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Variational Autoencoders

A latent-variable model trained by maximizing an evidence lower bound; the gap is KL(q_phi(z|x) || p_theta(z|x)), so the encoder is learned inference rather than just compression.

published · difficulty 4/5 · 20 min read

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Intuition

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Maximum likelihood asks for a model that assigns high log probability to the observed data:

logpθ(x).\log p_\theta(x).logpθ(x).

A variational autoencoder is a maximum-likelihood model with a hidden cause. It imagines that each observation xxx was produced from an unobserved latent variable zzz:

zp(z),xpθ(xz).\begin{aligned} z &\sim p(z), \\ x &\sim p_\theta(x\mid z). \end{aligned}zxp(z),pθ(xz).

Training would be easy if we could compute the marginal likelihood

pθ(x)=pθ(x,z)dz.\begin{aligned} p_\theta(x) &= \int p_\theta(x,z)\,dz. \end{aligned}pθ(x)=pθ(x,z)dz.

The problem is that this integral is usually hard for neural decoders. Bayesian inference tells us what we would like to use:

pθ(zx).p_\theta(z\mid x).pθ(zx).

But that posterior contains the same hard evidence term pθ(x)p_\theta(x)pθ(x). The VAE move is to learn an encoder

qϕ(zx)q_\phi(z\mid x)qϕ(zx)

that acts as a tractable approximate posterior.

The central mechanism is not "an autoencoder with noise." It is: replace the intractable posterior with a learned distribution qϕ(zx)q_\phi(z\mid x)qϕ(zx), then optimize a lower bound whose looseness is exactly a KL divergence from qϕq_\phiqϕ to the true posterior.

That is why VAEs sit at the intersection of maximum likelihood, Bayesian inference, and KL divergence.

Two natural next moves branch from this page. Normalizing flows ask what changes when the latent transformation is invertible and likelihood stays exact. Diffusion asks what changes when generation is learned as a gradual denoising process rather than as one sampled latent code.

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Latent variable likelihood

For one observed datapoint xxx, assume a prior p(z)p(z)p(z) and a decoder likelihood pθ(xz)p_\theta(x\mid z)pθ(xz). The latent-variable model, marginal likelihood, and true posterior are

pθ(x,z)=p(z)pθ(xz),pθ(x)=pθ(x,z)dz,pθ(zx)=pθ(x,z)pθ(x).\begin{aligned} p_\theta(x,z)&=p(z)p_\theta(x\mid z),\\ p_\theta(x)&=\int p_\theta(x,z)\,dz,\\ p_\theta(z\mid x)&=\frac{p_\theta(x,z)}{p_\theta(x)}. \end{aligned}pθ(x,z)pθ(x)pθ(zx)=p(z)pθ(xz),=pθ(x,z)dz,=pθ(x)pθ(x,z).

The evidence pθ(x)p_\theta(x)pθ(x) appears in the denominator, so exact posterior inference and exact likelihood training are tied to the same difficult integral. The claim-bearing VAE move is summarized by

logpθ(x)=L(θ,ϕ;x)+KL ⁣(qϕ(zx)pθ(zx)),L(θ,ϕ;x)=Eqϕ(zx)[logpθ(xz)]KL ⁣(qϕ(zx)p(z)),ϵN(0,I),z=μϕ(x)+σϕ(x)ϵ.\begin{aligned} \log p_\theta(x) &= \mathcal L(\theta,\phi;x) + \mathrm{KL}\!\left(q_\phi(z\mid x)\,\|\,p_\theta(z\mid x)\right),\\ \mathcal L(\theta,\phi;x) &= \mathbb E_{q_\phi(z\mid x)}[\log p_\theta(x\mid z)] - \mathrm{KL}\!\left(q_\phi(z\mid x)\,\|\,p(z)\right),\\ \epsilon&\sim\mathcal N(0,I), \qquad z=\mu_\phi(x)+\sigma_\phi(x)\odot\epsilon. \end{aligned}logpθ(x)L(θ,ϕ;x)ϵ=L(θ,ϕ;x)+KL(qϕ(zx)pθ(zx)),=Eqϕ(zx)[logpθ(xz)]KL(qϕ(zx)p(z)),N(0,I),z=μϕ(x)+σϕ(x)ϵ.

The first line says the ELBO gap is exactly the KL from the learned encoder qϕ(zx)q_\phi(z\mid x)qϕ(zx) to the true posterior. The second line separates reconstruction likelihood from prior pressure. The third line keeps randomness in external noise ϵ\epsilonϵ, so gradients of sampled reconstruction terms can flow through zzz into the encoder outputs.

The ELBO identity

Let qϕ(zx)q_\phi(z\mid x)qϕ(zx) be any approximate posterior whose support is compatible with the true posterior. To keep the equations readable, write q(z)q(z)q(z) for qϕ(zx)q_\phi(z\mid x)qϕ(zx) and Eq\mathbb E_qEq for expectation under that distribution:

Eq[]Eq(z)[].\mathbb E_q[\cdot] \equiv \mathbb E_{q(z)}[\cdot].Eq[]Eq(z)[].

Using Bayes' rule and rearranging gives the exact identity

logpθ(x)=L+G.\log p_\theta(x)=\mathcal L+G.logpθ(x)=L+G.

Here L\mathcal LL is the ELBO and GGG is the inference gap. Let p(z)p_*(z)p(z) denote the true posterior pθ(zx)p_\theta(z\mid x)pθ(zx). Then the gap is

G=KL(q(z)p(z)).G=\mathrm{KL}(q(z)\,\|\,p_*(z)).G=KL(q(z)p(z)).

Equivalently,

G=Eq[logq(z)logp(z)].G=\mathbb E_q[\log q(z)-\log p_*(z)].G=Eq[logq(z)logp(z)].

The ELBO term is

L=Eq[logpθ(x,z)logq(z)].\mathcal L = \mathbb E_q[\log p_\theta(x,z)-\log q(z)].L=Eq[logpθ(x,z)logq(z)].

The gap can also be read by subtraction:

G=logpθ(x)L.G=\log p_\theta(x)-\mathcal L.G=logpθ(x)L.

KL is nonnegative, so

L(θ,ϕ;x)logpθ(x).\mathcal L(\theta,\phi;x)\le \log p_\theta(x).L(θ,ϕ;x)logpθ(x).

Maximizing the ELBO improves this lower bound. The bound is tight exactly when the encoder distribution equals the true posterior, up to probability-zero events.

Reconstruction likelihood plus prior KL

Because

logpθ(x,z)=logpθ(xz)+logp(z),\log p_\theta(x,z) = \log p_\theta(x\mid z)+\log p(z),logpθ(x,z)=logpθ(xz)+logp(z),

the ELBO can be rewritten as

L=Eq[logpθ(xz)]KL(q(z)p(z)).\begin{aligned} \mathcal L &= \mathbb E_q[\log p_\theta(x\mid z)] \\ &\quad- \mathrm{KL}(q(z)\,\|\,p(z)). \end{aligned}L=Eq[logpθ(xz)]KL(q(z)p(z)).

The first term is a reconstruction log likelihood, not generically a pixel distance. The second term keeps the encoder's posterior close to the prior used for generation. At generation time we sample zp(z)z\sim p(z)zp(z), not zqϕ(zx)z\sim q_\phi(z\mid x)zqϕ(zx) for a training example, so the prior match is load-bearing.

Reconstruction likelihood is not always MSE

The reconstruction term is

Eq[logpθ(xz)].\mathbb E_q[\log p_\theta(x\mid z)].Eq[logpθ(xz)].

It becomes a familiar loss only after choosing a decoder distribution. With a fixed-variance Gaussian decoder centered at fθ(z)f_\theta(z)fθ(z), the negative log likelihood is a scaled squared error plus a constant. So MSE appears as a Gaussian negative log likelihood only after that modeling choice.

If xxx is binary and

pθ(xz)=Bernoulli(πθ(z)),p_\theta(x\mid z)=\operatorname{Bernoulli}(\pi_\theta(z)),pθ(xz)=Bernoulli(πθ(z)),

then the negative reconstruction log likelihood is binary cross-entropy.

Reparameterization trick

For a diagonal Gaussian encoder, the network outputs μϕ(x)\mu_\phi(x)μϕ(x) and σϕ(x)\sigma_\phi(x)σϕ(x). We sample with external noise:

ϵN(0,I),z=μϕ(x)+σϕ(x)ϵ.\epsilon\sim\mathcal N(0,I), \qquad z=\mu_\phi(x)+\sigma_\phi(x)\odot\epsilon.ϵN(0,I),z=μϕ(x)+σϕ(x)ϵ.

This keeps the randomness in ϵ\epsilonϵ and makes the sample differentiable with respect to the encoder outputs μϕ(x)\mu_\phi(x)μϕ(x) and σϕ(x)\sigma_\phi(x)σϕ(x).

Beta-VAE objective

A beta-VAE changes the training objective to

Lβ=Eq[logpθ(xz)]βKL(q(z)p(z)).\begin{aligned} \mathcal L_\beta &= \mathbb E_q[\log p_\theta(x\mid z)] \\ &\quad- \beta\,\mathrm{KL}(q(z)\,\|\,p(z)). \end{aligned}Lβ=Eq[logpθ(xz)]βKL(q(z)p(z)).

When β=1\beta=1β=1, this is the standard VAE ELBO. When β1\beta\ne 1β=1, it is a modified objective rather than the original ELBO. For β>1\beta>1β>1, it remains a lower bound because it subtracts extra nonnegative KL penalty, but it is no longer the standard maximum-likelihood ELBO. For β<1\beta<1β<1, it is generally not guaranteed to lower-bound logpθ(x)\log p_\theta(x)logpθ(x).

Larger β\betaβ puts more pressure on zzz to carry less information and stay close to the prior. This can encourage more factor-like representations in some settings, but it does not guarantee disentanglement. If the pressure is too strong, the encoder may approach qϕ(zx)p(z)q_\phi(z\mid x)\approx p(z)qϕ(zx)p(z), so zzz carries little information about xxx.

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Code

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This scalar linear-Gaussian example is small enough that we can compute the exact marginal likelihood, exact posterior, ELBO, and inference gap, then check a one-sample reparameterized reconstruction gradient by finite differences.

import math

def log_norm(x, mean, var):
    return -0.5 * (math.log(2 * math.pi * var) + (x - mean) ** 2 / var)

def kl_norm(mu0, var0, mu1, var1):
    return 0.5 * (var0 / var1 + (mu1 - mu0) ** 2 / var1 - 1 + math.log(var1 / var0))

x, w, b, sigma_x = 1.5, 1.2, -0.1, 0.3  # z~N(0,1), x|z~N(wz+b,sigma_x^2)
var_x = sigma_x ** 2
mu_q, logvar_q = 0.3, -0.7              # q(z|x)=N(mu_q, exp(logvar_q))
var_q = math.exp(logvar_q)

log_px = log_norm(x, b, w * w + var_x)
post_var = 1 / (1 + w * w / var_x)
post_mu = post_var * w * (x - b) / var_x
recon = -0.5 * (math.log(2 * math.pi * var_x) + ((x - b - w * mu_q) ** 2 + w * w * var_q) / var_x)
kl_prior = kl_norm(mu_q, var_q, 0, 1)
elbo = recon - kl_prior
gap = log_px - elbo
kl_post = kl_norm(mu_q, var_q, post_mu, post_var)
assert abs(gap - kl_post) < 1e-10

eps = -0.4
def sampled_recon(mu, logvar):
    sigma = math.exp(0.5 * logvar)
    z = mu + sigma * eps
    return log_norm(x, w * z + b, var_x), z, sigma

sample_loglik, z, sigma = sampled_recon(mu_q, logvar_q)
dloglik_dz = (x - (w * z + b)) * w / var_x
path_mu = dloglik_dz
path_logvar = dloglik_dz * 0.5 * sigma * eps
h = 1e-5
fd_mu = (sampled_recon(mu_q + h, logvar_q)[0] - sampled_recon(mu_q - h, logvar_q)[0]) / (2 * h)
fd_logvar = (sampled_recon(mu_q, logvar_q + h)[0] - sampled_recon(mu_q, logvar_q - h)[0]) / (2 * h)
assert abs(path_mu - fd_mu) < 1e-7
assert abs(path_logvar - fd_logvar) < 1e-7

print(round(elbo, 3), round(log_px, 3), round(gap, 3), round(sample_loglik, 3))

For a batched neural VAE, typical shapes are:

  • x: (B, D)
  • encoder outputs mu, logvar: (B, K)
  • noise eps: (S, B, K)
  • latent samples z = mu[None, :, :] + exp(0.5 * logvar)[None, :, :] * eps: (S, B, K)
  • decoder log likelihood per sample: (S, B)
  • Monte Carlo reconstruction estimate: (B,)
  • analytic diagonal-Gaussian KL: (B,)
  • per-example ELBO: (B,)
  • optimization loss -elbo.mean(): scalar
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Explore Variational Autoencoders

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difficulty 4/5undergraduatecode-aligned
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The demo keeps the latent variable one-dimensional so the hidden inference geometry can be revealed after a prediction. Move the approximate posterior q(zx)q(z\mid x)q(zx), inspect the prior and likelihood shape, then predict what the ELBO gap will diagnose.

After reveal, compare the target curve and identity values with your prediction. The point is to feel the ELBO as a lower bound whose looseness is measured by the mismatch between qqq and the hidden target distribution.

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Concept: Variational Autoencoders

What is the smallest example that makes Variational Autoencoders click without losing the math?

BeforeMaximum LikelihoodNow4/4 sections readyTryManipulate one control and predict the visible change.NextNormalizing Flows: Tractable Density via Invertible Transforms
Object contextGenerative Models
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Variational Autoencoders

What is the smallest example that makes Variational Autoencoders click without losing the math?

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Work hereVariational Autoencoders

A latent-variable model trained by maximizing an evidence lower bound; the gap is KL(q_phi(z|x) || p_theta(z|x)), so the encoder is learned inference rather than just compression.

Carry outNormalizing Flows: Tractable Density via Invertible Transforms

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A latent-variable model trained by maximizing an evidence lower bound; the gap is KL(q_phi(z|x) || p_theta(z|x)), so the encoder is learned inference rather than just compression.

Demo notes open01 / Intuition
Editorial generative-model illustration of data encoded into a latent distribution and decoded back into reconstructed samples.
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A latent-variable model trained by maximizing an evidence lower bound; the gap is KL(q_phi(z|x) || p_theta(z|x)), so the encoder is learned inference rather than just compression.

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Object - ConceptVariational AutoencodersQuestion

What is the smallest example that makes Variational Autoencoders click without losing the math?

concept:generative-models/vaes
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sources: kingma-2013-auto-encoding-variational-bayes, rezende-2014-stochastic-backprop

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selected object source · paper · 2013Auto-Encoding Variational BayesKingma and Welling
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Introduces the reparameterized VAE objective and the evidence lower bound training view.

Used here as

Kingma/Welling and Rezende/Mohamed/Wierstra both ground VAEs/deep latent-variable models in ELBO optimization with learned inference networks and reparameterized or stochastic backpropaga...

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The reconstruction term is an expectation under q_phi and often Monte Carlo estimated. Pathwise gradients require a differentiable transform of parameter-independent noise, so this does n...

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selected object source · paper · 2014Stochastic Backpropagation and Approximate Inference in Deep Generative ModelsRezende, Mohamed, and Wierstra
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Grounds stochastic backpropagation for latent-variable generative models with learned inference networks.

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Kingma/Welling and Rezende/Mohamed/Wierstra both ground VAEs/deep latent-variable models in ELBO optimization with learned inference networks and reparameterized or stochastic backpropaga...

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The reconstruction term is an expectation under q_phi and often Monte Carlo estimated. Pathwise gradients require a differentiable transform of parameter-independent noise, so this does n...

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A latent-variable model trained by maximizing an evidence lower bound; the gap is KL(q_phi(z|x) || p_theta(z|x)), so the encoder is learned inference rather than just compression.

Object - ConceptVariational AutoencodersQuestion

What is the smallest example that makes Variational Autoencoders click without losing the math?

concept:generative-models/vaes
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sources: kingma-2013-auto-encoding-variational-bayes, rezende-2014-stochastic-backprop

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A VAE fits a latent-variable generative model by maximizing the ELBO: q_phi(z|x) approximates the usually intractable posterior, E_q[log p_theta(x|z)] rewards reconstruction likelihood, KL(q_phi(z|x)||p(z)) penalizes deviation from the prior, and reparameterization gives pathwise gradients through z samples.
Used here as

Kingma/Welling and Rezende/Mohamed/Wierstra both ground VAEs/deep latent-variable models in ELBO optimization with learned inference networks and reparameterized or stochastic backpropagation estimators. Loc...

Local witness
Equation 1
pθ(x,z)=p(z)pθ(xz),pθ(x)=pθ(x,z)dz,pθ(zx)=pθ(x,z)pθ(x).\begin{aligned} p_\theta(x,z)&=p(z)p_\theta(x\mid z),\\ p_\theta(x)&=\int p_\theta(x,z)\,dz,\\ p_\theta(z\mid x)&=\frac{p_\theta(x,z)}{p_\theta(x)}. \end{aligned}
Equation 2
logpθ(x)=L(θ,ϕ;x)+KL ⁣(qϕ(zx)pθ(zx)),L(θ,ϕ;x)=Eqϕ(zx)[logpθ(xz)]KL ⁣(qϕ(zx)p(z)),ϵN(0,I),z=μϕ(x)+σϕ(x)ϵ.\begin{aligned} \log p_\theta(x) &= \mathcal L(\theta,\phi;x) + \mathrm{KL}\!\left(q_\phi(z\mid x)\,\|\,p_\theta(z\mid x)\right),\\ \mathcal L(\theta,\phi;x) &= \mathbb E_{q_\phi(z\mid x)}[\log p_\theta(x\mid z)] - \mathrm{KL}\!\left(q_\phi(z\mid x)\,\|\,p(z)\right),\\ \epsilon&\sim\mathcal N(0,I), \qquad z=\mu_\phi(x)+\sigma_\phi(x)\odot\epsilon. \end{aligned}
Caveat

The reconstruction term is an expectation under q_phi and often Monte Carlo estimated. Pathwise gradients require a differentiable transform of parameter-independent noise, so this does not cover discrete or...

Review stateCF editorial source-scope reviewClaim metadata: source checkedPublisher-side editorial review only; not independent replication. Check caveats and exact source scope.

Kingma/Welling support q_phi(z|x) as a learned recognition model for the intractable posterior, derive log p_theta(x)=ELBO+KL(q||posterior), decompose the ELBO into E_q log p_theta(x|z)-KL(q||p(z)), and give Gaussian reparameterization. Rezende et al. independently support the recognition-model, lower-bound/free-energy, reconstruction/regularization, and stochastic-backprop structure. Local math, code, and demo now witness the ELBO gap, prior KL, reparameterized sample, and prediction-gated posterior diagnostics.

Reviewer: codex+oracle+codex-5.3; reviewed 2026-05-08

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A latent-variable model trained by maximizing an evidence lower bound; the gap is KL(q_phi(z|x) || p_theta(z|x)), so the encoder is learned inference rather than just compression.

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Object - ConceptVariational AutoencodersQuestion

What is the smallest example that makes Variational Autoencoders click without losing the math?

concept:generative-models/vaes
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conceptGenerative Models

Variational Autoencoders

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What is the smallest example that makes Variational Autoencoders click without losing the math?

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  • The learner can predict how the mechanism changes under one perturbation
Object-attached AI handoff

I am working in Continuous Function's research reading room. Object: concept - Variational Autoencoders Object key: concept:generative-models/vaes Context: Generative Models Anchor id: concept/concept-notebook/generative-models/vaes Open question: What is the smallest example that makes Variational Autoencoders click without losing the math? Evidence to inspect: - Source ids to inspect: kingma-2013-auto-encoding-variational-bayes, rezende-2014-stochastic-backprop - Definition, prerequisite, and contrast concept links - The equation or code witness that makes the concept operational - One demo state that shows the invariant instead of a slogan Deterministic role lenses for this object: - Boundary: fixed perspectives, not people, community contributions, or independent review - Source-checking summary: Treat this as a mechanism object: connect the definition to one equation, code witness, or demo before broadening the discussion. - Proposed experiment: Ask the learner to perturb one representation, then check whether the same invariant survives in math, code, and demo. - Teach/transfer move: Turn the mechanism into one sentence that predicts a neighboring concept. - Assumptions: - Source ids kingma-2013-auto-encoding-variational-bayes, rezende-2014-stochastic-backprop must support the exact object, not just the surrounding topic. - The stable content-object key lets local drafts, prompts, and route memory attach without changing the source page. - The concept explanation is local atlas prose until checked against its math, code, and source support. - Prerequisite gaps should become a repair route, not a reason to leave the object vague. - Role-lens requests: - Learner: ask for "Ask what would make "Variational Autoencoders" feel predictable rather than familiar." | assumption: Source ids kingma-2013-auto-encoding-variational-bayes, rezende-2014-stochastic-backprop must support the exact object, not just the surrounding topic. | next action: The learner can state the mechanism in their own words - Researcher: ask for "Source ids to inspect: kingma-2013-auto-encoding-variational-bayes, rezende-2014-stochastic-backprop" | assumption: The stable content-object key lets local drafts, prompts, and route memory attach without changing the source page. | next action: The learner can name the prerequisite that would repair confusion - Experimenter: ask for "Choose one variable or condition to perturb before asking for an explanation." | assumption: The concept explanation is local atlas prose until checked against its math, code, and source support. | next action: The learner can predict how the mechanism changes under one perturbation - Professor: ask for "Find the smallest transferable rule a learner could reuse without the AI." | assumption: Prerequisite gaps should become a repair route, not a reason to leave the object vague. | next action: Teach or transfer: Turn the mechanism into one sentence that predicts a neighboring concept. What would resolve this: - The learner can state the mechanism in their own words - The learner can name the prerequisite that would repair confusion - The learner can predict how the mechanism changes under one perturbation Answer as a careful research tutor: stay source-grounded, separate verified evidence from assumptions, name the relevant math objects, and end with one next action. Current deterministic role lens for this object: - Role lens: Learner - Evidence request: Ask what would make "Variational Autoencoders" feel predictable rather than familiar. - Assumption to keep visible: Source ids kingma-2013-auto-encoding-variational-bayes, rezende-2014-stochastic-backprop must support the exact object, not just the surrounding topic. - Proposed experiment: Ask the learner to perturb one representation, then check whether the same invariant survives in math, code, and demo. - Next action: The learner can state the mechanism in their own words

concept/concept-notebook/generative-models/vaes concept:generative-models/vaes