We propose a non-parametric regression methodology, Random Forests on Distance Matrices (RFDM), for detecting genetic variants associated to quantitative phenotypes representing the human brain's structure or function, and obtained using neuroimaging techniques. RFDM, which is an extension of decision forests, requires a distance matrix as response that encodes all pair-wise phenotypic distances in the random sample. We discuss ways to learn such distances directly from the data using manifold learning techniques, and how to define such distances when the phenotypes are non-vectorial objects such as brain connectivity networks. We also describe an extension of RFDM to detect espistatic effects while keeping the computational complexity low. Extensive simulation results and an application to an imaging genetics study of Alzheimer's Disease are presented and discussed.

We propose a computationally efficient random walk on a convex body which rapidly mixes and closely tracks a time-varying log-concave distribution. We develop general theoretical guarantees on the required number of steps; this number can be calculated on the fly according to the distance from and the shape of the next distribution. We then illustrate the technique on several examples. Within the context of exponential families, the proposed method produces samples from a posterior distribution which is updated as data arrive in a streaming fashion. The sampling technique can be used to track time-varying truncated distributions, as well as to obtain samples from a changing mixture model, fitted in a streaming fashion to data. In the setting of linear optimization, the proposed method has oracle complexity with best known dependence on the dimension for certain geometries. In the context of online learning and repeated games, the algorithm is an efficient method for implementing no-regret mixture forecasting strategies. Remarkably, in some of these examples, only one step of the random walk is needed to track the next distribution.

We study the performance of a family of randomized parallel coordinate descent methods for minimizing the sum of a nonsmooth and separable convex functions. The problem class includes as a special case L1-regularized L1 regression and the minimization of the exponential loss ("AdaBoost problem"). We assume the input data defining the loss function is contained in a sparse $m\times n$ matrix $A$ with at most $\omega$ nonzeros in each row. Our methods need $O(n \beta/\tau)$ iterations to find an approximate solution with high probability, where $\tau$ is the number of processors and $\beta = 1 + (\omega-1)(\tau-1)/(n-1)$ for the fastest variant. The notation hides dependence on quantities such as the required accuracy and confidence levels and the distance of the starting iterate from an optimal point. Since $\beta/\tau$ is a decreasing function of $\tau$, the method needs fewer iterations when more processors are used. Certain variants of our algorithms perform on average only $O(\nnz(A)/n)$ arithmetic operations during a single iteration per processor and, because $\beta$ decreases when $\omega$ does, fewer iterations are needed for sparser problems.

Community detection has been one of the central problems in network studies and directed network is particularly challenging due to asymmetry among its links. In this paper, we found that incorporating the direction of links reveals new perspectives on communities regarding to two different roles, source and terminal, that a node plays in each community. Intriguingly, such communities appear to be connected with unique spectral property of the graph Laplacian of the adjacency matrix and we exploit this connection by using regularized SVD methods. We propose harvesting algorithms, coupled with regularized SVDs, that are linearly scalable for efficient identification of communities in huge directed networks. The proposed algorithm shows great performance and scalability on benchmark networks in simulations and successfully recovers communities in real network applications.

In this paper, we introduce a new stochastic approximation (SA) type algorithm, namely the randomized stochastic gradient (RSG) method, for solving an important class of nonlinear (possibly nonconvex) stochastic programming (SP) problems. We establish the complexity of this method for computing an approximate stationary point of a nonlinear programming problem. We also show that this method possesses a nearly optimal rate of convergence if the problem is convex. We discuss a variant of the algorithm which consists of applying a post-optimization phase to evaluate a short list of solutions generated by several independent runs of the RSG method, and show that such modification allows to improve significantly the large-deviation properties of the algorithm. These methods are then specialized for solving a class of simulation-based optimization problems in which only stochastic zeroth-order information is available.

Linear Discriminant Analysis (LDA) is a well-known method for dimensionality reduction and classification. Previous studies have also extended the binary-class case into multi-classes. However, many applications, such as object detection and keyframe extraction cannot provide consistent instance-label pairs, while LDA requires labels on instance level for training. Thus it cannot be directly applied for semi-supervised classification problem. In this paper, we overcome this limitation and propose a latent variable Fisher discriminant analysis model. We relax the instance-level labeling into bag-level, is a kind of semi-supervised (video-level labels of event type are required for semantic frame extraction) and incorporates a data-driven prior over the latent variables. Hence, our method combines the latent variable inference and dimension reduction in an unified bayesian framework. We test our method on MUSK and Corel data sets and yield competitive results compared to the baseline approach. We also demonstrate its capacity on the challenging TRECVID MED11 dataset for semantic keyframe extraction and conduct a human-factors ranking-based experimental evaluation, which clearly demonstrates our proposed method consistently extracts more semantically meaningful keyframes than challenging baselines.

Recent advances in high-throughput cDNA sequencing (RNA-Seq) technology have revolutionized transcriptome studies. A major motivation for RNA-Seq is to map the structure of expressed transcripts at nucleotide resolution. With accurate computational tools for transcript reconstruction, this technology may also become useful for genome (re-)annotation, which has mostly relied on de novo gene finding where gene structures are primarily inferred from the genome sequence. We developed a machine-learning method, called mTim (margin-based transcript inference method) for transcript reconstruction from RNA-Seq read alignments that is based on discriminatively trained hidden Markov support vector machines. In addition to features derived from read alignments, it utilizes characteristic genomic sequences, e.g. around splice sites, to improve transcript predictions. mTim inferred transcripts that were highly accurate and relatively robust to alignment errors in comparison to those from Cufflinks, a widely used transcript assembly method.

The combination of multiple classifiers using ensemble methods is increasingly important for making progress in a variety of difficult prediction problems. We present a comparative analysis of several ensemble methods through two case studies in genomics, namely the prediction of genetic interactions and protein functions, to demonstrate their efficacy on real-world datasets and draw useful conclusions about their behavior. These methods include simple aggregation, meta-learning, cluster-based meta-learning, and ensemble selection using heterogeneous classifiers trained on resampled data to improve the diversity of their predictions. We present a detailed analysis of these methods across 4 genomics datasets and find the best of these methods offer statistically significant improvements over the state of the art in their respective domains. In addition, we establish a novel connection between ensemble selection and meta-learning, demonstrating how both of these disparate methods establish a balance between ensemble diversity and performance.

HOL(y)Hammer is an online AI/ATP service for formal (computer-understandable) mathematics encoded in the HOL Light system. The service allows its users to upload and automatically process an arbitrary formal development (project) based on HOL Light, and to attack arbitrary conjectures that use the concepts defined in some of the uploaded projects. For that, the service uses several automated reasoning systems combined with several premise selection methods trained on all the project proofs. The projects that are readily available on the server for such query answering include the recent versions of the Flyspeck, Multivariate Analysis and Complex Analysis libraries. The service runs on a 48-CPU server, currently employing in parallel for each task 7 AI/ATP combinations and 4 decision procedures that contribute to its overall performance. The system is also available for local installation by interested users, who can customize it for their own proof development. An Emacs interface allowing parallel asynchronous queries to the service is also provided. The overall structure of the service is outlined, problems that arise and their solutions are discussed, and an initial account of using the system is given.

We present five methods to the problem of network anomaly detection. These methods cover most of the common techniques in the anomaly detection field, including Statistical Hypothesis Tests (SHT), Support Vector Machines (SVM) and clustering analysis. We evaluate all methods in a simulated network that consists of nominal data, three flow-level anomalies and one packet-level attack. Through analyzing the results, we point out the advantages and disadvantages of each method and conclude that combining the results of the individual methods can yield improved anomaly detection results.