26 papers · ranked by Valyu relevance
Jun He, Dejiao Zhang, Laura Balzano, Tao Tao
Robust high-dimensional data processing has witnessed an exciting development in recent years. Theoretical results have shown that it is possible using convex programming to optimize data fit to a low-rank component plus a sparse outlier component. This problem is also known as Robust PCA, and it has found application…
Yi Wang, Zihang He, Yunjie Yan
Multimodal spatial omics enables systematic characterization of tissue organization by jointly profiling molecular features across transcriptomic, proteomic, and metabolomic layers. However, integrative analysis across sections and modalities is frequently hindered by non-linear tissue distortions, mismatched spatial…
Sergiy Popovych, Thomas Macrina, Nico Kemnitz, Manuel Castro + 9 more
The reconstruction of neural circuits from serial section electron microscopy (ssEM) images is being accelerated by automatic image segmentation methods. Segmentation accuracy is often limited by the preceding step of aligning 2D section images to create a 3D image stack. Precise and robust alignment in the presence of…
Martyna Poreba, François Goulette
With the variety of measurement techniques available on the market today, fusing multi-source complementary information into one dataset is a matter of great interest. Target-based, point-based and feature-based methods are some of the approaches used to place data in a common reference frame by estimating its…
Yue Hu
Protein structure alignment is a fundamental task in computational biology. While the TM-score is a gold standard for evaluating structural similarity, its direct optimization is challenging. Many algorithms, therefore, rely on heuristic or combinatorial approaches. In this work, we present OTMalign, a novel algorithm…
Donatas Sederevičius, Atle Bjørnerud, Kristine B. Walhovd, Koen Van Leemput + 2 more
Variations in image intensities between magnetic resonance imaging (MRI) acquisitions affect the subsequent image processing and its derived outcomes. Therefore, it is necessary to normalize images of different scanners/acquisitions, especially for longitudinal studies where a change of scanner or pulse sequence often…
Yutaka Saito, Kengo Sato, Yasubumi Sakakibara
Background Computational prediction of noncoding RNAs (ncRNAs) is an important task in the post-genomic era. One common approach is to utilize the profile information contained in alignment data rather than single sequences. However, this strategy involves the possibility that the quality of input alignments can…
Jose Sergio Hleap, Melania E. Cristescu, Dirk Steinke
Amplicons to Global Gene (A2G^2^) is a Python wrapper that uses MAFFT and an “Amplicon to Gene” strategy to align very large numbers of sequences while improving alignment accuracy. It is specially developed to deal with conserved genes, where traditional aligners introduce a significant amount of gaps. A2G^2^…
Jieyu Zhang, Yuanying Qiu, Xuechao Duan, Kangli Xu + 1 more
Horizontal docking assembly is a fundamental process in the aerospace assembly, where intelligent measurement and adjustable support systems are urgently needed to achieve higher automation and precision. Thus, a laser scanning approach is employed to obtain the point cloud from a laser scanning sensor. And a method of…
Yue Hu, Zanxia Cao, Yingchao Liu
The Root-Mean-Square Deviation (RMSD) metric, coupled with the Kabsch algorithm for optimal superposition, represents a cornerstone of quantitative structural biology. However, its application is fundamentally limited to the comparison of structures with a pre-defined, one-to-one correspondence of equal length…
Davide Verzotto, Audrey S. M. Teo, Axel M. Hillmer, Niranjan Nagarajan
'Niranjan Nagarajan'] Background Resolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and genome-mapping technologies (for example, optical restriction mapping). In particular, mapping…
Lingjie Su, Wei Xu, Shuyang Zhao, Yuqi Cheng + 1 more
Clouds Considering Local Consistency Authors: ['Lingjie Su' 'Wei Xu' 'Shuyang Zhao' 'Yuqi Cheng' 'Wenlong Li'] Abstract— In robotic inspection, joint registration of multiple point clouds is an essential technique for estimating the transformation relationships between measured parts, such as multiple blades in a…
Verzotto Davide, Audrey S.M. Teo, Axel M. Hillmer, Nagarajan Niranjan
Resolution of complex repeat structures and rearrangements in the assembly and analysis of large eukaryotic genomes is often aided by a combination of high-throughput sequencing and mapping technologies (e.g. optical restriction mapping). In particular, mapping technologies can generate sparse maps of large DNA…
Yael Harpaz, Yoel Shkolnisky
A common task in cryo-electron microscopy data processing is to compare three-dimensional density maps of macromolecules. In this paper, we propose an algorithm for aligning three-dimensional density maps, which exploits common lines between projection images of the maps. The algorithm is fully automatic and handles…
Heng Yang, Luca Carlone
—We propose a robust approach for the registration of two sets of 3D points in the presence of a large amount of outliers. Our first contribution is to reformulate the registration problem using a Truncated Least Squares (TLS) cost that makes the estimation insensitive to a large fraction of spurious pointto-point…
Authors not listed
In molecular machine learning, the choice of the representation of molecules can have a significant impact on model performance. However, understanding the root causes of these performance differences often proves challenging. One promising approach to explore model behavior is representational alignment, which…
Weiwei Lyu, Xianghong Cheng, Jinling Wang
Transfer alignment on a moving base under a complex dynamic environment is one of the toughest challenges in a strapdown inertial navigation system (SINS). With the aim of improving rapidity and accuracy, velocity plus attitude matching is applied in the transfer alignment model. Meanwhile, the error compensation model…
Seong Hun Lee, Javier Civera
— In this work, we propose a novel method for robust single rotation averaging that can efficiently handle an extremely large fraction of outliers. Our approach is to minimize the total truncated least unsquared deviations (TLUD) cost of geodesic distances. The proposed algorithm consists of three steps: First, we…
Ibrahim Jubran, Alaa Maalouf, Ron Kimmel, Dan Feldman
The goal of the alignment problem is to align a (given) point cloud = {1, · · · , } to another (observed) point cloud = {1, · · · , }. That is, to compute a rotation matrix ∈ R 3×3 and a translation vector ∈ R 3 that minimize the sum of paired distances ∑︀ =1 ( − , ) for some distance function . A harder version is the…
Rasha Atwi, Ye Wang, Simone Sciabola, Adam Antoszewski
Efficient virtual screening techniques are critical in drug discovery for identifying potential drug candidates. We present an open-source package for molecular alignment and 3D similarity calculations optimized for large-scale virtual screening of small molecules. This work parallels widely used proprietary tools and…
Authors not listed
Tissue engineering and regenerative medicine applications require the integration of multifunctional materials, offering appropriate mechanical cues and geometric guidance to support tissue-specific cell differentiation. In this context, supramolecular gel noodles formed by ionic cross-linking of pre-assembled micellar…
Saeed Gholami Shahbandi, Martin Magnusson
In many applications of autonomous mobile robots the following problem is encountered. Two maps of the same environment are available, one a prior map and the other a sensor map built by the robot. To benefit from all available information in both maps, the robot must find the correct alignment between the two maps.…
Tiancheng Li, Peter Walker, Dima A. Hammoud, Liang Zhao + 1 more
Orthopedic Surgery Authors: ['Tiancheng Li' 'Peter Walker' 'Dima A. Hammoud' 'Liang Zhao' 'Shoudong Huang'] Abstract—In computer-assisted orthopedic surgery (CAOS), accurate pre-operative to intra-operative bone registration is an essential and critical requirement for providing navigational guidance. This registration…
Marjan Hadian-Jazi, Alireza Sadri, D. G. Waterman
This article introduces RGFlib, a Python package for robust statistical analysis. The package is a useful tool for a variety of tasks in X-ray crystallography data analysis, such as peak-finding, bad pixel mask making and other outlier-detection tasks.
Dimitris Gkoumas, Maria Liakata
The intersection of chemistry and Artificial Intelligence (AI) is an active area of research focused on accelerating scientific discovery. While using large language models (LLMs) with scientific modalities has shown potential, there are significant challenges to address, such as improving training efficiency and…
Joseph Redshaw, Darren Ting, Alex Brown, Jonathan Hirst + 1 more
Antimicrobial peptides (AMPs) represent a potential solution to the growing problem of antimicrobial resistance, yet their identification through wet-lab experiments is a costly and timeconsuming process. Accurate computational predictions would allow rapid in silico screening of candidate AMPs, thereby accelerating…