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Search · four archives
23 papers · ranked by Valyu relevance
Fulvia Mecatti, Charalambos Sismanidis, Emanuela Furfaro, Pier Luigi Conti
'Pier Luigi Conti'] A new class of sampling strategies is proposed that can be applied to population-based surveys targeting a rare trait that is unevenly spread over an area of interest. Our proposal is characterised by the ability to tailor the data collection to specific features and challenges of the survey at…
Kundu, Sampurna, Jayant Jha, Subir Kumar Bhandari
We propose an adaptive sequential framework for testing two simple hypotheses that analytically ensures finite exposure to the less effective treatment. Our proposed procedure employs a likelihood ratio–driven adaptive allocation rule, dynamically concentrating sampling effort on the superior population while…
Sarba Kundu, Jayant Jha, Subir Kumar Bhandari
Design Authors: ['Sarba Kundu' 'Jayant Jha' 'Subir Kumar Bhandari'] We revisit the procedure proposed by Bhandari et al. (2009) in the context of twotreatment clinical trials, with the objective of minimizing the applications of a less effective drug to the least number of patients. Our focus is on an adaptive…
Michel H Hof, Anita CJ Ravelli, Aeilko H Zwinderman
Background In population-based observational studies, non-participation and delayed response to the invitation to participate are complications that often arise during the recruitment of a sample. When both are not properly dealt with, the composition of the sample can be different from the desired composition.…
Yanqing Yi, Su-Fen Yang
protection zone during the COVID-19 pandemic, travellers were sampled to test for COVID infection at airports or harbours with limited PCR boxes and health workers were screened to prevent the spread of the disease in health care facilities. With limited PCR boxes or resources for testing, the question is which…
Nick Crang, Orlando Contreras-López, Remi-André Olsen, Fahri Hasby
Oxford Nanopore Technology (ONT) has developed a long-read sequencing method known as “adaptive” or “Read Until” sequencing. Unlike Illumina sequencing, this ONT read data is available in real-time during the run, rather than only being available when the sequencing run is complete and it focuses on a specified region…
Sebastian Krumscheid, Per Pettersson
Quantifyingthe effect of uncertainties in computationally complex systems where only point evaluations in the stochastic domain but no regularity conditions are available is limited to sampling-based techniques. This work presents an adaptive sequential stratification estimation method that uses Latin Hypercube…
Félix Mercier, Nizar Bouhlel, Angelina El Ghaziri, Joseph Ly Vu + 2 more
Digital phenotyping is rapidly advancing, generating increasing amounts of data, particularly in the case of temporal monitoring. We propose an adaptive sampling method that optimizes sampling, thereby reducing costs associated with data production, processing, and storage. The proposed method is based on Bayesian…
Lukas Weilguny, Nicola De Maio, Rory Munro, Charlotte Manser + 3 more
One particularly promising feature of nanopore sequencing is the ability to reject reads, enabling real-time selection of molecules without complex sample preparation. This is based on the idea of deciding whether a molecule warrants full sequencing depending on reading a small initial part. Previously, such decisions…
Luca Martino, Francisco Louzada
The adaptive rejection sampling (ARS) algorithm is a universal random generator for drawing samples efficiently from a univariate log-concave target probability density function (pdf). ARS generates independent samples from the target via rejection sampling with high acceptance rates. Indeed, ARS yields a sequence of…
Isabel S. Naarman-de Vries, Enio Gjerga, Catharina L.A. Gandor, Christoph Dieterich
ONT long-read sequencing provides real-time monitoring and controlling of individual nanopores. Adaptive sampling enriches or depletes specific sequences in Nanopore DNA sequencing, but was not applicable to direct sequencing of RNA so far. Here, we identify essential parameter settings for direct RNA sequencing (DRS).…
Jens-Uwe Ulrich, Lennard Epping, Tanja Pilz, Birgit Walther + 3 more
Bacterial plasmids play a major role in the spread of antibiotic resistance genes. However, their characterization via DNA sequencing suffers from the low abundance of plasmid DNA in those samples. Although sample preparation methods can enrich the proportion of plasmid DNA before sequencing, these methods are…
Finlay Clark, Graeme Robb, Daniel Cole, Julien Michel
Alchemical absolute binding free energy (ABFE) calculations have substantial potential in drug discovery, but are often prohibitively computationally expensive. To unlock their potential, efficient automated ABFE workflows are required to reduce both computational cost and human intervention. We present a…
Peter Norwood, Marie Davidian, Eric Laber
Response-adaptive randomization (RAR) has been studied extensively in conventional, single-stage clinical trials, where it has been shown to yield ethical and statistical benefits, especially in trials with many treatment arms. However, RAR and its potential benefits are understudied in sequential multiple assignment…
Authors not listed
Accurate and efficient calculation of alchemical free energies is a critical challenge in computational chemistry, frequently hindered by the inherent limitations of conventional Thermodynamic Integration (TI) methods. These limitations include poor phasespace overlap between discrete alchemical states, inefficient…
Elizabeth G. Ryan, Julie Bruce, Andrew J. Metcalfe, Nigel Stallard + 4 more
'Sarah E. Lamb' 'Kert Viele' 'Duncan Young' 'Simon Gates'] Background Bayesian adaptive designs can improve the efficiency of trials, and lead to trials that can produce high quality evidence more quickly, with fewer patients and lower costs than traditional methods. The aim of this work was to determine how Bayesian…
Jens-Uwe Ulrich, Ahmad Lutfi, Kilian Rutzen, Bernhard Y. Renard
Nanopore sequencers allow targeted sequencing of interesting nucleotide sequences by rejecting other sequences from individual pores. This feature facilitates the enrichment of low-abundant sequences by depleting overrepresented ones in-silico. Existing tools for adaptive sampling either apply signal alignment, which…
Alan Benson, Nial Friel
We consider the problem of Bayesian inference for changepoints where the number and position of the changepoints are both unknown. In particular, we consider product partition models where it is possible to integrate out model parameters for the regime between each changepoint, leaving a posterior distribution over a…
Ji Hyun Bak, Jonathan W. Pillow
Psychometric functions (PFs) quantify how external stimuli affect behavior and play an important role in building models of sensory and cognitive processes. Adaptive stimulus selection methods seek to select stimuli that are maximally informative about the PF given data observed so far in an experiment and thereby…
Noora Aho, Gerrit Groenhof, Pavel Buslaev
Molecular dynamics (MD) simulations are widely applied to estimate absolute binding free energies of protein-ligand and protein-protein complexes. A routinely used method for binding free energy calculations with MD is umbrella sampling (US), which calculates the potential of mean force (PMF) along a single reaction…
Zhimian Hao, Chonghuan Zhang, Alexei Lapkin
We propose a workflow for reduction in the time required for data generation during generation of statistical digital twins. This methodology is particularly relevant for real-world engineering problems when data generation is expensive. A prerequisite for building surrogates is sufficient input/output data, whereas…
Sterling Baird, Jason R. Hall, Taylor D. Sparks
Would you rather search for a line inside a cube or a point inside a square? Physics-based simulations and wet-lab experiments often have symmetries (degeneracies) that allow reducing problem dimensionality or search space, but constraining these degeneracies is often unsupported or difficult to implement in many…
Sterling Baird, Jason R. Hall, Taylor D. Sparks
Would you rather search for a line inside a cube or a point inside a square? This type of solution degeneracy often exists in physics-based simulations and wet-lab experiments, but constraining these degeneracies is often unsupported or difficult to implement in many optimization packages, requiring additional time and…