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J. Ramirez

Publications and source records attributed to J. Ramirez.

14 recordsLinked to original sources

Tunable mesoscopic numerical model for bacterial biofilms

We present a tunable mesoscale model to provide a basis for future rheological calculations of of bacterial biofilms, explicitly incorporating reversible crosslinking within the extracellular polymeric substance (EPS) matrix. Using a Dissipative Particle Dynamics framework combined with a Gillespie-inspired algorithm, bonds between polymers and bacteria dynamically form and break, capturing the intrinsically evolving nature of the network. We show that biofilm structure is governed by a competition between polymer-polymer and polymer-bacteria crosslinks, controlled by binding energy, linker availability, and bond stiffness and provide a minimal model that helps to understand the competition between both species.

physics.comp-ph

Comparison of Nb and Ta Pentoxide Loss Tangents for Superconducting Quantum Devices

Superconducting transmon qubits are commonly made with thin-film Nb wiring, but recent studies have shown increased performance with Ta wiring. In this work, we compare the resonator-induced single photon, millikelvin dielectric loss for pentoxides of Nb (Nb2O5) and Ta (Ta2O5) in order to further understand limiting losses in qubits. Nb and Ta pentoxides of three thicknesses are deposited via pulsed laser deposition onto identical coplanar waveguide resonators. The two-level system (TLS) loss in Nb2O5 is determined to be about 30% higher than that of Ta2O5. This work indicates that qubits with Nb wiring are affected by higher loss arising from the native pentoxide itself, likely in addition to the presence of suboxides, which are largely absent in Ta.

quant-ph

Unraveling the Autism spectrum heterogeneity: Insights from ABIDE I Database using data/model-driven permutation testing approaches

Autism Spectrum Condition (ASC) is a neurodevelopmental condition characterized by impairments in communication, social interaction and restricted or repetitive behaviors. Extensive research has been conducted to identify distinctions between individuals with ASC and neurotypical individuals. However, limited attention has been given to comprehensively evaluating how variations in image acquisition protocols across different centers influence these observed differences. This analysis focuses on structural magnetic resonance imaging (sMRI) data from the Autism Brain Imaging Data Exchange I (ABIDE I) database, evaluating subjects' condition and individual centers to identify disparities between ASC and control groups. Statistical analysis, employing permutation tests, utilizes two distinct statistical mapping methods: Statistical Agnostic Mapping (SAM) and Statistical Parametric Mapping (SPM). Results reveal the absence of statistically significant differences in any brain region, attributed to factors such as limited sample sizes within certain centers, noise effects and the problem of multicentrism in a heterogeneous condition such as autism. This study indicates limitations in using the ABIDE I database to detect structural differences in the brain between neurotypical individuals and those diagnosed with ASC. Furthermore, results from the SAM mapping method show greater consistency with existing literature.

q-bio.QM

Statistical Agnostic Regression: a machine learning method to validate regression models

Regression analysis is a central topic in statistical modeling, aimed at estimating the relationships between a dependent variable, commonly referred to as the response variable, and one or more independent variables, i.e., explanatory variables. Linear regression is by far the most popular method for performing this task in various fields of research, such as data integration and predictive modeling when combining information from multiple sources. Classical methods for solving linear regression problems, such as Ordinary Least Squares (OLS), Ridge, or Lasso regressions, often form the foundation for more advanced machine learning (ML) techniques, which have been successfully applied, though without a formal definition of statistical significance. At most, permutation or analyses based on empirical measures (e.g., residuals or accuracy) have been conducted, leveraging the greater sensitivity of ML estimations for detection. In this paper, we introduce Statistical Agnostic Regression (SAR) for evaluating the statistical significance of ML-based linear regression models. This is achieved by analyzing concentration inequalities of the actual risk (expected loss) and considering the worst-case scenario. To this end, we define a threshold that ensures there is sufficient evidence, with a probability of at least $1-\eta$, to conclude the existence of a linear relationship in the population between the explanatory (feature) and the response (label) variables. Simulations demonstrate the ability of the proposed agnostic (non-parametric) test to provide an analysis of variance similar to the classical multivariate $F$-test for the slope parameter, without relying on the underlying assumptions of classical methods. Moreover, the residuals computed from this method represent a trade-off between those obtained from ML approaches and the classical OLS.

stat.ML

A hypothesis-driven method based on machine learning for neuroimaging data analysis

There remains an open question about the usefulness and the interpretation of Machine learning (MLE) approaches for discrimination of spatial patterns of brain images between samples or activation states. In the last few decades, these approaches have limited their operation to feature extraction and linear classification tasks for between-group inference. In this context, statistical inference is assessed by randomly permuting image labels or by the use of random effect models that consider between-subject variability. These multivariate MLE-based statistical pipelines, whilst potentially more effective for detecting activations than hypotheses-driven methods, have lost their mathematical elegance, ease of interpretation, and spatial localization of the ubiquitous General linear Model (GLM). Recently, the estimation of the conventional GLM has been demonstrated to be connected to an univariate classification task when the design matrix is expressed as a binary indicator matrix. In this paper we explore the complete connection between the univariate GLM and MLE \emph{regressions}. To this purpose we derive a refined statistical test with the GLM based on the parameters obtained by a linear Support Vector Regression (SVR) in the \emph{inverse} problem (SVR-iGLM). Subsequently, random field theory (RFT) is employed for assessing statistical significance following a conventional GLM benchmark. Experimental results demonstrate how parameter estimations derived from each model (mainly GLM and SVR) result in different experimental design estimates that are significantly related to the predefined functional task. Moreover, using real data from a multisite initiative the proposed MLE-based inference demonstrates statistical power and the control of false positives, outperforming the regular GLM.

stat.ML

Uncertainty-driven ensembles of deep architectures for multiclass classification. Application to COVID-19 diagnosis in chest X-ray images

Respiratory diseases kill million of people each year. Diagnosis of these pathologies is a manual, time-consuming process that has inter and intra-observer variability, delaying diagnosis and treatment. The recent COVID-19 pandemic has demonstrated the need of developing systems to automatize the diagnosis of pneumonia, whilst Convolutional Neural Network (CNNs) have proved to be an excellent option for the automatic classification of medical images. However, given the need of providing a confidence classification in this context it is crucial to quantify the reliability of the model's predictions. In this work, we propose a multi-level ensemble classification system based on a Bayesian Deep Learning approach in order to maximize performance while quantifying the uncertainty of each classification decision. This tool combines the information extracted from different architectures by weighting their results according to the uncertainty of their predictions. Performance of the Bayesian network is evaluated in a real scenario where simultaneously differentiating between four different pathologies: control vs bacterial pneumonia vs viral pneumonia vs COVID-19 pneumonia. A three-level decision tree is employed to divide the 4-class classification into three binary classifications, yielding an accuracy of 98.06% and overcoming the results obtained by recent literature. The reduced preprocessing needed for obtaining this high performance, in addition to the information provided about the reliability of the predictions evidence the applicability of the system to be used as an aid for clinicians.

eess.IV

Spectral Clustering: An empirical study of Approximation Algorithms and its Application to the Attrition Problem

Clustering is the problem of separating a set of objects into groups (called clusters) so that objects within the same cluster are more similar to each other than to those in different clusters. Spectral clustering is a now well-known method for clustering which utilizes the spectrum of the data similarity matrix to perform this separation. Since the method relies on solving an eigenvector problem, it is computationally expensive for large datasets. To overcome this constraint, approximation methods have been developed which aim to reduce running time while maintaining accurate classification. In this article, we summarize and experimentally evaluate several approximation methods for spectral clustering. From an applications standpoint, we employ spectral clustering to solve the so-called attrition problem, where one aims to identify from a set of employees those who are likely to voluntarily leave the company from those who are not. Our study sheds light on the empirical performance of existing approximate spectral clustering methods and shows the applicability of these methods in an important business optimization related problem.

cs.LG

A New Comprehensive 2-D Model of the Point Spread Functions of the XMM-Newton EPIC Telescopes : Spurious Source Suppression and Improved Positional Accuracy

We describe here a new full 2-D parameterization of the PSFs of the three XMM-Newton EPIC telescopes as a function of instrument, energy, off-axis angle and azimuthal angle, covering the whole field-of-view of the three EPIC detectors. It models the general PSF envelopes, the primary and secondary spokes, their radial dependencies, and the large-scale azimuthal variations. This PSF model has been constructed via the stacking and centering of a large number of bright, but not significantly piled-up point sources from the full field-of-view of each EPIC detector, and azimuthally filtering the resultant PSF envelopes to form the spoke structures and the gross azimuthal shapes observed. This PSF model is available for use within the XMM-Newton Science Analysis System via the usage of Current Calibration Files XRTi_XPSF_0011.CCF and later versions. Initial source-searching tests showed substantial reductions in the numbers of spurious sources being detected in the wings of bright point sources. Furthermore, we have uncovered a systematic error in the previous PSF system, affecting the entire mission to date, whereby returned source RA and Dec values are seen to vary sinusoidally about the true position (amplitude ~0.8") with source azimuthal position. The new PSF system is now available and is seen as a major improvement with regard to the detection of spurious sources. The new PSF also largely removes the discovered astrometry error and is seen to improve the positional accuracy of EPIC. The modular nature of the PSF system allows for further refinements in the future.

astro-ph.IM

Long-term magnetic field monitoring of the Sun-like star Ksi Bootis A

Phase-resolved observations of the solar-type star Ksi Bootis A were obtained using the NARVAL spectropolarimeter at the Telescope Bernard Lyot (Pic du Midi, France) during years 2007, 2008, 2009 and 2010. The data sets enable us to study both the rotational modulation and the long-term evolution of various magnetic and activity tracers. Here, we focus on the large-scale photospheric magnetic field (reconstructed by Zeeman-Doppler Imaging), the Zeeman broadening of the FeI 846.84 nm magnetic line, and the chromospheric CaII H and H alpha emission.

astro-ph.SR

Toroidal versus poloidal magnetic fields in Sun-like stars: a rotation threshold

From a set of stellar spectropolarimetric observations, we report the detection of surface magnetic fields in a sample of four solar-type stars, namely HD 73350, HD 76151, HD 146233 (18 Sco) and HD 190771. Assuming that the observed variability of polarimetric signal is controlled by stellar rotation, we establish the rotation periods of our targets, with values ranging from 8.8 d (for HD 190771) to 22.7 d (for HD 146233). Apart from rotation, fundamental parameters of the selected objects are very close to the Sun's, making this sample a practical basis to investigate the specific impact of rotation on magnetic properties of Sun-like stars. We reconstruct the large-scale magnetic geometry of the targets as a low-order (l<10) spherical harmonics expansion of the surface magnetic field. From the set of magnetic maps, we draw two main conclusions. (a) The magnetic energy of the large-scale field increases with rotation rate. The increase of chromospheric emission with the mean magnetic field is flatter than observed in the Sun. Since the chromospheric flux is also sensitive to magnetic elements smaller than those contributing to the polarimetric signal, this observation suggests that a larger fraction of the surface magnetic energy is stored in large scales as rotation increases. (b) Whereas the magnetic field is mostly poloidal for low rotation rates, more rapid rotators host a large-scale toroidal component in their surface field. From our observations, we infer that a rotation period lower than ~12 days is necessary for the toroidal magnetic energy to dominate over the poloidal component.

astro-ph

Magnetism in Herbig Ae/Be stars and the link to the Ap/Bp stars

Among the A/B stars, about 5% host large-scale organised magnetic fields. These magnetic stars show also abundance anomalies in their spectra, and are therefore called the magnetic Ap/Bp stars. Most of these stars are also slow rotators compared to the normal A and B stars. Today, one of the greatest challenges concerning the Ap/Bp stars is to understand the origin of their slow rotation and their magnetic fields. The favoured hypothesis for the latter is that the fields are fosils, which implies that the magnetic fields subsist throughout the different evolutionary phases, and in particular during the pre-main sequence phase. The existence of magnetic fields at the pre-main sequence phase is also required to explain the slow rotation of Ap/Bp stars. During the last 3 years we performed a spectropolarimetric survey of the Herbig Ae/Be stars in the field and in young clusters, in order to investigate their magnetism and rotation. These investigations have resulted in the detection and/or confirmation of magnetic fields in 8 Herbig Ae/Be stars, ranging in mass from 2 to nearly 15 solar masses. In this paper I will present the results of our survey, as well as their implications for the origin and evolution of the magnetic fields and rotation of the A and B stars.

astro-ph

Magnetism in pre-MS intermediate-mass stars and the fossil field hypothesis

Today, one of the greatest challenges concerning the Ap/Bp stars is to understand the origin of their slow rotation and their magnetic fields. The favoured hypothesis for the latter is the fossil field, which implies that the magnetic fields subsist throughout the different evolutionary phases, and in particular during the pre-main sequence phase. The existence of magnetic fields at the pre-main sequence phase is also required to explain the slow rotation of Ap/Bp stars. However, until recently, essentially no information was available about the magnetic properties of intermediate-mass pre-main sequence stars, the so-called Herbig Ae/Be stars. The new high-resolution spectropolarimeter ESPaDOnS, installed in 2005 at the Canada-France-Hawaii telescope, provided the capability necessary to perform surveys of the Herbig Ae/Be stars in order to investigate their magnetism and rotation. These investigations have resulted in the detection and/or confirmation of magnetic fields in 8 Herbig Ae/Be stars, ranging in mass from 2 to nearly 15 solar masses. In this contribution I will present the results of our survey, as well as their implications for the origin and evolution of the magnetic fields and rotation.

astro-ph

A decoupled system of hyperbolic equations for linearized cosmological perturbations

A decoupled system of hyperbolic partial differential equations for linear perturbations around any spatially flat FRW universe is obtained for a wide class of perturbations. The considered perturbing energy momentum-tensors can be expressed as the sum of the perturbation of a minimally coupled scalar field plus an arbitrary (weak) energy-momentum tensor which is covariantly conserved with respect to the background. The key ingredient in obtaining the decoupling of the equations is the introduction of a new covariant gauge which plays a similar role as harmonic gauge does for perturbations around Minkowski space-time. The case of universes satysfying a linear equation of state is discussed in particular, and closed analytic expressions for the retarded Green's functions solving the de Sitter, dust and radiation dominated cases are given.

gr-qc

Generation of gravitational waves by generic sources in de Sitter space-time

We study the generation of gravitational radiation by sources moving in the de Sitter background. Exploiting the maximal symmetry and the conformal flatness of de Sitter space-time we prove that the derivation of this gravitational radiation can be done along the same lines as in Minkowski space-time. A gauge is chosen in which all the physical and unphysical modes of the graviton are those of a minimally coupled massless scalar field in de Sitter space-time and a massless field in Minkowski space-time. The graviton retarded Green's function and the Schwinger commutator function are computed in this gauge using Quantum Field Theory techniques. We obtain closed formulae for the spectral decomposition in frequencies of the linaearized gravitational field produced by the source, in terms of a suitable spectral decomposition of the source energy-momentum tensor. This spectral decomposition is dictated by the free (sourceless) gravitational wave modes in the de Sitter background

astro-ph