Multiple haplotype reconstruction from allele frequency data

Because haplotype information is of widespread interest in biomedical applications, effort has been put into their reconstruction. Here, we propose an efficient method, called haploSep, that is able to accurately infer major haplotypes and their frequencies just from multiple samples of allele frequency data. Even the accuracy of experimentally obtained allele frequencies can be improved by re-estimating them from our reconstructed haplotypes. From a methodological point of view, we model our problem as a multivariate regression problem where both the design matrix and the coefficient matrix are unknown. Compared to other methods, haploSep is very fast, with linear computational complexity in the haplotype length. We illustrate our method on simulated and real data focusing on experimental evolution and microbial data.

Testing for dependence on tree structures

Tree-like structures are abundant in the empirical sciences as they can summarize high-dimensional data and show latent structure among many samples in a single framework. Prominent examples include phylogenetic trees or hierarchical clustering derived from genetic data. Currently, users employ ad hoc methods to test for association between a given tree and a response variable, which reduces reproducibility and robustness. In this paper, we introduce treeSeg, a simple to use and widely applicable methodology with high power for testing between all levels of hierarchy for a given tree and the response while accounting for the overall false positive rate. Our method allows for precise uncertainty quantification and therefore, increases interpretability and reproducibility of such studies across many fields of science.

Tree structures, showing hierarchical relationships and the latent structures between samples, are ubiquitous in genomic and biomedical sciences. A common question in many studies is whether there is an association between a response variable measured on each sample and the latent group structure represented by some given tree. Currently, this is addressed on an ad hoc basis, usually requiring the user to decide on an appropriate number of clusters to prune out of the tree to be tested against the response variable. Here, we present a statistical method with statistical guarantees that tests for association between the response variable and a fixed tree structure across all levels of the tree hierarchy with high power while accounting for the overall false positive error rate. This enhances the robustness and reproducibility of such findings.

Low-Element Image Restoration Based on an Out-of-Order Elimination Algorithm

To reduce the consumption of receiving devices, a number of devices at the receiving end undergo low-element treatment (the number of devices at the receiving end is less than that at the transmitting ends). The underdetermined blind-source separation system is a classic low-element model at the receiving end. Blind signal extraction in an underdetermined system remains an ill-posed problem, as it is difficult to extract all the source signals. To realize fewer devices at the receiving end without information loss, this paper proposes an image restoration method for underdetermined blind-source separation based on an out-of-order elimination algorithm. Firstly, a chaotic system is used to perform hidden transmission of source signals, where the source signals can hardly be observed and confidentiality is guaranteed. Secondly, empirical mode decomposition is used to decompose and complement the missing observed signals, and the fast independent component analysis (FastICA) algorithm is used to obtain part of the source signals. Finally, all the source signals are successfully separated using the out-of-order elimination algorithm and the FastICA algorithm. The results show that the performance of the underdetermined blind separation algorithm is related to the configuration of the transceiver antenna. When the signal is 3 × 4 antenna configuration, the algorithm in this paper is superior to the comparison algorithm in signal recovery, and its separation performance is better for a lower degree of missing array elements. The end result is that the algorithms discussed in this paper can effectively and completely extract all the source signals.