ML and SM 2


  • Lecture 1 introduced idea of Variational Inference (VI)

  • Turns inference in latent variable models into optimization

  • Today: how to leverage neural networks & automatic differentiation

  • Model of choice: Variational Autoencoder

$$ \DeclareMathOperator*{\E}{\mathbb{E}} \newcommand{\cE}{\mathcal{E}} \newcommand{\R}{\mathbb{R}} \newcommand{\bx}{\mathbf{x}} \newcommand{\bz}{\mathbf{z}} \newcommand{\br}{\mathbf{r}} \newcommand{\bv}{\mathbf{v}} \newcommand{\bmu}{\boldsymbol{\mu}} \newcommand{\bSigma}{\boldsymbol{\Sigma}} \newcommand{\bzeta}{\boldsymbol{\zeta}} $$

VI redux

  • Model defined by prior $p(z)$ and generative model $p_\phi(x|z)$

  • Similar model for posterior $q_\theta(z|x)$

  • Two representatios of $p(x,z)$: forward and backward $$ p_\text{F}(x,z)= p_\theta(x|z)p(z),\qquad p_\text{B}(x,z)= q_\phi(z|x)p_\text{D}(x). $$ where $p_\text{D}(x)$ is data distribution

  • KL between these two models $$ D_\text{KL}(p_\text{B}||p_\text{F})= \E_{x\sim \text{Data}}\left[\E_{z\sim q_\phi(\cdot|x)}\left[\log\left(\frac{q_\phi(z|x)p_\text{D}(x)}{p_\theta(x|z)p(z)}\right)\right]\right]\geq 0. $$ or $$ H[p_\text{D}]\leq \E_{x\sim \text{Data}}\left[\E_{z\sim q_\phi(\cdot|x)}\left[\log\left(\frac{q_\phi(z|x)}{p_\theta(x|z)p(z)}\right)\right]\right]. $$

  • RHS doesn’t involve $p_\text{D}(x)$ explicitly, only expectation. This is implemented as empirical average over (batches of) data

  • RHS often presented as

$$ \E_{x\sim \text{Data}}\left[D_\text{KL}(q_\phi(\cdot|x)||p)-\E_{z\sim q_\phi(\cdot|x)}\left[\log p_\theta(x|z)\right]\right]. $$

  • First term small when posterior matches prior

  • Second small when model matches data (reconstruction error)

Variational autoencoder

Autoencoder schema

  • Autoencoder trained to return outputs close to inputs

  • Not trivial if $\text{dim}\,\textbf{h}<\text{dim}\,\textbf{x}$!

  • We have a loss function for VI in autoencoder framework $$ \mathcal{L}(\theta,\phi)=\E_{x\sim \text{Data}}\left[D_\text{KL}(q_\phi(\cdot|x)||p)-\E_{z\sim q_\phi(\cdot|x)}\left[\log p_\theta(x|z)\right]\right] $$

  • We need

    • To parameterize $p_\theta(x|z)$ and $q_\phi(z|x)$ using NNs.
    • To take gradients of the loss function to perform optimization.
  • Let’s look at these in turn.


  • $\bz\in \R^{H}$, $\bx\in \R^{D}$

  • For encoder $q_\phi(\bz|\bx)$, choose $\mathcal{N}(\bmu_\phi(\bx),\bSigma_\phi(\bx))$

  • If prior is $\mathcal{N}(0,\mathbb{1})$ the KL term loss can be evaluated explicitly.

  • $\bmu_\phi(\bx)$ and $\bSigma_\phi(\bx)$ are parameterized using NNs, with architecture adapted to the data e.g. Convolutional neural networks for images

  • Similarly for decoder $p_\theta(\cdot|\bz)=\mathcal{N}(\bmu'_\theta(\bz),\bSigma'_\theta(\bz))$

  • Second term of loss involves $$ -\log p_\theta(\bx|\bz) = \frac{1}{2}(\bx-\bmu'_\theta(\bz))^T\bSigma'^{-1}_\theta(\bz)(\bx-\bmu'_\theta(\bz))+\frac{1}{2}\log\det\bSigma_\theta'(\bz)+\text{const.}, $$ encourages mean output $\bmu'_\theta(\bz)$ to be close to $\bx$

  • Required expectation over $\bz$ requires Monte Carlo

  • Problem: expectation depends on parameters $\phi$, and we want derivatives

  • What do we do?

Reparameterization trick

  • If you have $\zeta\sim\mathcal{N}(0,1)$ then $\sigma \zeta +\mu\sim \mathcal{N}(\mu,\sigma^2)$

  • Separates parameters from sampling, so that a Monte Carlo estimate of an expectation $$ \E_{x\sim \mathcal{N}(\mu,\sigma^2)}\left[f(x)\right]\approx \frac{1}{S}\sum_{s=1}^S f(\sigma z_s + \mu) $$ is explicitly a function of $\sigma$ and $\mu$, so derivatives may be taken

  • Generalizes to multivariate Gaussian: $\bz\sim \bSigma_\phi^{1/2}(\bx)\bzeta+\mu_\phi(\bx)$.

More practicalities

  • In practice a single $\bz$ sample is usually found to provide useful gradients for optimization

  • Large datasets usually split into batches (sometimes called mini-batches)

  • For batch of size $B$ loss function is estimated using $B$ iid $ \bzeta_b\sim \mathcal{N}(0,\mathbb{1})$ $$ \mathcal{L}(\theta,\phi)\approx\frac{1}{B}\sum_{b=1}^B\left[D_\text{KL}(q_\phi(\cdot|\bx_b)||p)-\log p_\theta(\bx_b|\bSigma_\phi^{1/2}(\bx_b)\bzeta_b+\mu_\phi(\bx_b))\right] $$

  • Gradients calculated by automatic differentiation, implemented in all modern DL libraries

  • There’s a great deal of craft to the business of training…


  • One promise of latent variable models is an interpretable latent space

  • Moving in lower dimensional latent space $\R^H$ allows us to explore the manifold in which the data is embedded in $\R^D$

  • Some issues:

    1. Loss function doesn’t require that the latent space is used at all. If decoder model $p_\theta(\bx|\bz)$ is rich enough may have $p_\theta(\bx|\bz)\approx p_\text{D}(\bx)$. By Bayes' theorem posterior is $$ \frac{p_\theta(\bx|\bz)p(\bz)}{p_\text{D}(\bx)}\approx p(\bz), $$ same as the prior! This is posterior collapse

    2. No guarantee that latent space is used nicely, e.g. with variables for colour, shape, position, etc. (disentangled representation). One problem: prior $\mathcal{N}(0,\mathbb{1})$ is rotationally invariant, so lifting symmetry is necessary.

Compression with VAEs: bits back

  • In Lecture 1 I suggested that good probabilistic models could give better compression

  • How does this work for latent variable models like VAE?

  • Problem, as always, is that model doesn’t have explicit $p_\text{M}(x)$: marginalizing over latent variables is intractable.

  • Recall that loss function of VAE is based

$$ H[p_\text{D}]\leq \E_{x\sim \text{Data}}\left[\E_{z\sim q_\phi(\cdot|x)}\left[\log\left(\frac{q_\phi(z|x)}{p_\theta(x|z)p(z)}\right)\right]\right]. $$

  • Split RHS into three terms

$$ \E_{x\sim \text{Data}}\left[\E_{z\sim q_\phi(\cdot|x)}\left[\log\left(q_\phi(z|x)\right)-\log\left(p_\theta(x|z)\right)-\log\left(p(z)\right)\right]\right]. $$

  • Remember $-\log_2 p(x)$ is length in bits of optimal encoding of $x$. Last two terms could be interpreted as

    1. Given data $x$ we sample $z\sim q_\phi(\cdot|x)$.
    2. We encode $x$ using the distribution $p_\theta(\cdot|z)$, then
    3. Encode $z$ using the prior $p(\cdot)$.
  • For decoding, go in reverse

    1. Decode $z$ using the prior $p(z)$.
    2. Decode $x$ using $p_\theta(\cdot|z)$
  • We’ll never reach Shannon bound this way, however, because of the negative first term in

$$ \E_{x\sim \text{Data}}\left[\E_{z\sim q_\phi(\cdot|x)}\left[\log\left(q_\phi(z|x)\right)-\log\left(p_\theta(x|z)\right)-\log\left(p(z)\right)\right]\right]. $$

  • We need to make the code shorter. How?
  • Remember that Shannon bound applies in limit of $N\to\infty$ iid data

  • Imagine a semi-infinite bit stream mid-way through encoding

    • We decode part of already encoded bitstream using $q_\phi(\cdot|x)$

    • Result is $z\sim q_\phi(\cdot|x)$: use for encoding $x$ as described above

    • These are bits back: remove $H(q_\phi(\cdot|x))$ bits on average

    • Allows us to reach the Shannon bound

  • When decoding data, the last thing we do for each $x$ is encode $z$ back to the bitstream using $q_\phi(\cdot|x)$

The VAE framework is quite general, and in recent years has been elaborated in various ways.

Markov chain autoencoders (??)

  • Up to now our encoder and decoder were just Gaussian models

  • Can we produce a model with a richer distribution?

  • Make forward and backward models Markov processes with $T$ steps $$ p_\text{F}(z_0,\ldots x=z_T) = p_\theta(x=z_T|z_{T-1})p_\theta(z_{T-1}|z_{T-2})\cdots p_\theta(z_1|z_{0})p(z_0) $$ $$ p_\text{B}(z_0,\ldots \ldots x=z_T) = q_\phi(z_0|z_{1})\cdots q_\phi(z_{T-2}|z_{T-1})q_\phi(z_{T-1}|z_T)p_\text{D}(x=z_T) $$

  • Loss function is

$$ H[p_\text{D}]\leq \E_{z\sim p_\text{B}}\left[\log \left(\frac{q_\phi(z_0|z_1)}{p(z_0)}\right)+\sum_{t=0}^{T-2}\log\left(\frac{q_\phi(z_{t+1}|z_{t+2})}{p_\theta(z_{t+1}|z_t)}\right)\right]. $$

  • Can pass to continuous time limit, in which case $z_t$ described by stochastic differential equation (SDE). $$ dz_t = \mu_\theta(z_t)dt + dW_t $$ $W_t$ is $\R^H$ dimensional Brownian motion, $\mu_\theta(z_t)$ is a parameterized drift

  • One forward and one backward SDE

  • Model is separate from implementation of dynamics. Solve SDE by whatever method you like: AD through solution.

  • Possible applications

    1. Infer the trajectories that led to measured outcomes in stochastic dynamics.

      • Forward model describes a simulation of a physical system – e.g. molecular dynamics simulation of a biomolecule
      • Backward model can be used to infer trajectories that led to some measured states $z_T$.
    2. Fix the backward model and just learn the forward model. Seems strange from point of view of finding posterior

Denoising Diffusion Probabilistic Models

Normalizing flows

  • Autoencoders conceived for $H<D$

  • By taking $\R^H=\R^D$ can make contact with: Normalizing Flows

  • Take $\bSigma_\phi$ and $\bSigma'_\theta\to 0$, so that $q_\phi(\bz|\bx)$ and $p_\theta(\bx|\bz)$ become deterministic

$$ \bz = \mu_\phi(\bx),\qquad \bx = \mu'_\theta(\bz). $$

  • $D_\text{KL}\neq 0$ only if they are inverses
  • What is KL? $$ q_\phi(\cdot|\bx) = \frac{1}{\sqrt{(2\pi)^{D} \det\bSigma_\phi(\bx)}} \exp\left[-\frac{1}{2}(\bz-\bmu_\phi(\bx))^T\bSigma^{-1}_\phi(\bx)(\bz-\bmu_\phi(\bx))\right], $$

  • KL involves the ratio $$ \frac{q_\phi(\bz|\bx)}{p_\theta(\bx|\bz)} $$

  • When $\bz$ and $\bx$ are inverses $$ \frac{q_\phi(\bz|\bx)}{p_\theta(\bx|\bz)}\longrightarrow \sqrt{\frac{\det\bSigma'_\theta(\bz)}{\det\bSigma_\phi(\bx)}}=\det \left(\frac{\partial\bx}{\partial\bz}\right). $$

  • If $\bz$ described by $p(\bz)$ then $\bx=\mu'_\theta(\bz)$ has density $$ \det\left(\frac{\partial\bz}{\partial\bx}\right) p(\mu_\phi(\bx)). $$ i.e. we map to $\bz$ and evaluate density there, accounting for Jacobian

  • In deterministic limit, KL becomes $$ D_\text{KL}(p_\text{B}||p_\text{F})\longrightarrow -\E_{x\sim \text{Data}}\left[\log\det \left(\frac{\partial\bz}{\partial\bx}\right)+\log p(\mu_\phi(\bx))\right]. $$

  • Challenge: construct flexible, invertible models with tractable Jacobians (determinant is $O(D^3)$)

  • Stack simpler transformations, each invertible with known Jacobian.

Learning the path integral

Barr, Gispen, Lamacraft (2020)

Feynman–Kac formula

  • For “imaginary time” Schrödinger $$ \left[-\frac{\nabla^2}{2m}+V(\br_i)\right]\psi(\br,t) = -\partial_t\psi(\br,t) $$
  • Feynman–Kac formula expresses $\psi(\br,t)$ as expectation… $$ \psi(\br_2,t_2) = \E_{\br_t}\left[\exp\left(-\int_{t_1}^{t_2}V(\br_t)dt\right)\psi(\br_{t_1},t_1)\right] $$
...over Brownian paths with $\br_{t_{2}}=\br_{2}$
  • For $t\to\infty$: $\psi(\br,t)\to e^{-E_0 t}\varphi_0(\br)$
  • Path integral Monte Carlo

Ceperley, RMP (1995)

Loss function

  • FK formula defines path measure $\mathbb{P}_\text{FK}$

  • Jamison (1974): process is Markovian $$ d\br_t = d\mathbf{W}_t + \bv(\br_t,t)dt $$

  • Model drift $\bv(\br,t)$ defines measure $\mathbb{P}_\bv$

  • $D_\text{KL}(\mathbb{P}_\bv\lvert\rvert \mathbb{P}_\text{FK})=\E_{\mathbb{P}_\bv}\left[\log\left(\frac{d\mathbb{P}_\bv}{d\mathbb{P}_\text{FK}}\right)\right]$ is our loss function

  • RL / Optimal Control formulation of QM (Holland, 1977)


  • Relative likelihood (Radon–Nikodym derivative; Girsanov theorem)

$$ \log\left(\frac{d\mathbb{P}_{\bv}}{d\mathbb{P}_\text{FK}}\right) =\ell_T - E_0 T+\log\left(\frac{\varphi_0(\br_0)}{\varphi_0(\br_T)}\right) $$ $$ \ell_T\equiv \int_0^T \bv(\br_t) \cdot d\mathbf{W}_t+\int_0^T dt\left(\frac{1}{2}|\bv(\br_t)|^2+V(\br_t)\right) $$

  • Monte Carlo estimate of $D_\text{KL}(\mathbb{P}_\bv\lvert\rvert \mathbb{P}_\text{FK})=\E_{\mathbb{P}_\bv}\left[\log\left(\frac{d\mathbb{P}_\bv}{d\mathbb{P}_\text{FK}}\right)\right]$

  • $\br^{(b)}_{t}$ from SDE discretization. Analogous to reparameterization trick

  • $D_\text{KL}(\mathbb{P}_\bv\lvert\rvert \mathbb{P}_\text{FK})\geq 0$ so $\E_{\mathbb{P}_\bv}\left[\ell_T\right]\geq E_0T$

  • Suggests strategy:

    1. Represent $\bv_\theta(\br) = \textsf{NN}_\theta(\br)$
    2. Integrate batch of SDE trajectories
    3. Backprop through the (MC estimated) cost

Hydrogen Molecule

$$ H = -\frac{\nabla_1^2+\nabla_2^2}{2}+ \frac{1}{|\br_1-\br_2|}- \sum_{i=1,2}\left[\frac{1}{|\br_i-\hat{\mathbf{z}} R/2|} + \frac{1}{|\br_i+\hat{\mathbf{z}}R/2|}\right] $$

  • Equilibrium proton separation $R=1.401$, $E_0= -1.174476$

2D Gaussian Bosons

$$ \begin{align} H&=\frac{1}{2}\sum_i \left[-\nabla_i^2 +\br_i^2\right]+\sum_{i<j}U(\br_i-\br_j)\\ U(\br) &=\frac{g}{\pi s^2}e^{-\br^2/s^2} \end{align} $$

  • Drift Visualization ($g=15$, $s=1/2$)