Inferring the structure of gene regulatory networks (GRN) from gene expression data has many applications, from the elucidation of complex biological processes to the identification of potential drug targets. It is however a notoriously difficult problem, for which the many existing methods reach limited accuracy. In this paper, we formulate GRN inference as a sparse regression problem and investigate the performance of a popular feature selection method, least angle regression (LARS) combined with stability selection. We introduce a novel, robust and accurate scoring technique for stability selection, which improves the performance of feature selection with LARS. The resulting method, which we call TIGRESS (Trustful Inference of Gene REgulation using Stability Selection), was ranked among the top methods in the DREAM5 gene network reconstruction challenge. We investigate in depth the influence of the various parameters of the method and show that a fine parameter tuning can lead to significant improvements and state-of-the-art performance for GRN inference. TIGRESS reaches state-of-the-art performance on benchmark data. This study confirms the potential of feature selection techniques for GRN inference. Code and data are available on http://cbio.ensmp.fr/~ahaury. Running TIGRESS online is possible on GenePattern: http://www.broadinstitute.org/cancer/software/genepattern/.

Based on World Health Organization (WHO) fact sheet in the 2011, outbreaks of poultry diseases especially Avian Influenza in poultry may raise global public health concerns due to their effect on poultry populations, their potential to cause serious disease in people, and their pandemic potential. In this research, we built a Poultry Diseases Expert System using Dempster-Shafer Theory. In this Poultry Diseases Expert System We describe five symptoms which include depression, combs, wattle, bluish face region, swollen face region, narrowness of eyes, and balance disorders. The result of the research is that Poultry Diseases Expert System has been successfully identifying poultry diseases.

This paper is concerned with the inference of the conditional independence graph G of a multivariate random vector Y of dimension n, a problem sometimes referred to as structure learning. We focus here on undirected decomposable graphs, whose popularity is mainly due to the tractable factorization they allow for the likelihood ([9, 20]); related work for directed graphical models can be found in [18]. Learning the conditional 1 independence graph G is an onerous task due to the large number of graphs on a set of n nodes, or variables. It is possible using optimization methods to find the graph which best fits the data according to some metric [23, 30, 13]; alternatively Bayesian model averaging may be used to accommodate for uncertainty in the estimated graph, or maximum a posteriori estimation may be used to select a given model from the posterior over graphs. Such an approach relies on a prior distribution π(G) over the set of decomposable graphs of a given size; through Bayes theorem, this prior is updated based on the data to give an a posteriori estimate of the distribution over graphs.

Domain knowledge is crucial for effective performance in autonomous control systems. Typically, human effort is required to encode this knowledge into a control algorithm. In this paper, we present an approach to language grounding which automatically interprets text in the context of a complex control application, such as a game, and uses domain knowledge extracted from the text to improve control performance. Both text analysis and control strategies are learned jointly using only a feedback signal inherent to the application. To effectively leverage textual information, our method automatically extracts the text segment most relevant to the current game state, and labels it with a task-centric predicate structure. This labeled text is then used to bias an action selection policy for the game, guiding it towards promising regions of the action space. We encode our model for text analysis and game playing in a multi-layer neural network, representing linguistic decisions via latent variables in the hidden layers, and game action quality via the output layer. Operating within the Monte-Carlo Search framework, we estimate model parameters using feedback from simulated games. We apply our approach to the complex strategy game Civilization II using the official game manual as the text guide. Our results show that a linguistically-informed game-playing agent significantly outperforms its language-unaware counterpart, yielding a 34% absolute improvement and winning over 65% of games when playing against the built-in AI of Civilization.

In binary classification problems, mainly two approaches have been proposed; one is loss function approach and the other is uncertainty set approach. The loss function approach is applied to major learning algorithms such as support vector machine (SVM) and boosting methods. The loss function represents the penalty of the decision function on the training samples. In the learning algorithm, the empirical mean of the loss function is minimized to obtain the classifier. Against a backdrop of the development of mathematical programming, nowadays learning algorithms based on loss functions are widely applied to real-world data analysis. In addition, statistical properties of such learning algorithms are well-understood based on a lots of theoretical works. On the other hand, the learning method using the so-called uncertainty set is used in hard-margin SVM, mini-max probability machine (MPM) and maximum margin MPM. In the learning algorithm, firstly, the uncertainty set is defined for each binary label based on the training samples. Then, the best separating hyperplane between the two uncertainty sets is employed as the decision function. This is regarded as an extension of the maximum-margin approach. The uncertainty set approach has been studied as an application of robust optimization in the field of mathematical programming. The statistical properties of learning algorithms with uncertainty sets have not been intensively studied. In this paper, we consider the relation between the above two approaches. We point out that the uncertainty set is described by using the level set of the conjugate of the loss function. Based on such relation, we study statistical properties of learning algorithms using uncertainty sets.

Bayesian Optimization aims at optimizing an unknown non-convex/concave function that is costly to evaluate. We are interested in application scenarios where concurrent function evaluations are possible. Under such a setting, BO could choose to either sequentially evaluate the function, one input at a time and wait for the output of the function before making the next selection, or evaluate the function at a batch of multiple inputs at once. These two different settings are commonly referred to as the sequential and batch settings of Bayesian Optimization. In general, the sequential setting leads to better optimization performance as each function evaluation is selected with more information, whereas the batch setting has an advantage in terms of the total experimental time (the number of iterations). In this work, our goal is to combine the strength of both settings. Specifically, we systematically analyze Bayesian optimization using Gaussian process as the posterior estimator and provide a hybrid algorithm that, based on the current state, dynamically switches between a sequential policy and a batch policy with variable batch sizes. We provide theoretical justification for our algorithm and present experimental results on eight benchmark BO problems. The results show that our method achieves substantial speedup (up to %78) compared to a pure sequential policy, without suffering any significant performance loss.

Given the superposition of a low-rank matrix plus the product of a known fat compression matrix times a sparse matrix, the goal of this paper is to establish deterministic conditions under which exact recovery of the low-rank and sparse components becomes possible. This fundamental identifiability issue arises with traffic anomaly detection in backbone networks, and subsumes compressed sensing as well as the timely low-rank plus sparse matrix recovery tasks encountered in matrix decomposition problems. Leveraging the ability of $\ell_1$- and nuclear norms to recover sparse and low-rank matrices, a convex program is formulated to estimate the unknowns. Analysis and simulations confirm that the said convex program can recover the unknowns for sufficiently low-rank and sparse enough components, along with a compression matrix possessing an isometry property when restricted to operate on sparse vectors. When the low-rank, sparse, and compression matrices are drawn from certain random ensembles, it is established that exact recovery is possible with high probability. First-order algorithms are developed to solve the nonsmooth convex optimization problem with provable iteration complexity guarantees. Insightful tests with synthetic and real network data corroborate the effectiveness of the novel approach in unveiling traffic anomalies across flows and time, and its ability to outperform existing alternatives.

Traffic congestion in urban road networks is a costly problem that affects all major cities in developed countries. To tackle this problem, it is possible (i) to act on the supply side, increasing the number of roads or lanes in a network, (ii) to reduce the demand, restricting the access to urban areas at specific hours or to specific vehicles, or (iii) to improve the efficiency of the existing network, by means of a widespread use of so-called Intelligent Transportation Systems (ITS). In line with the recent advances in smart transportation management infrastructures, ITS has turned out to be a promising field of application for artificial intelligence techniques. In particular, multiagent systems seem to be the ideal candidates for the design and implementation of ITS. In fact, drivers can be naturally modelled as autonomous agents that interact with the transportation management infrastructure, thereby generating a large-scale, open, agent-based system. To regulate such a system and maintain a smooth and efficient flow of traffic, decentralised mechanisms for the management of the transportation infrastructure are needed. In this article we propose a distributed, market-inspired, mechanism for the management of a future urban road network, where intelligent autonomous vehicles, operated by software agents on behalf of their human owners, interact with the infrastructure in order to travel safely and efficiently through the road network. Building on the reservation-based intersection control model proposed by Dresner and Stone, we consider two different scenarios: one with a single intersection and one with a network of intersections. In the former, we analyse the performance of a novel policy based on combinatorial auctions for the allocation of reservations. In the latter, we analyse the impact that a traffic assignment strategy inspired by competitive markets has on the drivers' route choices. Finally we propose an adaptive management mechanism that integrates the auction-based traffic control policy with the competitive traffic assignment strategy.

Imaging spectrometers measure electromagnetic energy scattered in their instantaneous field view in hundreds or thousands of spectral channels with higher spectral resolution than multispectral cameras. Imaging spectrometers are therefore often referred to as hyperspectral cameras (HSCs). Higher spectral resolution enables material identification via spectroscopic analysis, which facilitates countless applications that require identifying materials in scenarios unsuitable for classical spectroscopic analysis. Due to low spatial resolution of HSCs, microscopic material mixing, and multiple scattering, spectra measured by HSCs are mixtures of spectra of materials in a scene. Thus, accurate estimation requires unmixing. Pixels are assumed to be mixtures of a few materials, called endmembers. Unmixing involves estimating all or some of: the number of endmembers, their spectral signatures, and their abundances at each pixel. Unmixing is a challenging, ill-posed inverse problem because of model inaccuracies, observation noise, environmental conditions, endmember variability, and data set size. Researchers have devised and investigated many models searching for robust, stable, tractable, and accurate unmixing algorithms. This paper presents an overview of unmixing methods from the time of Keshava and Mustard's unmixing tutorial [1] to the present. Mixing models are first discussed. Signal-subspace, geometrical, statistical, sparsity-based, and spatial-contextual unmixing algorithms are described. Mathematical problems and potential solutions are described. Algorithm characteristics are illustrated experimentally.

Heuristics used for solving hard real-time search problems have regions with depressions. Such regions are bounded areas of the search space in which the heuristic function is inaccurate compared to the actual cost to reach a solution. Early real-time search algorithms, like LRTA*, easily become trapped in those regions since the heuristic values of their states may need to be updated multiple times, which results in costly solutions. State-of-the-art real-time search algorithms, like LSS-LRTA* or LRTA*(k), improve LRTA*'s mechanism to update the heuristic, resulting in improved performance. Those algorithms, however, do not guide search towards avoiding depressed regions. This paper presents depression avoidance, a simple real-time search principle to guide search towards avoiding states that have been marked as part of a heuristic depression. We propose two ways in which depression avoidance can be implemented: mark-and-avoid and move-to-border. We implement these strategies on top of LSS-LRTA* and RTAA*, producing 4 new real-time heuristic search algorithms: aLSS-LRTA*, daLSS-LRTA*, aRTAA*, and daRTAA*. When the objective is to find a single solution by running the real-time search algorithm once, we show that daLSS-LRTA* and daRTAA* outperform their predecessors sometimes by one order of magnitude. Of the four new algorithms, daRTAA* produces the best solutions given a fixed deadline on the average time allowed per planning episode. We prove all our algorithms have good theoretical properties: in finite search spaces, they find a solution if one exists, and converge to an optimal after a number of trials.