22 papers · ranked by Valyu relevance
Joel Armstrong, Glenn Hickey, Mark Diekhans, Ian T. Fiddes + 17 more
'Adam M. Novak' 'Alden Deran' 'Qi Fang' 'Duo Xie' 'Shaohong Feng' 'Josefin Stiller' 'Diane Genereux' 'Jeremy Johnson' 'Voichita Dana Marinescu' 'Jessica Alföldi' 'Robert S. Harris' 'Kerstin Lindblad-Toh' 'David Haussler' 'Elinor Karlsson' 'Erich D. Jarvis' 'Guojie Zhang' 'Benedict Paten'] New genome assemblies have…
Joel Armstrong, Glenn Hickey, Mark Diekhans, Alden Deran + 13 more
Cactus, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequence. We describe progressive extensions to Cactus that enable reference-free alignment of…
Matthias Kruspe, Peter F Stadler
Background The quality of progressive sequence alignments strongly depends on the accuracy of the individual pairwise alignment steps since gaps that are introduced at one step cannot be removed at later aggregation steps. Adjacent insertions and deletions necessarily appear in arbitrary order in pairwise alignments…
Kieran Boyce, Fabian Sievers, Desmond G. Higgins
Background Progressive alignment is the standard approach used to align large numbers of sequences. As with all heuristics, this involves a tradeoff between alignment accuracy and computation time. Results We examine this tradeoff and find that, because of a loss of information in the early steps of the approach, the…
Mengmeng Kuang
This paper proposed a novel and straightforward approach to improve the accuracy of progressive multiple protein sequence alignment. We trained a decision-making model based on the convolutional neural networks and bi-directional long short term memory networks, and based on this model, we progressively aligned the…
Jaeyong Lee, Masato Mimura, Takafumi Moriya
Aligner-Encoders are recently proposed seq2seq end-to-end ASR models that replace decoder attention by predicting the uth token directly from the u-th encoder position, so the encoder must learn the alignment internally without cross-attention or a transducer lattice. In practice, this alignment often forms abruptly in…
Massimo Maiolo, Xiaolei Zhang, Manuel Gil, Maria Anisimova
Sequence alignment lies at the heart of many evolutionary and comparative genomics studies. However, the optimal alignment of multiple sequences is NP-hard, so that exact algorithms become impractical for more than a few sequences. Thus, state of the art alignment methods employ progressive heuristics, breaking the…
Cameron L.M. Gilchrist, Milot Mirdita, Martin Steinegger
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended our repository of available proteins structures, requiring fast and accurate MSTA methods. Here, we introduce FoldMason, a…
Tianyi Qiu, Yang Zhang, Xuchuan Huang, Jasmine Xinze Li + 2 more
'Yaodong Yang'] Frontier AI systems, including large language models (LLMs), hold increasing influence over the epistemology of human users. Such influence can reinforce prevailing societal values, potentially contributing to the lock-in of misguided moral beliefs and, consequently, the perpetuation of problematic…
Michał Modzelewski, Norbert Dojer
Background Progressive methods offer efficient and reasonably good solutions to the multiple sequence alignment problem. However, resulting alignments are biased by guide-trees, especially for relatively distant sequences. Results We propose MSARC, a new graph-clustering based algorithm that aligns sequence sets…
Adrienn Szabó, Ádám Novák, István Miklós, Jotun Hein
Background In this paper, we introduce a progressive corner cutting method called Reticular Alignment for multiple sequence alignment. Unlike previous corner-cutting methods, our approach does not define a compact part of the dynamic programming table. Instead, it defines a set of optimal and suboptimal alignments at…
Yuhang Zhang, Zhengyu Zhang, Muxin Liao, Shishun Tian + 3 more
—Generalizable semantic segmentation, aims to excel on unseen target domains, as a critical focus due to the widespread practical applications requiring high generalizability. Class-wise prototypes, which depict class-wise centroids, as a type of domain-invariant information are key to improving the model…
Mario João Jr., Alexandre C. Sena, Vinod E. F. Rebello, Yang Zhang
The problem of aligning multiple biological sequences has fascinated scientists for a long time. Over the last four decades, tens of heuristic-based Multiple Sequence Alignment (MSA) tools have been proposed, the vast majority being built on the concept of Progressive Alignment. It is known, however, that this approach…
Junyu Luo, Yusheng Zhao, Xiao Luo, Zhiping Xiao + 4 more
'Dacheng Tao' 'Ming Zhang'] Abstract—Unsupervised efficient domain adaptive retrieval aims to transfer knowledge from a labeled source domain to an unlabeled target domain, while maintaining low storage cost and high retrieval efficiency. However, existing methods typically fail to address potential noise in the target…
Álvaro Rubio-Largo, Miguel A. Vega-Rodríguez
The alignment among three or more nucleotides/amino-acids sequences at the same time is known as Multiple Sequence Alignment (MSA), an NP-hard optimization problem. The time complexity of finding an optimal alignment raises exponentially when the number of sequences to align increases. In this work, we deal with a…
Xiaobiao Huang
We propose a method to simultaneously determine the magnetic centers of multiple quadrupoles in a transport line or a storage ring. The method finds the magnet centers by correcting the orbit shift due to a change of the quadrupole gradient strengths with orbit correctors. The quadrupoles are selected with orbit…
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…
Maren Cosens, S. Wright, Aaron Brown, Michael P. Fitzgerald + 13 more
'Chris A. Johnson' 'Tucker Jones' 'Marc Kassis' 'Evan Kress' 'Renate Kupke' 'James Larkin' 'Kenneth Magnone' 'Rosalie McGurk' 'Nils-Erik Rundquist' 'Ji Man Sohn' 'Eric Wang' 'James Wiley' 'Sherry Yeh'] Maren Cosensa,b, Shelley A. Wrighta,b, Aaron Browna , Michael Fitzgeraldc , Chris Johnsonc , Tucker Jonesd , Marc…
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…
Peng Qiu, Xiang Lin, Hao Yan, Zebin Zhou + 3 more
beam-alignment-mechanism Authors: ['Peng Qiu' 'Xiang Lin' 'Hao Yan' 'Zebin Zhou' 'Hui‐Zong Duan' 'F. Zhu' 'H. Miao'] Abstract. Tilt-to-length (TTL) noise, caused by angular jitter and misalignment, is a major noise source in the inter-satellite interferometer for gravitational wave detection. However, the required…
Authors not listed
Generating molecules that rigorously satisfy three-dimensional (3D) pharmacophore constraints has remained a challenge in de novo drug design, despite rapid progress in molecular generative models. We present DiffPharm, a diffusion-based framework that embeds explicit pharmacophore control into the generative process.…
Justin Kwok, Giridar Vishwanathan, Kyung Sun Park, Bijal Patel + 3 more
Fluid flow is an inherent aspect of solution processing of conjugated polymers. Much of the existing work investigating the effect of flow has been phenomenological, lacking a direct and quantitative connection between the flow gradients and measurable quantities of the conformation or alignment of the conjugated…