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This paper studies the problem of encoding messages into sequences which can be uniquely recovered from some noisy observations about their substrings. The observed reads comprise consecutive substrings with some given minimum overlap. This…
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of…
Thinning is the removal of contour pixels/points of connected components in an image to produce their skeleton with retained connectivity and structural properties. The output requirements of a thinning procedure often vary with…
String diagrams are a graphical language used to represent processes that can be composed sequentially or in parallel, which correspond graphically to horizontal or vertical juxtaposition. In this paper we demonstrate how to compute the…
Results: We present an application that enables the quantitative analysis of multichannel 5-D (x, y, z, t, channel) and large montage confocal fluorescence microscopy images. The image sequences show stem cells together with blood vessels,…
Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. A standard approach to speed up this task is to compute "sketches" of the DNA reads (typically via…
Deep learning methods have been successfully used in various computer vision tasks. Inspired by that success, deep learning has been explored in magnetic resonance imaging (MRI) reconstruction. In particular, integrating deep learning and…
The recent success of implicit neural scene representations has presented a viable new method for how we capture and store 3D scenes. Unlike conventional 3D representations, such as point clouds, which explicitly store scene properties in…
Synthetic data is a scalable alternative to manual supervision, but it requires overcoming the sim-to-real domain gap. This discrepancy between virtual and real worlds is addressed by two seemingly opposed approaches: improving the realism…
Approximation of non-linear kernels using random feature maps has become a powerful technique for scaling kernel methods to large datasets. We propose $\textit{Tensor Sketch}$, an efficient random feature map for approximating polynomial…
We consider the compilation of a binary neural network's decision function into tractable representations such as Ordered Binary Decision Diagrams (OBDDs) and Sentential Decision Diagrams (SDDs). Obtaining this function as an OBDD/SDD…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
We propose a new abstraction set (SynopSet) that has a continuum of visual representations for the explanatory analysis of molecular dynamics simulations (MDS) in the DNA nanotechnology domain. By re-purposing the commonly used progress bar…
Crystal-structure phase mapping is a core, long-standing challenge in materials science that requires identifying crystal structures, or mixtures thereof, in synthesized materials. Materials science experts excel at solving simple systems…
We represent 3D shape by structured 2D representations of fixed length making it feasible to apply well investigated 2D convolutional neural networks (CNN) for both discriminative and geometric tasks on 3D shapes. We first provide a general…
The Watson-Crick complementary properties of DNA make DNA a useful tool for the self-assembly of various target complexes. Concepts from graph theory can be used to model the self-assembling process in which the vertices of the graph…
We study DNA self-assembly and DNA computation using a coarse-grained DNA model within the directional dynamic bonding framework {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. In our model, a single nucleotide or domain is…
A stretched DNA molecule which is also under- or overwound, undergoes a buckling transition forming intertwined looped domains called plectonemes. Here we develop a simple theory that extends the two-phase model of stretched supercoiled…
Deep language models learning a hierarchical representation proved to be a powerful tool for natural language processing, text mining and information retrieval. However, representations that perform well for retrieval must capture semantic…
DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…