Archive for manifold

manifold learning [BNP Seminar, 11/01/23]

Posted in Books, Statistics, University life with tags , , , , , , , , on January 9, 2023 by xi'an

An incoming BNP webinar on Zoom by Judith Rousseau and Paul Rosa (U of Oxford), on 11 January at 1700 Greenwich time:

Bayesian nonparametric manifold learning

In high dimensions it is common to assume that the data have a lower dimensional structure. We consider two types of low dimensional structure: in the first part the data is assumed to be concentrated near an unknown low dimensional manifold, in the second case it is assumed to be possibly concentrated on an unknown manifold. In both cases neither the manifold nor the density is known. Atypical example is for noisy observations on an unknown low dimensional manifold.

We first consider a family of Bayesian nonparametric density estimators based on location – scale Gaussian mixture priors and we study the asymptotic properties of the posterior distribution. Our work shows in particular that non conjuguate location-scale Gaussian mixture models can adapt to complex geometries and spatially varying regularity when the density is supported near a low dimensional manifold.

In the second part of the talk we will consider also the case where the distribution is supported on a low dimensional manifold. In this non dominated model,we study different types of posterior contraction rates: Wasserstein and L_1(\mu_\mathcal{M}) where \mu_\mathcal{M} is the Haussdorff measure on the manifold \mathcal{M} supporting the density. Some more generic results on Wasserstein contraction rates are also discussed.


asymptotically exact inference in likelihood-free models [a reply from the authors]

Posted in R, Statistics with tags , , , , , , , , , , , , , , , , , on December 1, 2016 by xi'an

[Following my post of lastTuesday, Matt Graham commented on the paper with force détails. Here are those comments. A nicer HTML version of the Markdown reply below is also available on Github.]

Thanks for the comments on the paper!

A few additional replies to augment what Amos wrote:

This however sounds somewhat intense in that it involves a quasi-Newton resolution at each step.

The method is definitely computationally expensive. If the constraint function is of the form of a function from an M-dimensional space to an N-dimensional space, with MN, for large N the dominant costs at each timestep are usually the constraint Jacobian (c/u) evaluation (with reverse-mode automatic differentiation this can be evaluated at a cost of O(N) generator / constraint evaluations) and Cholesky decomposition of the Jacobian product (c/u)(c/u) with O(N³) cost (though in many cases e.g. i.i.d. or Markovian simulated data, structure in the generator Jacobian can be exploited to give a significantly reduced cost). Each inner Quasi-Newton update involves a pair of triangular solve operations which have a O(N²) cost, two matrix-vector multiplications with O(MN) cost, and a single constraint / generator function evaluation; the number of Quasi-Newton updates required for convergence in the numerical experiments tended to be much less than N hence the Quasi-Newton iteration tended not to be the main cost.

The high computation cost per update is traded off however with often being able to make much larger proposed moves in high-dimensional state spaces with a high chance of acceptance compared to ABC MCMC approaches. Even in the relatively small Lotka-Volterra example we provide which has an input dimension of 104 (four inputs which map to ‘parameters’, and 100 inputs which map to ‘noise’ variables), the ABC MCMC chains using the coarse ABC kernel radius ϵ=100 with comparably very cheap updates were significantly less efficient in terms of effective sample size / computation time than the proposed constrained HMC approach. This was in large part due to the elliptical slice sampling updates in the ABC MCMC chains generally collapsing down to very small moves even for this relatively coarse ϵ. Performance was even worse using non-adaptive ABC MCMC methods and for smaller ϵ, and for higher input dimensions (e.g. using a longer sequence with correspondingly more random inputs) the comparison becomes even more favourable for the constrained HMC approach. Continue reading

asymptotically exact inference in likelihood-free models

Posted in Books, pictures, Statistics with tags , , , , , , , on November 29, 2016 by xi'an

“We use the intuition that inference corresponds to integrating a density across the manifold corresponding to the set of inputs consistent with the observed outputs.”

Following my earlier post on that paper by Matt Graham and Amos Storkey (University of Edinburgh), I now read through it. The beginning is somewhat unsettling, albeit mildly!, as it starts by mentioning notions like variational auto-encoders, generative adversial nets, and simulator models, by which they mean generative models represented by a (differentiable) function g that essentially turn basic variates with density p into the variates of interest (with intractable density). A setting similar to Meeds’ and Welling’s optimisation Monte Carlo. Another proximity pointed out in the paper is Meeds et al.’s Hamiltonian ABC.

“…the probability of generating simulated data exactly matching the observed data is zero.”

The section on the standard ABC algorithms mentions the fact that ABC MCMC can be (re-)interpreted as a pseudo-marginal MCMC, albeit one targeting the ABC posterior instead of the original posterior. The starting point of the paper is the above quote, which echoes a conversation I had with Gabriel Stolz a few weeks ago, when he presented me his free energy method and when I could not see how to connect it with ABC, because having an exact match seemed to cancel the appeal of ABC, all parameter simulations then producing an exact match under the right constraint. However, the paper maintains this can be done, by looking at the joint distribution of the parameters, latent variables, and observables. Under the implicit restriction imposed by keeping the observables constant. Which defines a manifold. The mathematical validation is achieved by designing the density over this manifold, which looks like

p(u)\left|\frac{\partial g^0}{\partial u}\frac{\partial g^0}{\partial u}^\text{T}\right|^{-\textonehalf}

if the constraint can be rewritten as g⁰(u)=0. (This actually follows from a 2013 paper by Diaconis, Holmes, and Shahshahani.) In the paper, the simulation is conducted by Hamiltonian Monte Carlo (HMC), the leapfrog steps consisting of an unconstrained move followed by a projection onto the manifold. This however sounds somewhat intense in that it involves a quasi-Newton resolution at each step. I also find it surprising that this projection step does not jeopardise the stationary distribution of the process, as the argument found therein about the approximation of the approximation is not particularly deep. But the main thing that remains unclear to me after reading the paper is how the constraint that the pseudo-data be equal to the observable data can be turned into a closed form condition like g⁰(u)=0. As mentioned above, the authors assume a generative model based on uniform (or other simple) random inputs but this representation seems impossible to achieve in reasonably complex settings.

Moment conditions and Bayesian nonparametrics

Posted in R, Statistics, University life with tags , , , , , , , , , , on August 6, 2015 by xi'an

Luke Bornn, Neil Shephard, and Reza Solgi (all from Harvard) have arXived a pretty interesting paper on simulating targets on a zero measure set. Although it is not initially presented this way, but rather in non-parametric terms as moment conditions


where θ is the parameter of the sampling distribution, constrained by the value of β. (Which also contains quantile regression.) The very problem of simulating under a hard constraint has been bugging me for years and it is hence very exciting to see them come up with a proposal towards solving this difficulty! Even though it is restricted here to observations with a finite support (hence allowing for the use of a parametric Dirichlet prior). One interesting extension (Section 3.6) processed in the paper is the case when the support is unknown, but finite, with some points in the support being unobserved. Maybe connecting with non-parametrics if a prior is added on the number of unobserved points.

The setting of constricting θ via a parameterised moment condition relates to moment defined econometrics models, in a similar spirit to Gallant’s paper I recently discussed, but equally to empirical likelihood, which would then benefit from a fully Bayesian treatment thanks to the approach advocated by the authors.

bornnshepardDespite the zero-measure difficulty, or more exactly the non-linear manifold structure of the parameter space, for instance

β = log {θ/(1-θ)}

the authors manage to define a “projected” [my words] measure on the set of admissible pairs (β,θ). In a sense this is related with the choice of a certain metric, but the so-called Hausdorff reference measure allows for an automated definition of the original prior. It took me a (wee) while to spot (p.7) that the starting point was not a (unconstrained) prior on that (unconstrained) pair (β,θ) but directly on the manifold


Which makes its construction a difficulty. Even though, as noted in Section 4, all that we need is a prior over θ since the Hausdorff-Jacobian identity defines the “joint”, in a sort of backward way. (This is a wee bit confusing in that β being a transform of θ, all we need is a prior over θ, but we nonetheless end up with a different density on the joint distribution on the pair (β,θ). Any connection with incompatible priors merged together into a consensus prior?) Another question extending the scope of the paper would be to define Jeffreys’ or reference priors in this manifold sense.

The authors also discuss (Section 4.3) the problem I originally thought they were processing, namely starting from an unconstrained pair (β,θ) and it corresponding prior. The projected prior can then be defined based on a version of the original density on the constrained space, but it is definitely arbitrary. In that sense the paper does not address the general problem.

bornnshepard1“…traditional simulation algorithms will fail because the prior and the posterior of the model are supported on a zero Lebesgue measure set…” (p.10)

I somewhat resist this presentation through the measure zero set: once the prior is defined on a manifold, the fact that it is a measure zero set in a larger space is moot. Provided one can simulate a proposal over that manifold, e.g., a random walk, absolutely continuous wrt the same dominating measure, and compute or estimate a Metropolis-Hastings ratio of densities against a common measure, one can formally run MCMC on manifolds as well as regular Euclidean spaces. A first and theoretically straightforward (?) solution is to solve the constraint


in β=β(θ). Then the joint prior p(β,θ) can be projected by the Hausdorff projection into p(θ). For instance, in the case of the above logit transform, the projected density is

p(θ)=p(β,θ) {1+1/θ²(1-θ)²}½

In practice, the inversion may be too costly and Bornn et al. directly simulate the pair (β,θ) within the manifold capitalising on the fact that the constraint is linear in θ given β. Indeed, in this setting, β is unconstrained and θ can be simulated from a proposal restricted to the hyperplane. Gibbs-like.

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