A Coverage Criterion for Spaced Seeds and its Applications to Support Vector Machine String Kernels and k-Mer Distances

Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower misclassification rate when used with Support Vector Machines (SVMs) (On-odera and Shibuya, 2013), We confirm by independent experiments these two results, and propose in this article to use a coverage criterion (Benson and Mak, 2008, Martin, 2013, Martin and No{\'e}, 2014), to measure the seed efficiency in both cases in order to design better seed patterns. We show first how this coverage criterion can be directly measured by a full automaton-based approach. We then illustrate how this criterion performs when compared with two other criteria frequently used, namely the single-hit and multiple-hit criteria, through correlation coefficients with the correct classification/the true distance. At the end, for alignment-free distances, we propose an extension by adopting the coverage criterion, show how it performs, and indicate how it can be efficiently computed.Comment: http://online.liebertpub.com/doi/abs/10.1089/cmb.2014.017

Kernel methods for detecting coherent structures in dynamical data

We illustrate relationships between classical kernel-based dimensionality reduction techniques and eigendecompositions of empirical estimates of reproducing kernel Hilbert space (RKHS) operators associated with dynamical systems. In particular, we show that kernel canonical correlation analysis (CCA) can be interpreted in terms of kernel transfer operators and that it can be obtained by optimizing the variational approach for Markov processes (VAMP) score. As a result, we show that coherent sets of particle trajectories can be computed by kernel CCA. We demonstrate the efficiency of this approach with several examples, namely the well-known Bickley jet, ocean drifter data, and a molecular dynamics problem with a time-dependent potential. Finally, we propose a straightforward generalization of dynamic mode decomposition (DMD) called coherent mode decomposition (CMD). Our results provide a generic machine learning approach to the computation of coherent sets with an objective score that can be used for cross-validation and the comparison of different methods

Pattern formation in binary fluid mixtures induced by short-range competing interactions

Molecular dynamics simulations and integral equation calculations of a simple equimolar mixture of diatomic molecules and monomers interacting via attractive and repulsive short-range potentials show the existence of pattern formation (microheterogeneity), mostly due to depletion forces away from the demixing region. Effective site-site potentials extracted from the pair correlation functions using an inverse Monte Carlo approach and an integral equation inversion procedure exhibit the features characteristic of a short-range attractive and long-range repulsive potential. When charges are incorporated into the model, this becomes a coarse grained representation of a room temperature ionic liquid, and as expected, intermediate range order becomes more pronounced and stable

Surface tension of the Widom-Rowlinson model

11 pags., 5 figs., 3 tabs.We consider the computation of the surface tension of the fluid-fluid interface for the Widom-Rowlinson [J. Chem. Phys. 52, 1670 (1970)] binary mixture from direct simulation of the inhomogeneous system. We make use of the standard mechanical route, in which the surface tension follows from the computation of the normal and tangential components of the pressure tensor of the system. In addition to the usual approach, which involves simulations of the inhomogeneous system in the canonical ensemble, we also consider the computation of the surface tension in an ensemble where the pressure perpendicular (normal) to the planar interface is kept fixed. Both approaches are seen to provide consistent values of the interfacial tension. The issue of the system-size dependence of the surface tension is addressed. In addition, simulations of the fluid-fluid coexistence properties of the mixture are performed in the semigrand canonical ensemble. Our results are compared with existing data of the Widom-Rowlinson mixture and are also examined in the light of the vapor-liquid equilibrium of the thermodynamically equivalent one-component penetrable sphere model. © 2007 American Institute of Physics.Financial support is due to the Spanish Dirección General de Investigación Project Nos. FIS2004-06627-C02-01 E.d.M. and FIS2004-02954-C03-01 N.G.A. and from Universidad de Huelva and Junta de Andalucía. Additional funding from the Dirección General de Universidades e Investigación Comunidad de Madrid, Spain under the MOSSNOHO-CM program Grant No. S0505/ESP/0299 and from the Engineering and Physical Sciences EPSRC of the UK Grant Nos. GR/N20317, GR/N03358, GR/N35991, GR/R09497, and EP/E016340, the Joint Research Equipment Initiative JREI GR/M94427, and the Royal Society Wolfson Foundation refurbishment grant is also acknowledged. Finally we are grateful to the Royal Society for the award of a International Short Visit grant which has facilitated the collaborative work

Blood inflammatory indices in goats around kidding

AbstractThe transition period of goats is often characterized by serious metabolic problems, mainly before parturition. These troubles are related to negative energy balance status, however all causes are not totally defined. To improve the knowledge about pathogenesis in this phase we have monitored the changes of some blood indices of lipomobilization and inflammation. Six blood samples were collected from 10 primiparous and 25 multiparous "Camosciata delle Alpi" goats after morning milking. Samples were collected around 20 and 7 days before parturition and on days 0, 3, 6 and 12 of lactation. Albumin, total protein, haptoglobin, ceruloplasmin, total cholesterol, NEFA, β-OH-butyrate (BHB), Ca, Mg and Zn were determined. Goats were grouped according to their BHB level before parturition: low (≤0.6 mmol/l; LOB), average (0.6÷1.09; AVB) and high (≥1.09 mmol/l; HIB) level. Furthermore, the AVB group was divided according to plasma haptoglobin level before parturition: low (<0.5 g/l) or high. The statistical..

Conformation Dynamics

This article surveys the present state of the transfer operator approach to the effective dynamics of metastable dynamical systems and the variety of algorithms associated with it

Spin injection in Silicon at zero magnetic field

In this letter, we show efficient electrical spin injection into a SiGe based \textit{p-i-n} light emitting diode from the remanent state of a perpendicularly magnetized ferromagnetic contact. Electron spin injection is carried out through an alumina tunnel barrier from a Co/Pt thin film exhibiting a strong out-of-plane anisotropy. The electrons spin polarization is then analysed through the circular polarization of emitted light. All the light polarization measurements are performed without an external applied magnetic field \textit{i.e.} in remanent magnetic states. The light polarization as a function of the magnetic field closely traces the out-of-plane magnetization of the Co/Pt injector. We could achieve a circular polarization degree of the emitted light of 3 % at 5 K. Moreover this light polarization remains almost constant at least up to 200 K.Comment: accepted in AP

Markov State Models Based on Milestoning

Markov State Models (MSMs) have become the tool of choice to analyze large amounts of molec- ular dynamics data by approximating them as a Markov jump process between suitably predefined states. Here we investigate ”Core Set MSMs”, a new type of MSMs that builds on metastable core sets acting as milestones for tracing the rare event kinetics. We present a thorough analysis of Core Set MSMs based on the existing milestoning framework, Bayesian estimation methods and Transi- tion Path Theory (TPT). As a result, Core Set MSMs can now be used to extract phenomenological rate constants between the metastable sets of the system and to approximate the evolution of certain key observables. The performance of Core Set MSMs in comparison to standard MSMs is analyzed and illustrated on a model potential and the torsion angle dynamics of Alanine dipeptide