Gremlin: an interactive visualization model for analyzing genomic rearrangements

In this work we present, apply, and evaluate a novel, interactive visualization model for comparative analysis of structural variants and rearrangements in human and cancer genomes, with emphasis on data integration and uncertainty visualization. To support both global trend analysis and local feature detection, this model enables explorations continuously scaled from the high-level, complete genome perspective, down to the low-level, structural rearrangement view, while preserving global context at all times. We have implemented these techniques in Gremlin, a genomic rearrangement explorer with multi-scale, linked interactions, which we apply to four human cancer genome data sets for evaluation. Using an insight-based evaluation methodology, we compare Gremlin to Circos, the state-of-the-art in genomic rearrangement visualization, through a small user study with computational biologists working in rearrangement analysis. Results from user study evaluations demonstrate that this visualization model enables more total insights, more insights per minute, and more complex insights than the current state-of-the-art for visual analysis and exploration of genome rearrangements.     

World lines

In this paper we present World Lines as a novel interactive visualization that provides complete control over multiple heterogeneous simulation runs. In many application areas, decisions can only be made by exploring alternative scenarios. The goal of the suggested approach is to support users in this decision making process. In this setting, the data domain is extended to a set of alternative worlds where only one outcome will actually happen. World Lines integrate simulation, visualization and computational steering into a single unified system that is capable of dealing with the extended solution space. World Lines represent simulation runs as causally connected tracks that share a common time axis. This setup enables users to interfere and add new information quickly. A World Line is introduced as a visual combination of user events and their effects in order to present a possible future. To quickly find the most attractive outcome, we suggest World Lines as the governing component in a system of multiple linked views and a simulation component. World Lines employ linking and brushing to enable comparative visual analysis of multiple simulations in linked views. Analysis results can be mapped to various visual variables that World Lines provide in order to highlight the most compelling solutions. To demonstrate this technique we present a flooding scenario and show the usefulness of the integrated approach to support informed decision making.     

Combinatorial Optimization and Performance Analysis of a Multi-arm Cartesian Robotic Fruit Harvester—Extensions of Graph Coloring

A mobile melon robotic harvester consisting of multiple Cartesian manipulators, each with three degrees of freedom, is being developed. In order to design an optimal robot in terms of number of arms, manipulator capabilities, and robot speed, a method of allocating the fruits to be picked by each manipulator in a way that yields the maximum harvest has been developed. Such a method has already been devised for a multi-arm robot with 2DOF each. The maximum robotic harvesting problem was shown there to be an example of the maximum k-colorable subgraph problem (MKCSP) on an interval graph. However, for manipulators with 3DOF, the additional longitudinal motion results in variable intervals. To overcome this issue, we devise a new model based on the color-dependent interval graph (CDIG). This enables the harvest by multiple robotic arms to be modeled as a modified version of the MKCSP. Based on previous research, we develop a greedy algorithm that solves the problem in polynomial time, and prove its optimality using induction. As with the multi-arm 2DOF robot, when simulated numerous times on a field of randomly distributed fruits, the algorithm yields a nearly identical percentage of fruit harvested for given robot parameters. The results of the probabilistic analysis developed for the 2DOF robot was modified to yield a formula for the expected harvest ratio of the 3DOF robot. The significance of this method is that it enables selecting the most efficient actuators, number of manipulators, and robot forward velocity for maximal robotic fruit harvest.     

Constraint based approach for the steady-state simulation of complex systems: Application to ship control

When the steady states are largely predominant with respect to transitional phases, steady-state simulation seems sufficient to predict the behavior of a complex system. Over the past 20 years, different modeling languages and dedicated tools have been developed to improve steady state simulation.In this paper, focus is made on steady-state simulation for system control and design. A model combining an emission sub-model with a ship propulsion sub-model was implemented in a constraint programming (CP) approach. It will help to determine the efficiency (i.e. the ability to model and solve the problem) and complexity of implementation (i.e. difficulties encountered during the implementation) of this approach.First, requirements for the steady-state simulation of complex systems are defined. Then, CP approach is shown to be able to answer these issues through experiments. This approach is then compared to one of the main simulation languages: Modelica.Although the two approaches (i.e Modelica and CP) are able to reverse models, the study shows that the use of Modelica principles for steady-state simulation involves some crippling limitations, such as the non-management of under/over-constrained systems, or inequalities.This study also shows that the constraint programming approach permits to meet some needs for steady-state simulation not yet covered by current approaches.     

Augmenting and structuring user queries to support efficient free-form code search

Source code terms such as method names and variable types are often different from conceptual words mentioned in a search query. This vocabulary mismatch problem can make code search inefficient. In this paper, we present COde voCABUlary (CoCaBu), an approach to resolving the vocabulary mismatch problem when dealing with free-form code search queries. Our approach leverages common developer questions and the associated expert answers to augment user queries with the relevant, but missing, structural code entities in order to improve the performance of matching relevant code examples within large code repositories. To instantiate this approach, we build GitSearch, a code search engine, on top of GitHub and Stack Overflow Q&A data. We evaluate GitSearch in several dimensions to demonstrate that (1) its code search results are correct with respect to user-accepted answers; (2) the results are qualitatively better than those of existing Internet-scale code search engines; (3) our engine is competitive against web search engines, such as Google, in helping users solve programming tasks; and (4) GitSearch provides code examples that are acceptable or interesting to the community as answers for Stack Overflow questions.     

Invisible emotion magnification algorithm (IEMA) for real-time micro-expression recognition with graph-based features

Multimedia Tools and Applications - The interest in real-time micro-expression recognition has increased with the current trend in human-computer interaction applications. Presently, there are...     

Virtual Organizations in Arigatoni

Arigatoni is a lightweight overlay network that deploys the Global Computing Paradigm over the Internet. Communication for over the behavioral units of the overlay is performed by a simple resource discovery protocol (RDP). Basic Global Computers Units (GC) can communicate by first registering to a brokering service and then by mutually asking and offering services.Colonies and communities are the main entities in the model. A colony is a simple virtual organization composed by exactly one leader and some set (possibly empty) of individuals. A community is a raw set of colonies and global computers (think it as a soup of colonies and global computer without a leader).We present an operational semantics via a labeled transition system, that describes the main operations necessary in the Arigatoni model to perform leader negotiation, joining/leaving a colony, linking two colonies and moving one GC from one colony to another. Our formalization results to be adequate w.r.t. the algorithm performing peer logging/delogging and colony aggregation.     

Nodes on ropes: a comprehensive data and control flow for steering ensemble simulations

Flood disasters are the most common natural risk and tremendous efforts are spent to improve their simulation and management. However, simulation-based investigation of actions that can be taken in case of flood emergencies is rarely done. This is in part due to the lack of a comprehensive framework which integrates and facilitates these efforts. In this paper, we tackle several problems which are related to steering a flood simulation. One issue is related to uncertainty. We need to account for uncertain knowledge about the environment, such as levee-breach locations. Furthermore, the steering process has to reveal how these uncertainties in the boundary conditions affect the confidence in the simulation outcome. Another important problem is that the simulation setup is often hidden in a black-box. We expose system internals and show that simulation steering can be comprehensible at the same time. This is important because the domain expert needs to be able to modify the simulation setup in order to include local knowledge and experience. In the proposed solution, users steer parameter studies through the World Lines interface to account for input uncertainties. The transport of steering information to the underlying data-flow components is handled by a novel meta-flow. The meta-flow is an extension to a standard data-flow network, comprising additional nodes and ropes to abstract parameter control. The meta-flow has a visual representation to inform the user about which control operations happen. Finally, we present the idea to use the data-flow diagram itself for visualizing steering information and simulation results. We discuss a case-study in collaboration with a domain expert who proposes different actions to protect a virtual city from imminent flooding. The key to choosing the best response strategy is the ability to compare different regions of the parameter space while retaining an understanding of what is happening inside the data-flow system.     

Fast computation of minimal elementary decompositions of metabolic flux vectors

The concept of elementary flux vector is valuable in a number of applications of metabolic engineering. For instance, in metabolic flux analysis, each admissible flux vector can be expressed as a non-negative linear combination of a small number of elementary flux vectors. However a critical issue concerns the total number of elementary flux vectors which may be huge because it combinatorially increases with the size of the metabolic network. In this paper we present a fast algorithm that randomly computes a decomposition of admissible flux vectors in a minimal number of elementary flux vectors without explicitly enumerating all of them.     

Ensemble of surrogates

The custom in surrogate-based modeling of complex engineering problems is to fit one or more surrogate models and select the one surrogate model that performs best. In this paper, we extend the utility of an ensemble of surrogates to (1) identify regions of possible high errors at locations where predictions of surrogates widely differ, and (2) provide a more robust approximation approach. We explore the possibility of using the best surrogate or a weighted average surrogate model instead of individual surrogate models. The weights associated with each surrogate model are determined based on the errors in surrogates. We demonstrate the advantages of an ensemble of surrogates using analytical problems and one engineering problem. We show that for a single problem the choice of test surrogate can depend on the design of experiments.