Related papers: Persistent topology for cryo-EM data analysis
Electron cryomicroscopy (cryo-EM) is a technique in structural biology used to reconstruct accurate volumetric maps of molecules. One step of the cryo-EM pipeline involves solving an inverse-problem. This inverse-problem, referred to as…
In this paper, we apply persistent entropy, a novel topological statistic, for characterization of images of epithelial tissues. We have found out that persistent entropy is able to summarize topological and geometric information encoded by…
Persistent homology, a technique from computational topology, has recently shown strong empirical performance in the context of graph classification. Being able to capture long range graph properties via higher-order topological features,…
This paper presents a detailed noise analysis and a noise-based optimization procedure for resonant MEMS structures. A design for high sensitivity of MEMS structures needs to take into account the noise shaping induced by damping phenomena…
Single-particle cryo-electron microscopy (cryo-EM) has recently joined X-ray crystallography and NMR spectroscopy as a high-resolution structural method to resolve biological macromolecules. In a cryo-EM experiment, the microscope produces…
Persistence-based topological optimization deforms a point cloud $X \subset \mathbb{R}^d$ by minimizing objectives of the form $L(X) = \ell(\mathrm{Dgm}(X))$, where $\mathrm{Dgm}(X)$ is a persistence diagram. In practice, optimization is…
Cryo-electron tomography (cryoET) is a technique that captures images of biological samples at different tilts, preserving their native state as much as possible. Along with the partial tilt series and noise, one of the major challenges in…
In this paper we study multidimensional persistence modules [5,13] via what we call tame functors and noise systems. A noise system leads to a pseudo-metric topology on the category of tame functors. We show how this pseudo-metric can be…
In single-particle cryo-electron microscopy (cryo-EM), the efficient determination of orientation parameters for 2D projection images poses a significant challenge yet is crucial for reconstructing 3D structures. This task is complicated by…
Cryo-electron microscopy (cryo-EM) emerges as a pivotal technology for determining the architecture of cells, viruses, and protein assemblies at near-atomic resolution. Traditional particle picking, a key step in cryo-EM, struggles with…
Persistent homology has been widely used to discover hidden topological structures in data across various applications, including music data. To apply persistent homology, a distance or metric must be defined between points in a point cloud…
With more distributed energy resources (DERs) connected to distribution grids, better monitoring and control are needed, where identifying the topology accurately is the prerequisite. However, due to frequent re-configurations, operators…
Persistent homology is a relatively new tool often used for \emph{qualitative} analysis of intrinsic topological features in images and data originated from scientific and engineering applications. In this paper, we report novel…
We study the grokking phenomenon through the lens of topology. Using persistent homology on point clouds derived from the embedding matrices of a range of models trained on modular arithmetic with varying primes, we identify a clear and…
Topological correctness is critical for segmentation of tubular structures, which pervade in biomedical images. Existing topological segmentation loss functions are primarily based on the persistent homology of the image. They match the…
High-resolution transmission electron microscopy (HRTEM) is crucial for observing material's structural and morphological evolution at Angstrom scales, but the electron beam can alter these processes. Devices such as CMOS-based…
Persistent homology is one of the most popular methods in topological data analysis. An initial step in its use involves constructing a nested sequence of simplicial complexes. There is an abundance of different complexes to choose from,…
Quantifying the correlation between the complex structures of amorphous materials and their physical properties has been a long-standing problem in materials science. In amorphous Si, a representative covalent amorphous solid, the presence…
Persistent homology is a popular and useful tool for analysing finite metric spaces, revealing features that can be used to distinguish sets of unlabeled points and as input into machine learning pipelines. The famous stability theorem of…
Topology applied to real world data using persistent homology has started to find applications within machine learning, including deep learning. We present a differentiable topology layer that computes persistent homology based on level set…