Going weighted: Parameterized algorithms for cluster editing

AbstractThe goal of the Cluster Editing problem is to make the fewest changes to the edge set of an input graph such that the resulting graph is a disjoint union of cliques. This problem is NP-complete but recently, several parameterized algorithms have been proposed. In this paper, we present a number of surprisingly simple search tree algorithms for Weighted Cluster Editing assuming that edge insertion and deletion costs are positive integers. We show that the smallest search tree has size O(1.82k) for edit cost k, resulting in the currently fastest parameterized algorithm, both for this problem and its unweighted counterpart. We have implemented and compared our algorithms, and achieved promising results.11This is an extended version of two articles published in: Proc. of the 6th Asia Pacific Bioinformatics Conference, APBC 2008, in: Series on Advances in Bioinformatics and Computational Biology, vol. 5, Imperial College Press, pp. 211–220; and in: Proc. of the 2nd Conference on Combinatorial Optimization and Applications, COCOA 2008, in: LNCS, vol. 5038, Springer, pp. 289–302

High Spatial Resolution Thermal-Infrared Spectroscopy with ALES: Resolved Spectra of the Benchmark Brown Dwarf Binary HD 130948BC

We present 2.9-4.1 micron integral field spectroscopy of the L4+L4 brown dwarf binary HD 130948BC, obtained with the Arizona Lenslets for Exoplanet Spectroscopy (ALES) mode of the Large Binocular Telescope Interferometer (LBTI). The HD 130948 system is a hierarchical triple system, in which the G2V primary is joined by two co-orbiting brown dwarfs. By combining the age of the system with the dynamical masses and luminosities of the substellar companions, we can test evolutionary models of cool brown dwarfs and extra-solar giant planets. Previous near-infrared studies suggest a disagreement between HD 130948BC luminosities and those derived from evolutionary models. We obtained spatially-resolved, low-resolution (R~20) L-band spectra of HD 130948B and C to extend the wavelength coverage into the thermal infrared. Jointly using JHK photometry and ALES L-band spectra for HD 130948BC, we derive atmospheric parameters that are consistent with parameters derived from evolutionary models. We leverage the consistency of these atmospheric quantities to favor a younger age (0.50 \pm 0.07 Gyr) of the system compared to the older age (0.79 \pm 0.22 Gyr) determined with gyrochronology in order to address the luminosity discrepancy.Comment: 17 pages, 9 figures, Accepted to Ap

Convolutional LSTM Networks for Subcellular Localization of Proteins

Machine learning is widely used to analyze biological sequence data. Non-sequential models such as SVMs or feed-forward neural networks are often used although they have no natural way of handling sequences of varying length. Recurrent neural networks such as the long short term memory (LSTM) model on the other hand are designed to handle sequences. In this study we demonstrate that LSTM networks predict the subcellular location of proteins given only the protein sequence with high accuracy (0.902) outperforming current state of the art algorithms. We further improve the performance by introducing convolutional filters and experiment with an attention mechanism which lets the LSTM focus on specific parts of the protein. Lastly we introduce new visualizations of both the convolutional filters and the attention mechanisms and show how they can be used to extract biological relevant knowledge from the LSTM networks

Autonomous detection and anticipation of jam fronts from messages propagated by inter-vehicle communication

In this paper, a minimalist, completely distributed freeway traffic information system is introduced. It involves an autonomous, vehicle-based jam front detection, the information transmission via inter-vehicle communication, and the forecast of the spatial position of jam fronts by reconstructing the spatiotemporal traffic situation based on the transmitted information. The whole system is simulated with an integrated traffic simulator, that is based on a realistic microscopic traffic model for longitudinal movements and lane changes. The function of its communication module has been explicitly validated by comparing the simulation results with analytical calculations. By means of simulations, we show that the algorithms for a congestion-front recognition, message transmission, and processing predict reliably the existence and position of jam fronts for vehicle equipment rates as low as 3%. A reliable mode of operation already for small market penetrations is crucial for the successful introduction of inter-vehicle communication. The short-term prediction of jam fronts is not only useful for the driver, but is essential for enhancing road safety and road capacity by intelligent adaptive cruise control systems.Comment: Published in the Proceedings of the Annual Meeting of the Transportation Research Board 200

High Contrast Thermal Infrared Spectroscopy with ALES: The 3-4μ\mum Spectrum of κ\kappa Andromedae b

We present the first $L-$band (2.8 to 4.1~$\mu$m) spectroscopy of $\kappa$~Andromedae~b, a $\sim20~M_{\mathrm{Jup}}$ companion orbiting at $1^{\prime\prime}$ projected separation from its B9-type stellar host. We combine our Large Binocular Telescope ALES integral field spectrograph data with measurements from other instruments to analyze the atmosphere and physical characteristics of $\kappa$~And~b. We report a discrepancy of $\sim20\%$ ($2\sigma$) in the $L^{\prime}$ flux of $\kappa$~And~b when comparing to previously published values. We add an additional $L^{\prime}$ constraint using an unpublished imaging dataset collected in 2013 using LBTI/LMIRCam, the instrument in which the ALES module has been built. The LMIRCam measurement is consistent with the ALES measurement, both suggesting a fainter $L$-band scaling than previous studies. The data, assuming the flux scaling measured by ALES and LMIRCam imaging, are well fit by an L3-type brown dwarf. Atmospheric model fits to measurements spanning 0.9-4.8~$\mu$m reveal some tension with the predictions of evolutionary models, but the proper choice of cloud parameters can provide some relief. In particular, models with clouds extending to very-low pressures composed of grains $\leq1~\mu$m appear to be necessary. If the brighter $L^{\prime}$ photometry is accurate, there is a hint that sub-solar metallicity may be required.Comment: Accepted for publication in A

L-band Integral Field Spectroscopy of the HR 8799 Planetary System

Understanding the physical processes sculpting the appearance of young gas-giant planets is complicated by degeneracies confounding effective temperature, surface gravity, cloudiness, and chemistry. To enable more detailed studies, spectroscopic observations covering a wide range of wavelengths is required. Here we present the first L-band spectroscopic observations of HR 8799 d and e and the first low-resolution wide bandwidth L-band spectroscopic measurements of HR 8799 c. These measurements were facilitated by an upgraded LMIRCam/ALES instrument at the LBT, together with a new apodizing phase plate coronagraph. Our data are generally consistent with previous photometric observations covering similar wavelengths, yet there exists some tension with narrowband photometry for HR 8799 c. With the addition of our spectra, each of the three innermost observed planets in the HR 8799 system have had their spectral energy distributions measured with integral field spectroscopy covering $\sim0.9$ to $4.1~\mu\mathrm{m}$. We combine these spectra with measurements from the literature and fit synthetic model atmospheres. We demonstrate that the bolometric luminosity of the planets is not sensitive to the choice of model atmosphere used to interpolate between measurements and extrapolate beyond them. Combining luminosity with age and mass constraints, we show that the predictions of evolutionary models are narrowly peaked for effective temperature, surface gravity, and planetary radius. By holding these parameters at their predicted values, we show that more flexible cloud models can provide good fits to the data while being consistent with the expectations of evolutionary models.Comment: 19 pages, 11 figures, accepted for publication in The Astronomical Journal; added reference, updated figure 6 and table

Comparative analysis of an experimental subcellular protein localization assay and in silico prediction methods

The subcellular localization of a protein can provide important information about its function within the cell. As eukaryotic cells and particularly mammalian cells are characterized by a high degree of compartmentalization, most protein activities can be assigned to particular cellular compartments. The categorization of proteins by their subcellular localization is therefore one of the essential goals of the functional annotation of the human genome. We previously performed a subcellular localization screen of 52 proteins encoded on human chromosome 21. In the current study, we compared the experimental localization data to the in silico results generated by nine leading software packages with different prediction resolutions. The comparison revealed striking differences between the programs in the accuracy of their subcellular protein localization predictions. Our results strongly suggest that the recently developed predictors utilizing multiple prediction methods tend to provide significantly better performance over purely sequence-based or homology-based predictions

Verification of doppler coherence imaging for 2D ion velocity measurements on DIII-D

Coherence Imaging Spectroscopy (CIS) has emerged as a powerful tool for investigating complex ion phenomena in the boundary of magnetically confined plasma devices. The combination of Fourier-transform interferometry and high-resolution fast-framing cameras has made it possible to make sensitive velocity measurements that are also spatially resolved. However, this sensitivity makes the diagnostic vulnerable to environmental effects including thermal drifts, vibration, and magnetic fields that can influence the velocity measurement. Additionally, the ability to provide an absolute calibration for these geometries can be impacted by differences in the light-collection geometry between the plasma and reference light source, spectral impurities, and the presence of thin-films on in-vessel optics. This paper discusses the mitigation of these effects and demonstration that environmental effects result in less than 0.5 km/s error on the DIII-D CIS systems. A diagnostic comparison is used to demonstrate agreement between CIS and traditional spectroscopy once tomographic artifacts are accounted for.This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Fusion Energy Sciences, using the DIII-D National Fusion Facility, a DOE Office of Science user facility, under Award Nos. DEFC02-04ER54698 (DIII-D), DE-AC52-07NA27344 (LLNL), and DE-AC05-00OR22725 (ORNL). DIII-D data shown in this paper can be obtained in digital format by following the links at https://fusion.gat.com/global/D3D DMP

Proteomic analysis of the Plasmodium male gamete reveals the key role for glycolysis in flagellar motility.

BACKGROUND: Gametogenesis and fertilization play crucial roles in malaria transmission. While male gametes are thought to be amongst the simplest eukaryotic cells and are proven targets of transmission blocking immunity, little is known about their molecular organization. For example, the pathway of energy metabolism that power motility, a feature that facilitates gamete encounter and fertilization, is unknown. METHODS: Plasmodium berghei microgametes were purified and analysed by whole-cell proteomic analysis for the first time. Data are available via ProteomeXchange with identifier PXD001163. RESULTS: 615 proteins were recovered, they included all male gamete proteins described thus far. Amongst them were the 11 enzymes of the glycolytic pathway. The hexose transporter was localized to the gamete plasma membrane and it was shown that microgamete motility can be suppressed effectively by inhibitors of this transporter and of the glycolytic pathway. CONCLUSIONS: This study describes the first whole-cell proteomic analysis of the malaria male gamete. It identifies glycolysis as the likely exclusive source of energy for flagellar beat, and provides new insights in original features of Plasmodium flagellar organization

Discrete Emotion Effects on Lexical Decision Response Times

Our knowledge about affective processes, especially concerning effects on cognitive demands like word processing, is increasing steadily. Several studies consistently document valence and arousal effects, and although there is some debate on possible interactions and different notions of valence, broad agreement on a two dimensional model of affective space has been achieved. Alternative models like the discrete emotion theory have received little interest in word recognition research so far. Using backward elimination and multiple regression analyses, we show that five discrete emotions (i.e., happiness, disgust, fear, anger and sadness) explain as much variance as two published dimensional models assuming continuous or categorical valence, with the variables happiness, disgust and fear significantly contributing to this account. Moreover, these effects even persist in an experiment with discrete emotion conditions when the stimuli are controlled for emotional valence and arousal levels. We interpret this result as evidence for discrete emotion effects in visual word recognition that cannot be explained by the two dimensional affective space account