High Dimensional Classification with combined Adaptive Sparse PLS and Logistic Regression

Motivation: The high dimensionality of genomic data calls for the development of specific classification methodologies, especially to prevent over-optimistic predictions. This challenge can be tackled by compression and variable selection, which combined constitute a powerful framework for classification, as well as data visualization and interpretation. However, current proposed combinations lead to instable and non convergent methods due to inappropriate computational frameworks. We hereby propose a stable and convergent approach for classification in high dimensional based on sparse Partial Least Squares (sparse PLS). Results: We start by proposing a new solution for the sparse PLS problem that is based on proximal operators for the case of univariate responses. Then we develop an adaptive version of the sparse PLS for classification, which combines iterative optimization of logistic regression and sparse PLS to ensure convergence and stability. Our results are confirmed on synthetic and experimental data. In particular we show how crucial convergence and stability can be when cross-validation is involved for calibration purposes. Using gene expression data we explore the prediction of breast cancer relapse. We also propose a multicategorial version of our method on the prediction of cell-types based on single-cell expression data. Availability: Our approach is implemented in the plsgenomics R-package.Comment: 9 pages, 3 figures, 4 tables + Supplementary Materials 8 pages, 3 figures, 10 table

Pairing dynamics in particle transport

We analyze the effect of pairing on particle transport in time-dependent theories based on the Hartree-Fock-Bogoliubov (HFB) or BCS approximations. The equations of motion for the HFB density matrices are unique and the theory respects the usual conservation laws defined by commutators of the conserved quantity with the Hamiltonian. In contrast, the theories based on the BCS approximation are more problematic. In the usual formulation of TDHF+BCS, the equation of continuity is violated and one sees unphysical oscillations in particle densities. This can be ameliorated by freezing the occupation numbers during the evolution in TDHF+BCS, but there are other problems with the BCS that make it doubtful for reaction dynamics. We also compare different numerical implementations of the time-dependent HFB equations. The equations of motion for the $U$ and $V$ Bogoliubov transformations are not unique, but it appears that the usual formulation is also the most efficient. Finally, we compare the time-dependent HFB solutions with numerically exact solutions of the two-particle Schrodinger equation. Depending on the treatment of the initial state, the HFB dynamics produces a particle emission rate at short times similar to that of the Schrodinger equation. At long times, the total particle emission can be quite different, due to inherent mean-field approximation of the HFB theory.Comment: 11 pages, 9 figure

Magnetic hyperthermia in single-domain monodisperse FeCo nanoparticles: Evidences for Stoner-Wohlfarth behaviour and large losses

We report on hyperthermia measurements on a colloidal solution of 15 nm monodisperse FeCo nanoparticles (NPs). Losses as a function of the magnetic field display a sharp increase followed by a plateau, which is what is expected for losses of ferromagnetic single-domain NPs. The frequency dependence of the coercive field is deduced from hyperthermia measurement and is in quantitative agreement with a simple model of non-interacting NPs. The measured losses (1.5 mJ/g) compare to the highest of the literature, though the saturation magnetization of the NPs is well below the bulk one.Comment: 14 pages, 3 figure

Transport Model Simulations of Projectile Fragmentation Reactions at 140 MeV/nucleon

The collisions in four different reaction systems using $^{40,48}$Ca and $^{58,64}$Ni isotope beams and a Be target have been simulated using the Heavy Ion Phase Space Exploration and the Antisymmetrized Molecular Dynamics models. The present study mainly focuses on the model predictions for the excitation energies of the hot fragments and the cross sections of the final fragments produced in these reactions. The effects of various factors influencing the final fragment cross sections, such as the choice of the statistical decay code and its parameters have been explored. The predicted fragment cross sections are compared to the projectile fragmentation cross sections measured with the A1900 mass separator. At $E/A=140$ MeV, reaction dynamics can significantly modify the detection efficiencies for the fragments and make them different from the efficiencies applied to the measured data reported in the previous work. The effects of efficiency corrections on the validation of event generator codes are discussed in the context of the two models.Comment: 28 pages, 13 figure

Description of Pairing correlation in Many-Body finite systems with density functional theory

Different steps leading to the new functional for pairing based on natural orbitals and occupancies proposed in ref. [D. Lacroix and G. Hupin, arXiv:1003.2860] are carefully analyzed. Properties of quasi-particle states projected onto good particle number are first reviewed. These properties are used (i) to prove the existence of such a functional (ii) to provide an explicit functional through a 1/N expansion starting from the BCS approach (iii) to give a compact form of the functional summing up all orders in the expansion. The functional is benchmarked in the case of the picked fence pairing Hamiltonian where even and odd systems, using blocking technique are studied, at various particle number and coupling strength, with uniform and random single-particle level spacing. In all cases, a very good agreement is found with a deviation inferior to 1% compared to the exact energy.Comment: 14 pages, 9 figure

Out of equilibrium transport through an Anderson impurity: Probing scaling laws within the equation of motion approach

We study non-equilibrium electron transport through a quantum impurity coupled to metallic leads using the equation of motion technique at finite temperature T. Assuming that the interactions are taking place solely in the impurity and focusing in the infinite Hubbard limit, we compute the out of equilibrium density of states and the differential conductance G_2(T,V) to test several scaling laws. We find that G_2(T,V)/G_2(T,0) is a universal function of both eV/T_K and T/T_K, being T_K the Kondo temperature. The effect of an in plane magnetic field on the splitting of the zero bias anomaly in the differential conductance is also analyzed. For a Zeeman splitting \Delta, the computed differential conductance peak splitting depends only on \Delta/T_K, and for large fields approaches the value of 2\Delta . Besides the traditional two leads setup, we also consider other configurations that mimics recent experiments, namely, an impurity embedded in a mesoscopic wire and the presence of a third weakly coupled lead. In these cases, a double peak structure of the Kondo resonance is clearly obtained in the differential conductance while the amplitude of the highest peak is shown to decrease as \ln(eV/T_K). Several features of these results are in qualitative agreement with recent experimental observations reported on quantum dots.Comment: 9 pages, 7 figure

Ordering in the pyrochlore antiferromagnet due to Dzyaloshinsky-Moriya interactions

The Heisenberg nearest neighbour antiferromagnet on the pyrochlore (3D) lattice is highly frustrated and does not order at low temperature where spin-spin correlations remain short ranged. Dzyaloshinsky-Moriya interactions (DMI) may be present in pyrochlore compounds as is shown, and the consequences of such interactions on the magnetic properties are investigated through mean field approximation and monte carlo simulations. It is found that DMI (if present) tremendously change the low temperature behaviour of the system. At a temperature of the order of the DMI a phase transition to a long range ordered state takes place. The ordered magnetic structures are explicited for the different possible DMI which are introduced on the basis of symmetry arguments. The relevance of such a scenario for pyrochlore compounds in which an ordered magnetic structure is observed experimentally is dicussed

Particle-Number Restoration within the Energy Density Functional Formalism

We give a detailed analysis of the origin of spurious divergences and finite steps that have been recently identified in particle-number restoration calculations within the nuclear energy density functional framework. We isolate two distinct levels of spurious contributions to the energy. The first one is encoded in the definition of the basic energy density functional itself whereas the second one relates to the canonical procedure followed to extend the use of the energy density functional to multi-reference calculations. The first level of spuriosity relates to the long-known self-interaction problem and to the newly discussed self-pairing interaction process which might appear when describing paired systems with energy functional methods using auxiliary reference states of Bogoliubov or BCS type. A minimal correction to the second level of spuriosity to the multi-reference nuclear energy density functional proposed in [D. Lacroix, T. Duguet, M. Bender, arXiv:0809.2041] is shown to remove completely the anomalies encountered in particle-number restored calculations. In particular, it restores sum-rules over (positive) particle numbers that are to be fulfilled by the particle-number-restored formalism. The correction is found to be on the order of several hundreds of keVs up to about 1 MeV in realistic calculations, which is small compared to the total binding energy, but often accounts for a substantial percentage of the energy gain from particle-number restoration and is on the same energy scale as the excitations one addresses with multi-reference energy density functional methods.Comment: 37 pages, 14 figures, accepted for publication in PR