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Structure-based molecular ML (SBML) models can be highly sensitive to input geometries and give predictions with large variance. We present an approach to mitigate the challenge of selecting conformations for such models by generating…
Clustering in image analysis is a central technique that allows to classify elements of an image. We describe a simple clustering technique that uses the method of similarity matrices. We expand upon recent results in spectral analysis for…
Formation, maintenance and physiology of high-density protein-enriched organized nanodomains, first observed in electron microscopy images, remains challenging to investigate due to their small sizes. However, these regions regulate…
Correlative computational microscopy can accelerate imaging and modeling of cellular dynamics by relaxing trade-offs inherent to dynamic imaging. Existing computational microscopy frameworks are either specialized or overly generic,…
Cryo-EM data processing typically focuses on the structure of the main conformational state under investigation and discards images that belong to other states. This approach can reach atomic resolution, but ignores vast amounts of valuable…
Cryo-electron microscopy (cryo-EM) is a powerful technique for determining high-resolution 3D biomolecular structures from imaging data. Its unique ability to capture structural variability has spurred the development of heterogeneous…
Multidimensional separations data have the capacity to reveal detailed information about complex biological samples. However, data analysis has been an ongoing challenge in the area since the peaks that represent chemical factors may drift…
Understanding structure-property relationships in complex materials requires integrating complementary measurements across multiple length scales. Here we propose an interpretable "multimodal" machine learning framework that unifies…
We present a structural clustering algorithm for large-scale datasets of small labeled graphs, utilizing a frequent subgraph sampling strategy. A set of representatives provides an intuitive description of each cluster, supports the…
Many proposals have already been made for realizing programmable matter, ranging from shape-changing molecules, DNA tiles, and synthetic cells to reconfigurable modular robotics. Envisioning systems of nano-sensors devices, we are…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
Luminescence imaging is invaluable for studying biological and material systems, particularly when advanced protocols that exploit temporal dynamics are employed. However, implementing such protocols often requires custom instrumentation,…
Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly…
We present the compact group approach to analysis of the long-wavelength dielectric and optical characteristics of substances which can be modeled as macroscopically homogeneous and isotropic systems of hard dielectric particles embedded…
Recent decades have seen the discovery of numerous complex materials. At the root of the complexity underlying many of these materials lies a large number of possible contending atomic- and larger-scale configurations and the intricate…
A transfer-matrix algorithm is presented herein as a beginning to study the transmission characteristics of coherent light through three-dimensional periodic microstructures, in which the structures are treated as two-dimensional-layer…
Cryogenic electron microscopy (cryo-EM) provides a unique opportunity to study the structural heterogeneity of biomolecules. Being able to explain this heterogeneity with atomic models would help our understanding of their functional…
High-throughput synthesis of solution-processable structurally variable small-molecule semiconductors is both an opportunity and a challenge. A large number of diverse molecules provide a possibility for quick material discovery and machine…
We present in this work a new methodology to design kernels on data which is structured with smaller components, such as text, images or sequences. This methodology is a template procedure which can be applied on most kernels on measures…
We present the graph-based molecule software Molassembler for building organic and inorganic molecules. Molassembler provides algorithms for the construction of molecules built from any set of elements from the periodic table. In…