We explore the hypothesis that the neuronal spike generation mechanism is an analog-to-digital converter, which rectifies low-pass filtered summed synaptic currents and encodes them into spike trains linearly decodable in post-synaptic neurons. To digitally encode an analog current waveform, the sampling rate of the spike generation mechanism must exceed its Nyquist rate. Such oversampling is consistent with the experimental observation that the precision of the spike-generation mechanism is an order of magnitude greater than the cut-off frequency of dendritic low-pass filtering. To achieve additional reduction in the error of analog-to-digital conversion, electrical engineers rely on noise-shaping. If noise-shaping were used in neurons, it would introduce correlations in spike timing to reduce low-frequency (up to Nyquist) transmission error at the cost of high-frequency one (from Nyquist to sampling rate). Using experimental data from three different classes of neurons, we demonstrate that biological neurons utilize noise-shaping. We also argue that rectification by the spike-generation mechanism may improve energy efficiency and carry out de-noising. Finally, the zoo of ion channels in neurons may be viewed as a set of predictors, various subsets of which are activated depending on the statistics of the input current.

Residue-residue contact prediction is a fundamental problem in protein structure prediction. Hower, despite considerable research efforts, contact prediction methods are still largely unreliable. Here we introduce a novel deep machine-learning architecture which consists of a multidimensional stack of learning modules. For contact prediction, the idea is implemented as a three-dimensional stack of Neural Networks NN^k_{ij}, where i and j index the spatial coordinates of the contact map and k indexes ''time''. The temporal dimension is introduced to capture the fact that protein folding is not an instantaneous process, but rather a progressive refinement. Networks at level k in the stack can be trained in supervised fashion to refine the predictions produced by the previous level, hence addressing the problem of vanishing gradients, typical of deep architectures. Increased accuracy and generalization capabilities of this approach are established by rigorous comparison with other classical machine learning approaches for contact prediction. The deep approach leads to an accuracy for difficult long-range contacts of about 30%, roughly 10% above the state-of-the-art. Many variations in the architectures and the training algorithms are possible, leaving room for further improvements. Furthermore, the approach is applicable to other problems with strong underlying spatial and temporal components.

Principal components analysis (PCA) is a standard tool for identifying good low-dimensional approximations to data sets in high dimension. Many current data sets of interest contain private or sensitive information about individuals. Algorithms which operate on such data should be sensitive to the privacy risks in publishing their outputs. Differential privacy is a framework for developing tradeoffs between privacy and the utility of these outputs. In this paper we investigate the theory and empirical performance of differentially private approximations to PCA and propose a new method which explicitly optimizes the utility of the output. We demonstrate that on real data, there this a large performance gap between the existing methods and our method. We show that the sample complexity for the two procedures differs in the scaling with the data dimension, and that our method is nearly optimal in terms of this scaling.

In the setting of active learning for the multi-armed bandit, where the goal of a learner is to estimate with equal precision the mean of a finite number of arms, recent results show that it is possible to derive strategies based on finite-time confidence bounds that are competitive with the best possible strategy. We here consider an extension of this problem to the case when the arms are the cells of a finite partition P of a continuous sampling space X \subset \Real^d. Our goal is now to build a piecewise constant approximation of a noisy function (where each piece is one region of P and P is fixed beforehand) in order to maintain the local quadratic error of approximation on each cell equally low. Although this extension is not trivial, we show that a simple algorithm based on upper confidence bounds can be proved to be adaptive to the function itself in a near-optimal way, when |P| is chosen to be of minimax-optimal order on the class of \alpha-Hölder functions.

Statistical relational learning models combine the power of first-order logic, the de facto tool for handling relational structure, with that of probabilistic graphical models, the de facto tool for handling uncertainty. Lifted probabilistic inference algorithms for them have been the subject of much recent research. The main idea in these algorithms is to improve the speed, accuracy and scalability of existing graphical models' inference algorithms by exploiting symmetry in the first-order representation. In this paper, we consider blocked Gibbs sampling, an advanced variation of the classic Gibbs sampling algorithm and lift it to the first-order level. We propose to achieve this by partitioning the first-order atoms in the relational model into a set of disjoint clusters such that exact lifted inference is polynomial in each cluster given an assignment to all other atoms not in the cluster. We propose an approach for constructing such clusters and determining their complexity and show how it can be used to trade accuracy with computational complexity in a principled manner. Our experimental evaluation shows that lifted Gibbs sampling is superior to the propositional algorithm in terms of accuracy and convergence.

In this paper, we consider Bayesian reinforcement learning (BRL) where actions incur costs in addition to rewards, and thus exploration has to be constrained in terms of the expected total cost while learning to maximize the expected long-term total reward. In order to formalize cost-sensitive exploration, we use the constrained Markov decision process (CMDP) as the model of the environment, in which we can naturally encode exploration requirements using the cost function. We extend BEETLE, a model-based BRL method, for learning in the environment with cost constraints. We demonstrate the cost-sensitive exploration behaviour in a number of simulated problems.

Bayesian inference provides a unifying framework for addressing problems in machine learning, artificial intelligence, and robotics, as well as the problems facing the human mind. Unfortunately, exact Bayesian inference is intractable in all but the simplest models. Therefore minds and machines have to approximate Bayesian inference. Approximate inference algorithms can achieve a wide range of time-accuracy tradeoffs, but what is the optimal tradeoff? We investigate time-accuracy tradeoffs using the Metropolis-Hastings algorithm as a metaphor for the mind's inference algorithm(s). We find that reasonably accurate decisions are possible long before the Markov chain has converged to the posterior distribution, i.e. during the period known as burn-in. Therefore the strategy that is optimal subject to the mind's bounded processing speed and opportunity costs may perform so few iterations that the resulting samples are biased towards the initial value. The resulting cognitive process model provides a rational basis for the anchoring-and-adjustment heuristic. The model's quantitative predictions are tested against published data on anchoring in numerical estimation tasks. Our theoretical and empirical results suggest that the anchoring bias is consistent with approximate Bayesian inference.

In this work we consider a setting where we have a very large number of related tasks with few examples from each individual task. Rather than either learning each task individually (and having a large generalization error) or learning all the tasks together using a single hypothesis (and suffering a potentially large inherent error), we consider learning a small pool of {\em shared hypotheses}. Each task is then mapped to a single hypothesis in the pool (hard association). We derive VC dimension generalization bounds for our model, based on the number of tasks, shared hypothesis and the VC dimension of the hypotheses class. We conducted experiments with both synthetic problems and sentiment of reviews, which strongly support our approach.

We consider derivative-free algorithms for stochastic optimization problems that use only noisy function values rather than gradients, analyzing their finite-sample convergence rates. We show that if pairs of function values are available, algorithms that use gradient estimates based on random perturbations suffer a factor of at most $\sqrt{\dim}$ in convergence rate over traditional stochastic gradient methods, where $\dim$ is the dimension of the problem. We complement our algorithmic development with information-theoretic lower bounds on the minimax convergence rate of such problems, which show that our bounds are sharp with respect to all problem-dependent quantities: they cannot be improved by more than constant factors.

Many tasks in text and speech processing and computational biology require estimating functionsmapping strings to real numbers. A broad class of such functions can be defined by weighted automata. Spectral methods based on the singular valuedecomposition of a Hankel matrix have been recently proposed for learning a probability distribution represented by a weighted automaton from a training sample drawn according to this same target distribution. In this paper, we show how spectral methods can be extended to the problem of learning a general weighted automaton from a sample generated by an arbitrary distribution. The main obstruction to this approach is that, in general, some entries of the Hankel matrix may be missing. We present a solution to this problem based on solving a constrained matrix completion problem. Combining these two ingredients, matrix completion and spectral method, a whole new family of algorithms for learning general weighted automata is obtained.