Analysis of Three-Dimensional Protein Images

A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains labor intensive and relies on an expert's ability to derive and evaluate a protein scene model. In this paper, the problem of protein structure determination is formulated as an exercise in scene analysis. A computational methodology is presented in which a 3D image of a protein is segmented into a graph of critical points. Bayesian and certainty factor approaches are described and used to analyze critical point graphs and identify meaningful substructures, such as alpha-helices and beta-sheets. Results of applying the methodologies to protein images at low and medium resolution are reported. The research is related to approaches to representation, segmentation and classification in vision, as well as to top-down approaches to protein structure prediction.Comment: See http://www.jair.org/ for any accompanying file

SAFS: A Deep Feature Selection Approach for Precision Medicine

In this paper, we propose a new deep feature selection method based on deep architecture. Our method uses stacked auto-encoders for feature representation in higher-level abstraction. We developed and applied a novel feature learning approach to a specific precision medicine problem, which focuses on assessing and prioritizing risk factors for hypertension (HTN) in a vulnerable demographic subgroup (African-American). Our approach is to use deep learning to identify significant risk factors affecting left ventricular mass indexed to body surface area (LVMI) as an indicator of heart damage risk. The results show that our feature learning and representation approach leads to better results in comparison with others

Indexing of fictional video content for event detection and summarisation

This paper presents an approach to movie video indexing that utilises audiovisual analysis to detect important and meaningful temporal video segments, that we term events. We consider three event classes, corresponding to dialogues, action sequences, and montages, where the latter also includes musical sequences. These three event classes are intuitive for a viewer to understand and recognise whilst accounting for over 90% of the content of most movies. To detect events we leverage traditional filmmaking principles and map these to a set of computable low-level audiovisual features. Finite state machines (FSMs) are used to detect when temporal sequences of specific features occur. A set of heuristics, again inspired by filmmaking conventions, are then applied to the output of multiple FSMs to detect the required events. A movie search system, named MovieBrowser, built upon this approach is also described. The overall approach is evaluated against a ground truth of over twenty-three hours of movie content drawn from various genres and consistently obtains high precision and recall for all event classes. A user experiment designed to evaluate the usefulness of an event-based structure for both searching and browsing movie archives is also described and the results indicate the usefulness of the proposed approach

Physics-based visual characterization of molecular interaction forces

Molecular simulations are used in many areas of biotechnology, such as drug design and enzyme engineering. Despite the development of automatic computational protocols, analysis of molecular interactions is still a major aspect where human comprehension and intuition are key to accelerate, analyze, and propose modifications to the molecule of interest. Most visualization algorithms help the users by providing an accurate depiction of the spatial arrangement: the atoms involved in inter-molecular contacts. There are few tools that provide visual information on the forces governing molecular docking. However, these tools, commonly restricted to close interaction between atoms, do not consider whole simulation paths, long-range distances and, importantly, do not provide visual cues for a quick and intuitive comprehension of the energy functions (modeling intermolecular interactions) involved. In this paper, we propose visualizations designed to enable the characterization of interaction forces by taking into account several relevant variables such as molecule-ligand distance and the energy function, which is essential to understand binding affinities. We put emphasis on mapping molecular docking paths obtained from Molecular Dynamics or Monte Carlo simulations, and provide time-dependent visualizations for different energy components and particle resolutions: atoms, groups or residues. The presented visualizations have the potential to support domain experts in a more efficient drug or enzyme design process.Peer ReviewedPostprint (author's final draft

Open source environment to define constraints in route planning for GIS-T

Route planning for transportation systems is strongly related to shortest path algorithms, an optimization problem extensively studied in the literature. To find the shortest path in a network one usually assigns weights to each branch to represent the difficulty of taking such branch. The weights construct a linear preference function ordering the variety of alternatives from the most to the least attractive.Postprint (published version