Automated Quantitative Description of Spiral Galaxy Arm-Segment Structure

We describe a system for the automatic quantification of structure in spiral galaxies. This enables translation of sky survey images into data needed to help address fundamental astrophysical questions such as the origin of spiral structure---a phenomenon that has eluded theoretical description despite 150 years of study (Sellwood 2010). The difficulty of automated measurement is underscored by the fact that, to date, only manual efforts (such as the citizen science project Galaxy Zoo) have been able to extract information about large samples of spiral galaxies. An automated approach will be needed to eliminate measurement subjectivity and handle the otherwise-overwhelming image quantities (up to billions of images) from near-future surveys. Our approach automatically describes spiral galaxy structure as a set of arcs, precisely describing spiral arm segment arrangement while retaining the flexibility needed to accommodate the observed wide variety of spiral galaxy structure. The largest existing quantitative measurements were manually-guided and encompassed fewer than 100 galaxies, while we have already applied our method to more than 29,000 galaxies. Our output matches previous information, both quantitatively over small existing samples, and qualitatively against human classifications from Galaxy Zoo.Comment: 9 pages;4 figures; 2 tables; accepted to CVPR (Computer Vision and Pattern Recognition), June 2012, Providence, Rhode Island, June 16-21, 201

SANA NetGO: A combinatorial approach to using Gene Ontology (GO) terms to score network alignments

Gene Ontology (GO) terms are frequently used to score alignments between protein-protein interaction (PPI) networks. Methods exist to measure the GO similarity between two proteins in isolation, but pairs of proteins in a network alignment are not isolated: each pairing is implicitly dependent upon every other pairing via the alignment itself. Current methods fail to take into account the frequency of GO terms across the networks, and attempt to account for common GO terms in an ad hoc fashion by imposing arbitrary rules on when to "allow" GO terms based on their location in the GO hierarchy, rather than using readily available frequency information in the PPI networks themselves. Here we develop a new measure, NetGO, that naturally weighs infrequent, informative GO terms more heavily than frequent, less informative GO terms, without requiring arbitrary cutoffs. In particular, NetGO down-weights the score of frequent GO terms according to their frequency in the networks being aligned. This is a global measure applicable only to alignments, independent of pairwise GO measures, in the same sense that the edge-based EC or S3 scores are global measures of topological similarity independent of pairwise topological similarities. We demonstrate the superiority of NetGO by creating alignments of predetermined quality based on homologous pairs of nodes and show that NetGO correlates with alignment quality much better than any existing GO-based alignment measures. We also demonstrate that NetGO provides a measure of taxonomic similarity between species, consistent with existing taxonomic measures--a feature not shared with existing GO-based network alignment measures. Finally, we re-score alignments produced by almost a dozen aligners from a previous study and show that NetGO does a better job than existing measures at separating good alignments from bad ones

Shadowing-based reliability decay in softened n-body simulations

A shadow of a numerical solution to a chaotic system is an_exact_ solution to the equations of motion that remains close to the numerical solution for a long time. In a collisionless n-body system, we know that particle motion is governed by the global potential rather than by inter-particle interactions. As a result, the trajectory of each individual particle in the system is independently shadowable. It is thus meaningful to measure the number of particles that have shadowable trajectories as a function of time. We find that the number of shadowable particles decays exponentially with time as exp(-mu t), and that for eps in [~0.2,1] (in units of the local mean inter-particle separation $\bar n$), there is an explicit relationship between the decay constant mu, the timestep h of the leapfrog integrator, the softening eps, and the number of particles N in the simulation. Thus, given N and eps, it is possible to pre-compute the timestep h necessary to acheive a desired fraction of shadowable particles after a given length of simulation time. We demonstrate that a large fraction of particles remain shadowable over ~100 crossing times even if particles travel up to about 1/3 of the softening length per timestep. However, a sharp decrease in the number of shadowable particles occurs if the timestep increases to allow particles to travel further than 1/3 the softening length in one timestep, or if the softening is decreased below ~0.2$\bar n$.Comment: 4 pages, 5 figure

Graphettes: Constant-time determination of graphlet and orbit identity including (possibly disconnected) graphlets up to size 8.

Graphlets are small connected induced subgraphs of a larger graph G. Graphlets are now commonly used to quantify local and global topology of networks in the field. Methods exist to exhaustively enumerate all graphlets (and their orbits) in large networks as efficiently as possible using orbit counting equations. However, the number of graphlets in G is exponential in both the number of nodes and edges in G. Enumerating them all is already unacceptably expensive on existing large networks, and the problem will only get worse as networks continue to grow in size and density. Here we introduce an efficient method designed to aid statistical sampling of graphlets up to size k = 8 from a large network. We define graphettes as the generalization of graphlets allowing for disconnected graphlets. Given a particular (undirected) graphette g, we introduce the idea of the canonical graphette [Formula: see text] as a representative member of the isomorphism group Iso(g) of g. We compute the mapping [Formula: see text], in the form of a lookup table, from all 2k(k - 1)/2 undirected graphettes g of size k ≤ 8 to their canonical representatives [Formula: see text], as well as the permutation that transforms g to [Formula: see text]. We also compute all automorphism orbits for each canonical graphette. Thus, given any k ≤ 8 nodes in a graph G, we can in constant time infer which graphette it is, as well as which orbit each of the k nodes belongs to. Sampling a large number N of such k-sets of nodes provides an approximation of both the distribution of graphlets and orbits across G, and the orbit degree vector at each node

A Methodology to Assess Post-Launch Efforts to Counter Mobile Tactical Ballistic Missile Launchers

The Department of Defense has a requirement to quantify the force enhancement effects from various configurations of an envisioned multilayered Theater Missile Defense (TMD) system. TMD research accomplished to date has focused primarily on the pre-launch and in-flight tactical ballistic missile (TBM) operational phases while ignoring the post-launch phase during which mobile transporter-erector-launchers (TELs) are vulnerable to attack. No methodology currently exists to measure the effectiveness of various post-launch counter-TEL system configurations or their potential contribution to the overall TMD mission. This research uses the decision analysis technique of influence diagrams to model the post-launch counter-TEL process using notional variable values to approximate Operation Desert Storm counter-TEL capabilities. A probability of kill (Pk) goal is established based on its effect on the number of enemy missile launches. The study reveals that the level of enemy deception is the leading factor in post-launch counter-TEL success. No single variable under the decision maker\u27s control can be altered to achieve the goal Pk. Additional analysis shows the most promising alternative for improving the baseline Pk is to improve the accuracy of launch point determinations and reduce the initial-sensor-to-shooter timeline; the joint effect being to drastically reduce the impact of enemy deception. Economic risk assessment of post-launch counter-TEL alternatives indicates the optimal decision policy may change according to the importance placed on cost. Finally, the methodology of using a two-level full-factorial design experiment to develop a meta-model is also examined

Expression of three GnRH receptors in specific tissues in male and female sea lampreys Petromyzon marinus at three distinct life stages

Two recently cloned gonadotropin-releasing hormone (GnRH) receptors (lamprey GnRH-R-2 and lamprey GnRH-R-3) along with lamprey (l) GnRH-R-1 were shown to share similar structural features and amino acid motifs common to other vertebrate receptors. Here we report on our findings of RNA expression of these three GnRH receptors in the three major life stages (larval, parasitic, and adult phases) of the sea lamprey, Petromyzon marinus, a basal vertebrate. For each stage, we examined the expression of messenger RNA encoding the receptors in the brain, pituitary, gonad, heart, muscle, liver, eye, intestine, kidney, skin, thyroid, gill, and endostyle by RT-PCR. In adult lampreys, the spatial expression of the three receptors in the brain and pituitary was investigated by in situ hybridization. In general, the receptors were more widely expressed in adult tissues as compared to parasitic-phase tissues and least widely expressed in the larval tissues. There were noted differences in male and female lampreys in the adult and parasitic phases for all three receptors. The data showed the presence of all three receptor transcripts in brain tissues for adult and parasitic phases and all three receptor transcripts were expressed in the adult pituitaries, but not in the parasitic pituitaries. However, in the larval phase, only lGnRH-R-1 was expressed in the larval brain and pituitary. In situ hybridization revealed that lGnRH-R-2 and -3 were expressed in the pineal tissue of adult female lampreys while lGnRH-R-1 was expressed in the pineal in adult male lampreys, all restricted to the pineal pellucida. In summary, these data provide an initial comparative analysis of expression of three lamprey GnRH receptors suggesting differential regulation within males and females at three different life/reproductive stages