ABSTRACT
Current visualizations in microbiome research rely on aggregations in taxonomic classifications or do not show less abundant taxa. We introduce Snowflake: a new visualization method that creates a clear overview of the microbiome composition in collected samples without losing any information due to classification or neglecting less abundant reads. Snowflake displays every observed OTU/ASV in the microbiome abundance table and provides a solution to include the data's hierarchical structure and additional information obtained from downstream analysis (e.g., alpha- and beta-diversity) and metadata. Based on the value-driven ICE-T evaluation methodology, Snowflake was positively received. Experts in microbiome research found the visualizations to be user-friendly and detailed and liked the possibility of including and relating additional information to the microbiome's composition. Exploring the topological structure of the microbiome abundance table allows them to quickly identify which taxa are unique to specific samples and which are shared among multiple samples (i.e., separating sample-specific taxa from the core microbiome), and see the compositional differences between samples. An R package for constructing and visualizing Snowflake microbiome composition graphs is available at https://gitlab.com/vda-lab/snowflake.
ABSTRACT
The lateral line organ of fish has inspired engineers to develop flow sensor arrays-dubbed artificial lateral lines (ALLs)-capable of detecting near-field hydrodynamic events for obstacle avoidance and object detection. In this paper, we present a comprehensive review and comparison of ten localisation algorithms for ALLs. Differences in the studied domain, sensor sensitivity axes, and available data prevent a fair comparison between these algorithms from their original works. We compare them with our novel quadrature method (QM), which is based on a geometric property specific to 2D-sensitive ALLs. We show how the area in which each algorithm can accurately determine the position and orientation of a simulated dipole source is affected by (1) the amount of training and optimisation data, and (2) the sensitivity axes of the sensors. Overall, we find that each algorithm benefits from 2D-sensitive sensors, with alternating sensitivity axes as the second-best configuration. From the machine learning approaches, an MLP required an impractically large training set to approach the optimisation-based algorithms' performance. Regardless of the data set size, QM performs best with both a large area for accurate predictions and a small tail of large errors.
