Related papers: Improvements of the REDCRAFT Software Package
Optimizing Neural networks is a difficult task which is still not well understood. On the other hand, fixed representation methods such as kernels and random features have provable optimization guarantees but inferior performance due to…
Modern technology for producing extremely bright and coherent X-ray laser pulses provides the possibility to acquire a large number of diffraction patterns from individual biological nanoparticles, including proteins, viruses, and DNA.…
The paper investigates the problem of fitting protein complexes into electron density maps. They are represented by high-resolution cryoEM density maps converted into overlapping matrices and partly show a structure of a complex. The…
Motivation: Cellular Electron CryoTomography (CECT) enables 3D visualization of cellular organization at near-native state and in sub-molecular resolution, making it a powerful tool for analyzing structures of macromolecular complexes and…
We present a new method for real-time non-rigid dense correspondence between point clouds based on structured shape construction. Our method, termed Deep Point Correspondence (DPC), requires a fraction of the training data compared to…
Despite a short history, neural image codecs have been shown to surpass classical image codecs in terms of rate-distortion performance. However, most of them suffer from significantly longer decoding times, which hinders the practical…
A new deep neural network based on the WaveNet architecture (WNN) is presented, which is designed to grasp specific patterns in the NMR spectra. When trained at a fixed non-uniform sampling (NUS) schedule, the WNN benefits from pattern…
When evaluating the performance of a pre-trained model transferred to a downstream task, it is imperative to assess not only the in-distribution (ID) accuracy of the downstream model but also its capacity to generalize and identify…
In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…
Numerous studies have investigated the differences and similarities between protein structures determined by solution NMR spectroscopy and those determined by x-ray crystallography. A fundamental question is whether any observed differences…
Computational protein design has the potential to deliver novel molecular structures, binders, and catalysts for myriad applications. Recent neural graph-based models that use backbone coordinate-derived features show exceptional…
Neutronic calculations for reactors are a daunting task when using Monte Carlo (MC) methods. As high-performance computing has advanced, the simulation of a reactor is nowadays more readily done, but design and optimization with multiple…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Ultra-low-dose positron emission tomography (PET) reconstruction holds significant potential for reducing patient radiation exposure and shortening examination times. However, it may also lead to increased noise and reduced imaging detail,…
Deep Neural Networks (DNNs) are ubiquitous in today's computer vision land-scape, despite involving considerable computational costs. The mainstream approaches for runtime acceleration consist in pruning connections (unstructured pruning)…
We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling…
Parameter Recombination (PR) methods aim to efficiently compose the weights of a neural network for applications like Parameter-Efficient FineTuning (PEFT) and Model Compression (MC), among others. Most methods typically focus on one…
Structural dynamics of macromolecules is critical to their structural-function relationship. Cryogenic electron microscopy (CryoEM) provides snapshots of vitrified protein at different compositional and conformational states, and the…
Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…