Related papers: Conformations of Macromolecules and their Complexe…

Motivation: Cellular Electron CryoTomography (CECT) enables 3D visualization of cellular organization at near-native state and in sub-molecular resolution, making it a powerful tool for analyzing structures of macromolecular complexes and…

Microstructure of materials is often characterized through image analysis to understand processing-structure-properties linkages. We propose a largely automated framework that integrates unsupervised and supervised learning methods to…

Different cell types aggregate and sort into hierarchical architectures during the formation of animal tissues. The resulting spatial organization depends (in part) on the strength of adhesion of one cell type to itself relative to other…

We demonstrate a smart laser-diffraction analysis technique for particle mixture identification. We retrieve information about the size, geometry, and ratio concentration of two-component heterogeneous particle mixtures with an efficiency…

We show that macro-molecular self-assembly can recognize and classify high-dimensional patterns in the concentrations of $N$ distinct molecular species. Similar to associative neural networks, the recognition here leverages dynamical…

In this paper we present a new dynamical systems algorithm for clustering in hyperspectral images. The main idea of the algorithm is that data points are \`pushed\' in the direction of increasing density and groups of pixels that end up in…

We describe a simple automated method to extract and quantify transient heterogeneous dynamical changes from large datasets generated in single molecule/particle tracking experiments. Based on wavelet transform, the method transforms raw…

This article presents a novel pretopology-based algorithm designed to address the challenges of clustering mixed data without the need for dimensionality reduction. Leveraging Disjunctive Normal Form, our approach formulates customizable…

Molecular conformation generation, a critical aspect of computational chemistry, involves producing the three-dimensional conformer geometry for a given molecule. Generating molecular conformation via diffusion requires learning to reverse…

We propose an algorithm for the computational homogenization of locally periodic hyperelastic structures undergoing large deformations due to external quasi-static loading. The algorithm performs clustering of macroscopic deformations into…

In many applications involving multi-media data, the definition of similarity between items is integral to several key tasks, e.g., nearest-neighbor retrieval, classification, and recommendation. Data in such regimes typically exhibits…

In coherent X-ray diffraction microscopy the diffraction pattern generated by a sample illuminated with coherent x-rays is recorded, and a computer algorithm recovers the unmeasured phases to synthesize an image. By avoiding the use of a…

Super-resolution imaging techniques have largely improved our capabilities to visualize nanometric structures in biological systems. Their application further enables one to potentially quantitate relevant parameters to determine the…

Finite mixtures of regression models offer a flexible framework for investigating heterogeneity in data with functional dependencies. These models can be conveniently used for unsupervised learning on data with clear regression…

Cryo-electron microscopy is a state-of-the-art method for determining high-resolution three-dimensional models of molecules, from their two-dimensional projection images taken by an electron microscope. A crucial step in this method is to…

Complex systems are usually represented as an intricate set of relations between their components forming a complex graph or network. The understanding of their functioning and emergent properties are strongly related to their structural…

To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…

Chemical structure extraction from documents remains a hard problem due to both false positive identification of structures during segmentation and errors in the predicted structures. Current approaches rely on handcrafted rules and…

Low-rank matrix approximations are often used to help scale standard machine learning algorithms to large-scale problems. Recently, matrix coherence has been used to characterize the ability to extract global information from a subset of…

A common task in cryo-electron microscopy (cryo-EM) data processing is to compare three-dimensional density maps of macromolecules. In this paper, we propose an algorithm for aligning three-dimensional density maps that exploits common…