Related papers: Correcting pervasive errors in RNA crystallography…
Accurate crystal structure determination is critical across all scientific disciplines involving crystalline materials. However, solving and refining inorganic crystal structures from powder X-ray diffraction (PXRD) data is traditionally a…
Augmentation for dense prediction typically relies on either sample mixing or generative synthesis. Mixing improves robustness but misaligned masks yield soft label ambiguity. Diffusion synthesis increases apparent diversity but, when…
We presented a new 3D refinement method for Cryo-EM single particle analysis which can improve the resolution of final electron density map in this paper. We proposed to enforce both sparsity and smoothness to improve the regularity of…
As an entry for the 2001 Gordon Bell Award in the "special" category, we describe our 3-d, hybrid, adaptive mesh refinement (AMR) code, Enzo, designed for high-resolution, multiphysics, cosmological structure formation simulations. Our…
Our world is ambiguous and this is reflected in the data we use to train our algorithms. This is particularly true when we try to model natural processes where collected data is affected by noisy measurements and differences in measurement…
Backtracking of RNA polymerase (RNAP) is an important pausing mechanism during DNA transcription that is part of the error correction process that enhances transcription fidelity. We model the backtracking mechanism of RNA polymerase, which…
We introduce the first learning-based dense matching algorithm, termed Equirectangular Projection-Oriented Dense Kernelized Feature Matching (EDM), specifically designed for omnidirectional images. Equirectangular projection (ERP) images,…
This paper presents novel strategies for spawning and fusing submaps within an elastic dense 3D reconstruction system. The proposed system uses spatial understanding of the scanned environment to control memory usage growth by fusing…
Models for RNA secondary structures (the topology of folded RNA) without pseudo knots are disordered systems with a complex state-space below a critical temperature. Hence, a complex dynamical (glassy) behavior can be expected, when…
Gravitational instabilities naturally give rise to multi-scale structure, which is difficult for traditional Eulerian hydrodynamic methods to accurately evolve. This can be circumvented by adaptively adding resolution (in the form of…
The estimation of a precision matrix is a crucial problem in various research fields, particularly when working with high dimensional data. In such settings, the most common approach is to use the penalized maximum likelihood. The…
The three-dimensional conformations of non-coding RNAs underpin their biochemical functions but have largely eluded experimental characterization. Here, we report that integrating a classic mutation/rescue strategy with high-throughput…
Dense light field depth estimation remains challenging due to sparse angular sampling, occlusion boundaries, textureless regions, and the cost of exhaustive multi-view matching. We propose \emph{Deep Spectral Epipolar Representation}…
Experimentally obtained X-ray diffraction (XRD) patterns can be difficult to solve, precluding the full characterization of materials, pharmaceuticals, and geological compounds. Herein, we propose a method based upon a multi-objective…
Consistently predicting biopolymer structure at atomic resolution from sequence alone remains a difficult problem, even for small sub-segments of large proteins. Such loop prediction challenges, which arise frequently in comparative…
The task of reassembly is a significant challenge across multiple domains, including archaeology, genomics, and molecular docking, requiring the precise placement and orientation of elements to reconstruct an original structure. In this…
Existing training criteria in automatic speech recognition(ASR) permit the model to freely explore more than one time alignments between the feature and label sequences. In this paper, we use entropy to measure a model's uncertainty, i.e.…
Dense retrieval systems increasingly need to handle complex queries. In many realistic settings, users express intent through long instructions or task-specific descriptions, while target documents remain relatively simple and static. This…
The structure of an RNA molecule plays a significant role in its biological function. Predicting structure given a one dimensional sequence of RNA nucleotide bases is a difficult and important problem. Many computer programs (known as in…
Entity resolution (ER) is a key data integration problem. Despite the efforts in 70+ years in all aspects of ER, there is still a high demand for democratizing ER - humans are heavily involved in labeling data, performing feature…