Feature Selection for Genomic Signal Processing: Unsupervised, Supervised, and Self-Supervised Scenarios

effective data mining system lies in the representation of pattern vectors. For many bioinformatic applications, data are represented as vectors of extremely high dimension. This motivates the research on feature selection. In the literature, there are plenty of reports on feature selection methods. In terms of training data types, they are divided into the unsupervised and supervised categories. In terms of selection methods, they fall into filter and wrapper categories. This paper will provide a brief overview on the state-of-the-arts feature selection methods on all these categories. Sample applications of these methods for genomic signal processing will be highlighted. This paper also describes a notion of self-supervision. A special method called vector index adaptive SVM (VIA-SVM) is described for selecting features under the self-supervision scenario. Furthermore, the paper makes use of a more powerful symmetric doubly supervised formulation, for which VIA-SVM is particularly useful. Based on several subcellular localization experiments, and microarray time course experiments, the VIA-SVM algorithm when combined with some filter-type metrics appears to deliver a substantial dimension reduction (one-order of magnitude) with only little degradation on accuracy

Hawking Radiation of Dirac Particles in an Arbitrarily Accelerating Kinnersley Black Hole

Quantum thermal effect of Dirac particles in an arbitrarily accelerating Kinnersley black hole is investigated by using the method of generalized tortoise coordinate transformation. Both the location and the temperature of the event horizon depend on the advanced time and the angles. The Hawking thermal radiation spectrum of Dirac particles contains a new term which represents the interaction between particles with spin and black holes with acceleration. This spin-acceleration coupling effect is absent from the thermal radiation spectrum of scalar particles.Comment: Revtex, 12pt, 16 pages, no figure, to appear in Gen. Rel. Grav. 34 (2002) N0.

Plane waves with negative phase velocity in Faraday chiral mediums

The propagation of plane waves in a Faraday chiral medium is investigated. Conditions for the phase velocity to be directed opposite to the direction of power flow are derived for propagation in an arbitrary direction; simplified conditions which apply to propagation parallel to the distinguished axis are also established. These negative phase-velocity conditions are explored numerically using a representative Faraday chiral medium, arising from the homogenization of an isotropic chiral medium and a magnetically biased ferrite. It is demonstrated that the phase velocity may be directed opposite to power flow, provided that the gyrotropic parameter of the ferrite component medium is sufficiently large compared with the corresponding nongyrotropic permeability parameters.Comment: accepted for publication in Phys. Rev.

Excess energy of an ultracold Fermi gas in a trapped geometry

We have analytically explored finite size and interparticle interaction corrections to the average energy of a harmonically trapped Fermi gas below and above the Fermi temperature, and have obtained a better fitting for the excess energy reported by DeMarco and Jin [Science $\textbf{285}$, 1703 (1999)]. We have presented a perturbative calculation within a mean field approximation.Comment: 8 pages, 4 figures; Accepted in European Physical Journal

Thermodynamic Measurements in a Strongly Interacting Fermi Gas

We conduct a series of measurements on the thermodynamic properties of an optically-trapped strongly interacting Fermi gas, including the energy $E$, entropy $S$, and sound velocity $c$. Our model-independent measurements of $E$ and $S$ enable a precision study of the finite temperature thermodynamics. The $E(S)$ data are directly compared to several recent predictions. The temperature in both the superfluid and normal fluid regime is obtained from the fundamental thermodynamic relation $T=\partial E/\partial S$ by parameterizing the $E(S)$ data. Our $E(S)$ data are also used to experimentally calibrate the endpoint temperatures obtained for adiabatic sweeps of the magnetic field between the ideal and strongly interacting regimes. This enables the first experimental calibration of the temperature scale used in experiments on fermionic pair condensation. Our calibration shows that the ideal gas temperature measured for the onset of pair condensation corresponds closely to the critical temperature estimated in the strongly interacting regime from the fits to our $E(S)$ data. The results are in very good agreement with recent predictions. Finally, using universal thermodynamic relations, we estimate the chemical potential and heat capacity of the trapped gas from the $E(S)$ data.Comment: 29 pages, 12 figures. To appear in JLTP online, and in the January, 2009 volum

Immersed boundary-finite element model of fluid-structure interaction in the aortic root

It has long been recognized that aortic root elasticity helps to ensure efficient aortic valve closure, but our understanding of the functional importance of the elasticity and geometry of the aortic root continues to evolve as increasingly detailed in vivo imaging data become available. Herein, we describe fluid-structure interaction models of the aortic root, including the aortic valve leaflets, the sinuses of Valsalva, the aortic annulus, and the sinotubular junction, that employ a version of Peskin's immersed boundary (IB) method with a finite element (FE) description of the structural elasticity. We develop both an idealized model of the root with three-fold symmetry of the aortic sinuses and valve leaflets, and a more realistic model that accounts for the differences in the sizes of the left, right, and noncoronary sinuses and corresponding valve cusps. As in earlier work, we use fiber-based models of the valve leaflets, but this study extends earlier IB models of the aortic root by employing incompressible hyperelastic models of the mechanics of the sinuses and ascending aorta using a constitutive law fit to experimental data from human aortic root tissue. In vivo pressure loading is accounted for by a backwards displacement method that determines the unloaded configurations of the root models. Our models yield realistic cardiac output at physiological pressures, with low transvalvular pressure differences during forward flow, minimal regurgitation during valve closure, and realistic pressure loads when the valve is closed during diastole. Further, results from high-resolution computations demonstrate that IB models of the aortic valve are able to produce essentially grid-converged dynamics at practical grid spacings for the high-Reynolds number flows of the aortic root

Simulation of the thermally induced austenitic phase transition in NiTi nanoparticles

The reverse martensitic ("austenitic") transformation upon heating of equiatomic nickel-titanium nanoparticles with diameters between 4 and 17 nm is analyzed by means of molecular-dynamics simulations with a semi-empirical model potential. After constructing an appropriate order parameter to distinguish locally between the monoclinic B19' at low and the cubic B2 structure at high temperatures, the process of the phase transition is visualized. This shows a heterogeneous nucleation of austenite at the surface of the particles, which propagates to the interior by plane sliding, explaining a difference in austenite start and end temperatures. Their absolute values and dependence on particle diameter are obtained and related to calculations of the surface induced size dependence of the difference in free energy between austenite and martensite.Comment: 6 pages, 4 figures, accepted for publication in "The European Physical Journal B

Advances in ab-initio theory of Multiferroics. Materials and mechanisms: modelling and understanding

Within the broad class of multiferroics (compounds showing a coexistence of magnetism and ferroelectricity), we focus on the subclass of "improper electronic ferroelectrics", i.e. correlated materials where electronic degrees of freedom (such as spin, charge or orbital) drive ferroelectricity. In particular, in spin-induced ferroelectrics, there is not only a {\em coexistence} of the two intriguing magnetic and dipolar orders; rather, there is such an intimate link that one drives the other, suggesting a giant magnetoelectric coupling. Via first-principles approaches based on density functional theory, we review the microscopic mechanisms at the basis of multiferroicity in several compounds, ranging from transition metal oxides to organic multiferroics (MFs) to organic-inorganic hybrids (i.e. metal-organic frameworks, MOFs)Comment: 22 pages, 9 figure

Spin dynamics in semiconductors

This article reviews the current status of spin dynamics in semiconductors which has achieved a lot of progress in the past years due to the fast growing field of semiconductor spintronics. The primary focus is the theoretical and experimental developments of spin relaxation and dephasing in both spin precession in time domain and spin diffusion and transport in spacial domain. A fully microscopic many-body investigation on spin dynamics based on the kinetic spin Bloch equation approach is reviewed comprehensively.Comment: a review article with 193 pages and 1103 references. To be published in Physics Reports

Search for a W' boson decaying to a bottom quark and a top quark in pp collisions at sqrt(s) = 7 TeV

Results are presented from a search for a W' boson using a dataset corresponding to 5.0 inverse femtobarns of integrated luminosity collected during 2011 by the CMS experiment at the LHC in pp collisions at sqrt(s)=7 TeV. The W' boson is modeled as a heavy W boson, but different scenarios for the couplings to fermions are considered, involving both left-handed and right-handed chiral projections of the fermions, as well as an arbitrary mixture of the two. The search is performed in the decay channel W' to t b, leading to a final state signature with a single lepton (e, mu), missing transverse energy, and jets, at least one of which is tagged as a b-jet. A W' boson that couples to fermions with the same coupling constant as the W, but to the right-handed rather than left-handed chiral projections, is excluded for masses below 1.85 TeV at the 95% confidence level. For the first time using LHC data, constraints on the W' gauge coupling for a set of left- and right-handed coupling combinations have been placed. These results represent a significant improvement over previously published limits.Comment: Submitted to Physics Letters B. Replaced with version publishe