Current computational models of bottom-up and top-down components of attention arepredictive of eye movements across a range of stimuli and of simple, fixed visual tasks (such as visual search for a target among distractors). However, todate there exists no computational framework which can reliably mimic human gaze behavior in more complex environments and tasks, such as driving a vehicle through traffic. Here, we develop a hybrid computational/behavioral framework, combining simple models for bottom-up salience and top-down relevance, andlooking for changes in the predictive power of these components at different critical event times during 4.7 hours (500,000 video frames) of observers playing car racing and flight combat video games. This approach is motivated by our observation that the predictive strengths of the salience and relevance models exhibitreliable temporal signatures during critical event windows in the task sequence--for example, when the game player directly engages an enemy plane in a flight combat game, the predictive strength of the salience model increases significantly, while that of the relevance model decreases significantly. Our new framework combines these temporal signatures to implement several event detectors. Critically,we find that an event detector based on fused behavioral and stimulus information (in the form of the model's predictive strength) is much stronger than detectors based on behavioral information alone (eye position) or image information alone(model prediction maps). This approach to event detection, based on eye tracking combined with computational models applied to the visual input, may have useful applications as a less-invasive alternative to other event detection approaches based on neural signatures derived from EEG or fMRI recordings.

This paper studies boosting algorithms that make a single pass over a set of base classifiers. Wefirst analyze a one-pass algorithm in the setting of boosting with diverse base classifiers. Our guarantee is the same as the best proved for any boosting algorithm, butour one-pass algorithm is much faster than previous approaches. We next exhibit a random source of examples for which a "picky" variant of AdaBoost thatskips poor base classifiers can outperform the standard AdaBoost algorithm, whichuses every base classifier, by an exponential factor. Experiments with Reuters and synthetic data show that one-pass boosting can substantially improveon the accuracy of Naive Bayes, and that picky boosting can sometimes lead to a further improvement in accuracy.

Motivation: Profile hidden Markov Models (pHMMs) are a popular and very useful tool in the detection of the remote homologue protein families. Unfortunately, their performance is not always satisfactory when proteins are in the 'twilight zone'. We present HMMER-STRUCT, a model construction algorithm and tool that tries to improve pHMM performance by using structural information while training pHMMs. As a first step, HMMER-STRUCT constructs a set of pHMMs. Each pHMM is constructed by weighting each residue in an aligned protein according to a specific structural property of the residue. Properties used were primary, secondary and tertiary structures, accessibility and packing. HMMER-STRUCT then prioritizes the results by voting. Results: We used the SCOP database to perform our experiments. Throughout, we apply leave-one-family-out cross-validation over protein superfamilies. First, we used the MAMMOTH-mult structural aligner to align the training set proteins. Then, we performed two sets of experiments. In a first experiment, we compared structure weighted models against standard pHMMs and against each other. In a second experiment, we compared the voting model against individual pHMMs. We compare method performance through ROC curves and through Precision/Recall curves, and assess significance through the paired two tailed t-test. Our results show significant performance improvements of all structurally weighted models over default HMMER, and a significant improvement in sensitivity of the combined models over both the original model and the structurally weighted models.

This paper proposes a novel solution to spam detection inspired by a model of the adaptive immune system known as the crossregulation model. We report on the testing of a preliminary algorithm on six e-mail corpora. We also compare our results statically and dynamically with those obtained by the Naive Bayes classifier and another binary classification method we developed previously for biomedical text-mining applications. We show that the cross-regulation model is competitive against those and thus promising as a bio-inspired algorithm for spam detection in particular, and binary classification in general.

Many complex disease syndromes such as asthma consist of a large number of highly related, rather than independent, clinical phenotypes, raising a new technical challenge in identifying genetic variations associated simultaneously with correlated traits. In this study, we propose a new statistical framework called graph-guided fused lasso (GFlasso) to address this issue in a principled way. Our approach explicitly represents the dependency structure among the quantitative traits as a network, and leverages this trait network to encode structured regularizations in a multivariate regression model over the genotypes and traits, so that the genetic markers that jointly influence subgroups of highly correlated traits can be detected with high sensitivity and specificity. While most of the traditional methods examined each phenotype independently and combined the results afterwards, our approach analyzes all of the traits jointly in a single statistical method, and borrow information across correlated phenotypes to discover the genetic markers that perturbe a subset of correlated triats jointly rather than a single trait. Using simulated datasets based on the HapMap consortium data and an asthma dataset, we compare the performance of our method with the single-marker analysis, and other sparse regression methods such as the ridge regression and the lasso that do not use any structural information in the traits. Our results show that there is a significant advantage in detecting the true causal SNPs when we incorporate the correlation pattern in traits using our proposed methods.

Networks have in recent years emerged as an invaluable tool for describing and quantifying complex systems in many branches of science. Recent studies suggest that networks often exhibit hierarchical organization, where vertices divide into groups that further subdivide into groups of groups, and so forth over multiple scales. In many cases these groups are found to correspond to known functional units, such as ecological niches in food webs, modules in biochemical networks (protein interaction networks, metabolic networks, or genetic regulatory networks), or communities in social networks. Here we present a general technique for inferring hierarchical structure from network data and demonstrate that the existence of hierarchy can simultaneously explain and quantitatively reproduce many commonly observed topological properties of networks, such as right-skewed degree distributions, high clustering coefficients, and short path lengths. We further show that knowledge of hierarchical structure can be used to predict missing connections in partially known networks with high accuracy, and for more general network structures than competing techniques. Taken together, our results suggest that hierarchy is a central organizing principle of complex networks, capable of offering insight into many network phenomena.

The paper presents the investigation and implementation of the relationship between diversity and the performance of multiple classifiers on classification accuracy. The study is critical as to build classifiers that are strong and can generalize better. The parameters of the neural network within the committee were varied to induce diversity; hence structural diversity is the focus for this study. The hidden nodes and the activation function are the parameters that were varied. The diversity measures that were adopted from ecology such as Shannon and Simpson were used to quantify diversity. Genetic algorithm is used to find the optimal ensemble by using the accuracy as the cost function. The results observed shows that there is a relationship between structural diversity and accuracy. It is observed that the classification accuracy of an ensemble increases as the diversity increases. There was an increase of 3%-6% in the classification accuracy.

Most works related to unithood were conducted as part of a larger effort for the determination of termhood. Consequently, the number of independent research that study the notion of unithood and produce dedicated techniques for measuring unithood is extremely small. We propose a new approach, independent of any influences of termhood, that provides dedicated measures to gather linguistic evidence from parsed text and statistical evidence from Google search engine for the measurement of unithood. Our evaluations revealed a precision and recall of 98.68% and 91.82% respectively with an accuracy at 95.42% in measuring the unithood of 1005 test cases.

We develop and demonstrate a probabilistic method for classifying rare objects in surveys with the particular goal of building very pure samples. It works by modifying the output probabilities from a classifier so as to accommodate our expectation (priors) concerning the relative frequencies of different classes of objects. We demonstrate our method using the Discrete Source Classifier, a supervised classifier currently based on Support Vector Machines, which we are developing in preparation for the Gaia data analysis. DSC classifies objects using their very low resolution optical spectra. We look in detail at the problem of quasar classification, because identification of a pure quasar sample is necessary to define the Gaia astrometric reference frame. By varying a posterior probability threshold in DSC we can trade off sample completeness and contamination. We show, using our simulated data, that it is possible to achieve a pure sample of quasars (upper limit on contamination of 1 in 40,000) with a completeness of 65% at magnitudes of G=18.5, and 50% at G=20.0, even when quasars have a frequency of only 1 in every 2000 objects. The star sample completeness is simultaneously 99% with a contamination of 0.7%. Including parallax and proper motion in the classifier barely changes the results. We further show that not accounting for class priors in the target population leads to serious misclassifications and poor predictions for sample completeness and contamination. (Truncated)

Machine learning techniques are gaining prevalence in the production of a wide range of classifiers for complex real-world applications with nonuniform testing and misclassification costs. The increasing complexity of these applications poses a real challenge to resource management during learning and classification. In this work we introduce ACT (anytime cost-sensitive tree learner), a novel framework for operating in such complex environments. ACT is an anytime algorithm that allows learning time to be increased in return for lower classification costs. It builds a tree top-down and exploits additional time resources to obtain better estimations for the utility of the different candidate splits. Using sampling techniques, ACT approximates the cost of the subtree under each candidate split and favors the one with a minimal cost. As a stochastic algorithm, ACT is expected to be able to escape local minima, into which greedy methods may be trapped. Experiments with a variety of datasets were conducted to compare ACT to the state-of-the-art cost-sensitive tree learners. The results show that for the majority of domains ACT produces significantly less costly trees. ACT also exhibits good anytime behavior with diminishing returns.