Circular Networks from Distorted Metrics

Trees have long been used as a graphical representation of species relationships. However complex evolutionary events, such as genetic reassortments or hybrid speciations which occur commonly in viruses, bacteria and plants, do not fit into this elementary framework. Alternatively, various network representations have been developed. Circular networks are a natural generalization of leaf-labeled trees interpreted as split systems, that is, collections of bipartitions over leaf labels corresponding to current species. Although such networks do not explicitly model specific evolutionary events of interest, their straightforward visualization and fast reconstruction have made them a popular exploratory tool to detect network-like evolution in genetic datasets. Standard reconstruction methods for circular networks, such as Neighbor-Net, rely on an associated metric on the species set. Such a metric is first estimated from DNA sequences, which leads to a key difficulty: distantly related sequences produce statistically unreliable estimates. This is problematic for Neighbor-Net as it is based on the popular tree reconstruction method Neighbor-Joining, whose sensitivity to distance estimation errors is well established theoretically. In the tree case, more robust reconstruction methods have been developed using the notion of a distorted metric, which captures the dependence of the error in the distance through a radius of accuracy. Here we design the first circular network reconstruction method based on distorted metrics. Our method is computationally efficient. Moreover, the analysis of its radius of accuracy highlights the important role played by the maximum incompatibility, a measure of the extent to which the network differs from a tree.Comment: Submitte

Reconstruction of tree branching structures from UAV-LiDAR data

The reconstruction of tree branching structures is a longstanding problem in Computer Graphics which has been studied over several data sources, from photogrammetry point clouds to Terrestrial and Aerial Laser Imaging Detection and Ranging technology. However, most data sources present acquisition errors that make the reconstruction more challenging. Among them, the main challenge is the partial or complete occlusion of branch segments, thus leading to disconnected components whether the reconstruction is resolved using graph-based approaches. In this work, we propose a hybrid method based on radius-based search and Minimum Spanning Tree for the tree branching reconstruction by handling occlusion and disconnected branches. Furthermore, we simplify previous work evaluating the similarity between ground-truth and reconstructed skeletons. Using this approach, our method is proved to be more effective than the baseline methods, regarding reconstruction results and response time. Our method yields better results on the complete explored radii interval, though the improvement is especially significant on the Ground Sampling Distance In terms of latency, an outstanding performance is achieved in comparison with the baseline method.Junta de Andalucia 1381202-GEU PYC20-RE-005-UJAEuropean Commission Spanish Government PID2021-126339OB-I00 FPU17/01902 FPU19/0010

Inference of single-cell phylogenies from lineage tracing data using Cassiopeia.

The pairing of CRISPR/Cas9-based gene editing with massively parallel single-cell readouts now enables large-scale lineage tracing. However, the rapid growth in complexity of data from these assays has outpaced our ability to accurately infer phylogenetic relationships. First, we introduce Cassiopeia-a suite of scalable maximum parsimony approaches for tree reconstruction. Second, we provide a simulation framework for evaluating algorithms and exploring lineage tracer design principles. Finally, we generate the most complex experimental lineage tracing dataset to date, 34,557 human cells continuously traced over 15 generations, and use it for benchmarking phylogenetic inference approaches. We show that Cassiopeia outperforms traditional methods by several metrics and under a wide variety of parameter regimes, and provide insight into the principles for the design of improved Cas9-enabled recorders. Together, these should broadly enable large-scale mammalian lineage tracing efforts. Cassiopeia and its benchmarking resources are publicly available at www.github.com/YosefLab/Cassiopeia

Fast Landmark Localization with 3D Component Reconstruction and CNN for Cross-Pose Recognition

Two approaches are proposed for cross-pose face recognition, one is based on the 3D reconstruction of facial components and the other is based on the deep Convolutional Neural Network (CNN). Unlike most 3D approaches that consider holistic faces, the proposed approach considers 3D facial components. It segments a 2D gallery face into components, reconstructs the 3D surface for each component, and recognizes a probe face by component features. The segmentation is based on the landmarks located by a hierarchical algorithm that combines the Faster R-CNN for face detection and the Reduced Tree Structured Model for landmark localization. The core part of the CNN-based approach is a revised VGG network. We study the performances with different settings on the training set, including the synthesized data from 3D reconstruction, the real-life data from an in-the-wild database, and both types of data combined. We investigate the performances of the network when it is employed as a classifier or designed as a feature extractor. The two recognition approaches and the fast landmark localization are evaluated in extensive experiments, and compared to stateof-the-art methods to demonstrate their efficacy.Comment: 14 pages, 12 figures, 4 table