JGraphT -- A Java library for graph data structures and algorithms

Mathematical software and graph-theoretical algorithmic packages to efficiently model, analyze and query graphs are crucial in an era where large-scale spatial, societal and economic network data are abundantly available. One such package is JGraphT, a programming library which contains very efficient and generic graph data-structures along with a large collection of state-of-the-art algorithms. The library is written in Java with stability, interoperability and performance in mind. A distinctive feature of this library is the ability to model vertices and edges as arbitrary objects, thereby permitting natural representations of many common networks including transportation, social and biological networks. Besides classic graph algorithms such as shortest-paths and spanning-tree algorithms, the library contains numerous advanced algorithms: graph and subgraph isomorphism; matching and flow problems; approximation algorithms for NP-hard problems such as independent set and TSP; and several more exotic algorithms such as Berge graph detection. Due to its versatility and generic design, JGraphT is currently used in large-scale commercial, non-commercial and academic research projects. In this work we describe in detail the design and underlying structure of the library, and discuss its most important features and algorithms. A computational study is conducted to evaluate the performance of JGraphT versus a number of similar libraries. Experiments on a large number of graphs over a variety of popular algorithms show that JGraphT is highly competitive with other established libraries such as NetworkX or the BGL.Comment: Major Revisio

Visualization and Correction of Automated Segmentation, Tracking and Lineaging from 5-D Stem Cell Image Sequences

Results: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels, enabling quantification of the dynamic behaviors of stem cells in relation to their vascular niche, with applications in developmental and cancer biology. Our application automatically segments, tracks, and lineages the image sequence data and then allows the user to view and edit the results of automated algorithms in a stereoscopic 3-D window while simultaneously viewing the stem cell lineage tree in a 2-D window. Using the GPU to store and render the image sequence data enables a hybrid computational approach. An inference-based approach utilizing user-provided edits to automatically correct related mistakes executes interactively on the system CPU while the GPU handles 3-D visualization tasks. Conclusions: By exploiting commodity computer gaming hardware, we have developed an application that can be run in the laboratory to facilitate rapid iteration through biological experiments. There is a pressing need for visualization and analysis tools for 5-D live cell image data. We combine accurate unsupervised processes with an intuitive visualization of the results. Our validation interface allows for each data set to be corrected to 100% accuracy, ensuring that downstream data analysis is accurate and verifiable. Our tool is the first to combine all of these aspects, leveraging the synergies obtained by utilizing validation information from stereo visualization to improve the low level image processing tasks.Comment: BioVis 2014 conferenc

A novel improved model for building energy consumption prediction based on model integration

Building energy consumption prediction plays an irreplaceable role in energy planning, management, and conservation. Constantly improving the performance of prediction models is the key to ensuring the efficient operation of energy systems. Moreover, accuracy is no longer the only factor in revealing model performance, it is more important to evaluate the model from multiple perspectives, considering the characteristics of engineering applications. Based on the idea of model integration, this paper proposes a novel improved integration model (stacking model) that can be used to forecast building energy consumption. The stacking model combines advantages of various base prediction algorithms and forms them into “meta-features” to ensure that the final model can observe datasets from different spatial and structural angles. Two cases are used to demonstrate practical engineering applications of the stacking model. A comparative analysis is performed to evaluate the prediction performance of the stacking model in contrast with existing well-known prediction models including Random Forest, Gradient Boosted Decision Tree, Extreme Gradient Boosting, Support Vector Machine, and K-Nearest Neighbor. The results indicate that the stacking method achieves better performance than other models, regarding accuracy (improvement of 9.5%–31.6% for Case A and 16.2%–49.4% for Case B), generalization (improvement of 6.7%–29.5% for Case A and 7.1%-34.6% for Case B), and robustness (improvement of 1.5%–34.1% for Case A and 1.8%–19.3% for Case B). The proposed model enriches the diversity of algorithm libraries of empirical models

Efficient MaxCount and threshold operators of moving objects

Calculating operators of continuously moving objects presents some unique challenges, especially when the operators involve aggregation or the concept of congestion, which happens when the number of moving objects in a changing or dynamic query space exceeds some threshold value. This paper presents the following six d-dimensional moving object operators: (1) MaxCount (or MinCount), which finds the Maximum (or Minimum) number of moving objects simultaneously present in the dynamic query space at any time during the query time interval. (2) CountRange, which finds a count of point objects whose trajectories intersect the dynamic query space during the query time interval. (3) ThresholdRange, which finds the set of time intervals during which the dynamic query space is congested. (4) ThresholdSum, which finds the total length of all the time intervals during which the dynamic query space is congested. (5) ThresholdCount, which finds the number of disjoint time intervals during which the dynamic query space is congested. And (6) ThresholdAverage, which finds the average length of time of all the time intervals when the dynamic query space is congested. For these operators separate algorithms are given to find only estimate or only precise values. Experimental results from more than 7,500 queries indicate that the estimation algorithms produce fast, efficient results with error under 5%

Tools for Assessing Climate Impacts on Fish and Wildlife

Climate change is already affecting many fish and wildlife populations. Managing these populations requires an understanding of the nature, magnitude, and distribution of current and future climate impacts. Scientists and managers have at their disposal a wide array of models for projecting climate impacts that can be used to build such an understanding. Here, we provide a broad overview of the types of models available for forecasting the effects of climate change on key processes that affect fish and wildlife habitat (hydrology, fire, and vegetation), as well as on individual species distributions and populations. We present a framework for how climate-impacts modeling can be used to address management concerns, providing examples of model-based assessments of climate impacts on salmon populations in the Pacific Northwest, fire regimes in the boreal region of Canada, prairies and savannas in the Willamette Valley-Puget Sound Trough-Georgia Basin ecoregion, and marten Martes americana populations in the northeastern United States and southeastern Canada. We also highlight some key limitations of these models and discuss how such limitations should be managed. We conclude with a general discussion of how these models can be integrated into fish and wildlife management