24 papers · ranked by Valyu relevance
Iztok Fister, Iztok Fister
The main deficiency of the algorithms running on digital computers nowadays is their inability to change themselves during the execution. In line with this, the paper introduces the so-called replicated algorithms, inspired by the concept of developing a human brain. Similar to the human brain, where the process of…
Andrey Grabovsky, Vitaly Vanchurin
We analyze algorithmic and computational aspects of biological phenomena, such as replication and programmed death, in the context of machine learning. We use two different measures of neuron efficiency to develop machine learning algorithms for adding neurons to the system (i.e. replication algorithm) and removing…
Junyu Zhu, Chuanhe Huang, Xiying Fan, Sipei Guo + 1 more
Efficient data dissemination in vehicular ad hoc networks (VANETs) is a challenging issue due to the dynamic nature of the network. To improve the performance of data dissemination, we study distributed data replication algorithms in VANETs for exchanging information and computing in an arbitrarily-connected network of…
Camille Coti
—Communication-avoiding algorithms allow redundant computations to minimize the number of inter-process communications. In this paper, we propose to exploit this redundancy for fault-tolerance purpose. We illustrate this idea with Q R factorization of tall and skinny matrices, and we evaluate the number of failures our…
Khatereh Sabaghian, Keyhan Khamforoosh, Abdolbaghi Ghaderzadeh, Mehdi Keshavarz-Ghorabaee
'Mehdi Keshavarz-Ghorabaee'] As the amounts of data and use of distributed systems for data storage and processing have increased, reducing the number of replications has turned into a crucial requirement in these systems, which has been addressed by plenty of research. In this paper, an algorithm has been proposed to…
Mahnaz Khojand, Mehdi Fatan Serj, S. H. H. N. Ashrafi, Vahideh Namaki
'Vahideh Namaki'] Data grid replication is an effective method to achieve efficient and fault tolerant data access while reducing access latency and bandwidth consumption in grids. Since we have storage limitation, a replica should be created in the best site. Through evaluation of previously suggested algorithms, we…
Foto Afrati, Anish Das Sarma, Semih Salihoğlu, Jeffrey D. Ullman
A significant amount of recent research work has addressed the problem of solving various data management problems in the cloud. The major algorithmic challenges in map-reduce computations involve balancing a multitude of factors such as the number of machines available for mappers/reducers, their memory requirements…
Foto Afrati, Anish Das Sarma, Semih Salihoğlu, Jeffrey D. Ullman
In this paper we study the tradeoff between parallelism and communication cost in a map-reduce computation. For any problem that is not "embarrassingly parallel," the finer we partition the work of the reducers so that more parallelism can be extracted, the greater will be the total communication between mappers and…
Scott Norton, Jorge Vaquero-Garcia, Yoseph Barash
A key component in many RNA-Seq based studies is contrasting multiple replicates from different experimental conditions. In this setup replicates play a key role as they allow to capture underlying biological variability inherent to the compared conditions, as well as experimental variability. However, what constitutes…
Nour Mostafa, Yehia Kotb, Zakwan Al-Arnaout, Samer Alabed + 2 more
'Ahmed Younes Shdefat' 'Gregor Schiele'] The design and management of smart cities and the IoT is a multidimensional problem. One of those dimensions is cloud and edge computing management. Due to the complexity of the problem, resource sharing is one of the vital and major components that when enhanced, the…
Simon J. Hickinbotham, Susan Stepney, Paulien Hogeweg
Parasitism emerges readily in models and laboratory experiments of RNA world and would lead to extinction unless prevented by compartmentalization or spatial patterning. Modelling replication as an active computational process opens up many degrees of freedom that are exploited to meet environmental challenges, and to…
Othon Michail
In this work, we consider a solution of automata similar to Population Protocols and Network Constructors. The automata (also called nodes) move passively in a well-mixed solution without being capable of controlling their movement. However, the nodes can cooperate by interacting in pairs. Every such interaction may…
J Kyle Medley, Shaik Asifullah, Joseph Hellerstein, Herbert M Sauro
Mechanistic kinetic models of biological pathways are an important tool for understanding biological systems. Constructing kinetic models requires fitting the parameters to experimental data. However, parameter fitting on these models is a non–convex, non–linear optimization problem. Many algorithms have been proposed…
Zhipeng Gui, Manzhu Yu, Chaowei Yang, Yunfeng Jiang + 8 more
'Jizhe Xia' 'Qunying Huang' 'Kai Liu' 'Zhenlong Li' 'Mohammed Anowarul Hassan' 'Baoxuan Jin' 'M. Sohel Rahman'] Dust storm has serious disastrous impacts on environment, human health, and assets. The developments and applications of dust storm models have contributed significantly to better understand and predict the…
Pelin Icer Baykal, Mike Simonov, Dhrithi Deshpande, Ful Belin Korukoglu + 8 more
Genomic research relies on accurate and reproducible computational analyses of DNA sequencing data to draw reliable biological conclusions. Read mapping, the process of aligning reads to a reference genome, is central to many applications, including variant detection and comparative genomics. While several tools have…
Finlay Clark, Graeme Robb, Daniel Cole, Julien Michel
Alchemical absolute binding free energy (ABFE) calculations have substantial potential in drug discovery, but are often prohibitively computationally expensive. To unlock their potential, efficient automated ABFE workflows are required to reduce both computational cost and human intervention. We present a…
Christoph Stelz, Lukas Hübner, Alexandros Stamatakis, Russell Schwartz
In Section 6.1, we evaluate the reproducibility of phylogenetic tree inferences on datasets from the TreeBASE () repository. For this, for each dataset, we execute the same RAxML-NG () application binary eight times, using identical hardware, search settings, and random seeds. For each of the eight runs we exclusively…
Daniel Liu
Unique Molecular Identifiers (UMI) are used in many experiments to find and remove PCR duplicates. Although there are many tools for solving the problem of deduplicating reads based on their finding reads with the same alignment coordinates and UMIs, many tools either cannot handle substitution errors, or require…
Omer Sabary, Alexander Yucovich, Guy Shapira, Eitan Yaakobi
In the trace reconstruction problem a length-n string x yields a collection of noisy copies, called traces, y_1_, …, y_t_ where each y_i_ is independently obtained from x by passing through a deletion channel, which deletes every symbol with some fixed probability. The main goal under this paradigm is to determine the…
Jeff Guo, Philippe Schwaller
Sample efficiency is a fundamental challenge in de novo molecular design. Ideally, molecular generative models should learn to satisfy desired objectives under minimal oracle evaluations (computational prediction or wet-lab experiment). This problem becomes more apparent when using oracles that can provide increased…
Authors not listed
Machine olfaction—the artificial replication of the sense of smell—faces significant challenges due to the absence of large, standardized training datasets. Unlike vision, language, and audio models, which benefit from extensive corpora such as ImageNet, GLUE, and AudioSet, olfaction lacks scaled equivalents and…
Qi Zhang, Chang Liu, Stephen Wu, Ryo Yoshida
In the last few years, de novo molecular design using machine learning has made great technical progress but its practical deployment has not been as successful. This is mostly owing to the cost and technical difficulty of synthesizing such computationally designed molecules. To overcome such barriers, various methods…
Authors not listed
With the ever-increasing demand for atomistic structures representative of real-life systems as well as the ad-vent of exascale computers, it has now become necessary and possible to use advanced global optimization (GO) techniques to intelligently sample the potential energy surface (PES). Given the previous studies…
Brianna Greenstein, Danielle Elsey, Geoffrey Hutchison
Genetic algorithms (GAs) are a powerful tool to search large chemical spaces for inverse molecular design. However, GAs have multiple hyperparameters that have not been thoroughly investigated for chemical space searches. In this work, we examine the general effects of a number of hyperparameters, such as population…