22 papers · ranked by Valyu relevance
Tiehang Duan, José P. Pinto, Xiaohui Xie
Motivation: With the development of droplet based systems, massive single cell transcriptome data has become available, which enables analysis of cellular and molecular processes at single cell resolution and is instrumental to understanding many biological processes. While state-of-the-art clustering methods have been…
Daniel Kornai, Xiyun Jiao, Jiayi Ji, Tomáš Flouri + 2 more
'Robert Thomson'] Title: Abstract The multispecies coalescent (MSC) model accommodates genealogical fluctuations across the genome and provides a natural framework for comparative analysis of genomic sequence data from closely related species to infer the history of species divergence and gene flow. Given a set of…
Huan Gao, Yanqing Cen, Bo Liu, Xianghui Song + 3 more
'Felipe Jiménez'] To solve the problems of congestion and accident risk when multiple vehicles merge into the merging area of a freeway, a platoon split collaborative merging (PSCM) method was proposed for an on-ramp connected and automated vehicle (CAV) platoon under a mixed traffic environment composed of…
Beatrice Åkerblom, Elias Castegren, Tobias Wrigstad
The array is a fundamental data structure that provides an efficient way to store and retrieve non-sparse data contiguous in memory. Arrays are important for the performance of many memory-intensive applications due to the design of modern memory hierarchies: contiguous storage facilitates spatial locality and…
Aniruddha R. Upadhye, Chaitanya Kolluru, Lindsey Druschel, Luna Al Lababidi + 13 more
Vagus nerve stimulation (VNS) is FDA approved for stroke rehabilitation, epilepsy and depression; however, the underlying vagus functional anatomy underlying the implant is poorly understood. We used microCT to quantify fascicular structure and neuroanatomy within human cervical vagus nerves. Fascicles split or merged…
Daniel Kornai, Tomáš Flouri, Ziheng Yang
The multispecies coalescent (MSC) model accommodates genealogical fluctuations across the genome and provides a natural framework for comparative analysis of genomic sequence data to infer the history of species divergence and gene flow. Given a set of populations, hypotheses of species delimitation (and species…
Patrick J. Monnahan, Jean-Michel Michno, Christine H. O’Connor, Alex B. Brohammer + 3 more
Advances in sequencing technologies have led to the release of reference genomes and annotations for multiple individuals within more well-studied systems. While each of these new genome assemblies shares significant portions of synteny between each other, the annotated structure of gene models within these regions can…
Patrick J. Monnahan, Jean-Michel Michno, Christine O’Connor, Alex B. Brohammer + 3 more
Background Advances in sequencing technologies have led to the release of reference genomes and annotations for multiple individuals within more well-studied systems. While each of these new genome assemblies shares significant portions of synteny between each other, the annotated structure of gene models within these…
Philip M. Hubbard, Stuart Berg, Ting Zhao, Donald J. Olbris + 6 more
Recent advances in automatic image segmentation and synapse prediction in electron microscopy (EM) datasets of the brain enable more efficient reconstruction of neural connectivity. In these datasets, a single neuron can span thousands of images containing complex tree-like arbors with thousands of synapses. While…
Brendan Celii, Stelios Papadopoulos, Zhuokun Ding, Paul G. Fahey + 54 more
We are now in the era of millimeter-scale electron microscopy (EM) volumes collected at nanometer resolution (1; Consortium et al., 2021). Dense reconstruction of cellular compartments in these EM volumes has been enabled by recent advances in Machine Learning (ML) (3; 4; 5; 6). Automated segmentation methods produce…
Philip Bille, Mikko Berggren Ettienne, Inge Li Gørtz
We revisit the mergeable dictionaries with shift problem, where the goal is to maintain a family of sets subject to search, split, merge, make-set, and shift operations. The search, split, and make-set operations are the usual well-known textbook operations. The merge operation merges two sets and the shift operation…
Jesper Larsson Träff
This note makes an observation that significantly simplifies a number of previous parallel, two-way merge algorithms based on binary search and sequential merge in parallel. First, it is shown that the additional merge step of distinguished elements as found in previous algorithms is not necessary, thus simplifying the…
Oded Green, Saher Odeh, Yitzhak Birk
We present a novel, visually intuitive approach to partitioning two input sorted arrays into pairs of contiguous sequences of elements, one from each array, such that 1) each pair comprises any desired total number of elements, and 2) the elements of each pair form a contiguous sequence in the output merged sorted…
Bérenger Bramas, Quentin Bramas
In this paper, we present several improvements in the parallelization of the in-place merge algorithm, which merges two contiguous sorted arrays into one with an O(T) space complexity (where T is the number of threads). The approach divides the two arrays into as many pairs of partitions as there are threads available…
Alessandro Bria, Massimo Bernaschi, Massimiliano Guarrasi, Giulio Iannello
'Giulio Iannello'] Due to the limited field of view of the microscopes, acquisitions of macroscopic specimens require many parallel image stacks to cover the whole volume of interest. Overlapping regions are introduced among stacks in order to make it possible automatic alignment by means of a 3D stitching tool. Since…
Xiaobo Sun, Jingjing Gao, Peng Jin, Celeste Eng + 7 more
For most bioinformatics researchers, their daily working environment is still traditional in-house HPC clusters or stand-alone powerful servers (with cores ≥16 and memory ≥200 GB) rather than heterogeneous cloud-based clusters. Therefore, we also implement a parallel multiway-merge program running on a single machine…
Trevor Gokey, David L. Mobley
Molecular mechanics force fields require a chemical perception model to assign parameters to molecules. A recent advancement in force fields is the use of the SMARTS substructure query language as the perception model. Although it is straightforward to write SMARTS patterns to define new force field parameters, it is…
Jamshed Khan, Tobias Rubel, Erin Molloy, Laxman Dhulipala + 1 more
Purpose String indexes such as the suffix array (sa) and the closely related longest common prefix (lcp) array are fundamental objects in bioinformatics and have a wide variety of applications. Despite their importance in practice, few scalable parallel algorithms for constructing these are known, and the existing…
Authors not listed
Genetic Algorithms are a powerful method to solve optimization problems with complex cost functions over vast search spaces that rely in particular on recombining parts of previous solutions. Crossover operators play a crucial role in this context. Here, we describe a large class of these operators designed for…
Guido Pauli, G. Joseph Ray, Anton Bzhelyansky, Birgit Jaki + 18 more
Classical 1D 1H NMR spectra are prototypic for NMR spectroscopy in that they represent a wealth of chemical information encoded into convoluted graphs or patterns that contain complex features (aka multiplets), even for seemingly simple molecules. Accordingly, the utility of NMR depends on the theoretical and visual…
Gunther Schadow, Yulia Borodina, Victorien Delannée, Wolf-Dietrich Ihlenfeldt + 2 more
There are numerous formats and data models for describing reaction-related data. However, each offers only a limited coverage of the multitude of information that can be of interest to a broad user base in the context of chemical reactions. Structured Product Labeling (SPL) is a robust yet fairly light public XML…
Authors not listed
Today, machine learning models are employed extensively to predict the physicochemical and biological properties of molecules. Their performance is typically evaluated on in-distribution (ID) data, i.e., data originating from the same distribution as the training data. However, the real-world applications of such…