## Monte Carlo fusion

Posted in Statistics with tags , , , , , , , , , on January 18, 2019 by xi'an

Hongsheng Dai, Murray Pollock (University of Warwick), and Gareth Roberts (University of Warwick) just arXived a paper we discussed together last year while I was at Warwick. Where fusion means bringing different parts of the target distribution

f(x)∝f¹(x)f²(x)…

together, once simulation from each part has been done. In the same spirit as in Scott et al. (2016) consensus Monte Carlo. Where for instance the components of the target cannot be computed simultaneously, either because of the size of the dataset, or because of privacy issues.The idea in this paper is to target an augmented density with the above marginal, using for each component of f, an auxiliary variable x¹,x²,…, and a target that is the product of the squared component, f¹(x¹)², f²(x²)², … by a transition density keeping f¹(.)²,f²(.)²,… invariant:

$f^c(x^c)^2 p_c(y|x^c) / f_c(y)$

as for instance the transition density of a Langevin diffusion. The marginal of

$\prod_c f^c(x^c)^2 p_c(y|x^c) / f_c(y)$

as a function of y is then the targeted original product. Simulating from this new extended target can be achieved by rejection sampling. (Any impact of the number of auxiliary variables on the convergence?) The practical implementation actually implies using the path-space rejection sampling methods in the Read Paper of Beskos et al. (2006). (An extreme case of the algorithm is actually an (exact) ABC version where the simulations x¹,x²,… from all components have to be identical and equal to y. The opposite extreme is the consensus Monte Carlo Algorithm, which explains why this algorithm is not an efficient solution.) An alternative is based on an Ornstein-Uhlenbeck bridge. While the paper remains at a theoretical level with toy examples, I heard from the same sources that applications to more realistic problems and implementation on parallel processors is under way.

## Langevin on a wrong bend

Posted in Books, Statistics with tags , , , , , , , on October 19, 2017 by xi'an

Arnak Dalayan and Avetik Karagulyan (CREST) arXived a paper the other week on a focussed study of the Langevin algorithm [not MALA] when the gradient of the target is incorrect. With the following improvements [quoting non-verbatim from the paper]:

1. a varying-step Langevin that reduces the number of iterations for a given Wasserstein precision, compared with recent results by e.g. Alan Durmus and Éric Moulines;
2. an extension of convergence results for error-prone evaluations of the gradient of the target (i.e., the gradient is replaced with a noisy version, under some moment assumptions that do not include unbiasedness);
3. a new second-order sampling algorithm termed LMCO’, with improved convergence properties.

What is particularly interesting to me in this setting is the use in all these papers of a discretised Langevin diffusion (a.k.a., random walk with a drift induced by the gradient of the log-target) without the original Metropolis correction. The results rely on an assumption of [strong?] log-concavity of the target, with “user-friendly” bounds on the Wasserstein distance depending on the constants appearing in this log-concavity constraint. And so does the adaptive step. (In the case of the noisy version, the bias and variance of the noise also matter. As pointed out by the authors, there is still applicability to scaling MCMC for large samples. Beyond pseudo-marginal situations.)

“…this, at first sight very disappointing behavior of the LMC algorithm is, in fact, continuously connected to the exponential convergence of the gradient descent.”

The paper concludes with an interesting mise en parallèle of Langevin algorithms and of gradient descent algorithms, since the convergence rates are the same.

## non-reversible Langevin samplers

Posted in Books, pictures, Statistics, Travel, University life with tags , , , , , , , , , , on February 6, 2017 by xi'an

In the train to Oxford yesterday night, I read through the recently arXived Duncan et al.’s Nonreversible Langevin Samplers: Splitting Schemes, Analysis and Implementation. Standing up the whole trip in the great tradition of British trains.

The paper is fairly theoretical and full of Foster-Lyapunov assumptions but aims at defending an approach based on a non-reversible diffusion. One idea is that the diffusion based on the drift {∇ log π(x) + γ(x)} is associated with the target π provided

∇ . {π(x)γ(x)} = 0

which holds for the Langevin diffusion when γ(x)=0, but produces a non-reversible process in the alternative. The Langevin choice γ(x)=0 happens to be the worst possible when considering the asymptotic variance. In practice however the diffusion need be discretised, which induces an approximation that may be catastrophic for convergence if not corrected, and a relapse into reversibility if corrected by Metropolis. The proposal in the paper is to use a Lie-Trotter splitting I had never heard of before to split between reversible [∇ log π(x)] and non-reversible [γ(x)] parts of the process. The deterministic part is chosen as γ(x)=∇ log π(x) [but then what is the point since this is Langevin?] or as the gradient of a power of π(x). Although I was mostly lost by that stage, the paper then considers the error induced by a numerical integrator related with this deterministic part, towards deriving asymptotic mean and variance for the splitting scheme. On the unit hypercube. Although the paper includes a numerical example for the warped normal target, I find it hard to visualise the implementation of this scheme. Having obviously not heeded Nicolas’ and James’ advice, the authors also analyse the Pima Indian dataset by a logistic regression!)

## scalable Langevin exact algorithm

Posted in Books, Statistics, Travel, University life with tags , , , , , , , , , , , on October 18, 2016 by xi'an

“By employing a modification to existing naïve subsampling techniques we can obtain an algorithm which is still exact but has sub-linear iterative cost as a function of data size.”

A few weeks ago Murray Pollock, Paul Fearnhead, Adam Johansen and Gareth Roberts (all from Warwick except for Paul) arXived a paper The Scalable Langevin Exact Algorithm: Bayesian Inference for Big Data. (This was also the topic of Murray’s talk last year at JSM in Seattle.) One major advance found in the paper is the derivation of an “exact” algorithm that is sub-linear in the data size. As discussed in the introduction, the current approaches to large data problems either suffer from being approximate (like divide-and-conquer methods) or do not achieve significant reduction in the computing time, being of order O(n). The authors mention Teh and Welling (2011) sand their tochastic gradient approximation to the Langevin diffusion, when the gradient is based on a subsample. Without the Metropolis correction that would ensure an exact target but at a cost of order O(n). (Which makes the technique rather difficult to recommend.)

A novel [for me] notion at the core of this paper is the concept of quasi-stationary distribution, which is the limiting distribution of a Markov chain X[t] conditional on a Markov stopping time [being larger than t]. The approach is based on diffusions with appropriate stationary distributions like the Langevin diffusion. (Actually, as in most papers I have read and remember, the current paper only considers the Langevin diffusion.) In order to avoid the issues with unadjusted and Metropolis-adjusted Langevin schemes, a killed Brownian motion is created, which means a Brownian motion conditional of being alive till time T when the instantaneous killing rate is a given function of the chain, Φ(X[t]), related with the stationary measure of the Langevin diffusion ν. Under appropriate conditions, the density of this killed Brownian motion converges [in T] to √ν. Which immediately hints at creating a new Langevin diffusion targeting ν² instead of ν. And killing it with the proper rate, which can be done by thinning a Poisson process. Simulating the original path can be done by path-space rejection sampling, following the technique set by Gareth Roberts and co-authors more than ten years ago. Based on finite dimensional realisations of the path on [0,T]. And including the killing part can be done by importance sampling and checking that the simulated killing time is larger than the current (exponentially simulated) time.

One practical difficulty in the implementation of this neat principle is the derivation of the normalising constant, which evaluation degrades with the time horizon T. The solution adopted in the paper is through a sequential Monte Carlo method, using another discretisation of the time interval [0,T] (relying on the original one would get too costly?). As for subsampling, since the survival probability for the Brownian motion is based on an unbiased estimator, subsampling does not hurt if conducted in a random manner. Although this increases the variance on principle, the use of a control variate computed just once helps in reducing the complexity to O(1).

This is a tough paper and I have not gone through the effort of trying to implement it, but this is an original and innovative construct I would like to monitor in further details on a toy example, maybe next week while in Warwick. Or at least to discuss it with the authors.

## JSM 2015 [day #4]

Posted in pictures, Running, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , , , on August 13, 2015 by xi'an

My first session today was Markov Chain Monte Carlo for Contemporary Statistical Applications with a heap of interesting directions in MCMC research! Now, without any possible bias (!), I would definitely nominate Murray Pollock (incidentally from Warwick) as the winner for best slides, funniest presentation, and most enjoyable accent! More seriously, the scalable Langevin algorithm he developed with Paul Fearnhead, Adam Johansen, and Gareth Roberts, is quite impressive in avoiding computing costly likelihoods. With of course caveats on which targets it applies to. Murali Haran showed a new proposal to handle high dimension random effect models by a projection trick that reduces the dimension. Natesh Pillai introduced us (or at least me!) to a spectral clustering that allowed for an automated partition of the target space, itself the starting point to his parallel MCMC algorithm. Quite exciting, even though I do not perceive partitions as an ideal solution to this problem. The final talk in the session was Galin Jones’ presentation of consistency results and conditions for multivariate quantities which is a surprisingly unexplored domain. MCMC is still alive and running!

The second MCMC session of the morning, Monte Carlo Methods Facing New Challenges in Statistics and Science, was equally diverse, with Lynn Kuo’s talk on the HAWK approach, where we discovered that harmonic mean estimators are still in use, e.g., in MrBayes software employed in phylogenetic inference. The proposal to replace this awful estimator that should never be seen again (!) was rather closely related to an earlier solution of us for marginal likelihood approximation, based there on a partition of the whole space rather than an HPD region in our case… Then, Michael Betancourt brilliantly acted as a proxy for Andrew to present the STAN language, with a flashy trailer he most recently designed. Featuring Andrew as the sole actor. And with great arguments for using it, including the potential to run expectation propagation (as a way of life). In fine, Faming Liang proposed a bootstrap subsampling version of the Metropolis-Hastings algorithm, where the likelihood acknowledging the resulting bias in the limiting distribution.

My first afternoon session was another entry on Statistical Phylogenetics, somewhat continued from yesterday’s session. Making me realised I had not seen a single talk on ABC for the entire meeting! The issues discussed in the session were linked with aligning sequences and comparing  many trees. Again in settings where likelihoods can be computed more or less explicitly. Without any expertise in the matter, I wondered at a construction that would turn all trees, like  into realizations of a continuous model. For instance by growing one branch at a time while removing the MRCA root… And maybe using a particle like method to grow trees. As an aside, Vladimir Minin told me yesterday night about genetic mutations that could switch on and off phenotypes repeatedly across generations… For instance  the ability to glow in the dark for species of deep sea fish.

When stating that I did not see a single talk about ABC, I omitted Steve Fienberg’s Fisher Lecture R.A. Fisher and the Statistical ABCs, keeping the morceau de choix for the end! Even though of course Steve did not mention the algorithm! A was for asymptotics, or ancilarity, B for Bayesian (or biducial??), C for causation (or cuffiency???)… Among other germs, I appreciated that Steve mentioned my great-grand father Darmois in connection with exponential families! And the connection with Jon Wellner’s LeCam Lecture from a few days ago. And reminding us that Savage was a Fisher lecturer himself. And that Fisher introduced fiducial distributions quite early. And for defending the Bayesian perspective. Steve also set some challenges like asymptotics for networks, Bayesian model assessment (I liked the notion of stepping out of the model), and randomization when experimenting with networks. And for big data issues. And for personalized medicine, building on his cancer treatment. No trace of the ABC algorithm, obviously, but a wonderful Fisher’s lecture, also most obviously!! Bravo, Steve, keep thriving!!!

Posted in Books, Mountains, pictures, Statistics, University life with tags , , , , , on May 26, 2015 by xi'an

[Here are comments made by Matt Graham that I thought would be more readable in a post format. The beautiful picture of the Alps above is his as well. I do not truly understand what Matt’s point is, as I did not cover continuous time processes in my discussion…]

In terms of interpretation of the diffusion with non-reversible drift component, I think this can be generalised from the Gaussian invariant density case by

dx = [ – (∂E/∂x) dt + √2 dw ] + S’ (∂E/∂x) dt

where ∂E/∂x is the usual gradient of the negative log (unnormalised) density / energy and S=-S’ is a skew symmetric matrix. In this form it seems the dynamic can be interpreted as the composition of an energy and volume conserving (non-canonical) Hamiltonian dynamic

dx/dt = S’ ∂E/∂x

and a (non-preconditioned) Langevin diffusion

dx = – (∂E/∂x) dt + √2 dw

As an alternative to discretising the combined dynamic, it might be interesting to compare to sequential alternation between ‘Hamiltonian’ steps either using a simple Euler discretisation

x’ = x + h S’ ∂E/∂x

or a symplectic method like implicit midpoint to maintain reversibility / volume preservation and then a standard MALA step

x’ = x – h (∂E/∂x) + √2 h w, w ~ N(0, I)

plus MH accept. If only one final MH accept step is done this overall dynamic will be reversible, however if a an intermediary MH accept was done after each Hamiltonian step (flipping the sign / transposing S on a rejection to maintain reversibility), the composed dynamic would in general be non-longer reversible and it would be interesting to compare performance in this case to that using a non-reversible MH acceptance on the combined dynamic (this alternative sidestepping the issues with finding an appropriate scale ε to maintain the non-negativity condition on the sum of the vorticity density and joint density on a proposed and current state).

With regards to your point on the positivity of g(x,y)+π(y)q(y,x), I’m not sure if I have fully understood your notation correctly or not, but I think you may have misread the definition of g(x,y) for the discretised Ornstein-Uhlenbeck case (apologies if instead the misinterpretation is mine!). The vorticity density is defined as the skew symmetric component of the density f of F(dx, dy) = µ(dx) Q(x, dy) with respect to the Lebesgue measure, where µ(dx) is the true invariant distribution of the Euler-Maruyama discretised diffusion based proposal density Q(x, dy) rather than g(x, y) being defined in terms of the skew-symmetric component of π(dx) Q(x, dy) which in general would lead to a vorticity density which does not meet the zero integral requirement as the target density π is not invariant in general with respect to Q.

## computational methods for statistical mechanics [day #4]

Posted in Mountains, pictures, Running, Statistics, Travel, University life with tags , , , , , , , , , , , , , , , , on June 7, 2014 by xi'an

My last day at this ICMS workshop on molecular simulation started [with a double loop of Arthur’s Seat thankfully avoiding the heavy rains of the previous night and then] Chris Chipot‘s magistral entry to molecular simulation for proteins with impressive slides and simulation movies, even though I could not follow the details to really understand the simulation challenges therein, just catching a few connections with earlier talks. A typical example of a cross-disciplinary gap, where the other discipline always seems to be stressing the ‘wrong” aspects. Although this is perfectly unrealistic, it would immensely to prepare talks in pairs for such interdisciplinary workshops! Then Gersende Fort presented results about convergence and efficiency for the Wang-Landau algorithm. The idea is to find the optimal rate for updating the weights of the elements of the partition towards reaching the flat histogram in minimal time. Showing massive gains on toy examples. The next talk went back to molecular biology with Jérôme Hénin‘s presentation on improved adaptive biased sampling. With an exciting notion of orthogonality aiming at finding the slowest directions in the target and putting the computational effort. He also discussed the tension between long single simulations and short repeated ones, echoing a long-going debate in the MCMC community. (He also had a slide with a picture of my first 1983 Apple IIe computer!) Then Antonietta Mira gave a broad perspective on delayed rejection and zero variance estimates. With impressive variance reductions (although some physicists then asked for reduction of order 10¹⁰!). Johannes Zimmer gave a beautiful maths talk on the connection between particle and diffusion limits (PDEs) and Wasserstein geometry and large deviations. (I did not get most of the talk, but it was nonetheless beautiful!) Bert Kappen concluded the day (and the workshop for me) by a nice introduction to control theory. Making connection between optimal control and optimal importance sampling. Which made me idly think of the following problem: what if control cannot be completely… controlled and hence involves a stochastic part? Presumably of little interest as the control would then be on the parameters of the distribution of the control.

“The alanine dipeptide is the fruit fly of molecular simulation.”

The example of this alanine dipeptide molecule was so recurrent during the talks that it justified the above quote by Michael Allen. Not that I am more proficient in the point of studying this protein or using it as a benchmark. Or in identifying the specifics of the challenges of molecular dynamics simulation. Not a criticism of the ICMS workshop obviously, but rather of my congenital difficulty with continuous time processes!!! So I do not return from Edinburgh with a new research collaborative project in molecular dynamics (if with more traditional prospects), albeit with the perception that a minimal effort could bring me to breach the vocabulary barrier. And maybe consider ABC ventures in those (new) domains. (Although I fear my talk on ABC did not impact most of the audience!)