A robust partial least squares method with applications

Partial least squares regression (PLS) is a linear regression technique developed to relate many regressors to one or several response variables. Robust methods are introduced to reduce or remove the effect of outlying data points. In this paper we show that if the sample covariance matrix is properly robustified further robustification of the linear regression steps of the PLS algorithm becomes unnecessary. The robust estimate of the covariance matrix is computed by searching for outliers in univariate projections of the data on a combination of random directions (Stahel-Donoho) and specific directions obtained by maximizing and minimizing the kurtosis coefficient of the projected data, as proposed by Peña and Prieto (2006). It is shown that this procedure is fast to apply and provides better results than other procedures proposed in the literature. Its performance is illustrated by Monte Carlo and by an example, where the algorithm is able to show features of the data which were undetected by previous methods

Projected health effects of realistic dietary changes to address freshwater constraints in India : a modelling study

Acknowledgements This study forms part of the Sustainable and Healthy Diets in India project supported by the Wellcome Trust's Our Planet, Our Health programme (grant number 103932). LA's PhD is funded by the Leverhulme Centre for Integrative Research on Agriculture and Health. SA is supported by a Wellcome Trust Capacity Strengthening Strategic Award-Extension phase (grant number WT084754/Z/08/A). We would like to thank Zaid Chalabi (London School of Hygiene & Tropical Medicine) for providing valuable guidance on the modelling methods.Peer reviewedPublisher PD

A confidence assessment of WCET estimates for software time randomized caches

Obtaining Worst-Case Execution Time (WCET) estimates is a required step in real-time embedded systems during software verification. Measurement-Based Probabilistic Timing Analysis (MBPTA) aims at obtaining WCET estimates for industrial-size software running upon hardware platforms comprising high-performance features. MBPTA relies on the randomization of timing behavior (functional behavior is left unchanged) of hard-to-predict events like the location of objects in memory — and hence their associated cache behavior — that significantly impact software's WCET estimates. Software time-randomized caches (sTRc) have been recently proposed to enable MBPTA on top of Commercial off-the-shelf (COTS) caches (e.g. modulo placement). However, some random events may challenge MBPTA reliability on top of sTRc. In this paper, for sTRc and programs with homogeneously accessed addresses, we determine whether the number of observations taken at analysis, as part of the normal MBPTA application process, captures the cache events significantly impacting execution time and WCET. If this is not the case, our techniques provide the user with the number of extra runs to perform to guarantee that cache events are captured for a reliable application of MBPTA. Our techniques are evaluated with synthetic benchmarks and an avionics application.The research leading to these results has received funding from the European Community’s Seventh Framework Programme [FP7/2007-2013] under the PROXIMA Project (www.proxima-project.eu), grant agreement no 611085. This work has also been partially supported by the Spanish Ministry of Science and Innovation under grant TIN2015-65316, the HiPEAC Network of Excellence, and COST Action IC1202: Timing Analysis On Code-Level (TACLe). Jaume Abella has been partially supported by the Ministry of Economy and Competitiveness under Ramon y Cajal postdoctoral fellowship number RYC-2013-14717.Peer ReviewedPostprint (author's final draft

A Bayesian space–time model for clustering areal units based on their disease trends

Population-level disease risk across a set of non-overlapping areal units varies in space and time, and a large research literature has developed methodology for identifying clusters of areal units exhibiting elevated risks. However, almost no research has extended the clustering paradigm to identify groups of areal units exhibiting similar temporal disease trends. We present a novel Bayesian hierarchical mixture model for achieving this goal, with inference based on a Metropolis-coupled Markov chain Monte Carlo ((MC) 3 ) algorithm. The effectiveness of the (MC) 3 algorithm compared to a standard Markov chain Monte Carlo implementation is demonstrated in a simulation study, and the methodology is motivated by two important case studies in the United Kingdom. The first concerns the impact on measles susceptibility of the discredited paper linking the measles, mumps, and rubella vaccination to an increased risk of Autism and investigates whether all areas in the Scotland were equally affected. The second concerns respiratory hospitalizations and investigates over a 10 year period which parts of Glasgow have shown increased, decreased, and no change in risk

ProTheRaMon : a GATE simulation framework for proton therapy range monitoring using PET imaging

Objective. This paper reports on the implementation and shows examples of the use of the ProTheRaMon framework for simulating the delivery of proton therapy treatment plans and range monitoring using positron emission tomography (PET). ProTheRaMon offers complete processing of proton therapy treatment plans, patient CT geometries, and intra-treatment PET imaging, taking into account therapy and imaging coordinate systems and activity decay during the PET imaging protocol specific to a given proton therapy facility. We present the ProTheRaMon framework and illustrate its potential use case and data processing steps for a patient treated at the Cyclotron Centre Bronowice (CCB) proton therapy center in Krakow, Poland. Approach. The ProTheRaMon framework is based on GATE Monte Carlo software, the CASToR reconstruction package and in-house developed Python and bash scripts. The framework consists of five separated simulation and data processing steps, that can be further optimized according to the user’s needs and specific settings of a given proton therapy facility and PET scanner design. Main results. ProTheRaMon is presented using example data from a patient treated at CCB and the J-PET scanner to demonstrate the application of the framework for proton therapy range monitoring. The output of each simulation and data processing stage is described and visualized. Significance. We demonstrate that the ProTheRaMon simulation platform is a high-performance tool, capable of running on a computational cluster and suitable for multi-parameter studies, with databases consisting of large number of patients, as well as different PET scanner geometries and settings for range monitoring in a clinical environment. Due to its modular structure, the ProTheRaMon framework can be adjusted for different proton therapy centers and/or different PET detector geometries. It is available to the community via github (Borys et al 2022)

Structure of a sheared soft-disk fluid from a nonequilibrium potential

The distortion of structure of a simple, inverse-12, soft-disk fluid undergoing two-dimensional plane Couette flow was studied by nonequilibrium molecular dynamics (NEMD) simulation and by equilibrium Monte Carlo (MC) simulation with a nonequilibrium potential, under which the equilibrium structure of the fluid is that of the nonequilibrium fluid. Extension of the iterative predictor-corrector method of [Reatto Phys. Rev. A 33 3451 (1986)] was used to extract the nonequilibrium potential with the structure input from the NEMD simulation. Very good agreement for the structural properties and pressure tensor generated by the NEMD and MC simulation methods was found, thus providing the evidence that nonequilibrium liquid structure can be accurately reproduced via simple equilibrium simulations or theories using a properly chosen nonequilibrium potential. The method developed in the present study and numerical results presented here can be used to guide and test theoretical developments, providing them with the "experimental" results for the nonequilibrium potential.open2

Bayesian logistic regression for presence-only data

Presence-only data are referred to situations in which a censoring mechanism acts on a binary response which can be partially observed only with respect to one outcome, usually denoting the \textit{presence} of an attribute of interest. A typical example is the recording of species presence in ecological surveys. In this work a Bayesian approach to the analysis of presence-only data based on a two levels scheme is presented. A probability law and a case-control design are combined to handle the double source of uncertainty: one due to censoring and the other one due to sampling. In the paper, through the use of a stratified sampling design with non-overlapping strata, a new formulation of the logistic model for presence-only data is proposed. In particular, the logistic regression with linear predictor is considered. Estimation is carried out with a new Markov Chain Monte Carlo algorithm with data augmentation, which does not require the a priori knowledge of the population prevalence. The performance of the new algorithm is validated by means of extensive simulation experiments using three scenarios and comparison with optimal benchmarks. An application to data existing in literature is reported in order to discuss the model behaviour in real world situations together with the results of an original study on termites occurrences data

Processing of false belief passages during natural story comprehension: An fMRI study

The neural correlates of theory of mind (ToM) are typically studied using paradigms which require participants to draw explicit, task-related inferences (e.g., in the false belief task). In a natural setup, such as listening to stories, false belief mentalizing occurs incidentally as part of narrative processing. In our experiment, participants listened to auditorily presented stories with false belief passages (implicit false belief processing) and immediately after each story answered comprehension questions (explicit false belief processing), while neural responses were measured with functional magnetic resonance imaging (fMRI). All stories included (among other situations) one false belief condition and one closely matched control condition. For the implicit ToM processing, we modeled the hemodynamic response during the false belief passages in the story and compared it to the hemodynamic response during the closely matched control passages. For implicit mentalizing, we found activation in typical ToM processing regions, that is the angular gyrus (AG), superior medial frontal gyrus (SmFG), precuneus (PCUN), middle temporal gyrus (MTG) as well as in the inferior frontal gyrus (IFG) billaterally. For explicit ToM, we only found AG activation. The conjunction analysis highlighted the left AG and MTG as well as the bilateral IFG as overlapping ToM processing regions for both implicit and explicit modes. Implicit ToM processing during listening to false belief passages, recruits the left SmFG and billateral PCUN in addition to the “mentalizing network” known form explicit processing tasks

JOINTLY MODELING CONTINUOUS AND BINARY OUTCOMES FOR BOOLEAN OUTCOMES: AN APPLICATION TO MODELING HYPERTENSION

Binary outcomes defined by logical (Boolean) and or or operations on original continuous and discrete outcomes arise commonly in medical diagnoses and epidemiological research. In this manuscript,we consider applying the “or” operator to two continuous variables above a threshold and a binary variable, a setting that occurs frequently in the modeling of hypertension. Rather than modeling the resulting composite outcome defined by the logical operator, we present a method that models the original outcomes thus utilizing all information in the data, yet continues to yield conclusions on the composite scale. A stratified propensity score adjustment is proposed to account for confounding variables. A Mantel-Haenszel style combination of strata-specific odds ratios is proposed to evaluate a risk factor. The benefits of the proposed approach include easy handling of missing data and the ability to estimate the correlations between the original outcomes. We emphasize that the model retains the ability to evaluate odds ratios on the simpler and more easily interpreted composite scale. The approach is evaluated by Monte Carlo simulations. An example of the analysis of the impact of sleep disordered breathing on a standard composite hypertension measure, based on blood pressure measurements and medication usage,is included