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Multiple sequence alignment is a basic procedure in molecular biology, and it is often treated as being essentially a solved computational problem. However, this is not so, and here I review the evidence for this claim, and outline the…

Populations and Evolution · Quantitative Biology 2018-08-24 David A. Morrison

This paper proposes a new algorithm for simultaneous graph matching and clustering. For the first time in the literature, these two problems are solved jointly and synergetically without relying on any training data, which brings advantages…

Computer Vision and Pattern Recognition · Computer Science 2021-10-22 Maximilian Krahn , Florian Bernard , Vladislav Golyanik

Reconfiguration is one of the central mechanisms in distributed systems. Due to failures and connectivity disruptions, the very set of service replicas (or servers) and their roles in the computation may have to be reconfigured over time.…

Distributed, Parallel, and Cluster Computing · Computer Science 2020-09-16 Petr Kuznetsov , Thibault Rieutord , Sara Tucci-Piergiovanni

Data replication is crucial in modern distributed systems as a means to provide high availability. Many techniques have been proposed to utilize replicas to improve a system's performance, often requiring expensive coordination or…

Databases · Computer Science 2019-03-04 Yi Lu , Xiangyao Yu , Samuel Madden

The tree is an essential data structure in many applications. In a distributed application, such as a distributed file system, the tree is replicated.To improve performance and availability, different clients should be able to update their…

Distributed, Parallel, and Cluster Computing · Computer Science 2022-01-20 Sreeja Nair , Filipe Meirim , Mário Pereira , Carla Ferreira , Marc Shapiro

Hierarchical time series are common in several applied fields. The forecasts for these time series are required to be coherent, that is, to satisfy the constraints given by the hierarchy. The most popular technique to enforce coherence is…

Machine Learning · Statistics 2023-10-13 Lorenzo Zambon , Dario Azzimonti , Giorgio Corani

Relating formal grammars is a hard problem that balances between language equivalence (which is known to be undecidable) and grammar identity (which is trivial). In this paper, we investigate several milestones between those two extremes…

Software Engineering · Computer Science 2015-03-31 Vadim Zaytsev

Consistent query answering is the problem of computing the answers from a database that are consistent with respect to certain integrity constraints that the database as a whole may fail to satisfy. Those answers are characterized as those…

Databases · Computer Science 2007-05-23 L. Bertossi , L. Bravo , E. Franconi , A. Lopatenko

Comparing and aligning large datasets is a pervasive problem occurring across many different knowledge domains. We introduce and study MREC, a recursive decomposition algorithm for computing matchings between data sets. The basic idea is to…

Machine Learning · Statistics 2020-02-24 Andrew J. Blumberg , Mathieu Carriere , Michael A. Mandell , Raul Rabadan , Soledad Villar

We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous…

Distributed, Parallel, and Cluster Computing · Computer Science 2020-01-29 Marquita Ellis , Giulia Guidi , Aydın Buluç , Leonid Oliker , Katherine Yelick

Serializability is a well-understood concurrency control mechanism that eases reasoning about highly-concurrent database programs. Unfortunately, enforcing serializability has a high-performance cost, especially on geographically…

Programming Languages · Computer Science 2021-03-10 Kia Rahmani , Kartik Nagar , Benjamin Delaware , Suresh Jagannathan

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…

Neural and Evolutionary Computing · Computer Science 2023-04-27 Iztok Fister , Iztok Fister

In numerous applications, it is required to produce forecasts for multiple time-series at different hierarchy levels. An obvious example is given by the supply chain in which demand forecasting may be needed at a store, city, or country…

Machine Learning · Computer Science 2021-01-06 Davide Burba , Trista Chen

This research started with an algebra for reasoning about rely/guarantee concurrency for a shared memory model. The approach taken led to a more abstract algebra of atomic steps, in which atomic steps synchronise (rather than interleave)…

Logic in Computer Science · Computer Science 2017-10-11 Ian J. Hayes , Larissa A. Meinicke , Kirsten Winter , Robert J. Colvin

We study phase retrieval from magnitude measurements of an unknown signal as an algebraic estimation problem. Indeed, phase retrieval from rank-one and more general linear measurements can be treated in an algebraic way. It is verified that…

Functional Analysis · Mathematics 2014-02-18 Franz J Király , Martin Ehler

Dual decomposition is widely utilized in distributed optimization of multi-agent systems. In practice, the dual decomposition algorithm is desired to admit an asynchronous implementation due to imperfect communication, such as time delay…

Optimization and Control · Mathematics 2021-03-05 Yifan Su , Zhaojian Wang , Ming Cao , Mengshuo Jia , Feng Liu

Graphs provide an efficient tool for object representation in various computer vision applications. Once graph-based representations are constructed, an important question is how to compare graphs. This problem is often formulated as a…

Machine Learning · Statistics 2010-04-30 Mikhail Zaslavskiy , Francis Bach , Jean-Philippe Vert

A novel approach is put forth that utilizes data similarity, quantified on a graph, to improve upon the reconstruction performance of principal component analysis. The tasks of data dimensionality reduction and reconstruction are formulated…

Machine Learning · Statistics 2018-09-26 Ioannis D. Schizas

We use the reconfiguration framework to analyze problems that involve the rearrangement of items among groups. In various applications, a group of items could correspond to the files or jobs assigned to a particular machine, and the goal of…

Data Structures and Algorithms · Computer Science 2024-10-29 Jeffrey Kam , Shahin Kamali , Avery Miller , Naomi Nishimura

We propose a new approach for modeling and reconciling conflicting data cleaning actions. Such conflicts arise naturally in collaborative data curation settings where multiple experts work independently and then aim to put their efforts…

Databases · Computer Science 2024-03-14 Yilin Xia , Shawn Bowers , Lan Li , Bertram Ludäscher