The advent of high throughput technologies in biology has opened novel opportunities to investigate biological processes from a comprehensive point of view. At the same time, the noisy and high dimensional nature of these data sets gives rise to formidable statistical challenges, and has led to systems biology becoming a fertile area for machine learning applications, as well as a motivation for novel modelling methodologies. In this paper, we are interested in jointly modelling mRNA measurements (transcrip-tomics) together with metabolite measurements in order to provide a platform for understanding the chemical regulation of gene expression. From the statistical perspective, this is naturally addressed using a latent variables framework: mRNA transcription is known to be controlled by the activation state of a class of proteins, transcription factors (TFs), which mediate metabolic signals through fast conformational changes (Alon, 2006). However, due to their fast dynamic and often low concentrations, TFs are particularly difficult to assay experimentally, leading to the need for statistical inference methodologies (Asif & Sanguinetti, 2011; Shi et al., 2008). Here, we adopt a model of transcriptional regulation which is based on a binary representation of transcription factor states, a Factorial Hidden Markov Model (FHMM).

Many feature subset selection (FSS) algorithms have been proposed, but not all of them are appropriate for a given feature selection problem. At the same time, so far there is rarely a good way to choose appropriate FSS algorithms for the problem at hand. Thus, FSS algorithm automatic recommendation is very important and practically useful. In this paper, a meta learning based FSS algorithm automatic recommendation method is presented. The proposed method first identifies the data sets that are most similar to the one at hand by the k-nearest neighbor classification algorithm, and the distances among these data sets are calculated based on the commonly-used data set characteristics. Then, it ranks all the candidate FSS algorithms according to their performance on these similar data sets, and chooses the algorithms with best performance as the appropriate ones. The performance of the candidate FSS algorithms is evaluated by a multi-criteria metric that takes into account not only the classification accuracy over the selected features, but also the runtime of feature selection and the number of selected features. The proposed recommendation method is extensively tested on 115 real world data sets with 22 well-known and frequently-used different FSS algorithms for five representative classifiers. The results show the effectiveness of our proposed FSS algorithm recommendation method.

Networks provide a skeleton for the spread of contagions, like, information, ideas, behaviors and diseases. Many times networks over which contagions diffuse are unobserved and need to be inferred. Here we apply survival theory to develop general additive and multiplicative risk models under which the network inference problems can be solved efficiently by exploiting their convexity. Our additive risk model generalizes several existing network inference models. We show all these models are particular cases of our more general model. Our multiplicative model allows for modeling scenarios in which a node can either increase or decrease the risk of activation of another node, in contrast with previous approaches, which consider only positive risk increments. We evaluate the performance of our network inference algorithms on large synthetic and real cascade datasets, and show that our models are able to predict the length and duration of cascades in real data.

We address the problem of analyzing sets of noisy time-varying signals that all report on the same process but confound straightforward analyses due to complex inter-signal heterogeneities and measurement artifacts. In particular we consider single-molecule experiments which indirectly measure the distinct steps in a biomolecular process via observations of noisy time-dependent signals such as a fluorescence intensity or bead position. Straightforward hidden Markov model (HMM) analyses attempt to characterize such processes in terms of a set of conformational states, the transitions that can occur between these states, and the associated rates at which those transitions occur; but require ad-hoc post-processing steps to combine multiple signals. Here we develop a hierarchically coupled HMM that allows experimentalists to deal with inter-signal variability in a principled and automatic way. Our approach is a generalized expectation maximization hyperparameter point estimation procedure with variational Bayes at the level of individual time series that learns an single interpretable representation of the overall data generating process.

In this paper, we study optimization methods consisting of iteratively minimizing surrogates of an objective function. By proposing several algorithmic variants and simple convergence analyses, we make two main contributions. First, we provide a unified viewpoint for several first-order optimization techniques such as accelerated proximal gradient, block coordinate descent, or Frank-Wolfe algorithms. Second, we introduce a new incremental scheme that experimentally matches or outperforms state-of-the-art solvers for large-scale optimization problems typically arising in machine learning.

In an online contract selection problem there is a seller which offers a set of contracts to sequentially arriving buyers whose types are drawn from an unknown distribution. If there exists a profitable contract for the buyer in the offered set, i.e., a contract with payoff higher than the payoff of not accepting any contracts, the buyer chooses the contract that maximizes its payoff. In this paper we consider the online contract selection problem to maximize the sellers profit. Assuming that a structural property called ordered preferences holds for the buyer's payoff function, we propose online learning algorithms that have sub-linear regret with respect to the best set of contracts given the distribution over the buyer's type. This problem has many applications including spectrum contracts, wireless service provider data plans and recommendation systems.

We give a highly efficient "semi-agnostic" algorithm for learning univariate probability distributions that are well approximated by piecewise polynomial density functions. Let $p$ be an arbitrary distribution over an interval $I$ which is $\tau$-close (in total variation distance) to an unknown probability distribution $q$ that is defined by an unknown partition of $I$ into $t$ intervals and $t$ unknown degree-$d$ polynomials specifying $q$ over each of the intervals. We give an algorithm that draws $\tilde{O}(t\new{(d+1)}/\eps^2)$ samples from $p$, runs in time $\poly(t,d,1/\eps)$, and with high probability outputs a piecewise polynomial hypothesis distribution $h$ that is $(O(\tau)+\eps)$-close (in total variation distance) to $p$. This sample complexity is essentially optimal; we show that even for $\tau=0$, any algorithm that learns an unknown $t$-piecewise degree-$d$ probability distribution over $I$ to accuracy $\eps$ must use $\Omega({\frac {t(d+1)} {\poly(1 + \log(d+1))}} \cdot {\frac 1 {\eps^2}})$ samples from the distribution, regardless of its running time. Our algorithm combines tools from approximation theory, uniform convergence, linear programming, and dynamic programming. We apply this general algorithm to obtain a wide range of results for many natural problems in density estimation over both continuous and discrete domains. These include state-of-the-art results for learning mixtures of log-concave distributions; mixtures of $t$-modal distributions; mixtures of Monotone Hazard Rate distributions; mixtures of Poisson Binomial Distributions; mixtures of Gaussians; and mixtures of $k$-monotone densities. Our general technique yields computationally efficient algorithms for all these problems, in many cases with provably optimal sample complexities (up to logarithmic factors) in all parameters.

When dealing with subjective, noisy, or otherwise nebulous features, the "wisdom of crowds" suggests that one may benefit from multiple judgments of the same feature on the same object. We give theoretically-motivated `feature multi-selection' algorithms that choose, among a large set of candidate features, not only which features to judge but how many times to judge each one. We demonstrate the effectiveness of this approach for linear regression on a crowdsourced learning task of predicting people's height and weight from photos, using features such as 'gender' and 'estimated weight' as well as culturally fraught ones such as 'attractive'.

In this paper, we propose an extension of our Mining for SAT framework to Constraint satisfaction Problem (CSP). We consider n-ary extensional constraints (table constraints). Our approach aims to reduce the size of the CSP by exploiting the structure of the constraints graph and of its associated microstructure. More precisely, we apply itemset mining techniques to search for closed frequent itemsets on these two representation. Using Tseitin extension, we rewrite the whole CSP to another compressed CSP equivalent with respect to satisfiability. Our approach contrast with previous proposed approach by Katsirelos and Walsh, as we do not change the structure of the constraints.

Recent improvements of the LEO-II theorem prover are presented. These improvements include a revised ATP interface, new translations into first-order logic, rule support for the axiom of choice, detection of defined equality, and more flexible strategy scheduling.