

julia> b⁻¹(y) ≈ invlink(dist, y) true

``````
Pretty neat, huh? `Inverse{Logit}` is also a `Bijector` where we've defined `(ib::Inverse{<:Logit})(y)` as the inverse transformation of `(b::Logit)(x)`. Note that it's not always the case that `inv(b) isa Inverse`, e.g. the inverse of `Exp` is simply `Log` so `inv(Exp()) isa Log` is true.

#### Dimensionality
One more thing. See the `0` in `Inverse{Logit{Float64}, 0}`? It represents the *dimensionality* of the bijector, in the same sense as for an `AbstractArray` with the exception of `0` which means it expects 0-dim input and output, i.e. `<:Real`. This can also be accessed through `dimension(b)`:
``````

julia> Bijectors.dimension(b) 0

julia> Bijectors.dimension(Exp{1}()) 1

``````
In most cases specification of the dimensionality is unnecessary as a `Bijector{N}` is usually only defined for a particular value of `N`, e.g. `Logit isa Bijector{0}` since it only makes sense to apply `Logit` to a real number (or a vector of reals if you're doing batch-computation). As a user, you'll rarely have to deal with this dimensionality specification. Unfortunately there are exceptions, e.g. `Exp` which can be applied to both real numbers and a vector of real numbers, in both cases treating it as a single input. This means that when `Exp` receives a vector input `x` as input, it's ambiguous whether or not to treat `x` as a *batch* of 0-dim inputs or as a single 1-dim input. As a result, to support batch-computation it is necessary to know the expected dimensionality of the input and output. Notice that we assume the dimensionality of the input and output to be the *same*. This is a reasonable assumption considering we're working with *bijections*.

#### Composition
Also, we can _compose_ bijectors:
``````

julia> id_y = (b ∘ b⁻¹) Composed{Tuple{Inverse{Logit{Float64},0},Logit{Float64}},0}((Inverse{Logit{Float64},0}(Logit{Float64}(0.0, 1.0)), Logit{Float64}(0.0, 1.0)))

julia> id_y(y) ≈ y true

``````
And since `Composed isa Bijector`:
``````

julia> id_x = inv(id_y) Composed{Tuple{Inverse{Logit{Float64},0},Logit{Float64}},0}((Inverse{Logit{Float64},0}(Logit{Float64}(0.0, 1.0)), Logit{Float64}(0.0, 1.0)))

julia> id_x(x) ≈ x true

``````
#### `logpdf` of `TransformedDistribution`
This far we've seen that we can replicate the functionality provided by `link` and `invlink`. To replicate `logpdf_with_trans` we instead provide a `TransformedDistribution <: Distribution` implementing the `Distribution` interface from Distributions.jl:
``````

julia> using Bijectors: TransformedDistribution

julia> td = transformed(dist) TransformedDistribution{Beta{Float64},Logit{Float64},Univariate}( dist: Beta{Float64}(α=2.0, β=2.0) transform: Logit{Float64}(0.0, 1.0) )

julia> td isa UnivariateDistribution true

julia> logpdf(td, y) -1.123311289915276

julia> logpdf_with_trans(dist, x, true) -1.123311289915276

``````
When computing `logpdf(td, y)` where `td` is the _transformed_ distribution corresponding to `Beta(2, 2)`, it makes more semantic sense to compute the pdf of the _transformed_ variable `y` rather than using the "un-transformed" variable `x` to do so, as we do in `logpdf_with_trans`. With that being said, we can also do
``````

julia> logpdf_forward(td, x) -1.123311289915276

``````
#### `logabsdetjac` and `forward`

In the computation of both `logpdf` and `logpdf_forward` we need to compute `log(abs(det(jacobian(inv(b), y))))` and `log(abs(det(jacobian(b, x))))`, respectively. This computation is available using the `logabsdetjac` method
``````

julia> logabsdetjac(b⁻¹, y) -1.4575353795716655

julia> logabsdetjac(b, x) 1.4575353795716655

``````
Notice that
``````

julia> logabsdetjac(b, x) ≈ -logabsdetjac(b⁻¹, y) true

``````
which is always the case for a differentiable bijection with differentiable inverse. Therefore if you want to compute `logabsdetjac(b⁻¹, y)` and we know that `logabsdetjac(b, b⁻¹(y))` is actually more efficient, we'll return `-logabsdetjac(b, b⁻¹(y))` instead. For some bijectors it might be easy to compute, say, the forward pass `b(x)`, but expensive to compute `b⁻¹(y)`. Because of this you might want to avoid doing anything "backwards", i.e. using `b⁻¹`. This is where `forward` comes to good use:
``````

julia> forward(b, x) (rv = -0.5369949942509267, logabsdetjac = 1.4575353795716655)

``````
Similarily
``````

julia> forward(inv(b), y) (rv = 0.3688868996596376, logabsdetjac = -1.4575353795716655)

``````
In fact, the purpose of `forward` is to just _do the right thing_, not necessarily "forward". In this function we'll have access to both the original value `x` and the transformed value `y`, so we can compute `logabsdetjac(b, x)` in either direction. Furthermore, in a lot of cases we can re-use a lot of the computation from `b(x)` in the computation of `logabsdetjac(b, x)`, or vice-versa. `forward(b, x)` will take advantage of such opportunities (if implemented).

#### Sampling from `TransformedDistribution`
At this point we've only shown that we can replicate the existing functionality. But we said `TransformedDistribution isa Distribution`, so we also have `rand`:
``````

julia> y = rand(td) # ∈ ℝ 0.999166054552483

julia> x = inv(td.transform)(y) # transform back to interval [0, 1] 0.7308945834125756

``````
This can be quite convenient if you have computations assuming input to be on the real line.

But the real utility of `TransformedDistribution` becomes more apparent when using `transformed(dist, b)` for any bijector `b`. To get the transformed distribution corresponding to the `Beta(2, 2)`, we called `transformed(dist)` before. This is simply an alias for `transformed(dist, bijector(dist))`. Remember `bijector(dist)` returns the constrained-to-constrained bijector for that particular `Distribution`. But we can of course construct a `TransformedDistribution` using different bijectors with the same `dist`. This is particularly useful in something called _Automatic Differentiation Variational Inference (ADVI)_.[2] An important part of ADVI is to approximate a constrained distribution, e.g. `Beta`, as follows:
1. Sample `x` from a `Normal` with parameters `μ` and `σ`, i.e. `x ~ Normal(μ, σ)`.
2. Transform `x` to `y` s.t. `y ∈ support(Beta)`, with the transform being a differentiable bijection with a differentiable inverse (a "bijector")

This then defines a probability density with same _support_ as `Beta`! Of course, it's unlikely that it will be the same density, but it's an _approximation_. Creating such a distribution becomes trivial with `Bijector` and `TransformedDistribution`:
``````

julia> dist = Beta(2, 2) Beta{Float64}(α=2.0, β=2.0)

julia> b = bijector(dist) # (0, 1) → ℝ Logit{Float64}(0.0, 1.0)

julia> b⁻¹ = inv(b) # ℝ → (0, 1) Inverse{Logit{Float64},0}(Logit{Float64}(0.0, 1.0))

julia> td = transformed(Normal(), b⁻¹) # x ∼ 𝓝(0, 1) then b(x) ∈ (0, 1) TransformedDistribution{Normal{Float64},Inverse{Logit{Float64},0},Univariate}( dist: Normal{Float64}(μ=0.0, σ=1.0) transform: Inverse{Logit{Float64},0}(Logit{Float64}(0.0, 1.0)) )

julia> x = rand(td) # ∈ (0, 1) 0.538956748141868

``````
It's worth noting that `support(Beta)` is the _closed_ interval `[0, 1]`, while the constrained-to-unconstrained bijection, `Logit` in this case, is only well-defined as a map `(0, 1) → ℝ` for the _open_ interval `(0, 1)`. This is of course not an implementation detail. `ℝ` is itself open, thus no continuous bijection exists from a _closed_ interval to `ℝ`. But since the boundaries of a closed interval has what's known as measure zero, this doesn't end up affecting the resulting density with support on the entire real line. In practice, this means that
``````

td = transformed(Beta())

inv(td.transform)(rand(td))

``````
will never result in `0` or `1` though any sample arbitrarily close to either `0` or `1` is possible. _Disclaimer: numerical accuracy is limited, so you might still see `0` and `1` if you're lucky._

We can also do _multivariate_ ADVI using the `Stacked` bijector. `Stacked` gives us a way to combine univariate and/or multivariate bijectors into a singe multivariate bijector. Say you have a vector `x` of length 2 and you want to transform the first entry using `Exp` and the second entry using `Log`. `Stacked` gives you an easy and efficient way of representing such a bijector.
``````

julia> Random.seed!(42);

julia> using Bijectors: Exp, Log, SimplexBijector

julia> # Original distributions dists = ( Beta(), InverseGamma(), Dirichlet(2, 3) );

julia> # Construct the corresponding ranges ranges = [];

julia> idx = 1;

julia> for i = 1:length(dists) d = dists[i] push!(ranges, idx:idx + length(d) - 1)

``````       global idx
idx += length(d)
end;
``````

julia> ranges 3-element Array{Any,1}: 1:1 2:2 3:4

julia> # Base distribution; mean-field normal num_params = ranges[end][end] 4

julia> d = MvNormal(zeros(num_params), ones(num_params)) DiagNormal( dim: 4 μ: [0.0, 0.0, 0.0, 0.0] Σ: [1.0 0.0 0.0 0.0; 0.0 1.0 0.0 0.0; 0.0 0.0 1.0 0.0; 0.0 0.0 0.0 1.0] )

julia> # Construct the transform bs = bijector.(dists) # constrained-to-unconstrained bijectors for dists (Logit{Float64}(0.0, 1.0), Log{0}(), SimplexBijector{true}())

julia> ibs = inv.(bs) # invert, so we get unconstrained-to-constrained (Inverse{Logit{Float64},0}(Logit{Float64}(0.0, 1.0)), Exp{0}(), Inverse{SimplexBijector{true},1}(SimplexBijector{true}()))

julia> sb = Stacked(ibs, ranges) # => Stacked <: Bijector Stacked{Tuple{Inverse{Logit{Float64},0},Exp{0},Inverse{SimplexBijector{true},1}},3}((Inverse{Logit{Float64},0}(Logit{Float64}(0.0, 1.0)), Exp{0}(), Inverse{SimplexBijector{true},1}(SimplexBijector{true}())), (1:1, 2:2, 3:4))

julia> # Mean-field normal with unconstrained-to-constrained stacked bijector td = transformed(d, sb);

julia> y = rand(td) 4-element Array{Float64,1}: 0.36446726136766217 0.6412195576273355 0.5067884173521743 0.4932115826478257

julia> 0.0 ≤ y[1] ≤ 1.0 # => true true

julia> 0.0 < y[2] # => true true

julia> sum(y[3:4]) ≈ 1.0 # => true true

``````
### Normalizing flows
A very interesting application is that of _normalizing flows_.[1] Usually this is done by sampling from a multivariate normal distribution, and then transforming this to a target distribution using invertible neural networks. Currently there are two such transforms available in Bijectors.jl: `PlanarLayer` and `RadialLayer`. Let's create a flow with a single `PlanarLayer`:
``````

julia> d = MvNormal(zeros(2), ones(2));

julia> b = PlanarLayer(2) PlanarLayer{Array{Float64,2},Array{Float64,1}}([1.77786; -1.1449], [-0.468606; 0.156143], [-2.64199])

julia> flow = transformed(d, b) TransformedDistribution{MvNormal{Float64,PDMats.PDiagMat{Float64,Array{Float64,1}},Array{Float64,1}},PlanarLayer{Array{Float64,2},Array{Float64,1}},Multivariate}( dist: DiagNormal( dim: 2 μ: [0.0, 0.0] Σ: [1.0 0.0; 0.0 1.0] )

transform: PlanarLayer{Array{Float64,2},Array{Float64,1}}([1.77786; -1.1449], [-0.468606; 0.156143], [-2.64199]) )

julia> flow isa MultivariateDistribution true

``````
That's it. Now we can sample from it using `rand` and compute the `logpdf`, like any other `Distribution`.
``````

julia> y = rand(flow) 2-element Array{Float64,1}: 1.3337915588180933 1.010861989639227

julia> logpdf(flow, y) # uses inverse of `b` -2.8996106373788293

julia> x = rand(flow.dist) 2-element Array{Float64,1}: 0.18702790710363
0.5181487878771377

julia> logpdf_forward(flow, x) # more efficent and accurate -1.9813114667203335

``````
Similarily to the multivariate ADVI example, we could use `Stacked` to get a _bounded_ flow:
``````

julia> d = MvNormal(zeros(2), ones(2));

julia> ibs = inv.(bijector.((InverseGamma(2, 3), Beta())));

julia> sb = stack(ibs...) # == Stacked(ibs) == Stacked(ibs, [i:i for i = 1:length(ibs)] Stacked{Tuple{Exp{0},Inverse{Logit{Float64},0}},2}((Exp{0}(), Inverse{Logit{Float64},0}(Logit{Float64}(0.0, 1.0))), (1:1, 2:2))

julia> b = sb ∘ PlanarLayer(2) Composed{Tuple{PlanarLayer{Array{Float64,2},Array{Float64,1}},Stacked{Tuple{Exp{0},Inverse{Logit{Float64},0}},2}},1}((PlanarLayer{Array{Float64,2},Array{Float64,1}}([1.49138; 0.367563], [-0.886205; 0.684565], [-1.59058]), Stacked{Tuple{Exp{0},Inverse{Logit{Float64},0}},2}((Exp{0}(), Inverse{Logit{Float64},0}(Logit{Float64}(0.0, 1.0))), (1:1, 2:2))))

julia> td = transformed(d, b);

julia> y = rand(td) 2-element Array{Float64,1}: 2.6493626783431035 0.1833391433092443

julia> 0 < y[1] true

julia> 0 ≤ y[2] ≤ 1 true

``````
Want to fit the flow?
``````

julia> using Tracker

julia> b = PlanarLayer(2, param) # construct parameters using `param` PlanarLayer{TrackedArray{…,Array{Float64,2}},TrackedArray{…,Array{Float64,1}}}(-1.05099; 0.502079, -0.216248; -0.706424, -4.33747)

julia> flow = transformed(d, b) TransformedDistribution{MvNormal{Float64,PDMats.PDiagMat{Float64,Array{Float64,1}},Array{Float64,1}},PlanarLayer{TrackedArray{…,Array{Float64,2}},TrackedArray{…,Array{Float64,1}}},Multivariate}( dist: DiagNormal( dim: 2 μ: [0.0, 0.0] Σ: [1.0 0.0; 0.0 1.0] )

transform: PlanarLayer{TrackedArray{…,Array{Float64,2}},TrackedArray{…,Array{Float64,1}}}(-1.05099; 0.502079, -0.216248; -0.706424, -4.33747) )

julia> rand(flow) Tracked 2-element Array{Float64,1}: 0.5992818950827451 -0.6264187818605164

julia> x = rand(flow.dist) 2-element Array{Float64,1}: -0.37240087577993225 0.36901028455183293

julia> Tracker.back!(logpdf_forward(flow, x), 1.0) # backprob

julia> Tracker.grad(b.w) 2×1 Array{Float64,2}: -0.00037431072968105417 0.0013039074681623036

``````
We can easily create more complex flows by simply doing `PlanarLayer(10) ∘ PlanarLayer(10) ∘ RadialLayer(10)` and so on.

In those cases, it might be useful to use Flux.jl's `Flux.params` to extract the parameters:
``````

julia> using Flux

julia> Flux.params(flow) Params([-1.05099; 0.502079, -0.216248; -0.706424, -4.33747])

``````
Another useful function is the `forward(d::Distribution)` method. It is similar to `forward(b::Bijector)` in the sense that it does a forward pass of the entire process "sample then transform" and returns all the most useful quantities in process using the most efficent computation path.
``````

julia> x, y, logjac, logpdf_y = forward(flow) # sample + transform and returns all the useful quantities in one pass (x = [-0.839739, 0.169613], y = -0.810354, 0.963392, logabsdetjac = -0.0017416108706436628 (tracked), logpdf = -2.203100286792651 (tracked))

``````
This method is for example useful when computing quantities such as the _expected lower bound (ELBO)_ between this transformed distribution and some other joint density. If no analytical expression is available, we have to approximate the ELBO by a Monte Carlo estimate. But one term in the ELBO is the entropy of the base density, which we _do_ know analytically in this case. Using the analytical expression for the entropy and then using a monte carlo estimate for the rest of the terms in the ELBO gives an estimate with lower variance than if we used the monte carlo estimate for the entire expectation.

### Normalizing flows with bounded support

There's mainly two ways you can implement your own `Bijector`, and which way you choose mainly depends on the following question: are you bothered enough to manually implement `logabsdetjac`? If the answer is "Yup!", then you subtype from `Bijector`, if "Naaaah" then you subtype `ADBijector`.

### `<:Bijector`
Here's a simple example taken from the source code, the `Identity`:
``````

import Bijectors: logabsdetjac

struct Identity{N} <: Bijector{N} end (::Identity)(x) = x # transform itself, "forward" (::Inverse{<: Identity})(y) = y # inverse tramsform, "backward"

# see the proper implementation for `logabsdetjac` in general

logabsdetjac(::Identity{0}, y::Real) = zero(eltype(y)) # ∂ₓid(x) = ∂ₓ x = 1 → log(abs(1)) = log(1) = 0

``````
A slightly more complex example is `Logit`:
``````

using StatsFuns: logit, logistic

struct Logit{T<:Real} <: Bijector{0} a::T b::T end

(b::Logit)(x::Real) = logit((x - b.a) / (b.b - b.a)) (b::Logit)(x) = map(b, x)

# `orig` contains the `Bijector` which was inverted

(ib::Inverse{<:Logit})(y::Real) = (ib.orig.b - ib.orig.a) * logistic(y) + ib.orig.a (ib::Inverse{<:Logit})(y) = map(ib, y)

logabsdetjac(b::Logit, x::Real) = - log((x - b.a) * (b.b - x) / (b.b - b.a)) logabsdetjac(b::Logit, x) = map(logabsdetjac, x)

``````
(Batch computation is not fully supported by all bijectors yet (see issue #35), but is actively worked on. In the particular case of `Logit` there's only one thing that makes sense, which is elementwise application. Therefore we've added `@.` to the implementation above, thus this works for any `AbstractArray{<:Real}`.)

Then
``````

julia> b = Logit(0.0, 1.0) Logit{Float64}(0.0, 1.0)

julia> b(0.6) 0.4054651081081642

julia> inv(b)(y) Tracked 2-element Array{Float64,1}: 0.3078149833748082 0.72380041667891

julia> logabsdetjac(b, 0.6) 1.4271163556401458

julia> logabsdetjac(inv(b), y) # defaults to `- logabsdetjac(b, inv(b)(x))` Tracked 2-element Array{Float64,1}: -1.546158373866469 -1.6098711387913573

julia> forward(b, 0.6) # defaults to `(rv=b(x), logabsdetjac=logabsdetjac(b, x))` (rv = 0.4054651081081642, logabsdetjac = 1.4271163556401458)

``````
For further efficiency, one could manually implement `forward(b::Logit, x)`:
``````

julia> import Bijectors: forward, Logit

julia> function forward(b::Logit{<:Real}, x) totally_worth_saving = @. (x - b.a) / (b.b - b.a) # spoiler: it's probably not y = logit.(totally_worth_saving) logjac = @. - log((b.b - x) * totally_worth_saving) return (rv=y, logabsdetjac = logjac) end forward (generic function with 16 methods)

julia> forward(b, 0.6) (rv = 0.4054651081081642, logabsdetjac = 1.4271163556401458)

julia> @which forward(b, 0.6) forward(b::Logit{#s4} where #s4<:Real, x) in Main at REPL[43]:2

``````
As you can see it's a very contrived example, but you get the idea.

We could also have implemented `Logit` as an `ADBijector`:
``````

using StatsFuns: logit, logistic using Bijectors: ADBackend

(b::ADLogit)(x) = @. logit((x - b.a) / (b.b - b.a)) (ib::Inverse{<:ADLogit{<:Real}})(y) = @. (ib.orig.b - ib.orig.a) * logistic(y) + ib.orig.a

``````
No implementation of `logabsdetjac`, but:
``````

``````
Neat! And just to verify that everything works:
``````

julia> b = Logit(0.0, 1.0) Logit{Float64}(0.0, 1.0)

julia> logabsdetjac(b, 0.6) 1.4271163556401458

julia> logabsdetjac(b_ad, 0.6) ≈ logabsdetjac(b, 0.6) true

``````
We can also use Tracker.jl for the AD, rather than ForwardDiff.jl:
``````

``````

### Reference
Most of the methods and types mention below will have docstrings with more elaborate explanation and examples, e.g.
``````

help?> Bijectors.Composed Composed(ts::A)

∘(b1::Bijector{N}, b2::Bijector{N})::Composed{<:Tuple} composel(ts::Bijector{N}...)::Composed{<:Tuple} composer(ts::Bijector{N}...)::Composed{<:Tuple}

where A refers to either

``````•    Tuple{Vararg{<:Bijector{N}}}: a tuple of bijectors of dimensionality N

•    AbstractArray{<:Bijector{N}}: an array of bijectors of dimensionality N
``````

A Bijector representing composition of bijectors. composel and composer results in a Composed for which application occurs from left-to-right and right-to-left, respectively.

Note that all the alternative ways of constructing a Composed returns a Tuple of bijectors. This ensures type-stability of implementations of all relating methdos, e.g. inv.

If you want to use an Array as the container instead you can do

Composed([b1, b2, ...])

In general this is not advised since you lose type-stability, but there might be cases where this is desired, e.g. if you have a insanely large number of bijectors to compose.

Examples ≡≡≡≡≡≡≡≡≡≡

It's important to note that ∘ does what is expected mathematically, which means that the bijectors are applied to the input right-to-left, e.g. first applying b2 and then b1:

(b1 ∘ b2)(x) == b1(b2(x)) # => true

But in the Composed struct itself, we store the bijectors left-to-right, so that

cb1 = b1 ∘ b2 # => Composed.ts == (b2, b1) cb2 = composel(b2, b1) # => Composed.ts == (b2, b1) cb1(x) == cb2(x) == b1(b2(x)) # => true

``````If anything is lacking or not clear in docstrings, feel free to open an issue or PR.

#### Types
The following are the bijectors available:
- Abstract:
- `Bijector`: super-type of all bijectors.
- `ADBijector{AD} <: Bijector`: subtypes of this only require the user to implement `(b::UserBijector)(x)` and `(ib::Inverse{<:UserBijector})(y)`. Automatic differentation will be used to compute the `jacobian(b, x)` and thus `logabsdetjac(b, x).
- Concrete:
- `Composed`: represents a composition of bijectors.
- `Stacked`: stacks univariate and multivariate bijectors
- `Identity`: does what it says, i.e. nothing.
- `Logit`
- `Exp`
- `Log`
- `Scale`: scaling by scalar value, though at the moment only well-defined `logabsdetjac` for univariate.
- `Shift`: shifts by a scalar value.
- `Permute`: permutes the input array using matrix multiplication
- `SimplexBijector`: mostly used as the constrained-to-unconstrained bijector for `SimplexDistribution`, e.g. `Dirichlet`.
- `PlanarLayer`: §4.1 Eq. (10) in [1]
- `RadialLayer`: §4.1 Eq. (14) in [1]

The distribution interface consists of:
- `TransformedDistribution <: Distribution`: implements the `Distribution` interface from Distributions.jl. This means `rand` and `logpdf` are provided at the moment.

#### Methods
The following methods are implemented by all subtypes of `Bijector`, this also includes bijectors such as `Composed`.
- `(b::Bijector)(x)`: implements the transform of the `Bijector`
- `inv(b::Bijector)`: returns the inverse of `b`, i.e. `ib::Bijector` s.t. `(ib ∘ b)(x) ≈ x`. In most cases this is `Inverse{<:Bijector}`.
- `logabsdetjac(b::Bijector, x)`: computes log(abs(det(jacobian(b, x)))).
- `forward(b::Bijector, x)`: returns named tuple `(rv=b(x), logabsdetjac=logabsdetjac(b, x))` in the most efficient manner.
- `∘`, `composel`, `composer`: convenient and type-safe constructors for `Composed`. `composel(bs...)` composes s.t. the resulting composition is evaluated left-to-right, while `composer(bs...)` is evaluated right-to-left. `∘` is right-to-left, as excepted from standard mathematical notation.
- `jacobian(b::Bijector, x)` [OPTIONAL]: returns the jacobian of the transformation. In some cases the analytical jacobian has been implemented for efficiency.
- `dimension(b::Bijector)`: returns the dimensionality of `b`.
- `isclosedform(b::Bijector)`: returns `true` or `false` depending on whether or not `b(x)` has a closed-form implementation.

For `TransformedDistribution`, together with default implementations for `Distribution`, we have the following methods:
- `bijector(d::Distribution)`: returns the default constrained-to-unconstrained bijector for `d`
- `transformed(d::Distribution)`, `transformed(d::Distribution, b::Bijector)`: constructs a `TransformedDistribution` from `d` and `b`.
- `logpdf_forward(d::Distribution, x)`, `logpdf_forward(d::Distribution, x, logjac)`: computes the `logpdf(td, td.transform(x))` using the forward pass, which is potentially faster depending on the transform at hand.
- `forward(d::Distribution)`: returns `(x = rand(dist), y = b(x), logabsdetjac = logabsdetjac(b, x), logpdf = logpdf_forward(td, x))` where `b = td.transform`. This combines sampling from base distribution and transforming into one function. The intention is that this entire process should be performed in the most efficient manner, e.g. the `logabsdetjac(b, x)` call might instead be implemented as `- logabsdetjac(inv(b), b(x))` depending on which is most efficient.

# Bibliography
1. Rezende, D. J., & Mohamed, S. (2015). Variational Inference With Normalizing Flows. [arXiv:1505.05770](https://arxiv.org/abs/1505.05770v6).
2. Kucukelbir, A., Tran, D., Ranganath, R., Gelman, A., & Blei, D. M. (2016). Automatic Differentiation Variational Inference. [arXiv:1603.00788](https://arxiv.org/abs/1603.00788v1).
``````

09/13/2018

12 days ago

155 commits