A new approach to model geomaterials with heterogeneous properties in thermo-hydro-mechanical coupled problems

The main objective of this article is to present a new approach to model coupled thermo-hydro-mechanical problems considering geomaterials with heterogeneous properties. This approach has been implemented in the software CODE_BRIGHT and it provides the possibility of considering geomaterials with a spatially correlated heterogeneous field of porosity, following a normal distribution. This spatial correlation can be isotropic or anisotropic. An important feature of this approach is that material properties such as intrinsic permeability, thermal conductivity, diffusivity, retention curve, elastic modulus or cohesion are defined as a function of porosity and, thus, they become heterogeneous with spatial correlation and, eventually, anisotropic. A validation exercise and other basic numerical examples have been carried out to illustrate the possibilities of the proposed approach. The results, which have been compared with a homogeneous case, show that considering heterogeneous fields can be relevant in different modelling problems, especially coupled thermo-hydro-mechanical problems.This research was supported by the CODE_BRIGHT Project (CIMNE, International Centre for Numerical Methods in Engineering) and by the DECOVALEX Project. The second author was supported by a CSC scholarship (No. 202008390058). The CODE_BRIGHT project is funded by a Consortium composed by SKB (Sweden), Posiva (Finland), GRS (Germany) and ANDRA (France). DECOVALEX is an international research project comprising participants from industry, government and academia, focusing on development of understanding, models and codes in complex coupled problems in sub-surface geological and engineering applications; DECOVALEX-2023 is the current phase of the project. The authors appreciate and thank the DECOVALEX-2023 Funding Organisations ANDRA, BASE, BGE, BGR, CAS, CNSC, COVRA, US DOE, ENRESA, ENSI, JAEA, KAERI, NWMO, NWS, SÚRAO, SSM and Taipower for their financial and technical support of the work described in this paper. The statements made in the paper are, however, solely those of the authors and do not necessarily reflect those of the Funding Organisations. Special thanks to I.P. Damians for facilitating the original numerical model used in his work (Damians et al., 2020), in which one of the models presented in this article has been based.Peer ReviewedPostprint (published version

Assessment of data processing to improve reliability of microarray experiments using genomic DNA reference

<p>Abstract</p> <p>Background</p> <p>Using genomic DNA as common reference in microarray experiments has recently been tested by different laboratories. Conflicting results have been reported with regard to the reliability of microarray results using this method. To explain it, we hypothesize that data processing is a critical element that impacts the data quality.</p> <p>Results</p> <p>Microarray experiments were performed in a γ-proteobacterium <it>Shewanella oneidensis</it>. Pair-wise comparison of three experimental conditions was obtained either with two labeled cDNA samples co-hybridized to the same array, or by employing <it>Shewanella </it>genomic DNA as a standard reference. Various data processing techniques were exploited to reduce the amount of inconsistency between both methods and the results were assessed. We discovered that data quality was significantly improved by imposing the constraint of minimal number of replicates, logarithmic transformation and random error analyses.</p> <p>Conclusion</p> <p>These findings demonstrate that data processing significantly influences data quality, which provides an explanation for the conflicting evaluation in the literature. This work could serve as a guideline for microarray data analysis using genomic DNA as a standard reference.</p

Convergence analysis of a block preconditioned steepest descent eigensolver with implicit deflation

Gradient-type iterative methods for solving Hermitian eigenvalue problems can be accelerated by using preconditioning and deflation techniques. A preconditioned steepest descent iteration with implicit deflation (PSD-id) is one of such methods. The convergence behavior of the PSD-id is recently investigated based on the pioneering work of Samokish on the preconditioned steepest descent method (PSD). The resulting non-asymptotic estimates indicate a superlinear convergence of the PSD-id under strong assumptions on the initial guess. The present paper utilizes an alternative convergence analysis of the PSD by Neymeyr under much weaker assumptions. We embed Neymeyr's approach into the analysis of the PSD-id using a restricted formulation of the PSD-id. More importantly, we extend the new convergence analysis of the PSD-id to a practically preferred block version of the PSD-id, or BPSD-id, and show the cluster robustness of the BPSD-id. Numerical examples are provided to validate the theoretical estimates.Comment: 26 pages, 10 figure

Biostatistical Considerations of the Use of Genomic DNA Reference in Microarrays

Using genomic DNA as common reference in microarray experiments has recently been tested by different laboratories (2, 3, 5, 7, 9, 20, 24-26). While some reported that experimental results of microarrays using genomic DNA reference conformed nicely to those obtained by cDNA: cDNA co-hybridization method, others acquired poor results. We hypothesized that these conflicting reports could be resolved by biostatistical analyses. To test it, microarray experiments were performed in a 4 proteobacterium Shewanella oneidensis. Pair-wise comparison of three experimental conditions was obtained either by direct cDNA: cDNA co-hybridization, or by indirect calculation through a Shewanella genomic DNA reference. Several major biostatistical techniques were exploited to reduce the amount of inconsistency between both methods and the results were assessed. We discovered that imposing the constraint of minimal number of replicates, logarithmic transformation and random error analyses significantly improved the data quality. These findings could potentially serve as guidelines for microarray data analysis using genomic DNA as reference

BASAR:Black-box Attack on Skeletal Action Recognition

Skeletal motion plays a vital role in human activity recognition as either an independent data source or a complement. The robustness of skeleton-based activity recognizers has been questioned recently, which shows that they are vulnerable to adversarial attacks when the full-knowledge of the recognizer is accessible to the attacker. However, this white-box requirement is overly restrictive in most scenarios and the attack is not truly threatening. In this paper, we show that such threats do exist under black-box settings too. To this end, we propose the first black-box adversarial attack method BASAR. Through BASAR, we show that adversarial attack is not only truly a threat but also can be extremely deceitful, because on-manifold adversarial samples are rather common in skeletal motions, in contrast to the common belief that adversarial samples only exist off-manifold. Through exhaustive evaluation and comparison, we show that BASAR can deliver successful attacks across models, data, and attack modes. Through harsh perceptual studies, we show that it achieves effective yet imperceptible attacks. By analyzing the attack on different activity recognizers, BASAR helps identify the potential causes of their vulnerability and provides insights on what classifiers are likely to be more robust against attack. Code is available at https://github.com/realcrane/BASAR-Black-box-Attack-on-Skeletal-Action-Recognition.Comment: Accepted in CVPR 202