Archive for astronomy
pictures, Travel with tags 67P/Churyumov–Gerasimenko, astronomy, comets, European Space Agency, Philae lander, Rosetta, space probe on September 30, 2016 by xi'an
R, Statistics, University life with tags astronomy, Bayesian inference, inverse problems, parallaxes on July 15, 2016 by xi'an
A s I figured out while working with astronomer colleagues last week, a strange if understandable difficulty proceeds from the simplest and most studied statistical model, namely the Normal model
Indeed, if one reparametrises this model as x~N(υ⁻¹,1) with υ>0, a single observation x brings very little information about υ! (This is not a toy problem as it corresponds to estimating distances from observations of parallaxes.) If x gets large, υ is very likely to be small, but if x is small or negative, υ is certainly large, with no power to discriminate between highly different values. For instance, Fisher’s information for this model and parametrisation is υ⁻² and thus collapses at zero.
While one can always hope for Bayesian miracles, they do not automatically occur. For instance, working with a Gamma prior Ga(3,10³) on υ [as informed by a large astronomy dataset] leads to a posterior expectation hardly impacted by the value of the observation x:
Books, pictures, Statistics, University life with tags ABC, ABC-PMC, abcpmc, astronomy, astrostatistics, cosmoabc, cosmology, likelihood-free methods, Mahalanobis distance, Python, semi-automatic ABC on May 4, 2015 by xi'an
Two papers appeared on arXiv in the past two days with the similar theme of applying ABC-PMC [one version of which we developed with Mark Beaumont, Jean-Marie Cornuet, and Jean-Michel Marin in 2009] to cosmological problems. (As a further coincidence, I had just started refereeing yet another paper on ABC-PMC in another astronomy problem!) The first paper cosmoabc: Likelihood-free inference via Population Monte Carlo Approximate Bayesian Computation by Ishida et al. [“et al” including Ewan Cameron] proposes a Python ABC-PMC sampler with applications to galaxy clusters catalogues. The paper is primarily a description of the cosmoabc package, including code snapshots. Earlier occurrences of ABC in cosmology are found for instance in this earlier workshop, as well as in Cameron and Pettitt earlier paper. The package offers a way to evaluate the impact of a specific distance, with a 2D-graph demonstrating that the minimum [if not the range] of the simulated distances increases with the parameters getting away from the best parameter values.
“We emphasis [sic] that the choice of the distance function is a crucial step in the design of the ABC algorithm and the reader must check its properties carefully before any ABC implementation is attempted.” E.E.O. Ishida et al.
The second [by one day] paper Approximate Bayesian computation for forward modelling in cosmology by Akeret et al. also proposes a Python ABC-PMC sampler, abcpmc. With fairly similar explanations: maybe both samplers should be compared on a reference dataset. While I first thought the description of the algorithm was rather close to our version, including the choice of the empirical covariance matrix with the factor 2, it appears it is adapted from a tutorial in the Journal of Mathematical Psychology by Turner and van Zandt. One out of many tutorials and surveys on the ABC method, of which I was unaware, but which summarises the pre-2012 developments rather nicely. Except for missing Paul Fearnhead’s and Dennis Prangle’s semi-automatic Read Paper. In the abcpmc paper, the update of the covariance matrix is the one proposed by Sarah Filippi and co-authors, which includes an extra bias term for faraway particles.
“For complex data, it can be difficult or computationally expensive to calculate the distance ρ(x; y) using all the information available in x and y.” Akeret et al.
In both papers, the role of the distance is stressed as being quite important. However, the cosmoabc paper uses an L1 distance [see (2) therein] in a toy example without normalising between mean and variance, while the abcpmc paper suggests using a Mahalanobis distance that turns the d-dimensional problem into a comparison of one-dimensional projections.
pictures, Travel with tags astronomy, Autour du Ciel, Guillaume Cannat, La Grande Motte, Montpellier, moonset on February 2, 2015 by xi'an
Books, Kids, pictures, Statistics, Travel, University life with tags ABC, Amazon, astronomy, astrostatistics, big data, conference, England, galaxies, pulsars, Statistics, supernovae, The Fourth Paradigm, The Large Synoptic Survey Telescope, University of Warwick, variational Bayes methods, workshop on September 3, 2014 by xi'an
Great poster session yesterday night and at lunch today. Saw an ABC poster (by Dennis Prangle, following our random forest paper) and several MCMC posters (by Marco Banterle, who actually won one of the speed-meeting mini-project awards!, Michael Betancourt, Anne-Marie Lyne, Murray Pollock), and then a rather different poster on Mondrian forests, that generalise random forests to sequential data (by Balaji Lakshminarayanan). The talks all had interesting aspects or glimpses about big data and some of the unnecessary hype about it (them?!), along with exposing the nefarious views of Amazon to become the Earth only seller!, but I particularly enjoyed the astronomy afternoon and even more particularly Steve Roberts sweep through astronomy machine-learning. Steve characterised variational Bayes as picking your choice of sufficient statistics, which made me wonder why there were no stronger connections between variational Bayes and ABC. He also quoted the book The Fourth Paradigm: Data-Intensive Scientific Discovery by Tony Hey as putting forward interesting notions. (A book review for the next vacations?!) And also mentioned zooniverse, a citizens science website I was not aware of. With a Bayesian analysis of the learning curve of those annotating citizens (in the case of supernovae classification). Big deal, indeed!!!
Statistics, University life with tags ABC, ABC-MCMC, astronomy, astrostatistics, BIC, Milky Way, thick disk, thin disk on July 9, 2014 by xi'an
“The facts that the thick-disc episode lasted for several billion years, that a contraction is observed during the collapse phase, and that the main thick disc has a constant scale height with no flare argue against the formation of the thick disc through radial migration. The most probable scenario for the thick disc is that it formed while the Galaxy was gravitationally collapsing from well-mixed gas-rich giant clumps that were sustained by high turbulence, which prevented a thin disc from forming for a time, as proposed previously.”
Following discussions with astronomers from Besancon on the use of ABC methods to approximate posteriors, I was associated with their paper on assessing a formation scenario of the Milky Way, which was accepted a few weeks ago in Astronomy & Astrophysics. The central problem (was there a thin-then-thick disk?) somewhat escapes me, but this collaboration started when some of the astronomers leading the study contacted me about convergence issues with their MCMC algorithms and I realised they were using ABC-MCMC without any idea that it was in fact called ABC-MCMC and had been studied previously in another corner of the literature… The scale in the kernel was chosen to achieve an average acceptance rate of 5%-10%. Model are then compared by the combination of a log-likelihood approximation resulting from the ABC modelling and of a BIC ranking of the models. (Incidentally, I was impressed at the number of papers published in Astronomy & Astrophysics. The monthly issue contains dozens of papers!)
Books, pictures, Running, Statistics, University life with tags ABC, acceptance rate, astronomy, astrostatistics, Bristol, convergence, Gibbs sampling, MCMC, Metropolis-Hastings algorithms, Monte Carlo Statistical Methods, simulated annealing, simulation on October 23, 2013 by xi'an
Following my earlier post about the young astronomer who feared he was running his MCMC for too long, here is an update from his visit to my office this morning. This visit proved quite an instructive visit for both of us. (Disclaimer: the picture of an observatory seen from across Brunel’s suspension bridge in Bristol is as earlier completely unrelated with the young astronomer!)
First, the reason why he thought MCMC was running too long was that the acceptance rate was plummeting down to zero, whatever the random walk scale. The reason for this behaviour is that he was actually running a standard simulated annealing algorithm, hence observing the stabilisation of the Markov chain in one of the (global) modes of the target function. In that sense, he was right that the MCMC was run for “too long”, as there was nothing to expect once the mode had been reached and the temperature turned down to zero. So the algorithm was working correctly.
Second, the astronomy problem he considers had a rather complex likelihood, for which he substituted a distance between the (discretised) observed data and (discretised) simulated data, simulated conditional on the current parameter value. Now…does this ring a bell? If not, here is a three letter clue: ABC… Indeed, the trick he had found to get around this likelihood calculation issue was to re-invent a version of ABC-MCMC! Except that the distance was re-introduced into a regular MCMC scheme as a substitute to the log-likelihood. And compared with the distance at the previous MCMC iteration. This is quite clever, even though this substitution suffers from a normalisation issue (that I already mentioned in the post about Holmes’ and Walker’s idea to turn loss functions into pseudo likelihoods. Regular ABC does not encounter this difficult, obviously. I am still bemused by this reinvention of ABC from scratch!
So we are now at a stage where my young friend will experiment with (hopefully) correct ABC steps, trying to derive the tolerance value from warmup simulations and use some of the accelerating tricks suggested by Umberto Picchini and Julie Forman to avoid simulating the characteristics of millions of stars for nothing. And we agreed to meet soon for an update. Indeed, a fairly profitable morning for both of us!