MOTIVATION: Architectural stripes in Hi-C and related data are crucial for gene regulation, development, and DNA repair. Despite their importance, few tools exist for automatic stripe detection. RESULTS: We introduce StripePy, which leverages computational geometry methods to identify and analyze architectural stripes in contact maps from Chromosome Conformation Capture experiments like Hi-C and Micro-C. StripePy outperforms existing tools, as shown through tests on various datasets and a newly developed simulated benchmark, StripeBench, providing a valuable resource for the community. AVAILABILITY AND IMPLEMENTATION: StripePy is released to the public as an open-source, MIT-licensed Python application. StripePy source code is hosted on GitHub at https://github.com/paulsengroup/StripePy and is archived on Zenodo. StripePy can be easily installed from source or PyPI using pip and from Bioconda using conda. Containerized versions of StripePy are regularly published on DockerHub.

Abstract We propose CurveML, a benchmark for evaluating and comparing methods for the classification and identification of plane curves represented as point sets. The dataset is composed of 520k curves, of which 280k are generated from specific families characterised by distinctive shapes, and 240k are obtained from Bézier or composite Bézier curves. The dataset was generated starting from the parametric equations of the selected curves making it easily extensible. It is split into training, validation, and test sets to make it usable by learning-based methods, and it contains curves perturbed with different kinds of point set artefacts. To evaluate the detection of curves in point sets, our benchmark includes various metrics with particular care on what concerns the classification and approximation accuracy. Finally, we provide a comprehensive set of accompanying demonstrations, showcasing curve classification, and parameter regression tasks using both ResNet-based and PointNet-based networks. These demonstrations encompass 14 experiments, with each network type comprising 7 runs: 1 for classification and 6 for regression of the 6 defining parameters of plane curves. The corresponding Jupyter notebooks with training procedures, evaluations, and pre-trained models are also included for a thorough understanding of the methodologies employed.

The three-dimensional organization of chromatin plays a crucial role in gene regulation and cellular processes like deoxyribonucleic acid (DNA) transcription, replication and repair. Hi-C and related techniques provide detailed views of spatial proximities within the nucleus. However, data analysis is challenging partially due to a lack of well-defined, underpinning mathematical frameworks. Recently, recognizing and analyzing geometric patterns in Hi-C data has emerged as a powerful approach. This review provides a summary of algorithms for automatic recognition and analysis of geometric patterns in Hi-C data and their correspondence with chromatin structure. We classify existing algorithms on the basis of the data representation and pattern recognition paradigm they make use of. Finally, we outline some of the challenges ahead and promising future directions.

The problem faced in this paper concerns the recognition of simple and complex geometric primitives in point clouds resulting from scans of mechanical CAD objects. A large number of points, the presence of noise, outliers, missing or redundant parts and uneven distribution are the main problems to be addressed to meet this need. In this article we propose a solution, based on the Hough transform, that can recognize simple and complex geometric primitives and is robust to noise, outliers, and missing parts. Additionally, we can extract a series of geometric descriptors that uniquely characterize a primitive and, based on them, aggregate the output into maximal or compound primitives, thus reducing oversegmentation. The results presented in the paper demonstrate the robustness of the method and its competitiveness with respect to other solutions proposed in the literature.

Voltage-gated sodium (Nav) channels constitute a prime target for drug design and discovery, given their implication in various diseases such as epilepsy, migraine and ataxia to name a few. In this regard, performing morphological analysis is a crucial step in comprehensively understanding their biological function and mechanism, as well as in uncovering subtle details of their mechanism that may be elusive to experimental observations. Despite their tremendous therapeutic potential, drug design resources are deficient, particularly in terms of accurate and comprehensive geometric information. This paper presents a geometric dataset of molecular surfaces that are representative of Nav channels in mammals. For each structure we provide three representations and a number of geometric measures, including length, volume and straightness of the recognized channels. To demonstrate the effective use of GEO-Nav, we have tested it on two methods belonging to two different categories of approaches: a sphere-based and a tessellation-based method.

In applications like computer aided design, geometric models are often represented numerically as polynomial splines or NURBS, even when they originate from primitive geometry. For purposes such as redesign and isogeometric analysis, it is of interest to extract information about the underlying geometry through reverse engineering. In this work we develop a novel method to determine these primitive shapes by combining clustering analysis with approximate implicitization. The proposed method is automatic and can recover algebraic hypersurfaces of any degree in any dimension. In exact arithmetic, the algorithm returns exact results. All the required parameters, such as the implicit degree of the patches and the number of clusters of the model, are inferred using numerical approaches in order to obtain an algorithm that requires as little manual input as possible. The effectiveness, efficiency and robustness of the method are shown both in a theoretical analysis and in numerical examples implemented in Python.

In this paper we investigate a local surface approximation, the Weighted Quasi Interpolant Spline Approximation (wQISA), specifically designed for large and noisy point clouds. We briefly describe the properties of the wQISA representation and introduce a novel data-driven implementation, which combines prediction capability and complexity efficiency. We provide an extended comparative analysis with other continuous approximations on real data, including different types of surfaces and levels of noise, such as 3D models, terrain data and digital environmental data.