Structured prediction tasks pose a fundamental trade-off between the need for model complexity to increase predictive power and the limited computational resources for inference in the exponentially-sized output spaces such models require. We formulate and develop the Structured Prediction Cascade architecture: a sequence of increasingly complex models that progressively filter the space of possible outputs. The key principle of our approach is that each model in the cascade is optimized to accurately filter and refine the structured output state space of the next model, speeding up both learning and inference in the next layer of the cascade. We learn cascades by optimizing a novel convex loss function that controls the trade-off between the filtering efficiency and the accuracy of the cascade, and provide generalization bounds for both accuracy and efficiency. We also extend our approach to intractable models using tree-decomposition ensembles, and provide algorithms and theory for this setting. We evaluate our approach on several large-scale problems, achieving state-of-the-art performance in handwriting recognition and human pose recognition. We find that structured prediction cascades allow tremendous speedups and the use of previously intractable features and models in both settings.

In mechanism design it is typical to impose incentive compatibility and then derive an optimal mechanism subject to this constraint. By replacing the incentive compatibility requirement with the goal of minimizing expected ex post regret, we are able to adapt statistical machine learning techniques to the design of payment rules. This computational approach to mechanism design is applicable to domains with multi-dimensional types and situations where computational efficiency is a concern. Specifically, given an outcome rule and access to a type distribution, we train a support vector machine with a special discriminant function structure such that it implicitly establishes a payment rule with desirable incentive properties. We discuss applications to a multi-minded combinatorial auction with a greedy winner-determination algorithm and to an assignment problem with egalitarian outcome rule. Experimental results demonstrate both that the construction produces payment rules with low ex post regret, and that penalizing classification errors is effective in preventing failures of ex post individual rationality.

Creating and monitoring competitive and cost-effective pay-per-click advertisement campaigns through the web-search channel is a resource demanding task in terms of expertise and effort. Assisting or even automating the work of an advertising specialist will have an unrivaled commercial value. In this paper we propose a methodology, an architecture, and a fully functional framework for semi- and fully- automated creation, monitoring, and optimization of cost-efficient pay-per-click campaigns with budget constraints. The campaign creation module generates automatically keywords based on the content of the web page to be advertised extended with corresponding ad-texts. These keywords are used to create automatically the campaigns fully equipped with the appropriate values set. The campaigns are uploaded to the auctioneer platform and start running. The optimization module focuses on the learning process from existing campaign statistics and also from applied strategies of previous periods in order to invest optimally in the next period. The objective is to maximize the performance (i.e. clicks, actions) under the current budget constraint. The fully functional prototype is experimentally evaluated on real world Google AdWords campaigns and presents a promising behavior with regards to campaign performance statistics as it outperforms systematically the competing manually maintained campaigns.

This note introduces the method of cross-conformal prediction, which is a hybrid of the methods of inductive conformal prediction and cross-validation, and studies its validity and predictive efficiency empirically.

Biological data objects often have both of the following features: (i) they are functions rather than single numbers or vectors, and (ii) they are correlated due to phylogenetic relationships. In this paper we give a flexible statistical model for such data, by combining assumptions from phylogenetics with Gaussian processes. We describe its use as a nonparametric Bayesian prior distribution, both for prediction (placing posterior distributions on ancestral functions) and model selection (comparing rates of evolution across a phylogeny, or identifying the most likely phylogenies consistent with the observed data). Our work is integrative, extending the popular phylogenetic Brownian Motion and Ornstein-Uhlenbeck models to functional data and Bayesian inference, and extending Gaussian Process regression to phylogenies. We provide a brief illustration of the application of our method.

Many biological characteristics of evolutionary interest are not scalar variables but continuous functions. Here we use phylogenetic Gaussian process regression to model the evolution of simulated function-valued traits. Given function-valued data only from the tips of an evolutionary tree and utilising independent principal component analysis (IPCA) as a method for dimension reduction, we construct distributional estimates of ancestral function-valued traits, and estimate parameters describing their evolutionary dynamics.

We analyze general model selection procedures using penalized empirical loss minimization under computational constraints. While classical model selection approaches do not consider computational aspects of performing model selection, we argue that any practical model selection procedure must not only trade off estimation and approximation error, but also the computational effort required to compute empirical minimizers for different function classes. We provide a framework for analyzing such problems, and we give algorithms for model selection under a computational budget. These algorithms satisfy oracle inequalities that show that the risk of the selected model is not much worse than if we had devoted all of our omputational budget to the optimal function class.

We generalize stochastic subgradient descent methods to situations in which we do not receive independent samples from the distribution over which we optimize, but instead receive samples that are coupled over time. We show that as long as the source of randomness is suitably ergodic---it converges quickly enough to a stationary distribution---the method enjoys strong convergence guarantees, both in expectation and with high probability. This result has implications for stochastic optimization in high-dimensional spaces, peer-to-peer distributed optimization schemes, decision problems with dependent data, and stochastic optimization problems over combinatorial spaces.

We propose a specialized string kernel for small bio-molecules, peptides and pseudo-sequences of binding interfaces. The kernel incorporates physico-chemical properties of amino acids and elegantly generalize eight kernels, such as the Oligo, the Weighted Degree, the Blended Spectrum, and the Radial Basis Function. We provide a low complexity dynamic programming algorithm for the exact computation of the kernel and a linear time algorithm for it's approximation. Combined with kernel ridge regression and SupCK, a novel binding pocket kernel, the proposed kernel yields biologically relevant and good prediction accuracy on the PepX database. For the first time, a machine learning predictor is capable of accurately predicting the binding affinity of any peptide to any protein. The method was also applied to both single-target and pan-specific Major Histocompatibility Complex class II benchmark datasets and three Quantitative Structure Affinity Model benchmark datasets. On all benchmarks, our method significantly (p-value < 0.057) outperforms the current state-of-the-art methods at predicting peptide-protein binding affinities. The proposed approach is flexible and can be applied to predict any quantitative biological activity. The method should be of value to a large segment of the research community with the potential to accelerate peptide-based drug and vaccine development.

We present a set of high-probability inequalities that control the concentration of weighted averages of multiple (possibly uncountably many) simultaneously evolving and interdependent martingales. Our results extend the PAC-Bayesian analysis in learning theory from the i.i.d. setting to martingales opening the way for its application to importance weighted sampling, reinforcement learning, and other interactive learning domains, as well as many other domains in probability theory and statistics, where martingales are encountered. We also present a comparison inequality that bounds the expectation of a convex function of a martingale difference sequence shifted to the [0,1] interval by the expectation of the same function of independent Bernoulli variables. This inequality is applied to derive a tighter analog of Hoeffding-Azuma's inequality.