We consider the problem of finding a subnetwork in a given biological network (i.e. target network) that is most similar to a given small query network. We aim to find the optimal solution (i.e. the subnetwork with th...
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We consider the problem of finding a subnetwork in a given biological network (i.e. target network) that is most similar to a given small query network. We aim to find the optimal solution (i.e. the subnetwork with the largest alignment score) with a provable confidence bound. There is no known polynomial time solution to this problem in the literature. Alon et al. has developed a state-of-the-art coloring method that reduces the cost of this problem. This method randomly colors the target network prior to alignment for many iterations until a user-supplied confidence is reached. Here we develop a novel coloring method, named k-hop coloring (k is a positive integer), that achieves a provable confidence value in a small number of iterations without sacrificing the optimality. Our method considers the color assignments already made in the neighborhood of each target network node while assigning a color to a node. This way, it preemptively avoids many color assignments that are guaranteed to fail to produce the optimal alignment. We also develop a filtering method that eliminates the nodes that cannot be aligned without reducing the alignment score after each coloring instance. We demonstrate both theoretically and experimentally that our coloring method outperforms that of Alon et al., which is also used by a number network alignment methods, including QPath and QNet, by a factor of three without reducing the confidence in the optimality of the result. Our experiments also suggest that the resulting alignment method is capable of identifying functionally enriched regions in the target network successfully.
Coded structured light method was proposed for surface three dimension measurement, where two primary colors of red and blue were used to generate Gray code projecting patterns, with advantages of one unit Hamming dis...
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ISBN:
(纸本)9780769549354
Coded structured light method was proposed for surface three dimension measurement, where two primary colors of red and blue were used to generate Gray code projecting patterns, with advantages of one unit Hamming distance and avoiding influence from the bright stripe to the dark one in grey coding. System mathematical model was established and simulation system was designed, then method and system in this paper were evaluated by simulation measurement experiments of plane and sphere. Experimental results of plane show that the maximal measuring error is less than 10mm and the maximal relative error is less than 0.8% in depth range 1200mm. Experimental results of sphere show that the maximal measuring error is less than 12mm and the maximal relative error is less than 1.0% for sphere with 170mm radius, at difference spheric center depth in range 1200mm.
Previous research has shown multihue scales to be well-suited to code categorical features and shown lightness scales to be well-suited to code ordinal quanti. ties. We introduce an algorithm, Motley, that produces co...
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Previous research has shown multihue scales to be well-suited to code categorical features and shown lightness scales to be well-suited to code ordinal quanti. ties. We introduce an algorithm, Motley, that produces color scales varying in both hue and lightness, intended to be effective for both categorical and ordinal coding, allowing users to determine both absolute and relative quantities efficiently and accurately. The algorithm first determines the lightnesses of scale colors to maximize perceived lightness differences and establish the lightness ordering, generating separate search spaces for each scale position. It then selects hues by heuristic search to maximize the discriminability of the scale. It produces scales that are ordered with respect to lightness but unordered with respect to hue and thus more discriminable than typical multihue lightness scales. In an experimental evaluation on human subjects, Motley's scales enabled accurate judgments of relative quantity, with response times superior to unordered multihue scales and comparable to ordered lightness scales, and enabled accuracy and speed of judgments of absolute quantity superior to lightness scales and comparable to multihue scales. (dagger)Published 2009 Wiley Periodicals, Inc. Col Res Appl, 35, 18-28, 2010;Published online 17 November 2009 in Wiley InterScience (***). DOI 10.1002/col.20559
color vision in mammals is based on the expression of at least two cone opsins that are sensitive to different wavelengths of light. Furthermore, retinal pathways conveying color-opponent signals are required for colo...
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color vision in mammals is based on the expression of at least two cone opsins that are sensitive to different wavelengths of light. Furthermore, retinal pathways conveying color-opponent signals are required for color discrimination. Most of the primates are trichromats, and "color-coded channels" of their retinas are unveiled to a large extent. In contrast, knowledge of cone-selective pathways in nonprimate dichromats is only slowly emerging, although retinas of dichromats like mice or rats are extensively studied as model systems for retinal information processing. Here, we review recent progress of research on color-coded pathways in nonprimate dichromats to identify differences or similarities between di- and trichromatic mammals. In addition, we applied immunohistochemical methods and confocal microscopy to retinas of different species and present data on their neuronal properties, which are expected to contribute to color vision. Basic neuronal features such as the "blue cone bipolar cell" exist in every species investigated so far. Moreover, there is increasing evidence for chromatic OFF channels in dichromats and retinal ganglion cells that relay color-opponent signals to the brain. In conclusion, di- and trichromats share similar retinal pathways for color transmission and processing.
In silico approaches for drug-induced toxicity evaluation are likely to enable improved screening of new chemical entities during drug discovery and development. Analysis of protein-protein interaction (PPI) networks ...
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ISBN:
(纸本)9780769545745
In silico approaches for drug-induced toxicity evaluation are likely to enable improved screening of new chemical entities during drug discovery and development. Analysis of protein-protein interaction (PPI) networks using an edge centrality-based measure has previously been shown to reveal protein modules that may be associated with drug-induced toxicity. Here, we extend the algorithm by integrating protein interaction information with in vitro gene expression data from tissue treated with drugs known to be associated with the toxicity. We evaluate the new measure for its ability to detect nonimmune neutropenia related proteins and propose a biomarker panel that may be valuable for screening future drug candidates.
In this paper, we first introduce three different geometric features including shape index, curvedness and sphericity ratio, for colonic polyp detection. A new color coding scheme is designed to highlight the detected...
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ISBN:
(纸本)9780819466327
In this paper, we first introduce three different geometric features including shape index, curvedness and sphericity ratio, for colonic polyp detection. A new color coding scheme is designed to highlight the detected polyps, and help radiologists to distinguish them from other tissues more easily. The key idea is to place the detected polyp candidates at the same locations in a newly created polygonal dataset with exactly the same topological and geometrical properties as the triangulated mesh surface of real colon dataset, and assign different colors to the two separated datasets to highlight the polyps. Finally, we validate the proposed polyp detection framework and color coding scheme by computer simulated and real colon datasets. For sixteen synthetic polyps with different shapes and different sizes, the sensitivity is 100%, and false positive is 0.
color difference calculations are usually applied to match or tolerance of small differences between large (>2 degrees) visual fields. In contrast, we examine here the application of ultra-large color differences t...
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color difference calculations are usually applied to match or tolerance of small differences between large (>2 degrees) visual fields. In contrast, we examine here the application of ultra-large color differences to enhance conspicuousness and discriminability of small (1 degrees subtense or smaller) visual targets, e.g., in visual information displays. We show that CIEDE2000, and color difference metrics based on the OSA Uniform color Space and CIECAM02 are superior to CIELAB and CIELUV. Considering gray scale only, we show that Whittle's JND metric of achromatic contrast is as good as L* for this purpose, while also modeling contrast polarity and "crispening." Furthermore, using this JND metric, we replicate Highnote's finding that elongation of small targets affects their apparent contrast. We discuss the perceived fading of color differences when targets become smaller, and suggest practical methods to mitigate the adverse effect on color conspicuousness and discriminability. (C) 2009 Wiley Periodicals, Inc. Cot Res Appl, 35, 4-17, 2010;Published online 17 November 2009 in Wiley InterScience (***). DOI 10.1002/col.20557
The New York area is well-known to have some of the most congested airspace and airports in the U. S. National Airspace System (NAS). The challenge to air traffic management results from high demand, proximity of busy...
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ISBN:
(纸本)9781424466177
The New York area is well-known to have some of the most congested airspace and airports in the U. S. National Airspace System (NAS). The challenge to air traffic management results from high demand, proximity of busy airports, and occasional disruptive weather events. A prototype capability called Integrated Departure Route Planning (IDRP) is being tested this year (2010), in its "Phase 1" version. It will be an adjunct capability to the Route Availability Planning Tool (RAPT), developed by the Massachusetts Institute of Technology/Lincoln Laboratory (MIT/LL), which has been used successfully in a prototype mode for several years. The IDRP display windows will be output onto the RAPT terminal device, which is now installed at the New York approach control, several en route centers, multiple towers, and several air carrier operations desks. IDRP provides a forecast horizon of fix- and route-specific loading for New York departures, with color-coding to alert traffic managers about fix congestion and possible weather impacts. Whereas the RAPT display shows route blockage/availability and is useful only in situations of convective weather, IDRP should have benefits during both good weather and convective activity. A benefits estimation process was undertaken to approximate the total annual dollar benefit that might be expected from the full deployment of IDRP (which is some years away) to deal with non-weather-related congestion. Analysis of archived data found cases where fix congestion, and the associated taxi-out delays could have been ameliorated by reassigning affected flights to uncongested alternate fixes, subject to airline acceptance.
We enhance understanding of the prejudice-induced "color coding" phenomenon among whites by determining whether racial and ethnic prejudices are associated with a previously unexplored policy outcome, spendi...
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