Modeling the time evolution of discrete sets of items (e.g., genetic mutations) is a fundamental problem in many biomedical applications. We approach this problem through the lens of continuous-time Markov chains, and show that the resulting learning task is generally underspecified in the usual setting of cross-sectional data. We explore a perhaps surprising remedy: including a number of additional independent items can help determine time order, and hence resolve underspecification. This is in sharp contrast to the common practice of limiting the analysis to a small subset of relevant items, which is followed largely due to poor scaling of existing methods. To put our theoretical insight into practice, we develop an approximate likelihood maximization method for learning continuous-time Markov chains, which can scale to hundreds of items and is orders of magnitude faster than previous methods. We demonstrate the effectiveness of our approach on synthetic and real cancer data.
We consider the classical problems of estimating the mean of an $n$-dimensional normally (with identity covariance matrix) or Poisson distributed vector under the squared loss. In a Bayesian setting the optimal estimator is given by the prior-dependent conditional mean. In a frequentist setting various shrinkage methods were developed over the last century. The framework of empirical Bayes, put forth by Robbins (1956), combines Bayesian and frequentist mindsets by postulating that the parameters are independent but with an unknown prior and aims to use a fully data-driven estimator to compete with the Bayesian oracle that knows the true prior. The central figure of merit is the regret, namely, the total excess risk over the Bayes risk in the worst case (over the priors). Although this paradigm was introduced more than 60 years ago, little is known about the asymptotic scaling of the optimal regret in the nonparametric setting. We show that for the Poisson model with compactly supported and subexponential priors, the optimal regret scales as $\Theta((\frac{\log n}{\log\log n})^2)$ and $\Theta(\log^3 n)$, respectively, both attained by the original estimator of Robbins. For the normal mean model, the regret is shown to be at least $\Omega((\frac{\log n}{\log\log n})^2)$ and $\Omega(\log^2 n)$ for compactly supported and subgaussian priors, respectively, the former of which resolves the conjecture of Singh (1979) on the impossibility of achieving bounded regret; before this work, the best regret lower bound was $\Omega(1)$. %Analogous results for subgaussian or subexponential priors are also obtained. In addition to the empirical Bayes setting, these results are shown to hold in the compound setting where the parameters are deterministic. As a side application, the construction in this paper also leads to improved or new lower bounds for mixture density estimation.
Many of the challenges facing today's reinforcement learning (RL) algorithms, such as robustness, generalization, transfer, and computational efficiency are closely related to compression. Prior work has convincingly argued why minimizing information is useful in the supervised learning setting, but standard RL algorithms lack an explicit mechanism for compression. The RL setting is unique because (1) its sequential nature allows an agent to use past information to avoid looking at future observations and (2) the agent can optimize its behavior to prefer states where decision making requires few bits. We take advantage of these properties to propose a method (RPC) for learning simple policies. This method brings together ideas from information bottlenecks, model-based RL, and bits-back coding into a simple and theoretically-justified algorithm. Our method jointly optimizes a latent-space model and policy to be self-consistent, such that the policy avoids states where the model is inaccurate. We demonstrate that our method achieves much tighter compression than prior methods, achieving up to 5x higher reward than a standard information bottleneck. We also demonstrate that our method learns policies that are more robust and generalize better to new tasks.
A key component of mathematical reasoning is the ability to formulate interesting conjectures about a problem domain at hand. In this paper, we give a brief overview of a theory exploration system called QuickSpec, which is able to automatically discover interesting conjectures about a given set of functions. QuickSpec works by interleaving term generation with random testing to form candidate conjectures. This is made tractable by starting from small sizes and ensuring that only terms that are irreducible with respect to already discovered conjectures are considered. QuickSpec has been successfully applied to generate lemmas for automated inductive theorem proving as well as to generate specifications of functional programs. We give an overview of typical use-cases of QuickSpec, as well as demonstrating how to easily connect it to a theorem prover of the user's choice.
Residual networks (ResNets) have displayed impressive results in pattern recognition and, recently, have garnered considerable theoretical interest due to a perceived link with neural ordinary differential equations (neural ODEs). This link relies on the convergence of network weights to a smooth function as the number of layers increases. We investigate the properties of weights trained by stochastic gradient descent and their scaling with network depth through detailed numerical experiments. We observe the existence of scaling regimes markedly different from those assumed in neural ODE literature. Depending on certain features of the network architecture, such as the smoothness of the activation function, one may obtain an alternative ODE limit, a stochastic differential equation or neither of these. These findings cast doubts on the validity of the neural ODE model as an adequate asymptotic description of deep ResNets and point to an alternative class of differential equations as a better description of the deep network limit.
Stochastic gradient Markov chain Monte Carlo (SGMCMC) has become a popular method for scalable Bayesian inference. These methods are based on sampling a discrete-time approximation to a continuous time process, such as the Langevin diffusion. When applied to distributions defined on a constrained space, such as the simplex, the time-discretisation error can dominate when we are near the boundary of the space. We demonstrate that while current SGMCMC methods for the simplex perform well in certain cases, they struggle with sparse simplex spaces; when many of the components are close to zero. However, most popular large-scale applications of Bayesian inference on simplex spaces, such as network or topic models, are sparse. We argue that this poor performance is due to the biases of SGMCMC caused by the discretization error. To get around this, we propose the stochastic CIR process, which removes all discretization error and we prove that samples from the stochastic CIR process are asymptotically unbiased. Use of the stochastic CIR process within a SGMCMC algorithm is shown to give substantially better performance for a topic model and a Dirichlet process mixture model than existing SGMCMC approaches.
Image segmentation is the process of partitioning the image into significant regions easier to analyze. Nowadays, segmentation has become a necessity in many practical medical imaging methods as locating tumors and diseases. Hidden Markov Random Field model is one of several techniques used in image segmentation. It provides an elegant way to model the segmentation process. This modeling leads to the minimization of an objective function. Conjugate Gradient algorithm (CG) is one of the best known optimization techniques. This paper proposes the use of the Conjugate Gradient algorithm (CG) for image segmentation, based on the Hidden Markov Random Field. Since derivatives are not available for this expression, finite differences are used in the CG algorithm to approximate the first derivative. The approach is evaluated using a number of publicly available images, where ground truth is known. The Dice Coefficient is used as an objective criterion to measure the quality of segmentation. The results show that the proposed CG approach compares favorably with other variants of Hidden Markov Random Field segmentation algorithms.
We consider the task of learning the parameters of a {\em single} component of a mixture model, for the case when we are given {\em side information} about that component, we call this the "search problem" in mixture models. We would like to solve this with computational and sample complexity lower than solving the overall original problem, where one learns parameters of all components. Our main contributions are the development of a simple but general model for the notion of side information, and a corresponding simple matrix-based algorithm for solving the search problem in this general setting. We then specialize this model and algorithm to four common scenarios: Gaussian mixture models, LDA topic models, subspace clustering, and mixed linear regression. For each one of these we show that if (and only if) the side information is informative, we obtain parameter estimates with greater accuracy, and also improved computation complexity than existing moment based mixture model algorithms (e.g. tensor methods). We also illustrate several natural ways one can obtain such side information, for specific problem instances. Our experiments on real data sets (NY Times, Yelp, BSDS500) further demonstrate the practicality of our algorithms showing significant improvement in runtime and accuracy.
High spectral dimensionality and the shortage of annotations make hyperspectral image (HSI) classification a challenging problem. Recent studies suggest that convolutional neural networks can learn discriminative spatial features, which play a paramount role in HSI interpretation. However, most of these methods ignore the distinctive spectral-spatial characteristic of hyperspectral data. In addition, a large amount of unlabeled data remains an unexploited gold mine for efficient data use. Therefore, we proposed an integration of generative adversarial networks (GANs) and probabilistic graphical models for HSI classification. Specifically, we used a spectral-spatial generator and a discriminator to identify land cover categories of hyperspectral cubes. Moreover, to take advantage of a large amount of unlabeled data, we adopted a conditional random field to refine the preliminary classification results generated by GANs. Experimental results obtained using two commonly studied datasets demonstrate that the proposed framework achieved encouraging classification accuracy using a small number of data for training.
We develop an approach to risk minimization and stochastic optimization that provides a convex surrogate for variance, allowing near-optimal and computationally efficient trading between approximation and estimation error. Our approach builds off of techniques for distributionally robust optimization and Owen's empirical likelihood, and we provide a number of finite-sample and asymptotic results characterizing the theoretical performance of the estimator. In particular, we show that our procedure comes with certificates of optimality, achieving (in some scenarios) faster rates of convergence than empirical risk minimization by virtue of automatically balancing bias and variance. We give corroborating empirical evidence showing that in practice, the estimator indeed trades between variance and absolute performance on a training sample, improving out-of-sample (test) performance over standard empirical risk minimization for a number of classification problems.
Robust estimation is much more challenging in high dimensions than it is in one dimension: Most techniques either lead to intractable optimization problems or estimators that can tolerate only a tiny fraction of errors. Recent work in theoretical computer science has shown that, in appropriate distributional models, it is possible to robustly estimate the mean and covariance with polynomial time algorithms that can tolerate a constant fraction of corruptions, independent of the dimension. However, the sample and time complexity of these algorithms is prohibitively large for high-dimensional applications. In this work, we address both of these issues by establishing sample complexity bounds that are optimal, up to logarithmic factors, as well as giving various refinements that allow the algorithms to tolerate a much larger fraction of corruptions. Finally, we show on both synthetic and real data that our algorithms have state-of-the-art performance and suddenly make high-dimensional robust estimation a realistic possibility.