Using syncmers improves long-read mapping

As sequencing datasets keep growing larger, time and memory efficiency of read mapping are becoming more critical. Many clever algorithms and data structures were used to develop mapping tools for next generation sequencing, and in the last few years also for third generation long reads. A key idea in mapping algorithms is to sketch sequences with their minimizers. Recently, syncmers were introduced as an alternative sketching method that is more robust to mutations and sequencing errors. Here we introduce parameterized syncmer schemes, and provide a theoretical analysis for multi-parameter schemes. By combining these schemes with downsampling or minimizers we can achieve any desired compression and window guarantee. We introduced syncmer schemes into the popular minimap2 and Winnowmap2 mappers. In tests on simulated and real long read data from a variety of genomes, the syncmer-based algorithms reduced unmapped reads by 20-60% at high compression while using less memory. The advantage of syncmer-based mapping was even more pronounced at lower sequence identity. At sequence identity of 65-75% and medium compression, syncmer mappers had 50-60% fewer unmapped reads, and ∼ 10% fewer of the reads that did map were incorrectly mapped. We conclude that syncmer schemes improve mapping under higher error and mutation rates. This situation happens, for example, when the high error rate of long reads is compounded by a high mutation rate in a cancer tumor, or due to differences between strains of viruses or bacteria.

Smooth Descent: a Ploidy-Aware Algorithm To Improve Linkage Mapping In The Presence of Genotyping Errors

Linkage mapping is an approach to order markers based on recombination events. Mapping algorithms cannot easily handle genotyping errors, which are common in high-throughput genotyping data. To solve this issue, strategies have been developed, aimed mostly at identifying and eliminating these errors. One such strategy is SMOOTH (van Os et al. 2005), an iterative algorithm to detect genotyping errors. Unlike other approaches, SMOOTH can also be used to impute the most probable alternative genotypes, but its application is limited to diploid species and to markers heterozygous in only one of the parents. In this study we adapted SMOOTH to expand its use to any marker type and to autopolyploids with the use of identity-by-descent probabilities, naming the updated algorithm Smooth Descent (SD). We applied SD to real and simulated data, showing that in the presence of genotyping errors this method produces better genetic maps in terms of marker order and map length. SD is particularly useful for error rates between 5% and 20% and when error rates are not homogeneous among markers or individuals. Moreover, the simplicity of the algorithm allows thousands of markers to be efficiently processed, thus being particularly useful for error detection in high-density datasets. We have implemented this algorithm in the R package SmoothDescent.

Augmented Reality in Precision Farming: Concepts and Applications

The amount of arable land is limited, yet the demand for agricultural food products is increasing. This issue has led to the notion of precision farming, where smart city-based technologies (e.g., Internet of Things, digital twins, artificial intelligence) are employed in combination to cater for increased production with fewer resources. Widely used in manufacturing, augmented reality has demonstrated impactful solutions for information communication, remote monitoring and increased interaction. Yet, the technology has only recently begun to find a footing alongside precision farming solutions, despite the many benefits possible to farmers through augmenting the physical world with digital objects. Therefore, this article reflects on literature discussing current applied solutions within agriculture, where augmented realty has demonstrated a significant impact for monitoring and production. The findings discuss that augmented reality must be coupled with other technologies (e.g., simultaneous localization and mapping algorithms, global positioning systems, and sensors), specifically 9 are identified across 2 application domains (livestock and crop farming) to be beneficial. Attention is also provided on how augmented reality should be employed within agriculture, where related-work examples are drawn from in order to discuss suitable hardware approaches and constraints (e.g., mobility).

Function Words at the Interface: A Two-Tier Approach

The distinction between function words and content words poses a challenge to theories of the syntax–prosody interface. On the one hand, function words are “ignored” by the mapping algorithms; that is, function words are not mapped to prosodic words. On the other hand, there are numerous accounts of function words which form prosodic words and can even be analysed as heads of larger prosodic units. Furthermore, function words seem to be a driving factor for the formation of prosodic structures in that they can largely be held accountable for the non-isomorphism between syntactic and prosodic constituency. This paper discusses these challenges with a focus on a particular function word, and the first-person nominative pronoun in Swabian, a Southern German dialect. By means of two corpus studies, it is shown that the pronoun occurs in two forms, the prosodic word [i:] and the enclitic [ə]. Depending on clause position and focus structure, the forms occur in complementary distribution. Occurrences of n-insertion allow for the establishment of a recursive prosodic word structure at the level of the phonological module. The findings support a new proposal in the form of a two-tier mapping approach to the interface between syntax and prosody.

Parameter Reduction and Optimisation for Point Cloud and Occupancy Mapping Algorithms

Occupancy mapping is widely used to generate volumetric 3D environment models from point clouds, informing a robotic platform which parts of the environment are free and which are not. The selection of the parameters that govern the point cloud generation algorithms and mapping algorithms affects the process and the quality of the final map. Although previous studies have been reported in the literature on optimising major parameter configurations, research in the process to identify optimal parameter sets to achieve best occupancy mapping performance remains limited. The current work aims to fill this gap with a two-step principled methodology that first identifies the most significant parameters by conducting Neighbourhood Component Analysis on all parameters and then optimise those using grid search with the area under the Receiver Operating Characteristic curve. This study is conducted on 20 data sets with specially designed targets, providing precise ground truths for evaluation purposes. The methodology is tested on OctoMap with point clouds created by applying StereoSGBM on the images from a stereo camera. A clear indication can be seen that mapping parameters are more important than point cloud generation parameters. Moreover, up to 15% improvement in mapping performance can be achieved over default parameters.

A dashboard for exploring clinical trials sponsorship and potential virtual monopolies

Objective To create a data visualization dashboard to advance research related to clinical trials sponsorship and monopolistic practices in the pharmaceuticals industry. Materials and Methods This R Shiny application aggregates data from ClinicialTrials.gov resulting from user’s queries by terms. Returned data are visualized through an interactive dashboard. Results The Clinical Trials Sponsorship Network Dashboard (CTSND) uses force-directed network mapping algorithms to visualize clinical trials sponsorship data. Interpretation of network visualization is further supported with data on sponsor classes, sponsorship timelines, evaluated products, and target conditions. The source code for the CTSND is available at https://github.com/sscottgraham/ConflictMetrics. Discussion Monopolistic practices have been identified as a likely contributor to high drug prices in the United States. CTSND data and visualizations support the analysis of clinical trials sponsorship networks and may aid in identifying current and emerging monopolistic practices. Conclusions CTSND data can support more robust deliberation about an understudied area of drug pricing.

Towards a Generic Neural Network Architecture for Approximating Tone Mapping Algorithms

Tone curves are a key feature in any image processing pipeline, and are used to change the pixel values of an input image to find an output image that looks better. Perhaps the most widely deployed tone curve algorithm is Contrast Limited Histogram Equalisation (CLHE). CLHE is an iterative algorithm that tone maps an input image so that the histogram of the output is (approximately) maximally uniform subject to the constraint that the tone curve has bounded slope (neither too large or too small).In this paper, we build upon a neural network framework [1] that was recently developed to deliver CLHE in fewer iterations (each layer in the neural network is analogous to a single iteration of CLHE, but the network has fewer layers than the number of iterations needed by CLHE). The key contribution of this paper is to show that the same network architecture can be used to implement a more complex (and more powerful) tone mapping algorithm. Experiments validate our method.