A critical evaluation of network and pathway based classifiers for outcome prediction in breast cancer

Recently, several classifiers that combine primary tumor data, like gene expression data, and secondary data sources, such as protein-protein interaction networks, have been proposed for predicting outcome in breast cancer. In these approaches, new composite features are typically constructed by aggregating the expression levels of several genes. The secondary data sources are employed to guide this aggregation. Although many studies claim that these approaches improve classification performance over single gene classifiers, the gain in performance is difficult to assess. This stems mainly from the fact that different breast cancer data sets and validation procedures are employed to assess the performance. Here we address these issues by employing a large cohort of six breast cancer data sets as benchmark set and by performing an unbiased evaluation of the classification accuracies of the different approaches. Contrary to previous claims, we find that composite feature classifiers do not outperform simple single gene classifiers. We investigate the effect of (1) the number of selected features; (2) the specific gene set from which features are selected; (3) the size of the training set and (4) the heterogeneity of the data set on the performance of composite feature and single gene classifiers. Strikingly, we find that randomization of secondary data sources, which destroys all biological information in these sources, does not result in a deterioration in performance of composite feature classifiers. Finally, we show that when a proper correction for gene set size is performed, the stability of single gene sets is similar to the stability of composite feature sets. Based on these results there is currently no reason to prefer prognostic classifiers based on composite features over single gene classifiers for predicting outcome in breast cancer.


Multi-criteria Anomaly Detection using Pareto Depth Analysis

We consider the problem of identifying patterns in a data set that exhibit anomalous behavior, often referred to as anomaly detection. In most anomaly detection algorithms, the dissimilarity between data samples is calculated by a single criterion, such as Euclidean distance. However, in many cases there may not exist a single dissimilarity measure that captures all possible anomalous patterns. In such a case, multiple criteria can be defined, and one can test for anomalies by scalarizing the multiple criteria using a linear combination of them. If the importance of the different criteria are not known in advance, the algorithm may need to be executed multiple times with different choices of weights in the linear combination. In this paper, we introduce a novel non-parametric multi-criteria anomaly detection method using Pareto depth analysis (PDA). PDA uses the concept of Pareto optimality to detect anomalies under multiple criteria without having to run an algorithm multiple times with different choices of weights. The proposed PDA approach scales linearly in the number of criteria and is provably better than linear combinations of the criteria.


How to Evaluate Dimensionality Reduction? - Improving the Co-ranking Matrix

The growing number of dimensionality reduction methods available for data visualization has recently inspired the development of quality assessment measures, in order to evaluate the resulting low-dimensional representation independently from a methods' inherent criteria. Several (existing) quality measures can be (re)formulated based on the so-called co-ranking matrix, which subsumes all rank errors (i.e. differences between the ranking of distances from every point to all others, comparing the low-dimensional representation to the original data). The measures are often based on the partioning of the co-ranking matrix into 4 submatrices, divided at the K-th row and column, calculating a weighted combination of the sums of each submatrix. Hence, the evaluation process typically involves plotting a graph over several (or even all possible) settings of the parameter K. Considering simple artificial examples, we argue that this parameter controls two notions at once, that need not necessarily be combined, and that the rectangular shape of submatrices is disadvantageous for an intuitive interpretation of the parameter. We debate that quality measures, as general and flexible evaluation tools, should have parameters with a direct and intuitive interpretation as to which specific error types are tolerated or penalized. Therefore, we propose to replace K with two parameters to control these notions separately, and introduce a differently shaped weighting on the co-ranking matrix. The two new parameters can then directly be interpreted as a threshold up to which rank errors are tolerated, and a threshold up to which the rank-distances are significant for the evaluation. Moreover, we propose a color representation of local quality to visually support the evaluation process for a given mapping, where every point in the mapping is colored according to its local contribution to the overall quality.


Injecting External Solutions Into CMA-ES

This report considers how to inject external candidate solutions into the CMA-ES algorithm. The injected solutions might stem from a gradient or a Newton step, a surrogate model optimizer or any other oracle or search mechanism. They can also be the result of a repair mechanism, for example to render infeasible solutions feasible. Only small modifications to the CMA-ES are necessary to turn injection into a reliable and effective method: too long steps need to be tightly renormalized. The main objective of this report is to reveal this simple mechanism. Depending on the source of the injected solutions, interesting variants of CMA-ES arise. When the best-ever solution is always (re-)injected, an elitist variant of CMA-ES with weighted multi-recombination arises. When \emph{all} solutions are injected from an \emph{external} source, the resulting algorithm might be viewed as \emph{adaptive encoding} with step-size control. In first experiments, injected solutions of very good quality lead to a convergence speed twice as fast as on the (simple) sphere function without injection. This means that we observe an impressive speed-up on otherwise difficult to solve functions. Single bad injected solutions on the other hand do no significant harm.


A Reliable Effective Terascale Linear Learning System

We present a system and a set of techniques for learning linear predictors with convex losses on terascale datasets, with trillions of features, {The number of features here refers to the number of non-zero entries in the data matrix.} billions of training examples and millions of parameters in an hour using a cluster of 1000 machines. Individually none of the component techniques are new, but the careful synthesis required to obtain an efficient implementation is. The result is, up to our knowledge, the most scalable and efficient linear learning system reported in the literature (as of 2011 when our experiments were conducted). We describe and thoroughly evaluate the components of the system, showing the importance of the various design choices.


An Optimal Algorithm for Linear Bandits

We provide the first algorithm for online bandit linear optimization whose regret after T rounds is of order sqrt{Td ln N} on any finite class X of N actions in d dimensions, and of order d*sqrt{T} (up to log factors) when X is infinite. These bounds are not improvable in general. The basic idea utilizes tools from convex geometry to construct what is essentially an optimal exploration basis. We also present an application to a model of linear bandits with expert advice. Interestingly, these results show that bandit linear optimization with expert advice in d dimensions is no more difficult (in terms of the achievable regret) than the online d-armed bandit problem with expert advice (where EXP4 is optimal).


Aspiration Learning in Coordination Games

We consider the problem of distributed convergence to efficient outcomes in coordination games through dynamics based on aspiration learning. Under aspiration learning, a player continues to play an action as long as the rewards received exceed a specified aspiration level. Here, the aspiration level is a fading memory average of past rewards, and these levels also are subject to occasional random perturbations. A player becomes dissatisfied whenever a received reward is less than the aspiration level, in which case the player experiments with a probability proportional to the degree of dissatisfaction. Our first contribution is the characterization of the asymptotic behavior of the induced Markov chain of the iterated process in terms of an equivalent finite-state Markov chain. We then characterize explicitly the behavior of the proposed aspiration learning in a generalized version of coordination games, examples of which include network formation and common-pool games. In particular, we show that in generic coordination games the frequency at which an efficient action profile is played can be made arbitrarily large. Although convergence to efficient outcomes is desirable, in several coordination games, such as common-pool games, attainability of fair outcomes, i.e., sequences of plays at which players experience highly rewarding returns with the same frequency, might also be of special interest. To this end, we demonstrate through analysis and simulations that aspiration learning also establishes fair outcomes in all symmetric coordination games, including common-pool games.


Data-dependent kernels in nearly-linear time

We propose a method to efficiently construct data-dependent kernels which can make use of large quantities of (unlabeled) data. Our construction makes an approximation in the standard construction of semi-supervised kernels in Sindhwani et al. 2005. In typical cases these kernels can be computed in nearly-linear time (in the amount of data), improving on the cubic time of the standard construction, enabling large scale semi-supervised learning in a variety of contexts. The methods are validated on semi-supervised and unsupervised problems on data sets containing upto 64,000 sample points.


Learning Hierarchical and Topographic Dictionaries with Structured Sparsity

Recent work in signal processing and statistics have focused on defining new regularization functions, which not only induce sparsity of the solution, but also take into account the structure of the problem. We present in this paper a class of convex penalties introduced in the machine learning community, which take the form of a sum of l_2 and l_infinity-norms over groups of variables. They extend the classical group-sparsity regularization in the sense that the groups possibly overlap, allowing more flexibility in the group design. We review efficient optimization methods to deal with the corresponding inverse problems, and their application to the problem of learning dictionaries of natural image patches: On the one hand, dictionary learning has indeed proven effective for various signal processing tasks. On the other hand, structured sparsity provides a natural framework for modeling dependencies between dictionary elements. We thus consider a structured sparse regularization to learn dictionaries embedded in a particular structure, for instance a tree or a two-dimensional grid. In the latter case, the results we obtain are similar to the dictionaries produced by topographic independent component analysis.


Kernel Topic Models

Latent Dirichlet Allocation models discrete data as a mixture of discrete distributions, using Dirichlet beliefs over the mixture weights. We study a variation of this concept, in which the documents' mixture weight beliefs are replaced with squashed Gaussian distributions. This allows documents to be associated with elements of a Hilbert space, admitting kernel topic models (KTM), modelling temporal, spatial, hierarchical, social and other structure between documents. The main challenge is efficient approximate inference on the latent Gaussian. We present an approximate algorithm cast around a Laplace approximation in a transformed basis. The KTM can also be interpreted as a type of Gaussian process latent variable model, or as a topic model conditional on document features, uncovering links between earlier work in these areas.


Web search queries can predict stock market volumes

We live in a computerized and networked society where many of our actions leave a digital trace and affect other people's actions. This has lead to the emergence of a new data-driven research field: mathematical methods of computer science, statistical physics and sociometry provide insights on a wide range of disciplines ranging from social science to human mobility. A recent important discovery is that query volumes (i.e., the number of requests submitted by users to search engines on the www) can be used to track and, in some cases, to anticipate the dynamics of social phenomena. Successful exemples include unemployment levels, car and home sales, and epidemics spreading. Few recent works applied this approach to stock prices and market sentiment. However, it remains unclear if trends in financial markets can be anticipated by the collective wisdom of on-line users on the web. Here we show that trading volumes of stocks traded in NASDAQ-100 are correlated with the volumes of queries related to the same stocks. In particular, query volumes anticipate in many cases peaks of trading by one day or more. Our analysis is carried out on a unique dataset of queries, submitted to an important web search engine, which enable us to investigate also the user behavior. We show that the query volume dynamics emerges from the collective but seemingly uncoordinated activity of many users. These findings contribute to the debate on the identification of early warnings of financial systemic risk, based on the activity of users of the www.


Wikipedia Edit Number Prediction based on Temporal Dynamics Only

In this paper, we describe our approach to the Wikipedia Participation Challenge which aims to predict the number of edits a Wikipedia editor will make in the next 5 months. The best submission from our team, "zeditor", achieved 41.7% improvement over WMF's baseline predictive model and the final rank of 3rd place among 96 teams. An interesting characteristic of our approach is that only temporal dynamics features (i.e., how the number of edits changes in recent periods, etc.) are used in a self-supervised learning framework, which makes it easy to be generalised to other application domains.


Quilting Stochastic Kronecker Product Graphs to Generate Multiplicative Attribute Graphs

We describe the first sub-quadratic sampling algorithm for the Multiplicative Attribute Graph Model (MAGM) of Kim and Leskovec (2010). We exploit the close connection between MAGM and the Kronecker Product Graph Model (KPGM) of Leskovec et al. (2010), and show that to sample a graph from a MAGM it suffices to sample small number of KPGM graphs and \emph{quilt} them together. Under a restricted set of technical conditions our algorithm runs in $O((\log_2(n))^3 |E|)$ time, where $n$ is the number of nodes and $|E|$ is the number of edges in the sampled graph. We demonstrate the scalability of our algorithm via extensive empirical evaluation; we can sample a MAGM graph with 8 million nodes and 20 billion edges in under 6 hours.


Optimal discovery with probabilistic expert advice

We consider an original problem that arises from the issue of security analysis of a power system and that we name optimal discovery with probabilistic expert advice. We address it with an algorithm based on the optimistic paradigm and the Good-Turing missing mass estimator. We show that this strategy uniformly attains the optimal discovery rate in a macroscopic limit sense, under some assumptions on the probabilistic experts. We also provide numerical experiments suggesting that this optimal behavior may still hold under weaker assumptions.


Inducing Probabilistic Programs by Bayesian Program Merging

This report outlines an approach to learning generative models from data. We express models as probabilistic programs, which allows us to capture abstract patterns within the examples. By choosing our language for programs to be an extension of the algebraic data type of the examples, we can begin with a program that generates all and only the examples. We then introduce greater abstraction, and hence generalization, incrementally to the extent that it improves the posterior probability of the examples given the program. Motivated by previous approaches to model merging and program induction, we search for such explanatory abstractions using program transformations. We consider two types of transformation: Abstraction merges common subexpressions within a program into new functions (a form of anti-unification). Deargumentation simplifies functions by reducing the number of arguments. We demonstrate that this approach finds key patterns in the domain of nested lists, including parameterized sub-functions and stochastic recursion.


Discussion on "Techniques for Massive-Data Machine Learning in Astronomy" by A. Gray

Astronomy is increasingly encountering two fundamental truths: (1) The field is faced with the task of extracting useful information from extremely large, complex, and high dimensional datasets; (2) The techniques of astroinformatics and astrostatistics are the only way to make this tractable, and bring the required level of sophistication to the analysis. Thus, an approach which provides these tools in a way that scales to these datasets is not just desirable, it is vital. The expertise required spans not just astronomy, but also computer science, statistics, and informatics. As a computer scientist and expert in machine learning, Alex's contribution of expertise and a large number of fast algorithms designed to scale to large datasets, is extremely welcome. We focus in this discussion on the questions raised by the practical application of these algorithms to real astronomical datasets. That is, what is needed to maximally leverage their potential to improve the science return? This is not a trivial task. While computing and statistical expertise are required, so is astronomical expertise. Precedent has shown that, to-date, the collaborations most productive in producing astronomical science results (e.g, the Sloan Digital Sky Survey), have either involved astronomers expert in computer science and/or statistics, or astronomers involved in close, long-term collaborations with experts in those fields. This does not mean that the astronomers are giving the most important input, but simply that their input is crucial in guiding the effort in the most fruitful directions, and coping with the issues raised by real data. Thus, the tools must be useable and understandable by those whose primary expertise is not computing or statistics, even though they may have quite extensive knowledge of those fields.


The multi-armed bandit problem with covariates

We consider a multi-armed bandit problem in a setting where each arm produces a noisy reward realization which depends on an observable random covariate. As opposed to the traditional static multi-armed bandit problem, this setting allows for dynamically changing rewards that better describe applications where side information is available. We adopt a nonparametric model where the expected rewards are smooth functions of the covariate and where the hardness of the problem is captured by a margin parameter. To maximize the expected cumulative reward, we introduce a policy called Adaptively Binned Successive Elimination (abse) that adaptively decomposes the global problem into suitably "localized" static bandit problems. This policy constructs an adaptive partition using a variant of the Successive Elimination (se) policy. Our results include sharper regret bounds for the se policy in a static bandit problem and minimax optimal regret bounds for the abse policy in the dynamic problem.


Deciding of HMM parameters based on number of critical points for gesture recognition from motion capture data

This paper presents a method of choosing number of states of a HMM based on number of critical points of the motion capture data. The choice of Hidden Markov Models(HMM) parameters is crucial for recognizer's performance as it is the first step of the training and cannot be corrected automatically within HMM. In this article we define predictor of number of states based on number of critical points of the sequence and test its effectiveness against sample data.


PAC-Bayes-Bernstein Inequality for Martingales and its Application to Multiarmed Bandits

We develop a new tool for data-dependent analysis of the exploration-exploitation trade-off in learning under limited feedback. Our tool is based on two main ingredients. The first ingredient is a new concentration inequality that makes it possible to control the concentration of weighted averages of multiple (possibly uncountably many) simultaneously evolving and interdependent martingales. The second ingredient is an application of this inequality to the exploration-exploitation trade-off via importance weighted sampling. We apply the new tool to the stochastic multiarmed bandit problem, however, the main importance of this paper is the development and understanding of the new tool rather than improvement of existing algorithms for stochastic multiarmed bandits. In the follow-up work we demonstrate that the new tool can improve over state-of-the-art in structurally richer problems, such as stochastic multiarmed bandits with side information (Seldin et al., 2011a).


PAC-Bayesian Inequalities for Martingales

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.


Text-Independent Speaker Recognition for Low SNR Environments with Encryption

Recognition systems are commonly designed to authenticate users at the access control levels of a system. A number of voice recognition methods have been developed using a pitch estimation process which are very vulnerable in low Signal to Noise Ratio (SNR) environments thus, these programs fail to provide the desired level of accuracy and robustness. Also, most text independent speaker recognition programs are incapable of coping with unauthorized attempts to gain access by tampering with the samples or reference database. The proposed text-independent voice recognition system makes use of multilevel cryptography to preserve data integrity while in transit or storage. Encryption and decryption follow a transform based approach layered with pseudorandom noise addition whereas for pitch detection, a modified version of the autocorrelation pitch extraction algorithm is used. The experimental results show that the proposed algorithm can decrypt the signal under test with exponentially reducing Mean Square Error over an increasing range of SNR. Further, it outperforms the conventional algorithms in actual identification tasks even in noisy environments. The recognition rate thus obtained using the proposed method is compared with other conventional methods used for speaker identification.


Diffusion Adaptation Strategies for Distributed Optimization and Learning over Networks

We propose an adaptive diffusion mechanism to optimize a global cost function in a distributed manner over a network of nodes. The cost function is assumed to consist of a collection of individual components. Diffusion adaptation allows the nodes to cooperate and diffuse information in real-time; it also helps alleviate the effects of stochastic gradient noise and measurement noise through a continuous learning process. We analyze the mean-square-error performance of the algorithm in some detail, including its transient and steady-state behavior. We also apply the diffusion algorithm to two problems: distributed estimation with sparse parameters and distributed localization. Compared to well-studied incremental methods, diffusion methods do not require the use of a cyclic path over the nodes and are robust to node and link failure. Diffusion methods also endow networks with adaptation abilities that enable the individual nodes to continue learning even when the cost function changes with time. Examples involving such dynamic cost functions with moving targets are common in the context of biological networks.


Revisiting k-means: New Algorithms via Bayesian Nonparametrics

Bayesian models offer great flexibility for clustering applications---Bayesian nonparametrics can be used for modeling infinite mixtures, and hierarchical Bayesian models can be utilized for sharing clusters across multiple data sets. For the most part, such flexibility is lacking in classical clustering methods such as k-means. In this paper, we revisit the k-means clustering algorithm from a Bayesian nonparametric viewpoint. Inspired by the asymptotic connection between k-means and mixtures of Gaussians, we show that a Gibbs sampling algorithm for the Dirichlet process mixture approaches a hard clustering algorithm in the limit, and further that the resulting algorithm monotonically minimizes an elegant underlying k-means-like clustering objective that includes a penalty for the number of clusters. We generalize this analysis to the case of clustering multiple data sets through a similar asymptotic argument with the hierarchical Dirichlet process. We also discuss further extensions that highlight the benefits of our analysis: i) a spectral relaxation involving thresholded eigenvectors, and ii) a normalized cut graph clustering algorithm that does not fix the number of clusters in the graph.


Approximate Stochastic Subgradient Estimation Training for Support Vector Machines

Subgradient algorithms for training support vector machines have been quite successful for solving large-scale and online learning problems. However, they have been restricted to linear kernels and strongly convex formulations. This paper describes efficient subgradient approaches without such limitations. Our approaches make use of randomized low-dimensional approximations to nonlinear kernels, and minimization of a reduced primal formulation using an algorithm based on robust stochastic approximation, which do not require strong convexity. Experiments illustrate that our approaches produce solutions of comparable prediction accuracy with the solutions acquired from existing SVM solvers, but often in much shorter time. We also suggest efficient prediction schemes that depend only on the dimension of kernel approximation, not on the number of support vectors.


Online Learning with Preference Feedback

We propose a new online learning model for learning with preference feedback. The model is especially suited for applications like web search and recommender systems, where preference data is readily available from implicit user feedback (e.g. clicks). In particular, at each time step a potentially structured object (e.g. a ranking) is presented to the user in response to a context (e.g. query), providing him or her with some unobserved amount of utility. As feedback the algorithm receives an improved object that would have provided higher utility. We propose a learning algorithm with provable regret bounds for this online learning setting and demonstrate its effectiveness on a web-search application. The new learning model also applies to many other interactive learning problems and admits several interesting extensions.


Computing a Nonnegative Matrix Factorization -- Provably

In the Nonnegative Matrix Factorization (NMF) problem we are given an $n \times m$ nonnegative matrix $M$ and an integer $r > 0$. Our goal is to express $M$ as $A W$ where $A$ and $W$ are nonnegative matrices of size $n \times r$ and $r \times m$ respectively. In some applications, it makes sense to ask instead for the product $AW$ to approximate $M$ -- i.e. (approximately) minimize $\norm{M - AW}_F$ where $\norm{}_F$ denotes the Frobenius norm; we refer to this as Approximate NMF. This problem has a rich history spanning quantum mechanics, probability theory, data analysis, polyhedral combinatorics, communication complexity, demography, chemometrics, etc. In the past decade NMF has become enormously popular in machine learning, where $A$ and $W$ are computed using a variety of local search heuristics. Vavasis proved that this problem is NP-complete. We initiate a study of when this problem is solvable in polynomial time: 1. We give a polynomial-time algorithm for exact and approximate NMF for every constant $r$. Indeed NMF is most interesting in applications precisely when $r$ is small. 2. We complement this with a hardness result, that if exact NMF can be solved in time $(nm)^{o(r)}$, 3-SAT has a sub-exponential time algorithm. This rules out substantial improvements to the above algorithm. 3. We give an algorithm that runs in time polynomial in $n$, $m$ and $r$ under the separablity condition identified by Donoho and Stodden in 2003. The algorithm may be practical since it is simple and noise tolerant (under benign assumptions). Separability is believed to hold in many practical settings. To the best of our knowledge, this last result is the first example of a polynomial-time algorithm that provably works under a non-trivial condition on the input and we believe that this will be an interesting and important direction for future work.


Tight Bounds on Proper Equivalence Query Learning of DNF

We prove a new structural lemma for partial Boolean functions $f$, which we call the seed lemma for DNF. Using the lemma, we give the first subexponential algorithm for proper learning of DNF in Angluin's Equivalence Query (EQ) model. The algorithm has time and query complexity $2^{(\tilde{O}{\sqrt{n}})}$, which is optimal. We also give a new result on certificates for DNF-size, a simple algorithm for properly PAC-learning DNF, and new results on EQ-learning $\log n$-term DNF and decision trees.


Universal MMSE Filtering With Logarithmic Adaptive Regret

We consider the problem of online estimation of a real-valued signal corrupted by oblivious zero-mean noise using linear estimators. The estimator is required to iteratively predict the underlying signal based on the current and several last noisy observations, and its performance is measured by the mean-square-error. We describe and analyze an algorithm for this task which: 1. Achieves logarithmic adaptive regret against the best linear filter in hindsight. This bound is assyptotically tight, and resolves the question of Moon and Weissman [1]. 2. Runs in linear time in terms of the number of filter coefficients. Previous constructions required at least quadratic time.


Nonparametric Bayesian Estimation of Periodic Functions

Many real world problems exhibit patterns that have periodic behavior. For example, in astrophysics, periodic variable stars play a pivotal role in understanding our universe. An important step when analyzing data from such processes is the problem of identifying the period: estimating the period of a periodic function based on noisy observations made at irregularly spaced time points. This problem is still a difficult challenge despite extensive study in different disciplines. The paper makes several contributions toward solving this problem. First, we present a nonparametric Bayesian model for period finding, based on Gaussian Processes (GP), that does not make strong assumptions on the shape of the periodic function. As our experiments demonstrate, the new model leads to significantly better results in period estimation when the target function is non-sinusoidal. Second, we develop a new algorithm for parameter optimization for GP which is useful when the likelihood function is very sensitive to the setting of the hyper-parameters with numerous local minima, as in the case of period estimation. The algorithm combines gradient optimization with grid search and incorporates several mechanisms to overcome the high complexity of inference with GP. Third, we develop a novel approach for using domain knowledge, in the form of a probabilistic generative model, and incorporate it into the period estimation algorithm. Experimental results on astrophysics data validate our approach showing significant improvement over the state of the art in this domain.


Confidence Estimation in Structured Prediction

Structured classification tasks such as sequence labeling and dependency parsing have seen much interest by the Natural Language Processing and the machine learning communities. Several online learning algorithms were adapted for structured tasks such as Perceptron, Passive- Aggressive and the recently introduced Confidence-Weighted learning . These online algorithms are easy to implement, fast to train and yield state-of-the-art performance. However, unlike probabilistic models like Hidden Markov Model and Conditional random fields, these methods generate models that output merely a prediction with no additional information regarding confidence in the correctness of the output. In this work we fill the gap proposing few alternatives to compute the confidence in the output of non-probabilistic algorithms.We show how to compute confidence estimates in the prediction such that the confidence reflects the probability that the word is labeled correctly. We then show how to use our methods to detect mislabeled words, trade recall for precision and active learning. We evaluate our methods on four noun-phrase chunking and named entity recognition sequence labeling tasks, and on dependency parsing for 14 languages.


Efficient Nonparametric Conformal Prediction Regions

We investigate and extend the conformal prediction method due to Vovk,Gammerman and Shafer (2005) to construct nonparametric prediction regions. These regions have guaranteed distribution free, finite sample coverage, without any assumptions on the distribution or the bandwidth. Explicit convergence rates of the loss function are established for such regions under standard regularity conditions. Approximations for simplifying implementation and data driven bandwidth selection methods are also discussed. The theoretical properties of our method are demonstrated through simulations.


Robust Interactive Learning

In this paper we propose and study a generalization of the standard active-learning model where a more general type of query, class conditional query, is allowed. Such queries have been quite useful in applications, but have been lacking theoretical understanding. In this work, we characterize the power of such queries under two well-known noise models. We give nearly tight upper and lower bounds on the number of queries needed to learn both for the general agnostic setting and for the bounded noise model. We further show that our methods can be made adaptive to the (unknown) noise rate, with only negligible loss in query complexity.


UPAL: Unbiased Pool Based Active Learning

In this paper we address the problem of pool based active learning, and provide an algorithm, called UPAL, that works by minimizing the unbiased estimator of the risk of a hypothesis in a given hypothesis space. For the space of linear classifiers and the squared loss we show that UPAL is equivalent to an exponentially weighted average forecaster. Exploiting some recent results regarding the spectra of random matrices allows us to establish consistency of UPAL when the true hypothesis is a linear hypothesis. Empirical comparison with an active learner implementation in Vowpal Wabbit, and a previously proposed pool based active learner implementation show good empirical performance and better scalability.


Analysis of Thompson Sampling for the multi-armed bandit problem

The multi-armed bandit problem is a popular model for studying exploration/exploitation trade-off in sequential decision problems. Many algorithms are now available for this well-studied problem. One of the earliest algorithms, given by W. R. Thompson, dates back to 1933. This algorithm, referred to as Thompson Sampling, is a natural Bayesian algorithm. The basic idea is to choose an arm to play according to its probability of being the best arm. Thompson Sampling algorithm has experimentally been shown to be close to optimal. In addition, it is efficient to implement and exhibits several desirable properties such as small regret for delayed feedback. However, theoretical understanding of this algorithm was quite limited. In this paper, for the first time, we show that Thompson Sampling algorithm achieves logarithmic expected regret for the multi-armed bandit problem. More precisely, for the two-armed bandit problem, the expected regret in time $T$ is $O(\frac{\ln T}{\Delta} + \frac{1}{\Delta^3})$. And, for the $N$-armed bandit problem, the expected regret in time $T$ is $O([(\sum_{i=2}^N \frac{1}{\Delta_i^2})^2] \ln T)$. Our bounds are optimal but for the dependence on $\Delta_i$ and the constant factors in big-Oh.


Pushing Your Point of View: Behavioral Measures of Manipulation in Wikipedia

As a major source for information on virtually any topic, Wikipedia serves an important role in public dissemination and consumption of knowledge. As a result, it presents tremendous potential for people to promulgate their own points of view; such efforts may be more subtle than typical vandalism. In this paper, we introduce new behavioral metrics to quantify the level of controversy associated with a particular user: a Controversy Score (C-Score) based on the amount of attention the user focuses on controversial pages, and a Clustered Controversy Score (CC-Score) that also takes into account topical clustering. We show that both these measures are useful for identifying people who try to "push" their points of view, by showing that they are good predictors of which editors get blocked. The metrics can be used to triage potential POV pushers. We apply this idea to a dataset of users who requested promotion to administrator status and easily identify some editors who significantly changed their behavior upon becoming administrators. At the same time, such behavior is not rampant. Those who are promoted to administrator status tend to have more stable behavior than comparable groups of prolific editors. This suggests that the Adminship process works well, and that the Wikipedia community is not overwhelmed by users who become administrators to promote their own points of view.


Generic Multiplicative Methods for Implementing Machine Learning Algorithms on MapReduce

In this paper we introduce a generic model for multiplicative algorithms which is suitable for the MapReduce parallel programming paradigm. We implement three typical machine learning algorithms to demonstrate how similarity comparison, gradient descent, power method and other classic learning techniques fit this model well. Two versions of large-scale matrix multiplication are discussed in this paper, and different methods are developed for both cases with regard to their unique computational characteristics and problem settings. In contrast to earlier research, we focus on fundamental linear algebra techniques that establish a generic approach for a range of algorithms, rather than specific ways of scaling up algorithms one at a time. Experiments show promising results when evaluated on both speedup and accuracy. Compared with a standard implementation with computational complexity $O(m^3)$ in the worst case, the large-scale matrix multiplication experiments prove our design is considerably more efficient and maintains a good speedup as the number of cores increases. Algorithm-specific experiments also produce encouraging results on runtime performance.


Scaling Up Estimation of Distribution Algorithms For Continuous Optimization

Since Estimation of Distribution Algorithms (EDA) were proposed, many attempts have been made to improve EDAs' performance in the context of global optimization. So far, the studies or applications of multivariate probabilistic model based continuous EDAs are still restricted to rather low dimensional problems (smaller than 100D). Traditional EDAs have difficulties in solving higher dimensional problems because of the curse of dimensionality and their rapidly increasing computational cost. However, scaling up continuous EDAs for higher dimensional optimization is still necessary, which is supported by the distinctive feature of EDAs: Because a probabilistic model is explicitly estimated, from the learnt model one can discover useful properties or features of the problem. Besides obtaining a good solution, understanding of the problem structure can be of great benefit, especially for black box optimization. We propose a novel EDA framework with Model Complexity Control (EDA-MCC) to scale up EDAs. By using Weakly dependent variable Identification (WI) and Subspace Modeling (SM), EDA-MCC shows significantly better performance than traditional EDAs on high dimensional problems. Moreover, the computational cost and the requirement of large population sizes can be reduced in EDA-MCC. In addition to being able to find a good solution, EDA-MCC can also produce a useful problem structure characterization. EDA-MCC is the first successful instance of multivariate model based EDAs that can be effectively applied a general class of up to 500D problems. It also outperforms some newly developed algorithms designed specifically for large scale optimization. In order to understand the strength and weakness of EDA-MCC, we have carried out extensive computational studies of EDA-MCC. Our results have revealed when EDA-MCC is likely to outperform others on what kind of benchmark functions.


Improved Bound for the Nystrom's Method and its Application to Kernel Classification

We develop two approaches for analyzing the approximation error bound for the Nystr\"{o}m method, one based on the concentration inequality of integral operator, and one based on the compressive sensing theory. We show that the approximation error, measured in the spectral norm, can be improved from $O(N/\sqrt{m})$ to $O(N/m^{1 - \rho})$ in the case of large eigengap, where $N$ is the total number of data points, $m$ is the number of sampled data points, and $\rho \in (0, 1/2)$ is a positive constant that characterizes the eigengap. When the eigenvalues of the kernel matrix follow a $p$-power law, our analysis based on compressive sensing theory further improves the bound to $O(N/m^{p - 1})$ under an incoherence assumption, which explains why the Nystr\"{o}m method works well for kernel matrix with skewed eigenvalues. We present a kernel classification approach based on the Nystr\"{o}m method and derive its generalization performance using the improved bound. We show that when the eigenvalues of kernel matrix follow a $p$-power law, we can reduce the number of support vectors to $N^{2p/(p^2 - 1)}$, a number less than $N$ when $p > 1+\sqrt{2}$, without seriously sacrificing its generalization performance.


A Collaborative Mechanism for Crowdsourcing Prediction Problems

Machine Learning competitions such as the Netflix Prize have proven reasonably successful as a method of "crowdsourcing" prediction tasks. But these competitions have a number of weaknesses, particularly in the incentive structure they create for the participants. We propose a new approach, called a Crowdsourced Learning Mechanism, in which participants collaboratively "learn" a hypothesis for a given prediction task. The approach draws heavily from the concept of a prediction market, where traders bet on the likelihood of a future event. In our framework, the mechanism continues to publish the current hypothesis, and participants can modify this hypothesis by wagering on an update. The critical incentive property is that a participant will profit an amount that scales according to how much her update improves performance on a released test set.


Using Contextual Information as Virtual Items on Top-N Recommender Systems

Traditionally, recommender systems for the Web deal with applications that have two dimensions, users and items. Based on access logs that relate these dimensions, a recommendation model can be built and used to identify a set of N items that will be of interest to a certain user. In this paper we propose a method to complement the information in the access logs with contextual information without changing the recommendation algorithm. The method consists in representing context as virtual items. We empirically test this method with two top-N recommender systems, an item-based collaborative filtering technique and association rules, on three data sets. The results show that our method is able to take advantage of the context (new dimensions) when it is informative.


A Bayesian Model for Plan Recognition in RTS Games applied to StarCraft

The task of keyhole (unobtrusive) plan recognition is central to adaptive game AI. "Tech trees" or "build trees" are the core of real-time strategy (RTS) game strategic (long term) planning. This paper presents a generic and simple Bayesian model for RTS build tree prediction from noisy observations, which parameters are learned from replays (game logs). This unsupervised machine learning approach involves minimal work for the game developers as it leverage players' data (com- mon in RTS). We applied it to StarCraft1 and showed that it yields high quality and robust predictions, that can feed an adaptive AI.


No Free Lunch versus Occam's Razor in Supervised Learning

The No Free Lunch theorems are often used to argue that domain specific knowledge is required to design successful algorithms. We use algorithmic information theory to argue the case for a universal bias allowing an algorithm to succeed in all interesting problem domains. Additionally, we give a new algorithm for off-line classification, inspired by Solomonoff induction, with good performance on all structured problems under reasonable assumptions. This includes a proof of the efficacy of the well-known heuristic of randomly selecting training data in the hope of reducing misclassification rates.


Sequential search based on kriging: convergence analysis of some algorithms

Let $\FF$ be a set of real-valued functions on a set $\XX$ and let $S:\FF \to \GG$ be an arbitrary mapping. We consider the problem of making inference about $S(f)$, with $f\in\FF$ unknown, from a finite set of pointwise evaluations of $f$. We are mainly interested in the problems of approximation and optimization. In this article, we make a brief review of results concerning average error bounds of Bayesian search methods that use a random process prior about $f$.


The No-U-Turn Sampler: Adaptively Setting Path Lengths in Hamiltonian Monte Carlo

Hamiltonian Monte Carlo (HMC) is a Markov chain Monte Carlo (MCMC) algorithm that avoids the random walk behavior and sensitivity to correlated parameters that plague many MCMC methods by taking a series of steps informed by first-order gradient information. These features allow it to converge to high-dimensional target distributions much more quickly than simpler methods such as random walk Metropolis or Gibbs sampling. However, HMC's performance is highly sensitive to two user-specified parameters: a step size {\epsilon} and a desired number of steps L. In particular, if L is too small then the algorithm exhibits undesirable random walk behavior, while if L is too large the algorithm wastes computation. We introduce the No-U-Turn Sampler (NUTS), an extension to HMC that eliminates the need to set a number of steps L. NUTS uses a recursive algorithm to build a set of likely candidate points that spans a wide swath of the target distribution, stopping automatically when it starts to double back and retrace its steps. Empirically, NUTS perform at least as efficiently as and sometimes more efficiently than a well tuned standard HMC method, without requiring user intervention or costly tuning runs. We also derive a method for adapting the step size parameter {\epsilon} on the fly based on primal-dual averaging. NUTS can thus be used with no hand-tuning at all. NUTS is also suitable for applications such as BUGS-style automatic inference engines that require efficient "turnkey" sampling algorithms.


Parametrized Stochastic Multi-armed Bandits with Binary Rewards

In this paper, we consider the problem of multi-armed bandits with a large, possibly infinite number of correlated arms. We assume that the arms have Bernoulli distributed rewards, independent across time, where the probabilities of success are parametrized by known attribute vectors for each arm, as well as an unknown preference vector, each of dimension $n$. For this model, we seek an algorithm with a total regret that is sub-linear in time and independent of the number of arms. We present such an algorithm, which we call the Two-Phase Algorithm, and analyze its performance. We show upper bounds on the total regret which applies uniformly in time, for both the finite and infinite arm cases. The asymptotics of the finite arm bound show that for any $f \in \omega(\log(T))$, the total regret can be made to be $O(n \cdot f(T))$. In the infinite arm case, the total regret is $O(\sqrt{n^3 T})$.


Efficient Regression in Metric Spaces via Approximate Lipschitz Extension

We present a framework for performing efficient regression in general metric spaces. Roughly speaking, our regressor predicts the value at a new point by computing a Lipschitz extension --- the smoothest function consistent with the observed data --- after performing structural risk minimization to avoid overfitting. We obtain finite-sample risk bounds with minimal structural and noise assumptions, and a natural speed-precision tradeoff. The offline (learning) and online (prediction) stages can be solved by convex programming, but this naive approach has runtime complexity $O(n^3)$, which is prohibitive for large datasets. We design instead a regression algorithm whose speed and generalization performance depend on the intrinsic dimension of the data, to which the algorithm adapts. While our main innovation is algorithmic, the statistical results may also be of independent interest.


Large Scale Spectral Clustering Using Approximate Commute Time Embedding

Spectral clustering is a novel clustering method which can detect complex shapes of data clusters. However, it requires the eigen decomposition of the graph Laplacian matrix, which is proportion to $O(n^3)$ and thus is not suitable for large scale systems. Recently, many methods have been proposed to accelerate the computational time of spectral clustering. These approximate methods usually involve sampling techniques by which a lot information of the original data may be lost. In this work, we propose a fast and accurate spectral clustering approach using an approximate commute time embedding, which is similar to the spectral embedding. The method does not require using any sampling technique and computing any eigenvector at all. Instead it uses random projection and a linear time solver to find the approximate embedding. The experiments in several synthetic and real datasets show that the proposed approach has better clustering quality and is faster than the state-of-the-art approximate spectral clustering methods.


Bayesian optimization using sequential Monte Carlo

We consider the problem of optimizing a real-valued continuous function $f$ using a Bayesian approach, where the evaluations of $f$ are chosen sequentially by combining prior information about $f$, which is described by a random process model, and past evaluation results. The main difficulty with this approach is to be able to compute the posterior distributions of quantities of interest which are used to choose evaluation points. In this article, we decide to use a Sequential Monte Carlo (SMC) approach.


Stochastic gradient descent on Riemannian manifolds

Stochastic gradient descent is a simple approach to find the local minima of a cost function whose evaluations are corrupted by noise. In this paper, we develop a procedure extending stochastic gradient descent algorithms to the case where the function is defined on a Riemannian manifold. We prove that, as in the Euclidian case, the gradient descent algorithm converges to a critical point of the cost function. The algorithm has numerous potential applications, and is illustrated here by four examples. In particular a novel gossip algorithm on the set of covariance matrices is derived and tested numerically.


The Graphical Lasso: New Insights and Alternatives

The graphical lasso \citep{FHT2007a} is an algorithm for learning the structure in an undirected Gaussian graphical model, using $\ell_1$ regularization to control the number of zeros in the precision matrix ${\B\Theta}={\B\Sigma}^{-1}$ \citep{BGA2008,yuan_lin_07}. The {\texttt R} package \GL\ \citep{FHT2007a} is popular, fast, and allows one to efficiently build a path of models for different values of the tuning parameter. Convergence of \GL\ can be tricky; the converged precision matrix might not be the inverse of the estimated covariance, and occasionally it fails to converge with warm starts. In this paper we explain this behavior, and propose new algorithms that appear to outperform \GL. By studying the "normal equations" we see that, \GL\ is solving the {\em dual} of the graphical lasso penalized likelihood, by block coordinate ascent; a result which can also be found in \cite{BGA2008}. In this dual, the target of estimation is $\B\Sigma$, the covariance matrix, rather than the precision matrix $\B\Theta$. We propose similar primal algorithms \PGL\ and \DPGL, that also operate by block-coordinate descent, where $\B\Theta$ is the optimization target. We study all of these algorithms, and in particular different approaches to solving their coordinate sub-problems. We conclude that \DPGL\ is superior from several points of view.


Falsification and future performance

We information-theoretically reformulate two measures of capacity from statistical learning theory: empirical VC-entropy and empirical Rademacher complexity. We show these capacity measures count the number of hypotheses about a dataset that a learning algorithm falsifies when it finds the classifier in its repertoire minimizing empirical risk. It then follows from that the future performance of predictors on unseen data is controlled in part by how many hypotheses the learner falsifies. As a corollary we show that empirical VC-entropy quantifies the message length of the true hypothesis in the optimal code of a particular probability distribution, the so-called actual repertoire.


Trading Regret for Efficiency: Online Convex Optimization with Long Term Constraints

In this paper we propose a framework for solving constrained online convex optimization problem. Our motivation stems from the observation that most algorithms proposed for online convex optimization require a projection onto the convex set $\mathcal{K}$ from which the decisions are made. While for simple shapes (e.g. Euclidean ball) the projection is straightforward, for arbitrary complex sets this is the main computational challenge and may be inefficient in practice. In this paper, we consider an alternative online convex optimization problem. Instead of requiring decisions belong to $\mathcal{K}$ for all rounds, we only require that the constraints which define the set $\mathcal{K}$ be satisfied in the long run. We show that our framework can be utilized to solve a relaxed version of online learning with side constraints addressed in \cite{DBLP:conf/colt/MannorT06} and \cite{DBLP:conf/aaai/KvetonYTM08}. By turning the problem into an online convex-concave optimization problem, we propose an efficient algorithm which achieves $\tilde{\mathcal{O}}(\sqrt{T})$ regret bound and $\tilde{\mathcal{O}}(T^{3/4})$ bound for the violation of constraints. Then we modify the algorithm in order to guarantee that the constraints are satisfied in the long run. This gain is achieved at the price of getting $\tilde{\mathcal{O}}(T^{3/4})$ regret bound. Our second algorithm is based on the Mirror Prox method \citep{nemirovski-2005-prox} to solve variational inequalities which achieves $\tilde{\mathcal{\mathcal{O}}}(T^{2/3})$ bound for both regret and the violation of constraints when the domain $\K$ can be described by a finite number of linear constraints. Finally, we extend the result to the setting where we only have partial access to the convex set $\mathcal{K}$ and propose a multipoint bandit feedback algorithm with the same bounds in expectation as our first algorithm.


Learning a Factor Model via Regularized PCA

We consider the problem of learning a linear factor model. We propose a regularized form of principal component analysis (PCA) and demonstrate through experiments with synthetic and real data the superiority of resulting estimates to those produced by pre-existing factor analysis approaches. We also establish theoretical results that explain how our algorithm corrects the biases induced by conventional approaches. An important feature of our algorithm is that its computational requirements are similar to those of PCA, which enjoys wide use in large part due to its efficiency.


Robust Max-Product Belief Propagation

We study the problem of optimizing a graph-structured objective function under \emph{adversarial} uncertainty. This problem can be modeled as a two-persons zero-sum game between an Engineer and Nature. The Engineer controls a subset of the variables (nodes in the graph), and tries to assign their values to maximize an objective function. Nature controls the complementary subset of variables and tries to minimize the same objective. This setting encompasses estimation and optimization problems under model uncertainty, and strategic problems with a graph structure. Von Neumann's minimax theorem guarantees the existence of a (minimax) pair of randomized strategies that provide optimal robustness for each player against its adversary. We prove several structural properties of this strategy pair in the case of graph-structured payoff function. In particular, the randomized minimax strategies (distributions over variable assignments) can be chosen in such a way to satisfy the Markov property with respect to the graph. This significantly reduces the problem dimensionality. Finally we introduce a message passing algorithm to solve this minimax problem. The algorithm generalizes max-product belief propagation to this new domain.


Regret Bound by Variation for Online Convex Optimization

In citep{Hazan-2008-extract}, the authors showed that the regret of online linear optimization can be bounded by the total variation of the cost vectors. In this paper, we extend this result to general online convex optimization. We first analyze the limitations of the algorithm in \citep{Hazan-2008-extract} when applied it to online convex optimization. We then present two algorithms for online convex optimization whose regrets are bounded by the variation of cost functions. We finally consider the bandit setting, and present a randomized algorithm for online bandit convex optimization with a variation-based regret bound. We show that the regret bound for online bandit convex optimization is optimal when the variation of cost functions is independent of the number of trials.


Learning with Submodular Functions: A Convex Optimization Perspective

Submodular functions are relevant to machine learning for at least two reasons: (1) some problems may be expressed directly as the optimization of submodular functions and (2) the lovasz extension of submodular functions provides a useful set of regularization functions for supervised and unsupervised learning. In this monograph, we present the theory of submodular functions from a convex analysis perspective, presenting tight links between certain polyhedra, combinatorial optimization and convex optimization problems. In particular, we show how submodular function minimization is equivalent to solving a wide variety of convex optimization problems. This allows the derivation of new efficient algorithms for approximate and exact submodular function minimization with theoretical guarantees and good practical performance. By listing many examples of submodular functions, we review various applications to machine learning, such as clustering, experimental design, sensor placement, graphical model structure learning or subset selection, as well as a family of structured sparsity-inducing norms that can be derived and used from submodular functions.


A kernel-based framework for learning graded relations from data

Driven by a large number of potential applications in areas like bioinformatics, information retrieval and social network analysis, the problem setting of inferring relations between pairs of data objects has recently been investigated quite intensively in the machine learning community. To this end, current approaches typically consider datasets containing crisp relations, so that standard classification methods can be adopted. However, relations between objects like similarities and preferences are often expressed in a graded manner in real-world applications. A general kernel-based framework for learning relations from data is introduced here. It extends existing approaches because both crisp and graded relations are considered, and it unifies existing approaches because different types of graded relations can be modeled, including symmetric and reciprocal relations. This framework establishes important links between recent developments in fuzzy set theory and machine learning. Its usefulness is demonstrated through various experiments on synthetic and real-world data.


Fast Private Data Release Algorithms for Sparse Queries

We revisit the problem of accurately answering large classes of statistical queries while preserving differential privacy. Previous approaches to this problem have either been very general but have not had run-time polynomial in the size of the database, have applied only to very limited classes of queries, or have relaxed the notion of worst-case error guarantees. In this paper we consider the large class of sparse queries, which take non-zero values on only polynomially many universe elements. We give efficient query release algorithms for this class, in both the interactive and the non-interactive setting. Our algorithms also achieve better accuracy bounds than previous general techniques do when applied to sparse queries: our bounds are independent of the universe size. In fact, even the runtime of our interactive mechanism is independent of the universe size, and so can be implemented in the "infinite universe" model in which no finite universe need be specified by the data curator.


Multivariate information measures: an experimentalist's perspective

Information theory is widely accepted as a powerful tool for analyzing complex systems and it has been applied in many disciplines. Recently, some central components of information theory - multivariate information measures - have found expanded use in the study of several phenomena. These information measures differ in subtle yet significant ways. Here, we will review the information theory behind each measure, as well as examine the differences between these measures by applying them to several simple model systems. In addition to these systems, we will illustrate the usefulness of the information measures by analyzing neural spiking data from a dissociated culture through early stages of its development. We hope that this work will aid other researchers as they seek the best multivariate information measure for their specific research goals and system. Finally, we have made software available online which allows the user to calculate all of the information measures discussed within this paper.


Structure Learning of Probabilistic Graphical Models: A Comprehensive Survey

Probabilistic graphical models combine the graph theory and probability theory to give a multivariate statistical modeling. They provide a unified description of uncertainty using probability and complexity using the graphical model. Especially, graphical models provide the following several useful properties: - Graphical models provide a simple and intuitive interpretation of the structures of probabilistic models. On the other hand, they can be used to design and motivate new models. - Graphical models provide additional insights into the properties of the model, including the conditional independence properties. - Complex computations which are required to perform inference and learning in sophisticated models can be expressed in terms of graphical manipulations, in which the underlying mathematical expressions are carried along implicitly. The graphical models have been applied to a large number of fields, including bioinformatics, social science, control theory, image processing, marketing analysis, among others. However, structure learning for graphical models remains an open challenge, since one must cope with a combinatorial search over the space of all possible structures. In this paper, we present a comprehensive survey of the existing structure learning algorithms.


Efficient Discovery of Association Rules and Frequent Itemsets through Sampling with Tight Performance Guarantees

The tasks of extracting (top-$K$) Frequent Itemsets (FI's) and Association Rules (AR's) are fundamental primitives in data mining and database applications. Exact algorithms for these problems exist and are widely used, but their running time is hindered by the need of scanning the entire dataset, possibly multiple times. High quality approximations of FI's and AR's are sufficient for most practical uses, and a number of recent works explored the application of sampling for fast discovery of approximate solutions to the problems. However, these works do not provide satisfactory performance guarantees on the quality of the approximation, due to the difficulty of bounding the probability of under- or over-sampling any one of an unknown number of frequent itemsets. In this work we circumvent this issue by applying the statistical concept of \emph{Vapnik-Chervonenkis (VC) dimension} to develop a novel technique for providing tight bounds on the sample size that guarantees approximation within user-specified parameters. Our technique applies both to absolute and to relative approximations of (top-$K$) FI's and AR's. The resulting sample size is linearly dependent on the VC-dimension of a range space associated with the dataset to be mined. The main theoretical contribution of this work is a proof that the VC-dimension of this range space is upper bounded by an easy-to-compute characteristic quantity of the dataset which we call \emph{d-index}, and is the maximum integer $d$ such that the dataset contains at least $d$ transactions of length at least $d$ such that no one of them is a superset of or equal to another. We show that this bound is strict for a large class of datasets.


Optoelectronic Reservoir Computing

Reservoir computing is a recently introduced, highly efficient bio-inspired approach for processing time dependent data. The basic scheme of reservoir computing consists of a non linear recurrent dynamical system coupled to a single input layer and a single output layer. Within these constraints many implementations are possible. Here we report an opto-electronic implementation of reservoir computing based on a recently proposed architecture consisting of a single non linear node and a delay line. Our implementation is sufficiently fast for real time information processing. We illustrate its performance on tasks of practical importance such as nonlinear channel equalization and speech recognition, and obtain results comparable to state of the art digital implementations.


A Learning Framework for Self-Tuning Histograms

In this paper, we consider the problem of estimating self-tuning histograms using query workloads. To this end, we propose a general learning theoretic formulation. Specifically, we use query feedback from a workload as training data to estimate a histogram with a small memory footprint that minimizes the expected error on future queries. Our formulation provides a framework in which different approaches can be studied and developed. We first study the simple class of equi-width histograms and present a learning algorithm, EquiHist, that is competitive in many settings. We also provide formal guarantees for equi-width histograms that highlight scenarios in which equi-width histograms can be expected to succeed or fail. We then go beyond equi-width histograms and present a novel learning algorithm, SpHist, for estimating general histograms. Here we use Haar wavelets to reduce the problem of learning histograms to that of learning a sparse vector. Both algorithms have multiple advantages over existing methods: 1) simple and scalable extensions to multi-dimensional data, 2) scalability with number of histogram buckets and size of query feedback, 3) natural extensions to incorporate new feedback and handle database updates. We demonstrate these advantages over the current state-of-the-art, ISOMER, through detailed experiments on real and synthetic data. In particular, we show that SpHist obtains up to 50% less error than ISOMER on real-world multi-dimensional datasets.


Clustering under Perturbation Resilience

Motivated by the fact that distances between data points in many real-world clustering instances are often based on heuristic measures, Bilu and Linial~\cite{BL} proposed analyzing objective based clustering problems under the assumption that the optimum clustering to the objective is preserved under small multiplicative perturbations to distances between points. The hope is that by exploiting the structure in such instances, one can overcome worst case hardness results. In this paper, we provide several results within this framework. For center-based objectives, we present an algorithm that can optimally cluster instances resilient to perturbations of factor $(1 + \sqrt{2})$, solving an open problem of Awasthi et al.~\cite{ABS10}. For $k$-median, a center-based objective of special interest, we additionally give algorithms for a more relaxed assumption in which we allow the optimal solution to change in a small $\epsilon$ fraction of the points after perturbation. We give the first bounds known for $k$-median under this more realistic and more general assumption. We also provide positive results for min-sum clustering which is typically a harder objective than center-based objectives from approximability standpoint. Our algorithms are based on new linkage criteria that may be of independent interest. Additionally, we give sublinear-time algorithms, showing algorithms that can return an implicit clustering from only access to a small random sample.


Learning in embodied action-perception loops through exploration

Although exploratory behaviors are ubiquitous in the animal kingdom, their computational underpinnings are still largely unknown. Behavioral Psychology has identified learning as a primary drive underlying many exploratory behaviors. Exploration is seen as a means for an animal to gather sensory data useful for reducing its ignorance about the environment. While related problems have been addressed in Data Mining and Reinforcement Learning, the computational modeling of learning-driven exploration by embodied agents is largely unrepresented. Here, we propose a computational theory for learning-driven exploration based on the concept of missing information that allows an agent to identify informative actions using Bayesian inference. We demonstrate that when embodiment constraints are high, agents must actively coordinate their actions to learn efficiently. Compared to earlier approaches, our exploration policy yields more efficient learning across a range of worlds with diverse structures. The improved learning in turn affords greater success in general tasks including navigation and reward gathering. We conclude by discussing how the proposed theory relates to previous information-theoretic objectives of behavior, such as predictive information and the free energy principle, and how it might contribute to a general theory of exploratory behavior.


Multi-timescale Nexting in a Reinforcement Learning Robot

The term "nexting" has been used by psychologists to refer to the propensity of people and many other animals to continually predict what will happen next in an immediate, local, and personal sense. The ability to "next" constitutes a basic kind of awareness and knowledge of one's environment. In this paper we present results with a robot that learns to next in real time, predicting thousands of features of the world's state, including all sensory inputs, at timescales from 0.1 to 8 seconds. This was achieved by treating each state feature as a reward-like target and applying temporal-difference methods to learn a corresponding value function with a discount rate corresponding to the timescale. We show that two thousand predictions, each dependent on six thousand state features, can be learned and updated online at better than 10Hz on a laptop computer, using the standard TD(lambda) algorithm with linear function approximation. We show that this approach is efficient enough to be practical, with most of the learning complete within 30 minutes. We also show that a single tile-coded feature representation suffices to accurately predict many different signals at a significant range of timescales. Finally, we show that the accuracy of our learned predictions compares favorably with the optimal off-line solution.


An Identity for Kernel Ridge Regression

This paper derives an identity connecting the square loss of ridge regression in on-line mode with the loss of the retrospectively best regressor. Some corollaries about the properties of the cumulative loss of on-line ridge regression are also obtained.


Active Learning of Halfspaces under a Margin Assumption

We derive and analyze a new, efficient, pool-based active learning algorithm for halfspaces, called ALuMA. Most previous algorithms show exponential improvement in the label complexity assuming that the distribution over the instance space is close to uniform. This assumption rarely holds in practical applications. Instead, we study the label complexity under a large-margin assumption -- a much more realistic condition, as evident by the success of margin-based algorithms such as SVM. Our algorithm is computationally efficient and comes with formal guarantees on its label complexity. It also naturally extends to the non-separable case and to non-linear kernels. Experiments illustrate the clear advantage of ALuMA over other active learning algorithms.


SLA Establishment with Guaranteed QoS in the Interdomain Network: A Stock Model

The new model that we present in this paper is introduced in the context of guaranteed QoS and resources management in the inter-domain routing framework. This model, called the stock model, is based on a reverse cascade approach and is applied in a distributed context. So transit providers have to learn the right capacities to buy and to stock and, therefore learning theory is applied through an iterative process. We show that transit providers manage to learn how to strategically choose their capacities on each route in order to maximize their benefits, despite the very incomplete information. Finally, we provide and analyse some simulation results given by the application of the model in a simple case where the model quickly converges to a stable state.


Using Taxonomies to Facilitate the Analysis of the Association Rules

The Data Mining process enables the end users to analyze, understand and use the extracted knowledge in an intelligent system or to support in the decision-making processes. However, many algorithms used in the process encounter large quantities of patterns, complicating the analysis of the patterns. This fact occurs with association rules, a Data Mining technique that tries to identify intrinsic patterns in large data sets. A method that can help the analysis of the association rules is the use of taxonomies in the step of post-processing knowledge. In this paper, the GART algorithm is proposed, which uses taxonomies to generalize association rules, and the RulEE-GAR computational module, that enables the analysis of the generalized rules.


Recovery of a Sparse Integer Solution to an Underdetermined System of Linear Equations

We consider a system of m linear equations in n variables Ax=b where A is a given m x n matrix and b is a given m-vector known to be equal to Ax' for some unknown solution x' that is integer and k-sparse: x' in {0,1}^n and exactly k entries of x' are 1. We give necessary and sufficient conditions for recovering the solution x exactly using an LP relaxation that minimizes l1 norm of x. When A is drawn from a distribution that has exchangeable columns, we show an interesting connection between the recovery probability and a well known problem in geometry, namely the k-set problem. To the best of our knowledge, this connection appears to be new in the compressive sensing literature. We empirically show that for large n if the elements of A are drawn i.i.d. from the normal distribution then the performance of the recovery LP exhibits a phase transition, i.e., for each k there exists a value m' of m such that the recovery always succeeds if m > m' and always fails if m < m'. Using the empirical data we conjecture that m' = nH(k/n)/2 where H(x) = -(x)log_2(x) - (1-x)log_2(1-x) is the binary entropy function.


Extended UCB Policy for Multi-Armed Bandit with Light-Tailed Reward Distributions

We consider the multi-armed bandit problems in which a player aims to accrue reward by sequentially playing a given set of arms with unknown reward statistics. In the classic work, policies were proposed to achieve the optimal logarithmic regret order for some special classes of light-tailed reward distributions, e.g., Auer et al.'s UCB1 index policy for reward distributions with finite support. In this paper, we extend Auer et al.'s UCB1 index policy to achieve the optimal logarithmic regret order for all light-tailed (or equivalently, locally sub-Gaussian) reward distributions defined by the (local) existence of the moment-generating function.


Bootstrapping Intrinsically Motivated Learning with Human Demonstrations

This paper studies the coupling of internally guided learning and social interaction, and more specifically the improvement owing to demonstrations of the learning by intrinsic motivation. We present Socially Guided Intrinsic Motivation by Demonstration (SGIM-D), an algorithm for learning in continuous, unbounded and non-preset environments. After introducing social learning and intrinsic motivation, we describe the design of our algorithm, before showing through a fishing experiment that SGIM-D efficiently combines the advantages of social learning and intrinsic motivation to gain a wide repertoire while being specialised in specific subspaces.


Bipartite ranking algorithm for classification and survival analysis

Unsupervised aggregation of independently built univariate predictors is explored as an alternative regularization approach for noisy, sparse datasets. Bipartite ranking algorithm Smooth Rank implementing this approach is introduced. The advantages of this algorithm are demonstrated on two types of problems. First, Smooth Rank is applied to two-class problems from bio-medical field, where ranking is often preferable to classification. In comparison against SVMs with radial and linear kernels, Smooth Rank had the best performance on 8 out of 12 benchmark benchmarks. The second area of application is survival analysis, which is reduced here to bipartite ranking in a way which allows one to use commonly accepted measures of methods performance. In comparison of Smooth Rank with Cox PH regression and CoxPath methods, Smooth Rank proved to be the best on 9 out of 10 benchmark datasets.


Chinese Restaurant Game - Part II: Applications to Wireless Networking, Cloud Computing, and Online Social Networking

In Part I of this two-part paper [1], we proposed a new game, called Chinese restaurant game, to analyze the social learning problem with negative network externality. The best responses of agents in the Chinese restaurant game with imperfect signals are constructed through a recursive method, and the influence of both learning and network externality on the utilities of agents is studied. In Part II of this two-part paper, we illustrate three applications of Chinese restaurant game in wireless networking, cloud computing, and online social networking. For each application, we formulate the corresponding problem as a Chinese restaurant game and analyze how agents learn and make strategic decisions in the problem. The proposed method is compared with four common-sense methods in terms of agents' utilities and the overall system performance through simulations. We find that the proposed Chinese restaurant game theoretic approach indeed helps agents make better decisions and improves the overall system performance. Furthermore, agents with different decision orders have different advantages in terms of their utilities, which also verifies the conclusions drawn in Part I of this two-part paper.


Chinese Restaurant Game - Part I: Theory of Learning with Negative Network Externality

In a social network, agents are intelligent and have the capability to make decisions to maximize their utilities. They can either make wise decisions by taking advantages of other agents' experiences through learning, or make decisions earlier to avoid competitions from huge crowds. Both these two effects, social learning and negative network externality, play important roles in the decision process of an agent. While there are existing works on either social learning or negative network externality, a general study on considering both these two contradictory effects is still limited. We find that the Chinese restaurant process, a popular random process, provides a well-defined structure to model the decision process of an agent under these two effects. By introducing the strategic behavior into the non-strategic Chinese restaurant process, in Part I of this two-part paper, we propose a new game, called Chinese Restaurant Game, to formulate the social learning problem with negative network externality. Through analyzing the proposed Chinese restaurant game, we derive the optimal strategy of each agent and provide a recursive method to achieve the optimal strategy. How social learning and negative network externality influence each other under various settings is also studied through simulations.


Adaptive Forgetting Factor Fictitious Play

It is now well known that decentralised optimisation can be formulated as a potential game, and game-theoretical learning algorithms can be used to find an optimum. One of the most common learning techniques in game theory is fictitious play. However fictitious play is founded on an implicit assumption that opponents' strategies are stationary. We present a novel variation of fictitious play that allows the use of a more realistic model of opponent strategy. It uses a heuristic approach, from the online streaming data literature, to adaptively update the weights assigned to recently observed actions. We compare the results of the proposed algorithm with those of stochastic and geometric fictitious play in a simple strategic form game, a vehicle target assignment game and a disaster management problem. In all the tests the rate of convergence of the proposed algorithm was similar or better than the variations of fictitious play we compared it with. The new algorithm therefore improves the performance of game-theoretical learning in decentralised optimisation.


Low-rank optimization with trace norm penalty

The paper addresses the problem of low-rank trace norm minimization. We propose an algorithm that alternates between fixed-rank optimization and rank-one updates. The fixed-rank optimization is characterized by an efficient factorization that makes the trace norm differentiable in the search space and the computation of duality gap numerically tractable. The search space is nonlinear but is equipped with a particular Riemannian structure that leads to efficient computations. We present a second-order trust-region algorithm with a guaranteed quadratic rate of convergence. Overall, the proposed optimization scheme converges super-linearly to the global solution while maintaining complexity that is linear in the number of rows and columns of the matrix. To compute a set of solutions efficiently for a grid of regularization parameters we propose a predictor-corrector approach that outperforms the naive warm-restart approach on the fixed-rank quotient manifold. The performance of the proposed algorithm is illustrated on problems of low-rank matrix completion and multivariate linear regression.


Random Differential Privacy

We propose a relaxed privacy definition called {\em random differential privacy} (RDP). Differential privacy requires that adding any new observation to a database will have small effect on the output of the data-release procedure. Random differential privacy requires that adding a {\em randomly drawn new observation} to a database will have small effect on the output. We show an analog of the composition property of differentially private procedures which applies to our new definition. We show how to release an RDP histogram and we show that RDP histograms are much more accurate than histograms obtained using ordinary differential privacy. We finally show an analog of the global sensitivity framework for the release of functions under our privacy definition.


Robust Learning via Cause-Effect Models

We consider the problem of function estimation in the case where the data distribution may shift between training and test time, and additional information about it may be available at test time. This relates to popular scenarios such as covariate shift, concept drift, transfer learning and semi-supervised learning. This working paper discusses how these tasks could be tackled depending on the kind of changes of the distributions. It argues that knowledge of an underlying causal direction can facilitate several of these tasks.


A new order theory of set systems and better quasi-orderings

By reformulating a learning process of a set system L as a game between Teacher (presenter of data) and Learner (updater of the abstract independent set), we define the order type dim L of L to be the order type of the game tree. The theory of this new order type and continuous, monotone function between set systems corresponds to the theory of well quasi-orderings (WQOs). As Nash-Williams developed the theory of WQOs to the theory of better quasi-orderings (BQOs), we introduce a set system that has order type and corresponds to a BQO. We prove that the class of set systems corresponding to BQOs is closed by any monotone function. In (Shinohara and Arimura. "Inductive inference of unbounded unions of pattern languages from positive data." Theoretical Computer Science, pp. 191-209, 2000), for any set system L, they considered the class of arbitrary (finite) unions of members of L. From viewpoint of WQOs and BQOs, we characterize the set systems L such that the class of arbitrary (finite) unions of members of L has order type. The characterization shows that the order structure of the set system L with respect to the set-inclusion is not important for the resulting set system having order type. We point out continuous, monotone function of set systems is similar to positive reduction to Jockusch-Owings' weakly semirecursive sets.


Analysis and Extension of Arc-Cosine Kernels for Large Margin Classification

We investigate a recently proposed family of positive-definite kernels that mimic the computation in large neural networks. We examine the properties of these kernels using tools from differential geometry; specifically, we analyze the geometry of surfaces in Hilbert space that are induced by these kernels. When this geometry is described by a Riemannian manifold, we derive results for the metric, curvature, and volume element. Interestingly, though, we find that the simplest kernel in this family does not admit such an interpretation. We explore two variations of these kernels that mimic computation in neural networks with different activation functions. We experiment with these new kernels on several data sets and highlight their general trends in performance for classification.


Nonnegative Matrix Factorization for Semi-supervised Dimensionality Reduction

We show how to incorporate information from labeled examples into nonnegative matrix factorization (NMF), a popular unsupervised learning algorithm for dimensionality reduction. In addition to mapping the data into a space of lower dimensionality, our approach aims to preserve the nonnegative components of the data that are important for classification. We identify these components from the support vectors of large-margin classifiers and derive iterative updates to preserve them in a semi-supervised version of NMF. These updates have a simple multiplicative form like their unsupervised counterparts; they are also guaranteed at each iteration to decrease their loss function---a weighted sum of I-divergences that captures the trade-off between unsupervised and supervised learning. We evaluate these updates for dimensionality reduction when they are used as a precursor to linear classification. In this role, we find that they yield much better performance than their unsupervised counterparts. We also find one unexpected benefit of the low dimensional representations discovered by our approach: often they yield more accurate classifiers than both ordinary and transductive SVMs trained in the original input space.


Strongly Convex Programming for Exact Matrix Completion and Robust Principal Component Analysis

The common task in matrix completion (MC) and robust principle component analysis (RPCA) is to recover a low-rank matrix from a given data matrix. These problems gained great attention from various areas in applied sciences recently, especially after the publication of the pioneering works of Cand`es et al.. One fundamental result in MC and RPCA is that nuclear norm based convex optimizations lead to the exact low-rank matrix recovery under suitable conditions. In this paper, we extend this result by showing that strongly convex optimizations can guarantee the exact low-rank matrix recovery as well. The result in this paper not only provides sufficient conditions under which the strongly convex models lead to the exact low-rank matrix recovery, but also guides us on how to choose suitable parameters in practical algorithms.


Clustering and Latent Semantic Indexing Aspects of the Nonnegative Matrix Factorization

This paper provides a theoretical support for clustering aspect of the nonnegative matrix factorization (NMF). By utilizing the Karush-Kuhn-Tucker optimality conditions, we show that NMF objective is equivalent to graph clustering objective, so clustering aspect of the NMF has a solid justification. Different from previous approaches which usually discard the nonnegativity constraints, our approach guarantees the stationary point being used in deriving the equivalence is located on the feasible region in the nonnegative orthant. Additionally, since clustering capability of a matrix decomposition technique can sometimes imply its latent semantic indexing (LSI) aspect, we will also evaluate LSI aspect of the NMF by showing its capability in solving the synonymy and polysemy problems in synthetic datasets. And more extensive evaluation will be conducted by comparing LSI performances of the NMF and the singular value decomposition (SVD), the standard LSI method, using some standard datasets.


epsilon-Samples of Kernels

We study the worst case error of kernel density estimates via subset approximation. A kernel density estimate of a distribution is the convolution of that distribution with a fixed kernel (e.g. Gaussian kernel). Given a subset (i.e. a point set) of the input distribution, we can compare the kernel density estimates of the input distribution with that of the subset and bound the worst case error. If the maximum error is eps, then this subset can be thought of as an eps-sample (aka an eps-approximation) of the range space defined with the input distribution as the ground set and the fixed kernel representing the family of ranges. Interestingly, in this case the ranges are not binary, but have a continuous range (for simplicity we focus on kernels with range of [0,1]); these allow for smoother notions of range spaces. It turns out, the use of this smoother family of range spaces has an added benefit of greatly decreasing the size required for eps-samples. For instance, in the plane the size is O((1/eps^{4/3}) log^{2/3}(1/eps)) for disks (based on VC-dimension arguments) but is only O((1/eps) sqrt{log (1/eps)}) for Gaussian kernels and for kernels with bounded slope that only affect a bounded domain. These bounds are accomplished by studying the discrepancy of these "kernel" range spaces, and here the improvement in bounds are even more pronounced. In the plane, we show the discrepancy is O(sqrt{log n}) for these kernels, whereas for balls there is a lower bound of Omega(n^{1/4}).


Evaluation of Performance Measures for Classifiers Comparison

The selection of the best classification algorithm for a given dataset is a very widespread problem, occuring each time one has to choose a classifier to solve a real-world problem. It is also a complex task with many important methodological decisions to make. Among those, one of the most crucial is the choice of an appropriate measure in order to properly assess the classification performance and rank the algorithms. In this article, we focus on this specific task. We present the most popular measures and compare their behavior through discrimination plots. We then discuss their properties from a more theoretical perspective. It turns out several of them are equivalent for classifiers comparison purposes. Futhermore. they can also lead to interpretation problems. Among the numerous measures proposed over the years, it appears that the classical overall success rate and marginal rates are the more suitable for classifier comparison task.


Online Learning for Classification of Low-rank Representation Features and Its Applications in Audio Segment Classification

In this paper, a novel framework based on trace norm minimization for audio segment is proposed. In this framework, both the feature extraction and classification are obtained by solving corresponding convex optimization problem with trace norm regularization. For feature extraction, robust principle component analysis (robust PCA) via minimization a combination of the nuclear norm and the $\ell_1$-norm is used to extract low-rank features which are robust to white noise and gross corruption for audio segments. These low-rank features are fed to a linear classifier where the weight and bias are learned by solving similar trace norm constrained problems. For this classifier, most methods find the weight and bias in batch-mode learning, which makes them inefficient for large-scale problems. In this paper, we propose an online framework using accelerated proximal gradient method. This framework has a main advantage in memory cost. In addition, as a result of the regularization formulation of matrix classification, the Lipschitz constant was given explicitly, and hence the step size estimation of general proximal gradient method was omitted in our approach. Experiments on real data sets for laugh/non-laugh and applause/non-applause classification indicate that this novel framework is effective and noise robust.


A geometric analysis of subspace clustering with outliers

This paper considers the problem of clustering a collection of unlabeled data points assumed to lie near a union of lower-dimensional planes. As is common in computer vision or unsupervised learning applications, we do not know in advance how many subspaces there are nor do we have any information about their dimensions. We develop a novel geometric analysis of an algorithm named sparse subspace clustering (SSC) [In IEEE Conference on Computer Vision and Pattern Recognition, 2009. CVPR 2009 (2009) 2790-2797. IEEE], which significantly broadens the range of problems where it is provably effective. For instance, we show that SSC can recover multiple subspaces, each of dimension comparable to the ambient dimension. We also prove that SSC can correctly cluster data points even when the subspaces of interest intersect. Further, we develop an extension of SSC that succeeds when the data set is corrupted with possibly overwhelmingly many outliers. Underlying our analysis are clear geometric insights, which may bear on other sparse recovery problems. A numerical study complements our theoretical analysis and demonstrates the effectiveness of these methods.


Performance Analysis of Enhanced Clustering Algorithm for Gene Expression Data

Microarrays are made it possible to simultaneously monitor the expression profiles of thousands of genes under various experimental conditions. It is used to identify the co-expressed genes in specific cells or tissues that are actively used to make proteins. This method is used to analysis the gene expression, an important task in bioinformatics research. Cluster analysis of gene expression data has proved to be a useful tool for identifying co-expressed genes, biologically relevant groupings of genes and samples. In this paper we applied K-Means with Automatic Generations of Merge Factor for ISODATA- AGMFI. Though AGMFI has been applied for clustering of Gene Expression Data, this proposed Enhanced Automatic Generations of Merge Factor for ISODATA- EAGMFI Algorithms overcome the drawbacks of AGMFI in terms of specifying the optimal number of clusters and initialization of good cluster centroids. Experimental results on Gene Expression Data show that the proposed EAGMFI algorithms could identify compact clusters with perform well in terms of the Silhouette Coefficients cluster measure.