Related papers: Comparing unsupervised learning methods for local …

Uniform Manifold Approximation and Projection (UMAP) is a widely used manifold learning technique for dimensionality reduction. This paper studies UMAP, supervised UMAP, and several competing dimensionality reduction methods, including…

We introduce a simple, fast, and easy to implement unsupervised learning algorithm for detecting different local environments on a single-particle level in colloidal systems. In this algorithm, we use a vector of standard bond-orientational…

We apply a recently developed unsupervised machine learning scheme for local atomic environments to characterize large-scale, disordered aggregates formed by sequence-defined macromolecules. This method provides new insight into the…

Owing to the advances in computational techniques and the increase in computational power, atomistic simulations of materials can simulate large systems with higher accuracy. Complex phenomena can be observed in such state-of-the-art…

UMAP (Uniform Manifold Approximation and Projection) is a novel manifold learning technique for dimension reduction. UMAP is constructed from a theoretical framework based in Riemannian geometry and algebraic topology. The result is a…

I present a strategy for unsupervised manifold learning on local atomic environments in molecular simulations based on simple rotation- and permutation-invariant three-body features. These features are highly descriptive, generalize to…

Uniform Manifold Approximation and Projection (UMAP) is one of the state-of-the-art methods for dimensionality reduction and data visualization. This is a tutorial and survey paper on UMAP and its variants. We start with UMAP algorithm…

We propose an unsupervised learning methodology with descriptors based on Topological Data Analysis (TDA) concepts to describe the local structural properties of materials at the atomic scale. Based only on atomic positions and without a…

One of the outstanding analytical problems in X-ray single particle imaging (SPI) is the classification of structural heterogeneity, which is especially difficult given the low signal-to-noise ratios of individual patterns and that even…

Molecular dynamics (MD) simulations present a data-mining challenge, given that they can generate a considerable amount of data but often rely on limited or biased human interpretation to examine their information content. By not asking the…

We present a new nonlinear dimensionality reduction method, MAPLE, that enhances UMAP by improving manifold modeling. MAPLE employs a self-supervised learning approach to more efficiently encode low-dimensional manifold geometry. Central to…

Identifying crystal defects is vital for unraveling the origins of many physical phenomena. Traditionally used order parameters are system-dependent and can be computationally expensive to calculate for long molecular dynamics simulations.…

Evaluating the (dis)similarity of crystalline, disordered and molecular compounds is a critical step in the development of algorithms to navigate automatically the configuration space of complex materials. For instance, a structural…

Unsupervised anomaly detection aims to detect defective parts of a sample by having access, during training, to a set of normal, i.e. defect-free, data. It has many applications in fields, such as industrial inspection or medical imaging,…

Manifold learning approaches seek the intrinsic, low-dimensional data structure within a high-dimensional space. Mainstream manifold learning algorithms, such as Isomap, UMAP, $t$-SNE, Diffusion Map, and Laplacian Eigenmaps do not use data…

Learning structures of 3D shapes is a fundamental problem in the field of computer graphics and geometry processing. We present a simple yet interpretable unsupervised method for learning a new structural representation in the form of 3D…

UMAP is a non-parametric graph-based dimensionality reduction algorithm using applied Riemannian geometry and algebraic topology to find low-dimensional embeddings of structured data. The UMAP algorithm consists of two steps: (1) Compute a…

Detecting structures at the particle scale within plastically deformed crystalline materials allows a better understanding of the occurring phenomena. While previous approaches mostly relied on applying hand-chosen criteria on different…

Deep clustering has increasingly been demonstrating superiority over conventional shallow clustering algorithms. Deep clustering algorithms usually combine representation learning with deep neural networks to achieve this performance,…

Dimensionality reduction is a fundamental technique in machine learning and data analysis, enabling efficient representation and visualization of high-dimensional data. This paper explores five key methods: Principal Component Analysis…