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Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to…

Genomics · Quantitative Biology 2025-01-09 Lucas Czech , Moises Exposito-Alonso

Choosing and developing performant database solutions helps organizations optimize their operational practices and decision-making. Since graph data is becoming more common, it is crucial to develop and use them in big data with complex…

Databases · Computer Science 2024-02-01 Johan Sandell , Einar Asplund , Workneh Yilma Ayele , Martin Duneld

Skip graphs are a novel distributed data structure, based on skip lists, that provide the full functionality of a balanced tree in a distributed system where resources are stored in separate nodes that may fail at any time. They are…

Data Structures and Algorithms · Computer Science 2007-05-23 James Aspnes , Gauri Shah

LLMs excel in localized code completion but struggle with repository-level tasks due to limited context windows and complex semantic and structural dependencies across codebases. While Retrieval-Augmented Generation (RAG) mitigates context…

Software Engineering · Computer Science 2025-09-09 Xingliang Wang , Baoyi Wang , Chen Zhi , Junxiao Han , Xinkui Zhao , Jianwei Yin , Shuiguang Deng

Web archives are a valuable resource for researchers of various disciplines. However, to use them as a scholarly source, researchers require a tool that provides efficient access to Web archive data for extraction and derivation of smaller…

Digital Libraries · Computer Science 2017-02-06 Helge Holzmann , Vinay Goel , Avishek Anand

Graph computing has become increasingly crucial in processing large-scale graph data, with numerous systems developed for this purpose. Two years ago, we introduced GraphScope as a system addressing a wide array of graph computing needs,…

Distributed, Parallel, and Cluster Computing · Computer Science 2023-12-20 Tao He , Shuxian Hu , Longbin Lai , Dongze Li , Neng Li , Xue Li , Lexiao Liu , Xiaojian Luo , Binqing Lyu , Ke Meng , Sijie Shen , Li Su , Lei Wang , Jingbo Xu , Wenyuan Yu , Weibin Zeng , Lei Zhang , Siyuan Zhang , Jingren Zhou , Xiaoli Zhou , Diwen Zhu

The notion of complex systems is common to many domains, from Biology to Economy, Computer Science, Physics, etc. Often, these systems are made of sets of entities moving in an evolving environment. One of their major characteristics is the…

Mathematical Software · Computer Science 2008-12-18 Yoann Pigné , Antoine Dutot , Frédéric Guinand , Damien Olivier

Repository-level code generation aims to generate code within the context of a specified repository. Existing approaches typically employ retrieval-augmented generation (RAG) techniques to provide LLMs with relevant contextual information…

Software Engineering · Computer Science 2025-11-04 Yang Liu , Li Zhang , Fang Liu , Zhuohang Wang , Donglin Wei , Zhishuo Yang , Kechi Zhang , Jia Li , Lin Shi

The dramatic success of deep neural networks across multiple application areas often relies on experts painstakingly designing a network architecture specific to each task. To simplify this process and make it more accessible, an emerging…

Machine Learning · Computer Science 2018-01-17 Kamil Bennani-Smires , Claudiu Musat , Andreea Hossmann , Michael Baeriswyl

We present Geo2DR (Geometric to Distributed Representations), a GPU ready Python library for unsupervised learning on graph-structured data using discrete substructure patterns and neural language models. It contains efficient…

Machine Learning · Computer Science 2020-07-10 Paul Scherer , Pietro Lio

Graph mining applications, such as subgraph pattern matching and mining, are widely used in real-world domains such as bioinformatics, social network analysis, and computer vision. Such applications are considered a new class of…

Hardware Architecture · Computer Science 2023-06-21 Jiya Su , Peng Jiang , Rujia Wang

Large scale graph processing is a major research area for Big Data exploration. Vertex centric programming models like Pregel are gaining traction due to their simple abstraction that allows for scalable execution on distributed systems…

Distributed, Parallel, and Cluster Computing · Computer Science 2019-05-10 Yogesh Simmhan , Alok Kumbhare , Charith Wickramaarachchi , Soonil Nagarkar , Santosh Ravi , Cauligi Raghavendra , Viktor Prasanna

All-pairs shortest paths (APSP) remains a major bottleneck for large-scale graph analytics, as data movement with cubic complexity overwhelms the bandwidth of conventional memory hierarchies. In this work, we propose RAPID-Graph to address…

Hardware Architecture · Computer Science 2026-01-29 Yanru Chen , Zheyu Li , Keming Fan , Runyang Tian , John Hsu , Weihong Xu , Minxuan Zhou , Tajana Rosing

Graph Neural Networks (GNNs) have achieved great successes in many learning tasks performed on graph structures. Nonetheless, to propagate information GNNs rely on a message passing scheme which can become prohibitively expensive when…

Machine Learning · Computer Science 2022-11-09 Ariel R. Ramos Vela , Johannes F. Lutzeyer , Anastasios Giovanidis , Michalis Vazirgiannis

Graph processing is used extensively in areas from social networking mining to web indexing. We demonstrate that the performance and dependability of such applications critically hinges on the graph data structure used, because a fixed,…

Programming Languages · Computer Science 2014-12-30 Amlan Kusum , Iulian Neamtiu , Rajiv Gupta

Repository summarization is a crucial research question in development and maintenance for software engineering. Existing repository summarization techniques primarily focus on summarizing code according to the directory tree, which is…

Software Engineering · Computer Science 2025-10-14 Yifeng Zhu , Xianlin Zhao , Xutian Li , Yanzhen Zou , Haizhuo Yuan , Yue Wang , Bing Xie

Graph databases have become essential tools for managing complex and interconnected data, which is common in areas like social networks, bioinformatics, and recommendation systems. Unlike traditional relational databases, graph databases…

Databases · Computer Science 2026-02-24 Miguel E. Coimbra , Lucie Svitáková , Domagoj Vrgoč , Alexandre P. Francisco , Luís Veiga

We present GRIP, a graph neural network accelerator architecture designed for low-latency inference. AcceleratingGNNs is challenging because they combine two distinct types of computation: arithmetic-intensive vertex-centric operations and…

Hardware Architecture · Computer Science 2020-07-31 Kevin Kiningham , Christopher Re , Philip Levis

Design/methodology/approach This research evaluated the databases of SQL, No-SQL and graph databases to compare and contrast efficiency and performance. To perform this experiment the data were collected from multiple sources including…

Computational Finance · Quantitative Finance 2024-01-17 Partha Sen , Sumana Sen

Analyzing large-scale graphs provides valuable insights in different application scenarios. While many graph processing systems working on top of distributed infrastructures have been proposed to deal with big graphs, the tasks of profiling…

Distributed, Parallel, and Cluster Computing · Computer Science 2017-09-05 Alessio Arleo , Walter Didimo , Giuseppe Liotta , Fabrizio Montecchiani
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