13 papers · ranked by Valyu relevance
Peter L. Bartlett, Chris Junchi Li, Jingfeng Wu, Bin Yu
In the field of optimization, developing accelerated methods for solving minimax and fixed-point problems remains a fundamental challenge. This paper presents a novel family of dual accelerated algorithms that achieve optimal convergence rates for both minimax and fixed-point problems. By exploring new anchoring…
Harisankar Sadasivan, Milos Maric, Eric Dawson, Vishanth Iyer + 2 more
Long read sequencing technology is becoming increasingly popular for Precision Medicine applications like variant calling from Whole Genome Sequencing (WGS) and for metagenomics applications like microbial abundance estimation. Minimap2 is the state-of-the-art aligner and mapper used by the leading long read sequencing…
Yaniv Swiel, Jean-Tristan Brandenburg, Mahtaab Hayat, Wenlong Carl Chen + 2 more
Genome-wide association studies (GWASs) analyse genetic variation over the genomes of many individuals in an attempt to identify single nucleotide polymorphisms (SNPs) associated with complex phenotypes. To capture a large amount of genetic variation and increase the chance of detecting associated SNPs, modern GWASs…
Anders Pitman, Cathy Yang, Yi Qiao
Next-generation sequencing now produces whole-genome data in hours, but downstream variant calling remains a multi-hour to multi-day bottleneck that excludes genomic analysis from time-critical clinical settings. GPU acceleration offers a natural path forward — variant calling is inherently parallelizable across…
Zhejian Yu
Fast simulation of next-generation sequencing (NGS) data is vital for software development and benchmarking. Here we describe art_modern, an accelerated ART simulator that can simulate various NGS data. We accelerated ART using updated sampling algorithms, single-instruction multiple-data (SIMD) instruction-set…
Felix Kallenborn, Fawaz Dabbaghie, Martin Steinegger, Bertil Schmidt
The continually increasing volume of sequence data results in a growing demand for fast implementations of core algorithms. Computation of pairwise alignments based on dynamic programming is an important part in many bioinformatics pipelines and a major contributor to overall runtime due to the associated quadratic…
Peiyu Zong, Wenpeng Deng, Jian Liu, Jue Ruan
The rapid advancements in sequencing length necessitate the adoption of increasingly efficient sequence alignment algorithms. The Needleman-Wunsch method introduces the foundational dynamic programming (DP) matrix calculation for global alignment, which evaluates the overall alignment of sequences. However, this method…
Tim Anderson, Travis J. Wheeler
Sequence alignment lies at the heart of genome sequence annotation. While the BLAST suite of alignment tools has long held an important role in alignment-based sequence database search, greater sensitivity is achieved through the use of profile hidden Markov models (pHMMs). The Forward algorithm that provides much of…
Kisaru Liyanage, Hiruna Samarakoon, Sri Parameswaran, Hasindu Gamaarachchi
minimap2 is the gold-standard software for reference-based sequence mapping in third-generation long-read sequencing. While minimap2 is relatively fast, further speedup is desirable, especially when processing a multitude of large datasets. In this work, we present minimap2-fpga, a hardware-accelerated version of…
Hossein Mokhtarzzadeh, Rosie Richards, Thomas Geijtenbeek
Self-paced treadmills are increasingly used in clinical and research settings. Using self-paced (SP) treadmills, researchers can simulate overground walking while participants can walk with different but comfortable gait speeds in a controlled environment. Several algorithms have been designed for self-paced treadmills…
Ragnar Groot Koerkamp, Igor Martayan
Because of the rapidly-growing amount of sequencing data, computing sketches of large textual datasets has become an essential preprocessing task. These sketches are typically much smaller than the input sequences, but preserve sufficient information for downstream analysis. Minimizers are an especially popular…
Sumit Walia, Zexing Chen, Yu-Hsiang Tseng, Yatish Turakhia
Distance-based methods are commonly used to reconstruct phylogenies for a variety of applications, owing to their excellent speed, scalability, and theoretical guarantees. However, classical de novo algorithms are hindered by cubic time and quadratic memory complexity, which makes them impractical for emerging datasets…
Zhengwu Zhang, Arun Venkataraman, Martin Cole, Tianrui Ye + 3 more
Accelerated imaging has been broadly adopted in diffusion MRI studies, yet little is known about its impacts. Acceleration can achieve higher spatial and q-space resolution in shorter time, reduce motion artifacts, and reduce patient burden. However, it leads to noise amplification, and its impacts in clinical cohorts…