results for au:Ravanbakhsh_S in:cs

- A grand challenge of the 21st century cosmology is to accurately estimate the cosmological parameters of our Universe. A major approach to estimating the cosmological parameters is to use the large-scale matter distribution of the Universe. Galaxy surveys provide the means to map out cosmic large-scale structure in three dimensions. Information about galaxy locations is typically summarized in a "single" function of scale, such as the galaxy correlation function or power-spectrum. We show that it is possible to estimate these cosmological parameters directly from the distribution of matter. This paper presents the application of deep 3D convolutional networks to volumetric representation of dark-matter simulations as well as the results obtained using a recently proposed distribution regression framework, showing that machine learning techniques are comparable to, and can sometimes outperform, maximum-likelihood point estimates using "cosmological models". This opens the way to estimating the parameters of our Universe with higher accuracy.
- In this paper, we study the problem of designing objective functions for machine learning problems defined on finite \emphsets. In contrast to traditional objective functions defined for machine learning problems operating on finite dimensional vectors, the new objective functions we propose are operating on finite sets and are invariant to permutations. Such problems are widespread, ranging from estimation of population statistics \citeppoczos13aistats, via anomaly detection in piezometer data of embankment dams \citepJung15Exploration, to cosmology \citepNtampaka16Dynamical,Ravanbakhsh16ICML1. Our main theorem characterizes the permutation invariant objective functions and provides a family of functions to which any permutation invariant objective function must belong. This family of functions has a special structure which enables us to design a deep network architecture that can operate on sets and which can be deployed on a variety of scenarios including both unsupervised and supervised learning tasks. We demonstrate the applicability of our method on population statistic estimation, point cloud classification, set expansion, and image tagging.
- We propose to study equivariance in deep neural networks through parameter symmetries. In particular, given a group $\mathcal{G}$ that acts discretely on the input and output of a standard neural network layer $\phi_{W}: \Re^{M} \to \Re^{N}$, we show that $\phi_{W}$ is equivariant with respect to $\mathcal{G}$-action iff $\mathcal{G}$ explains the symmetries of the network parameters $W$. Inspired by this observation, we then propose two parameter-sharing schemes to induce the desirable symmetry on $W$. Our procedures for tying the parameters achieve $\mathcal{G}$-equivariance and, under some conditions on the action of $\mathcal{G}$, they guarantee sensitivity to all other permutation groups outside $\mathcal{G}$.
- We introduce a simple permutation equivariant layer for deep learning with set structure.This type of layer, obtained by parameter-sharing, has a simple implementation and linear-time complexity in the size of each set. We use deep permutation-invariant networks to perform point-could classification and MNIST-digit summation, where in both cases the output is invariant to permutations of the input. In a semi-supervised setting, where the goal is make predictions for each instance within a set, we demonstrate the usefulness of this type of layer in set-outlier detection as well as semi-supervised learning with clustering side-information.
- Restricted Boltzmann Machine (RBM) is a bipartite graphical model that is used as the building block in energy-based deep generative models. Due to numerical stability and quantifiability of the likelihood, RBM is commonly used with Bernoulli units. Here, we consider an alternative member of exponential family RBM with leaky rectified linear units -- called leaky RBM. We first study the joint and marginal distributions of leaky RBM under different leakiness, which provides us important insights by connecting the leaky RBM model and truncated Gaussian distributions. The connection leads us to a simple yet efficient method for sampling from this model, where the basic idea is to anneal the leakiness rather than the energy; -- i.e., start from a fully Gaussian/Linear unit and gradually decrease the leakiness over iterations. This serves as an alternative to the annealing of the temperature parameter and enables numerical estimation of the likelihood that are more efficient and more accurate than the commonly used annealed importance sampling (AIS). We further demonstrate that the proposed sampling algorithm enjoys faster mixing property than contrastive divergence algorithm, which benefits the training without any additional computational cost.
- Understanding the nature of dark energy, the mysterious force driving the accelerated expansion of the Universe, is a major challenge of modern cosmology. The next generation of cosmological surveys, specifically designed to address this issue, rely on accurate measurements of the apparent shapes of distant galaxies. However, shape measurement methods suffer from various unavoidable biases and therefore will rely on a precise calibration to meet the accuracy requirements of the science analysis. This calibration process remains an open challenge as it requires large sets of high quality galaxy images. To this end, we study the application of deep conditional generative models in generating realistic galaxy images. In particular we consider variations on conditional variational autoencoder and introduce a new adversarial objective for training of conditional generative networks. Our results suggest a reliable alternative to the acquisition of expensive high quality observations for generating the calibration data needed by the next generation of cosmological surveys.
- We propose a Laplace approximation that creates a stochastic unit from any smooth monotonic activation function, using only Gaussian noise. This paper investigates the application of this stochastic approximation in training a family of Restricted Boltzmann Machines (RBM) that are closely linked to Bregman divergences. This family, that we call exponential family RBM (Exp-RBM), is a subset of the exponential family Harmoniums that expresses family members through a choice of smooth monotonic non-linearity for each neuron. Using contrastive divergence along with our Gaussian approximation, we show that Exp-RBM can learn useful representations using novel stochastic units.
- Boolean matrix factorization and Boolean matrix completion from noisy observations are desirable unsupervised data-analysis methods due to their interpretability, but hard to perform due to their NP-hardness. We treat these problems as maximum a posteriori inference problems in a graphical model and present a message passing approach that scales linearly with the number of observations and factors. Our empirical study demonstrates that message passing is able to recover low-rank Boolean matrices, in the boundaries of theoretically possible recovery and compares favorably with state-of-the-art in real-world applications, such collaborative filtering with large-scale Boolean data.
- Graphical models use the intuitive and well-studied methods of graph theory to implicitly represent dependencies between variables in large systems. They can model the global behaviour of a complex system by specifying only local factors. This thesis studies inference in discrete graphical models from an algebraic perspective and the ways inference can be used to express and approximate NP-hard combinatorial problems. We investigate the complexity and reducibility of various inference problems, in part by organizing them in an inference hierarchy. We then investigate tractable approximations for a subset of these problems using distributive law in the form of message passing. The quality of the resulting message passing procedure, called Belief Propagation (BP), depends on the influence of loops in the graphical model. We contribute to three classes of approximations that improve BP for loopy graphs A) loop correction techniques; B) survey propagation, another message passing technique that surpasses BP in some settings; and C) hybrid methods that interpolate between deterministic message passing and Markov Chain Monte Carlo inference. We then review the existing message passing solutions and provide novel graphical models and inference techniques for combinatorial problems under three broad classes: A) constraint satisfaction problems such as satisfiability, coloring, packing, set / clique-cover and dominating / independent set and their optimization counterparts; B) clustering problems such as hierarchical clustering, K-median, K-clustering, K-center and modularity optimization; C) problems over permutations including assignment, graph morphisms and alignment, finding symmetries and traveling salesman problem. In many cases we show that message passing is able to find solutions that are either near optimal or favourably compare with today's state-of-the-art approaches.
- This paper studies the form and complexity of inference in graphical models using the abstraction offered by algebraic structures. In particular, we broadly formalize inference problems in graphical models by viewing them as a sequence of operations based on commutative semigroups. We then study the computational complexity of inference by organizing various problems into an "inference hierarchy". When the underlying structure of an inference problem is a commutative semiring -- i.e. a combination of two commutative semigroups with the distributive law -- a message passing procedure called belief propagation can leverage this distributive law to perform polynomial-time inference for certain problems. After establishing the NP-hardness of inference in any commutative semiring, we investigate the relation between algebraic properties in this setting and further show that polynomial-time inference using distributive law does not (trivially) extend to inference problems that are expressed using more than two commutative semigroups. We then extend the algebraic treatment of message passing procedures to survey propagation, providing a novel perspective using a combination of two commutative semirings. This formulation generalizes the application of survey propagation to new settings.
- Many diseases cause significant changes to the concentrations of small molecules (aka metabolites) that appear in a person's biofluids, which means such diseases can often be readily detected from a person's "metabolic profile". This information can be extracted from a biofluid's NMR spectrum. Today, this is often done manually by trained human experts, which means this process is relatively slow, expensive and error-prone. This paper presents a tool, Bayesil, that can quickly, accurately and autonomously produce a complex biofluid's (e.g., serum or CSF) metabolic profile from a 1D1H NMR spectrum. This requires first performing several spectral processing steps then matching the resulting spectrum against a reference compound library, which contains the "signatures" of each relevant metabolite. Many of these steps are novel algorithms and our matching step views spectral matching as an inference problem within a probabilistic graphical model that rapidly approximates the most probable metabolic profile. Our extensive studies on a diverse set of complex mixtures, show that Bayesil can autonomously find the concentration of all NMR-detectable metabolites accurately (~90% correct identification and ~10% quantification error), in <5minutes on a single CPU. These results demonstrate that Bayesil is the first fully-automatic publicly-accessible system that provides quantitative NMR spectral profiling effectively -- with an accuracy that meets or exceeds the performance of trained experts. We anticipate this tool will usher in high-throughput metabolomics and enable a wealth of new applications of NMR in clinical settings. Available at http://www.bayesil.ca.
- Jun 05 2014 cs.AI arXiv:1406.0941v1The cutting plane method is an augmentative constrained optimization procedure that is often used with continuous-domain optimization techniques such as linear and convex programs. We investigate the viability of a similar idea within message passing -- which produces integral solutions -- in the context of two combinatorial problems: 1) For Traveling Salesman Problem (TSP), we propose a factor-graph based on Held-Karp formulation, with an exponential number of constraint factors, each of which has an exponential but sparse tabular form. 2) For graph-partitioning (a.k.a., community mining) using modularity optimization, we introduce a binary variable model with a large number of constraints that enforce formation of cliques. In both cases we are able to derive surprisingly simple message updates that lead to competitive solutions on benchmark instances. In particular for TSP we are able to find near-optimal solutions in the time that empirically grows with N^3, demonstrating that augmentation is practical and efficient.
- A new approach to maximum likelihood learning of discrete graphical models and RBM in particular is introduced. Our method, Perturb and Descend (PD) is inspired by two ideas (I) perturb and MAP method for sampling (II) learning by Contrastive Divergence minimization. In contrast to perturb and MAP, PD leverages training data to learn the models that do not allow efficient MAP estimation. During the learning, to produce a sample from the current model, we start from a training data and descend in the energy landscape of the "perturbed model", for a fixed number of steps, or until a local optima is reached. For RBM, this involves linear calculations and thresholding which can be very fast. Furthermore we show that the amount of perturbation is closely related to the temperature parameter and it can regularize the model by producing robust features resulting in sparse hidden layer activation.
- We introduce an efficient message passing scheme for solving Constraint Satisfaction Problems (CSPs), which uses stochastic perturbation of Belief Propagation (BP) and Survey Propagation (SP) messages to bypass decimation and directly produce a single satisfying assignment. Our first CSP solver, called Perturbed Blief Propagation, smoothly interpolates two well-known inference procedures; it starts as BP and ends as a Gibbs sampler, which produces a single sample from the set of solutions. Moreover we apply a similar perturbation scheme to SP to produce another CSP solver, Perturbed Survey Propagation. Experimental results on random and real-world CSPs show that Perturbed BP is often more successful and at the same time tens to hundreds of times more efficient than standard BP guided decimation. Perturbed BP also compares favorably with state-of-the-art SP-guided decimation, which has a computational complexity that generally scales exponentially worse than our method (wrt the cardinality of variable domains and constraints). Furthermore, our experiments with random satisfiability and coloring problems demonstrate that Perturbed SP can outperform SP-guided decimation, making it the best incomplete random CSP-solver in difficult regimes.
- Belief Propagation (BP) is one of the most popular methods for inference in probabilistic graphical models. BP is guaranteed to return the correct answer for tree structures, but can be incorrect or non-convergent for loopy graphical models. Recently, several new approximate inference algorithms based on cavity distribution have been proposed. These methods can account for the effect of loops by incorporating the dependency between BP messages. Alternatively, region-based approximations (that lead to methods such as Generalized Belief Propagation) improve upon BP by considering interactions within small clusters of variables, thus taking small loops within these clusters into account. This paper introduces an approach, Generalized Loop Correction (GLC), that benefits from both of these types of loop correction. We show how GLC relates to these two families of inference methods, then provide empirical evidence that GLC works effectively in general, and can be significantly more accurate than both correction schemes.