Markov random fields are used to model high dimensional distributions in a number of applied areas. Much recent interest has been devoted to the reconstruction of the dependency structure from independent samples from the Markov random fields. We analyze a simple algorithm for reconstructing the underlying graph defining a Markov random field on @math nodes and maximum degree @math given observations. We show that under mild non-degeneracy conditions it reconstructs the generating graph with high probability using @math samples where @math depend on the local interactions. For most local interaction @math are of order @math . Our results are optimal as a function of @math up to a multiplicative constant depending on @math and the strength of the local interactions. Our results seem to be the first results for general models that guarantee that the generating model is reconstructed. Furthermore, we provide explicit @math running time bound. In cases where the measure on the graph has correlation decay, the running time is @math for all fixed @math . We also discuss the effect of observing noisy samples and show that as long as the noise level is low, our algorithm is effective. On the other hand, we construct an example where large noise implies non-identifiability even for generic noise and interactions. Finally, we briefly show that in some simple cases, models with hidden nodes can also be recovered.
Chow and Liu @cite_4 considered the problem of estimating Markov random fields whose underlying graphs are trees, and provided an efficient (polynomial-time) algorithm based on the fact that in the tree case maximum-likelihood estimation amounts to the computation of a maximum-weight spanning tree with edge weights equal to pairwise empirical mutual information. Unfortunately, their approach does not generalize to the estimation of Markov random fields whose graphs have cycles. Much work in mathematical biology is devoted to reconstructing tree Markov fields when there are hidden models. For trees, given data that is generated from the model, the tree can be reconstructed efficiently from samples at a subset of the nodes given mild non-degeneracy conditions. See @cite_6 @cite_5 @cite_2 for some of the most recent and tightest results in this setup.
@cite_5 @cite_4 @cite_6 @cite_2
2124988974 1846857138 2102902005 2127856808
The problem of maximum-likelihood (ML) estimation of discrete tree-structured distributions is considered. Chow and Liu established that ML-estimation reduces to the construction of a maximum-weight spanning tree using the empirical mutual information quantities as the edge weights. Using the theory of large-deviations, we analyze the exponent associated with the error probability of the event that the ML-estimate of the Markov tree structure differs from the true tree structure, given a set of independently drawn samples. By exploiting the fact that the output of ML-estimation is a tree, we establish that the error exponent is equal to the exponential rate of decay of a single dominant crossover event. We prove that in this dominant crossover event, a non-neighbor node pair replaces a true edge of the distribution that is along the path of edges in the true tree graph connecting the nodes in the non-neighbor pair. Using ideas from Euclidean information theory, we then analyze the scenario of ML-estimation in the very noisy learning regime and show that the error exponent can be approximated as a ratio, which is interpreted as the signal-to-noise ratio (SNR) for learning tree distributions. We show via numerical experiments that in this regime, our SNR approximation is accurate. We apply the theory of Markov random fields on trees to derive a phase transition in the number of samples needed in order to reconstruct phylogenies. We consider the Cavender-Farris-Neyman model of evolution on trees, where all the inner nodes have degree at least 3, and the net transition on each edge is bounded by e. Motivated by a conjecture by M. Steel, we show that if 2(1 - 2∈) 2 > 1, then for balanced trees, the topology of the underlying tree, having n leaves, can be reconstructed from O(logn) samples (characters) at the leaves. On the other hand, we show that if 2(1 - 2∈) 2 < 1, then there exist topologies which require at least n Ω(1) samples for reconstruction. Our results are the first rigorous results to establish the role of phase transitions for Markov random fields on trees, as studied in probability, statistical physics and information theory, for the study of phylogenies in mathematical biology. Consider a Markov chain on an infinite tree T = (V,E) rooted at . In such a chain, once the initial root state ( ) is chosen, each vertex iteratively chooses its state from the one of its parent by an application of a Markov transition rule (and all such applications are independent). Let µj denote the resulting measure for ( ) = j. µj is defined on configurations = ( (x))x2V 2 A V , where A is some finite set. Let µ n denote the restriction of µ to the sigma-algebra generated by the variables (x) where x is at distance exactly n from . Letting n = maxi,j2A dTV (µ n ,µ n ), where dTV denotes total variation distance, we say that the reconstruction problem is solvable if liminfn!1 n > 0. Reconstruction solvability roughly means that the n’th level of the tree contains a non-vanishing amount of information on the root of the tree, as n ! 1. In this paper we study the problem of robust reconstruction. Let be a non degenerate distribution on A and > 0. Let be chosen according to µ n and 0 be obtained from by letting for each node independently (v) = 0 (v) with probability 1 and 0 (v) to be an independent sample from otherwise. We denote by µ n [, ] the resulting measure on 0 . The measure µ n [, ] is a perturbation of the measure µ n . Letting n(, ) = maxi,j2A dTV (µ n [, ],µ n [, ]), we say that the reconstruction problem is -robust-solvable if liminfn!1 n(, ) > 0 for all 0 1, where 2(M) is the second largest eigenvalue of M (in absolute value), then for all non-degenerate , the reconstruction problem is -robust-solvable. We prove a converse and show that the reconstruction problem is not -robust-solvable if B| 2(M)| 2 < 1. This proves a conjecture by the second author and Peres. We also consider other models of noise and general trees. Until recently, the lack of ground truth data has hindered the application of discriminative structured prediction techniques to the stereo problem. In this paper we use ground truth data sets that we have recently constructed to explore different model structures and parameter learning techniques. To estimate parameters in Markov random fields (MRFs) via maximum likelihood one usually needs to perform approximate probabilistic inference. Conditional random fields (CRFs) are discriminative versions of traditional MRFs. We explore a number of novel CRF model structures including a CRF for stereo matching with an explicit occlusion model. CRFs require expensive inference steps for each iteration of optimization and inference is particularly slow when there are many discrete states. We explore belief propagation, variational message passing and graph cuts as inference methods during learning and compare with learning via pseudolikelihood. To accelerate approximate inference we have developed a new method called sparse variational message passing which can reduce inference time by an order of magnitude with negligible loss in quality. Learning using sparse variational message passing improves upon previous approaches using graph cuts and allows efficient learning over large data sets when energy functions violate the constraints imposed by graph cuts.