Calculating Expected Value of Sample Information Adjusting for Imperfect Implementation

Background The expected value of sample information (EVSI) calculates the value of collecting additional information through a research study with a given design. However, standard EVSI analyses do not account for the slow and often incomplete implementation of the treatment recommendations that follow research. Thus, standard EVSI analyses do not correctly capture the value of the study. Previous research has developed measures to calculate the research value while adjusting for implementation challenges, but estimating these measures is a challenge. Methods Based on a method that assumes the implementation level is related to the strength of evidence in favor of the treatment, 2 implementation-adjusted EVSI calculation methods are developed. These novel methods circumvent the need for analytical calculations, which were restricted to settings in which normality could be assumed. The first method developed in this article uses computationally demanding nested simulations, based on the definition of the implementation-adjusted EVSI. The second method is based on adapting the moment matching method, a recently developed efficient EVSI computation method, to adjust for imperfect implementation. The implementation-adjusted EVSI is then calculated with the 2 methods across 3 examples. Results The maximum difference between the 2 methods is at most 6% in all examples. The efficient computation method is between 6 and 60 times faster than the nested simulation method in this case study and could be used in practice. Conclusions This article permits the calculation of an implementation-adjusted EVSI using realistic assumptions. The efficient estimation method is accurate and can estimate the implementation-adjusted EVSI in practice. By adapting standard EVSI estimation methods, adjustments for imperfect implementation can be made with the same computational cost as a standard EVSI analysis. Highlights Standard expected value of sample information (EVSI) analyses do not account for the fact that treatment implementation following research is often slow and incomplete, meaning they incorrectly capture the value of the study. Two methods, based on nested Monte Carlo sampling and the moment matching EVSI calculation method, are developed to adjust EVSI calculations for imperfect implementation when the speed and level of the implementation of a new treatment depends on the strength of evidence in favor of the treatment. The 2 methods we develop provide similar estimates for the implementation-adjusted EVSI. Our methods extend current EVSI calculation algorithms and thus require limited additional computational complexity.

Dictionary learning allows model-free pseudotime estimation of transcriptomic data

Background Pseudotime estimation from dynamic single-cell transcriptomic data enables characterisation and understanding of the underlying processes, for example developmental processes. Various pseudotime estimation methods have been proposed during the last years. Typically, these methods start with a dimension reduction step because the low-dimensional representation is usually easier to analyse. Approaches such as PCA, ICA or t-SNE belong to the most widely used methods for dimension reduction in pseudotime estimation methods. However, these methods usually make assumptions on the derived dimensions, which can result in important dataset properties being missed. In this paper, we suggest a new dictionary learning based approach, dynDLT, for dimension reduction and pseudotime estimation of dynamic transcriptomic data. Dictionary learning is a matrix factorisation approach that does not restrict the dependence of the derived dimensions. To evaluate the performance, we conduct a large simulation study and analyse 8 real-world datasets. Results The simulation studies reveal that firstly, dynDLT preserves the simulated patterns in low-dimension and the pseudotimes can be derived from the low-dimensional representation. Secondly, the results show that dynDLT is suitable for the detection of genes exhibiting the simulated dynamic patterns, thereby facilitating the interpretation of the compressed representation and thus the dynamic processes. For the real-world data analysis, we select datasets with samples that are taken at different time points throughout an experiment. The pseudotimes found by dynDLT have high correlations with the experimental times. We compare the results to other approaches used in pseudotime estimation, or those that are method-wise closely connected to dictionary learning: ICA, NMF, PCA, t-SNE, and UMAP. DynDLT has the best overall performance for the simulated and real-world datasets. Conclusions We introduce dynDLT, a method that is suitable for pseudotime estimation. Its main advantages are: (1) It presents a model-free approach, meaning that it does not restrict the dependence of the derived dimensions; (2) Genes that are relevant in the detected dynamic processes can be identified from the dictionary matrix; (3) By a restriction of the dictionary entries to positive values, the dictionary atoms are highly interpretable.

Understanding bias when estimating life expectancy from age at death: a simulation approach applied to Morquio syndrome A

Objective Life expectancy can be estimated accurately from a cohort of individuals born in the same year and followed from birth to death. However, due to the resource-consuming nature of following a cohort prospectively, life expectancy is often assessed based upon retrospective death record reviews. This conventional approach may lead to potentially biased estimates, in particular when estimating life expectancy of rare diseases such as Morquio syndrome A. We investigated the accuracy of life expectancy estimation using death records by simulating the survival of individuals with Morquio syndrome A under four different scenarios. Results When life expectancy was constant during the entire period, using death data did not result in a biased estimate. However, when life expectancy increased over time, as is often expected to be the case in rare diseases, using only death data led to a substantial underestimation of life expectancy. We emphasize that it is therefore crucial to understand how estimates of life expectancy are obtained, to interpret them in an appropriate context, and to assess estimation methods within a sensitivity analysis framework, similar to the simulations performed herein.

Structural Convergence between African Countries: Empirical Evidence

This paper aims to investigate structural convergence in selected African countries over the period 1994-2019. Using panel data for 48 African countries and several estimation methods [Panel-Corrected Standard Errors (PCSE), Feasible Generalized Least Squares (FGLS), tobit model, instrumental variable, and Granger non-causality], the results show the existence of the phenomenon of sectoral structural convergence in Africa, i.e. a greater similarity in sectoral structures while income gaps are narrowing. The paper also highlights the service sector's low relative productivity level and industrial sector's low labor force attractiveness despite a significant shift in labor from the agricultural sector and a higher level of relative productivity respectively. To address this issue, the development and acquisition of human and physical capital would be necessary to develop the industrial sector and increase the service sector's productivity.

The Macroeconomic Controversy Over Price Rigidity — How to Resolve it and How Bayesian Estimation has Led us Astray

Price rigidity plays a central role in macroeconomic models but remains controversial. Those espousing it look to Bayesian estimated models in support, while those assuming price flexibility largely impose it on their models. So controversy continues unresolved by testing on the data. In a Monte Carlo experiment we ask how different estimation methods could help to resolve this controversy. We find Bayesian estimation creates a large potential estimation bias compared with standard estimation techniques. Indirect estimation where the bias is found to be low appears to do best, and offers the best way forward for settling the price rigidity controversy.

Single-Stage Adaptive Multi-Scale Point Cloud Noise Filtering Algorithm Based on Feature Information

This paper proposes a single-stage adaptive multi-scale noise filtering algorithm for point clouds, based on feature information, which aims to mitigate the fact that the current laser point cloud noise filtering algorithm has difficulty quickly completing the single-stage adaptive filtering of multi-scale noise. The feature information from each point of the point cloud is obtained based on the efficient k-dimensional (k-d) tree data structure and amended normal vector estimation methods, and the adaptive threshold is used to divide the point cloud into large-scale noise, a feature-rich region, and a flat region to reduce the computational time. The large-scale noise is removed directly, the feature-rich and flat regions are filtered via improved bilateral filtering algorithm and weighted average filtering algorithm based on grey relational analysis, respectively. Simulation results show that the proposed algorithm performs better than the state-of-art comparison algorithms. It was, thus, verified that the algorithm proposed in this paper can quickly and adaptively (i) filter out large-scale noise, (ii) smooth small-scale noise, and (iii) effectively maintain the geometric features of the point cloud. The developed algorithm provides research thought for filtering pre-processing methods applicable in 3D measurements, remote sensing, and target recognition based on point clouds.

The Scientific Profiles of Documented Collections via Publication Data: Past, Present, and Future Directions in Forensic Anthropology

Human osteological documented collections (DCs), also referred to as “identified collections”, are a valuable resource in biological and forensic anthropology, as they offer the possibility for hypothesis-driven research on sex and age-at-death estimation methods, human variability, and other morphometric-based parameters of individual identification. Consequently, they feature in many publications addressing the forensic sciences. The paper aims to explore the scientific profiles of DCs via publication using bibliometric data. The Dimensions databases were used to select the DC-related keywords in the title and abstracts of the publications. The search result analysis and extraction were conducted using VOSviewer. A total of 376 articles were found, published between 1969 and 2021 (November). The number of publications has increased over the years, specifically after 2011. The results show that most of the publications are associated with countries such as the United States and Portugal (the latter highlights the University of Coimbra), that the research tends to focus on human biological profiling (e.g., age, sex assessments), and that the journals with the highest numbers of publications were related to forensic sciences. This analysis shows a positive correlation between DC publications and the growth of forensic anthropology in recent years, with a slight shift towards the leading institutions that publish DC-based research. Hence, we can anticipate a change in the institutional leading profiles in the years to come.

Recent Progress on Methods for Estimating and Updating Large Phylogenies

With the increased availability of sequence data and even of fully sequenced and assembled genomes, phylogeny estimation of very large trees (even of hundreds of thousands of sequences) is now a goal for some biologists. Yet, the construction of these phylogenies is a complex pipeline presenting analytical and computational challenges, especially when the number of sequences is very large. In the last few years, new methods have been developed that aim to enable highly accurate phylogeny estimations on these large datasets, including divide-and-conquer techniques for multiple sequence alignment and/or tree estimation, methods that can estimate species trees from multi-locus datasets while addressing heterogeneity due to biological processes (e.g., incomplete lineage sorting and gene duplication and loss), and methods to add sequences into large gene trees or species trees. Here we present some of these recent advances and discuss opportunities for future improvements.

Diameter distribution model development of tropical hybrid Eucalyptus clonal plantations in Sumatera, Indonesia: A comparison of estimation methods

Background: Effective forest management and planning often requires information about the distribution of volume by size and product classes. Size-class models describe the diameter distribution and provide information by diameter class, such as the number of trees, basal area, and volume per unit of area. A successful diameter-distribution model requires high flexibility yet robust prediction of its parameters. To our knowledge, there are no studies regarding diameter distribution models for Eucalyptus hybrids in Indonesia. Therefore, the aim of this study was to compare different recovery methods for predicting parameters of the 3-parameter Weibull distribution for characterising diameter distributions of Eucalyptus hybrid clone plantations, on Sumatera Island of Indonesia. Methods: The parameter recovery approach was proposed to be compatible with stand-average growth and yield models developed based on the same data. Three approaches where compared: moment-based recovery, percentile-based prediction and hybrid methods. The ultimate goal was to recover Weibull parameters from future stand attributes, which were predicted from current stand attributes using regression models. Results: In this study, the moment method was found to give the overall lowest mean error-index and Kolmogorov– Smirnov (KS) statistic, followed by the hybrid and percentile methods. The moment-based method better fit long tails on both sides of the distribution and exhibited slightly greater flexibility in describing plots with larger variance than the other methods. Conclusions: The Weibull approach appeared relatively robust in determining diameter distributions of Eucalyptus hybrid clone plantation in Indonesia, yet some refinements may be necessary to characterize more complex distributions.