Capturing Surface Complementarity in Proteins using Unsupervised Learning and Robust Curvature Measure

The structure of a protein plays a pivotal role in determining its function. Often, the protein surface’s shape and curvature dictate its nature of interaction with other proteins and biomolecules. However, marked by corrugations and roughness, a protein’s surface representation poses significant challenges for its curvature-based characterization. In the present study, we employ unsupervised machine learning to segment the protein surface into patches. To measure the surface curvature of a patch, we present an algebraic sphere fitting method that is fast, accurate, and robust. Moreover, we use local curvatures to show the existence of “shape complementarity” in protein-protein, antigen-antibody, and protein-ligand interfaces. We believe that the current approach could help understand the relationship between protein structure and its biological function and can be used to find binding partners of a given protein.

Detecting network anomalies using Forman–Ricci curvature and a case study for human brain networks

We analyze networks of functional correlations between brain regions to identify changes in their structure caused by Attention Deficit Hyperactivity Disorder (adhd). We express the task for finding changes as a network anomaly detection problem on temporal networks. We propose the use of a curvature measure based on the Forman–Ricci curvature, which expresses higher-order correlations among two connected nodes. Our theoretical result on comparing this Forman–Ricci curvature with another well-known notion of network curvature, namely the Ollivier–Ricci curvature, lends further justification to the assertions that these two notions of network curvatures are not well correlated and therefore one of these curvature measures cannot be used as an universal substitute for the other measure. Our experimental results indicate nine critical edges whose curvature differs dramatically in brains of adhd patients compared to healthy brains. The importance of these edges is supported by existing neuroscience evidence. We demonstrate that comparative analysis of curvature identifies changes that more traditional approaches, for example analysis of edge weights, would not be able to identify.

A Review of and Some Results for Ollivier–Ricci Network Curvature

Characterizing topological properties and anomalous behaviors of higher-dimensional topological spaces via notions of curvatures is by now quite common in mainstream physics and mathematics, and it is therefore natural to try to extend these notions from the non-network domains in a suitable way to the network science domain. In this article we discuss one such extension, namely Ollivier’s discretization of Ricci curvature. We first motivate, define and illustrate the Ollivier–Ricci Curvature. In the next section we provide some “not-previously-published” bounds on the exact and approximate computation of the curvature measure. In the penultimate section we review a method based on the linear sketching technique for efficient approximate computation of the Ollivier–Ricci network curvature. Finally in the last section we provide concluding remarks with pointers for further reading.

A Method to Identify Geochemical Mineralization on Linear Transects

Mineral exploration in biogeochemistry is related to the detection of anomalies in soil, which is driven by many factors and thus a complex problem. Mikšová, Rieser, and Filzmoser (2019b) have introduced a method for the identification of spatial patterns with increased element concentrations in samples along a linear sampling transect. This procedure is based on fitting Generalized Additive Models (GAMs) to the concentration data, and computing a curvature measure from the pairwise log-ratios of these fits. The higher the curvature, the more likely one or both elements of the pair indicate local mineralization. This method is applied on two geochemical data sets which have been collected specifically for the purpose of mineral exploration. The aim is to test the technique for its ability to identify pathfinder elements to detect mineralized zones, and to verify whether the method can indicate which sampling material is best suited for this purpose.

A curvature operator for a regular tetrahedron shape in LQG

An alternative approach introducing a 3-dimensional (3D) Ricci scalar curvature quantum operator given in terms of volume and area as well as new edge length operators is proposed. An example of monochromatic 4-valent node intertwiner state (equilateral tetrahedra) is studied and the scalar curvature measure for a regular tetrahedron shape is constructed. It is shown that all regular tetrahedron states are in the negative scalar curvature regime and for the semi-classical limit the spectrum is very close to the Euclidean regime.