AtPID: Arabidopsis thaliana protein interactome database—an integrative platform for plant systems biology

Arabidopsis thaliana Protein Interactome Database (AtPID) is an object database that integrates data from several bioinformatics prediction methods and manually collected information from the literature. It contains data relevant to protein–protein interaction, protein subcellular location, ortholog maps, domain attributes and gene regulation. The predicted protein interaction data were obtained from ortholog interactome, microarray profiles, GO annotation, and conserved domain and genome contexts. This database holds 28 062 protein–protein interaction pairs with 23 396 pairs generated from prediction methods. Among the rest 4666 pairs, 3866 pairs of them involving 1875 proteins were manually curated from the literature and 800 pairs were from enzyme complexes in KEGG. In addition, subcellular location information of 5562 proteins is available. AtPID was built via an intuitive query interface that provides easy access to the important features of proteins. Through the incorporation of both experimental and computational methods, AtPID is a rich source of information for system-level understanding of gene function and biological processes in A. thaliana. Public access to the AtPID database is available at http://atpid.biosino.org/

Applied Bayesian Networks

A Bayesian Network is a stochastic graphical model that can be used to maintain and propagate conditional probability tables among its nodes. Here, we use a Bayesian Network to model results from a numerical riverine model. We develop an discretization optimization algorithm that improves efficiency and concurrently increases the overall accuracy of the resulting network. We measure accuracy using a new prediction accuracy criteria that includes an a posteriori soft correction. Furthermore, we show that this accuracy quickly asymptotes and begins to show diminishing returns on large data sets

Predicting human intention in visual observations of hand/object interactions

Abstract—The main contribution of this paper is a prob-abilistic method for predicting human manipulation intention from image sequences of human-object interaction. Predicting intention amounts to inferring the imminent manipulation task when human hand is observed to have stably grasped the object. Inference is performed by means of a probabilistic graphical model that encodes object grasping tasks over the 3D state of the observed scene. The 3D state is extracted from RGB-D image sequences by a novel vision-based, markerless hand-object 3D tracking framework. To deal with the high-dimensional state-space and mixed data types (discrete and continuous) involved in grasping tasks, we introduce a generative vector quantization method using mixture models and self-organizing maps. This yields a compact model for encoding of grasping actions, able of handling uncertain and partial sensory data. Experimentation showed that the model trained on simulated data can provide a potent basis for accurate goal-inference with partial and noisy observations of actual real-world demonstrations. We also show a grasp selection process, guided by the inferred human intention, to illustrate the use of the system for goal-directed grasp imitation. I

Probabilistic modelling of oil rig drilling operations for business decision support: a real world application of Bayesian networks and computational intelligence.

This work investigates the use of evolved Bayesian networks learning algorithms based on computational intelligence meta-heuristic algorithms. These algorithms are applied to a new domain provided by the exclusive data, available to this project from an industry partnership with ODS-Petrodata, a business intelligence company in Aberdeen, Scotland. This research proposes statistical models that serve as a foundation for building a novel operational tool for forecasting the performance of rig drilling operations. A prototype for a tool able to forecast the future performance of a drilling operation is created using the obtained data, the statistical model and the experts' domain knowledge. This work makes the following contributions: applying K2GA and Bayesian networks to a real-world industry problem; developing a well-performing and adaptive solution to forecast oil drilling rig performance; using the knowledge of industry experts to guide the creation of competitive models; creating models able to forecast oil drilling rig performance consistently with nearly 80% forecast accuracy, using either logistic regression or Bayesian network learning using genetic algorithms; introducing the node juxtaposition analysis graph, which allows the visualisation of the frequency of nodes links appearing in a set of orderings, thereby providing new insights when analysing node ordering landscapes; exploring the correlation factors between model score and model predictive accuracy, and showing that the model score does not correlate with the predictive accuracy of the model; exploring a method for feature selection using multiple algorithms and drastically reducing the modelling time by multiple factors; proposing new fixed structure Bayesian network learning algorithms for node ordering search-space exploration. Finally, this work proposes real-world applications for the models based on current industry needs, such as recommender systems, an oil drilling rig selection tool, a user-ready rig performance forecasting software and rig scheduling tools

A Comparison of Bayesian Network Learning Algorithms from Continuous Data

Learning a Bayesian network from data is an important problem in biomedicine for the automatic construction of decision support systems and inference of plausible causal relations. Most Bayesian network learning algorithms require discrete data; however discretization may impact the quality of the learned structure. In this project, we present a comparison of different approaches for learning from continuous data to identify the most promising one and to quantify the impact of discretization in Bayesian network learning