We expand the item response theory to study the case of "cheating students" for a set of exams, trying to detect them by applying a greedy algorithm of inference. This extended model is closely related to the Boltzmann machine learning. In this paper we aim to infer the correct biases and interactions of our model by considering a relatively small number of sets of training data. Nevertheless, the greedy algorithm that we employed in the present study exhibits good performance with a few number of training data. The key point is the sparseness of the interactions in our problem in the context of the Boltzmann machine learning: the existence of cheating students is expected to be very rare (possibly even in real world). We compare a standard approach to infer the sparse interactions in the Boltzmann machine learning to our greedy algorithm and we find the latter to be superior in several aspects.

When the design matrix has orthonormal columns, "soft thresholding" the ordinary least squares (OLS) solution produces the Lasso solution [Tibshirani, 1996]. If one uses the Puffer preconditioned Lasso [Jia and Rohe, 2012], then this result generalizes from orthonormal designs to full rank designs (Theorem 1). Theorem 2 refines the Puffer preconditioner to make the Lasso select the same model as removing the elements of the OLS solution with the largest p-values. Using a generalized Puffer preconditioner, Theorem 3 relates ridge regression to the preconditioned Lasso; this result is for the high dimensional setting, p > n. Where the standard Lasso is akin to forward selection [Efron et al., 2004], Theorems 1, 2, and 3 suggest that the preconditioned Lasso is more akin to backward elimination. These results hold for sparse penalties beyond l1; for a broad class of sparse and non-convex techniques (e.g. SCAD and MC+), the results hold for all local minima.

According to Cobanoglu et al and Murphy, it is now widely acknowledged that the single target paradigm (one protein or target, one disease, one drug) that has been the dominant premise in drug development in the recent past is untenable. More often than not, a drug-like compound (ligand) can be promiscuous - that is, it can interact with more than one target protein. In recent years, in in silico target prediction methods the promiscuity issue has been approached computationally in different ways. In this study we confine attention to the so-called ligand-based target prediction machine learning approaches, commonly referred to as target-fishing. With a few exceptions, the target-fishing approaches that are currently ubiquitous in cheminformatics literature can be essentially viewed as single-label multi-classification schemes; these approaches inherently bank on the single target paradigm assumption that a ligand can home in on one specific target. In order to address the ligand promiscuity issue, one might be able to cast target-fishing as a multi-label multi-class classification problem. For illustrative and comparison purposes, single-label and multi-label Naive Bayes classification models (denoted here by SMM and MMM, respectively) for target-fishing were implemented. The models were constructed and tested on 65,587 compounds and 308 targets retrieved from the ChEMBL17 database. SMM and MMM performed differently: for 16,344 test compounds, the MMM model returned recall and precision values of 0.8058 and 0.6622, respectively; the corresponding recall and precision values yielded by the SMM model were 0.7805 and 0.7596, respectively. However, at a significance level of 0.05 and one degree of freedom McNemar test performed on the target prediction results returned by SMM and MMM for the 16,344 test ligands gave a chi-squared value of 15.656, in favour of the MMM approach.

Nonparametric two sample testing deals with the question of consistently deciding if two distributions are different, given samples from both, without making any parametric assumptions about the form of the distributions. The current literature is split into two kinds of tests - those which are consistent without any assumptions about how the distributions may differ (\textit{general} alternatives), and those which are designed to specifically test easier alternatives, like a difference in means (\textit{mean-shift} alternatives). The main contribution of this paper is to explicitly characterize the power of a popular nonparametric two sample test, designed for general alternatives, under a mean-shift alternative in the high-dimensional setting. Specifically, we explicitly derive the power of the linear-time Maximum Mean Discrepancy statistic using the Gaussian kernel, where the dimension and sample size can both tend to infinity at any rate, and the two distributions differ in their means. As a corollary, we find that if the signal-to-noise ratio is held constant, then the test's power goes to one if the number of samples increases faster than the dimension increases. This is the first explicit power derivation for a general nonparametric test in the high-dimensional setting, and also the first analysis of how tests designed for general alternatives perform when faced with easier ones.

In this paper, we consider the matrix completion problem when the observations are one-bit measurements of some underlying matrix M, and in particular the observed samples consist only of ones and no zeros. This problem is motivated by modern applications such as recommender systems and social networks where only "likes" or "friendships" are observed. The problem of learning from only positive and unlabeled examples, called PU (positive-unlabeled) learning, has been studied in the context of binary classification. We consider the PU matrix completion problem, where an underlying real-valued matrix M is first quantized to generate one-bit observations and then a subset of positive entries is revealed. Under the assumption that M has bounded nuclear norm, we provide recovery guarantees for two different observation models: 1) M parameterizes a distribution that generates a binary matrix, 2) M is thresholded to obtain a binary matrix. For the first case, we propose a "shifted matrix completion" method that recovers M using only a subset of indices corresponding to ones, while for the second case, we propose a "biased matrix completion" method that recovers the (thresholded) binary matrix. Both methods yield strong error bounds --- if M is n by n, the Frobenius error is bounded as O(1/((1-rho)n), where 1-rho denotes the fraction of ones observed. This implies a sample complexity of O(n\log n) ones to achieve a small error, when M is dense and n is large. We extend our methods and guarantees to the inductive matrix completion problem, where rows and columns of M have associated features. We provide efficient and scalable optimization procedures for both the methods and demonstrate the effectiveness of the proposed methods for link prediction (on real-world networks consisting of over 2 million nodes and 90 million links) and semi-supervised clustering tasks.

In this work, we propose a simple yet effective solution to the problem of connectome inference in calcium imaging data. The proposed algorithm consists of two steps. First, processing the raw signals to detect neural peak activities. Second, inferring the degree of association between neurons from partial correlation statistics. This paper summarises the methodology that led us to win the Connectomics Challenge, proposes a simplified version of our method, and finally compares our results with respect to other inference methods.

This paper studies large-scale dynamical networks where the current state of the system is a linear transformation of the previous state, contaminated by a multivariate Gaussian noise. Examples include stock markets, human brains and gene regulatory networks. We introduce a transition matrix to describe the evolution, which can be translated to a directed Granger transition graph, and use the concentration matrix of the Gaussian noise to capture the second-order relations between nodes, which can be translated to an undirected conditional dependence graph. We propose regularizing the two graphs jointly in topology identification and dynamics estimation. Based on the notion of joint association graph (JAG), we develop a joint graphical screening and estimation (JGSE) framework for efficient network learning in big data. In particular, our method can pre-determine and remove unnecessary edges based on the joint graphical structure, referred to as JAG screening, and can decompose a large network into smaller subnetworks in a robust manner, referred to as JAG decomposition. JAG screening and decomposition can reduce the problem size and search space for fine estimation at a later stage. Experiments on both synthetic data and real-world applications show the effectiveness of the proposed framework in large-scale network topology identification and dynamics estimation.

We study the problem of variable selection in convex nonparametric regression. Under the assumption that the true regression function is convex and sparse, we develop a screening procedure to select a subset of variables that contains the relevant variables. Our approach is a two-stage quadratic programming method that estimates a sum of one-dimensional convex functions, followed by one-dimensional concave regression fits on the residuals. In contrast to previous methods for sparse additive models, the optimization is finite dimensional and requires no tuning parameters for smoothness. Under appropriate assumptions, we prove that the procedure is faithful in the population setting, yielding no false negatives. We give a finite sample statistical analysis, and introduce algorithms for efficiently carrying out the required quadratic programs. The approach leads to computational and statistical advantages over fitting a full model, and provides an effective, practical approach to variable screening in convex regression.

Random ferns is a machine learning algorithm proposed by [11] for matching same elements between two images of the same scene, allowing one to recognise certain objects or trace them on videos. The original motivation behind this method was to create a simple and efficient algorithm by extending the Naïve Bayes classifier; still the authors acknowledged its strong connection to the decision tree ensembles like the Random forest [2] algorithm. Since introduction, Random ferns have been applied in numerous computer vision application, like image recognition [1], action recognition [10] or augmented reality [14]. However, it has not gathered attention outside this field; thus, this work aims to bring this algorithm to a much wider spectrum of applications. In order to do that, I propose a generalised version of the algorithm, implemented as an R [13] package rFerns. The paper is organised as follows. Section 2 briefly recalls the Bayesian derivation of the original version of Random ferns, presents the decision tree ensemble interpretation of the algorithm and lists modifications leading to the rFerns variant.

Scene parsing is an important and challenging prob- lem in computer vision. It requires labeling each pixel in an image with the category it belongs to. Tradition- ally, it has been approached with hand-engineered features from color information in images. Recently convolutional neural networks (CNNs), which automatically learn hierar- chies of features, have achieved record performance on the task. These approaches typically include a post-processing technique, such as superpixels, to produce the final label- ing. In this paper, we propose a novel network architecture that combines deep deconvolutional neural networks with CNNs. Our experiments show that deconvolutional neu- ral networks are capable of learning higher order image structure beyond edge primitives in comparison to CNNs. The new network architecture is employed for multi-patch training, introduced as part of this work. Multi-patch train- ing makes it possible to effectively learn spatial priors from scenes. The proposed approach yields state-of-the-art per- formance on four scene parsing datasets, namely Stanford Background, SIFT Flow, CamVid, and KITTI. In addition, our system has the added advantage of having a training system that can be completely automated end-to-end with- out requiring any post-processing.