Related papers: Improvements of the REDCRAFT Software Package
Forest mapping provides critical observational data needed to understand the dynamics of forest environments. Notably, tree diameter at breast height (DBH) is a metric used to estimate forest biomass and carbon dioxide sequestration. Manual…
Discovering the 3D atomic structure of molecules such as proteins and viruses is a fundamental research problem in biology and medicine. Electron Cryomicroscopy (Cryo-EM) is a promising vision-based technique for structure estimation which…
This review article provides an overview of structurally oriented experimental datasets that can be used to benchmark protein force fields, focusing on data generated by nuclear magnetic resonance (NMR) spectroscopy and room temperature…
Functional or non-coding RNAs are attracting more attention as they are now potentially considered valuable resources in the development of new drugs intended to cure several human diseases. The identification of drugs targeting the…
Most molecular diagram parsers recover chemical structure from raster images (e.g., PNGs). However, many PDFs include commands giving explicit locations and shapes for characters, lines, and polygons. We present a new parser that uses these…
Neural network decoding algorithms are recently introduced by Nachmani et al. to decode high-density parity-check (HDPC) codes. In contrast with iterative decoding algorithms such as sum-product or min-sum algorithms in which the weight of…
Accurate treatment of amide resonance is important in electronic structure calculation of protein, for Resonance-Assisted Hydrogen Bonding in the hydrogen bonded chains of backbone amides of protein secondary structures such as beta sheets…
Far-UV circular dichroism (CD) spectroscopy provides a rapid, sensitive, nondestructive tool to analyze protein conformation by monitoring secondary structure composition. Originally intended for educational purposes, a spreadsheet-based…
Identification and alignment of three-dimensional folding of proteins may yield useful information about relationships too remote to be detected by conventional methods, such as sequence comparison, and may potentially lead to prediction of…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
We challenge the common assumption that deeper decoder architectures always yield better performance in point cloud reconstruction. Our analysis reveals that, beyond a certain depth, increasing decoder complexity leads to overfitting and…
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…
We present MRPC, an R package that learns causal graphs with improved accuracy over existing packages, such as pcalg and bnlearn. Our algorithm builds on the powerful PC algorithm, the canonical algorithm in computer science for learning…
Several well known large scale linear programming decomposition methodologies exist. Benders Decomposition, which covers the case where some small subset of variables link the otherwise separable subproblems. Dantzig-Wolfe decomposition and…
Interactions of protons with nuclei are modeled in a form that is suitable for Monte Carlo simulation of proton transport. The differential cross section (DCS) for elastic collisions of protons with neutral atoms is expressed as the product…
Given the amino acid sequence of a protein, researchers often infer its structure and function by finding homologous, or evolutionarily-related, proteins of known structure and function. Since structure is typically more conserved than…
The problem of reconstructing and identifying intracellular protein signaling and biochemical networks is of critical importance in biology today. We sought to develop a mathematical approach to this problem using, as a test case, one of…
Segmentation is one of the most significant steps in image processing. Segmenting an image is a technique that makes it possible to separate a digital image into various areas based on the different characteristics of pixels in the image.…
The interaction between proteins and nucleic acids is crucial for processes that sustain cellular function, including DNA maintenance and the regulation of gene expression and translation. Amino acid mutations in protein-nucleic acid…
Quality control (QC) of MR images is essential to ensure that downstream analyses such as segmentation can be performed successfully. Currently, QC is predominantly performed visually and subjectively, at significant time and operator cost.…