Cryo-electron microscopy (cryo-EM) studies using single particle reconstruction are extensively used to reveal structural information on macromolecular complexes. Aiming at the highest achievable resolution, state of the art electron microscopes automatically acquire thousands of high-quality micrographs. Particles are detected on and boxed out from each micrograph using fully- or semi-automated approaches. However, the obtained particles still require laborious manual post-picking classification, which is one major bottleneck for single particle analysis of large datasets. We introduce MAPPOS, a supervised post-picking strategy for the classification of boxed particle images, as additional strategy adding to the already efficient automated particle picking routines. MAPPOS employs machine learning techniques to train a robust classifier from a small number of characteristic image features. In order to accurately quantify the performance of MAPPOS we used simulated particle and non-particle images. In addition, we verified our method by applying it to an experimental cryo-EM dataset and comparing the results to the manual classification of the same dataset. Comparisons between MAPPOS and manual post-picking classification by several human experts demonstrated that merely a few hundred sample images are sufficient for MAPPOS to classify an entire dataset with a human-like performance. MAPPOS was shown to greatly accelerate the throughput of large datasets by reducing the manual workload by orders of magnitude while maintaining a reliable identification of non-particle images.

Topic models provide a useful method for dimensionality reduction and exploratory data analysis in large text corpora. Most approaches to topic model inference have been based on a maximum likelihood objective. Efficient algorithms exist that approximate this objective, but they have no provable guarantees. Recently, algorithms have been introduced that provide provable bounds, but these algorithms are not practical because they are inefficient and not robust to violations of model assumptions. In this paper we present an algorithm for topic model inference that is both provable and practical. The algorithm produces results comparable to the best MCMC implementations while running orders of magnitude faster.

We consider online planning in Markov decision processes (MDPs). In online planning, the agent focuses on its current state only, deliberates about the set of possible policies from that state onwards and, when interrupted, uses the outcome of that exploratory deliberation to choose what action to perform next. The performance of algorithms for online planning is assessed in terms of simple regret, which is the agent's expected performance loss when the chosen action, rather than an optimal one, is followed. To date, state-of-the-art algorithms for online planning in general MDPs are either best effort, or guarantee only polynomial-rate reduction of simple regret over time. Here we introduce a new Monte-Carlo tree search algorithm, BRUE, that guarantees exponential-rate reduction of simple regret and error probability. This algorithm is based on a simple yet non-standard state-space sampling scheme, MCTS2e, in which different parts of each sample are dedicated to different exploratory objectives. Our empirical evaluation shows that BRUE not only provides superior performance guarantees, but is also very effective in practice and favorably compares to state-of-the-art. We then extend BRUE with a variant of "learning by forgetting." The resulting set of algorithms, BRUE(alpha), generalizes BRUE, improves the exponential factor in the upper bound on its reduction rate, and exhibits even more attractive empirical performance.

We propose a generative model of a group EEG analysis, based on appropriate kernel assumptions on EEG data. We derive the variational inference update rule using various approximation techniques. The proposed model outperforms the current state-of-the-art algorithms in terms of common pattern extraction. The validity of the proposed model is tested on the BCI competition dataset.

We propose a probabilistic model for the parallel execution of Las Vegas algorithms, i.e., randomized algorithms whose runtime might vary from one execution to another, even with the same input. This model aims at predicting the parallel performances (i.e., speedups) by analysis the runtime distribution of the sequential runs of the algorithm. Then, we study in practice the case of a particular Las Vegas algorithm for combinatorial optimization, on three classical problems, and compare with an actual parallel implementation up to 256 cores. We show that the prediction can be quite accurate, matching the actual speedups very well up to 100 parallel cores and then with a deviation of about 20% up to 256 cores.

Given a multivariate data set, sparse principal component analysis (SPCA) aims to extract several linear combinations of the variables that together explain the variance in the data as much as possible, while controlling the number of nonzero loadings in these combinations. In this paper we consider 8 different optimization formulations for computing a single sparse loading vector; these are obtained by combining the following factors: we employ two norms for measuring variance (L2, L1) and two sparsity-inducing norms (L0, L1), which are used in two different ways (constraint, penalty). Three of our formulations, notably the one with L0 constraint and L1 variance, have not been considered in the literature. We give a unifying reformulation which we propose to solve via a natural alternating maximization (AM) method. We show the the AM method is nontrivially equivalent to GPower (Journ\'{e}e et al; JMLR 11:517--553, 2010) for all our formulations. Besides this, we provide 24 efficient parallel SPCA implementations: 3 codes (multi-core, GPU and cluster) for each of the 8 problems. Parallelism in the methods is aimed at i) speeding up computations (our GPU code can be 100 times faster than an efficient serial code written in C++), ii) obtaining solutions explaining more variance and iii) dealing with big data problems (our cluster code is able to solve a 357 GB problem in about a minute).

Large-scale L1-regularized loss minimization problems arise in high-dimensional applications such as compressed sensing and high-dimensional supervised learning, including classification and regression problems. High-performance algorithms and implementations are critical to efficiently solving these problems. Building upon previous work on coordinate descent algorithms for L1-regularized problems, we introduce a novel family of algorithms called block-greedy coordinate descent that includes, as special cases, several existing algorithms such as SCD, Greedy CD, Shotgun, and Thread-Greedy. We give a unified convergence analysis for the family of block-greedy algorithms. The analysis suggests that block-greedy coordinate descent can better exploit parallelism if features are clustered so that the maximum inner product between features in different blocks is small. Our theoretical convergence analysis is supported with experimental re- sults using data from diverse real-world applications. We hope that algorithmic approaches and convergence analysis we provide will not only advance the field, but will also encourage researchers to systematically explore the design space of algorithms for solving large-scale L1-regularization problems.

This paper presents a model based on an hybrid system to numerically simulate the climbing phase of an aircraft. This model is then used within a trajectory prediction tool. Finally, the Covariance Matrix Adaptation Evolution Strategy (CMA-ES) optimization algorithm is used to tune five selected parameters, and thus improve the accuracy of the model. Incorporated within a trajectory prediction tool, this model can be used to derive the order of magnitude of the prediction error over time, and thus the domain of validity of the trajectory prediction. A first validation experiment of the proposed model is based on the errors along time for a one-time trajectory prediction at the take off of the flight with respect to the default values of the theoretical BADA model. This experiment, assuming complete information, also shows the limit of the model. A second experiment part presents an on-line trajectory prediction, in which the prediction is continuously updated based on the current aircraft position. This approach raises several issues, for which improvements of the basic model are proposed, and the resulting trajectory prediction tool shows statistically significantly more accurate results than those of the default model.

Nowadays, huge efforts are made to modernize the air traffic management systems to cope with uncertainty, complexity and sub-optimality. An answer is to enhance the information sharing between the stakeholders. This paper introduces a framework that bridges the gap between air traffic management and air traffic control on the one hand, and bridges the gap between the ground, the approach and the en-route centers on the other hand. An original system is presented, that has three essential components: the trajectory models, the optimization process, and the monitoring process. The uncertainty of the trajectory is modeled with a Bayesian Network, where the nodes are associated to two types of random variables: the time of overflight on metering points of the airspace, and the traveling time of the routes linking these points. The resulting Bayesian Network covers the complete airspace, and Monte- Carlo simulations are done to estimate the probabilities of sector congestion and delays. On top of this trajectory model, an optimization process minimizes these probabilities by tuning the parameters of the Bayesian trajectory model related to overflight times on metering points. The last component is the monitoring process, that continuously updates the situation of the airspace, modifying the trajectories uncertainties according to actual positions of aircraft. After each update, a new optimal set of overflight times is computed, and can be communicated to the controllers as clearances for the aircraft pilots. The paper presents a formal specification of this global optimization problem, whose underlying rationale was derived with the help of air traffic controllers at Thales Air Systems.

The sum-product or belief propagation (BP) algorithm is a widely used message-passing technique for computing approximate marginals in graphical models. We introduce a new technique, called stochastic orthogonal series message-passing (SOSMP), for computing the BP fixed point in models with continuous random variables. It is based on a deterministic approximation of the messages via orthogonal series expansion, and a stochastic approximation via Monte Carlo estimates of the integral updates of the basis coefficients. We prove that the SOSMP iterates converge to a \delta-neighborhood of the unique BP fixed point for any tree-structured graph, and for any graphs with cycles in which the BP updates satisfy a contractivity condition. In addition, we demonstrate how to choose the number of basis coefficients as a function of the desired approximation accuracy \delta and smoothness of the compatibility functions. We illustrate our theory with both simulated examples and in application to optical flow estimation.