Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 1403.1317

Hardware software co-design of the Aho-Corasick algorithm: Scalable for protein identification?

S. M. Vidanagamachchi·S. D. Dewasurendra·R. G. Ragel
View original source ↗Read source document ↗Export metadata ↓

Abstract

Pattern matching is commonly required in many application areas and bioinformatics is a major area of interest that requires both exact and approximate pattern matching. Much work has been done in this area, yet there is still a significant space for improvement in efficiency, flexibility, and throughput. This paper presents a hardware software co-design of Aho-Corasick algorithm in Nios II soft-processor and a study on its scalability for a pattern matching application. A software only approach is used to compare the throughput and the scalability of the hardware software co-design approach. According to the results we obtained, we conclude that the hardware software co-design implementation shows a maximum of 10 times speed up for pattern size of 1200 peptides compared to the software only implementation. The results also show that the hardware software co-design approach scales well for increasing data size compared to the software only approach.

Explore related subjects

cs.CE

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

S. M. Vidanagamachchi, S. D. Dewasurendra, R. G. Ragel. 2014-03-06. Hardware software co-design of the Aho-Corasick algorithm: Scalable for protein identification?. https://doi.org/10.1109/iciinfs.2013.6732003

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Synthetic Human Mobility Data Generation: A Structured Review of Representations, Methods, and Practical Capabilities

Human mobility data has become an increasingly important component of urban analytics. Although the range of available mobility data sources has expanded substantially, access remains highly constrained by commercial restrictions, privacy concerns, and institutional barriers. Data protection procedures also often reduce the analytical value of released datasets. Synthetic mobility data has emerged as a promising solution, but existing methods differ substantially in their underlying mechanisms, the information they preserve, the outputs they generate, and the analytical questions they can support. Their comparative strengths and trade-offs remain insufficiently understood for urban analytics. This paper presents a structured review of synthetic human mobility data generation from an urban analytics perspective. We review the literature by methodological family and index it by the mobility outputs each family generates natively and the analytical capabilities those outputs enable. We first provide a taxonomy of synthetic data products, including population and persona representations, activity schedules, trip and tour records, trajectories, and aggregate mobility patterns. We then review the major methodological families, spanning mechanistic models, survey-driven population synthesis, activity- and agent-based simulation, deep generative models, transformer-based mobility language models, and LLM-agentic systems. Building on this synthesis, we introduce a Meaning-Population-Autonomy framework that characterises these methods along three dimensions: behavioural meaning, population grounding and scale, and generation autonomy. We consider these dimensions the principal requirements for downstream urban analytics. Few methods deliver behavioural meaning, population grounding and autonomous generation at once, and fewer still with generation constrained to feasible trajectories.

cs.CE↗
arXiv2026

TERRA-NG v1.0: Extreme-Scale, GPU-accelerated Mantle Convection

We present TERRA-NG, a portable, GPU-accelerated, matrix-free mantle-convection code. A single Kokkos C++ implementation runs at scale on NVIDIA, AMD, and Intel GPU supercomputers. TERRA-NG has a deliberately narrow design: built on a radially extruded mesh of spherical wedges, tailored to the spherical shell geometry, which enables domain-specific optimizations like single quadrature-point integral-evaluations, radial coordinate storage compression and radial shared-memory tiling. The corresponding low-order $W_1$-iso-$W_2/W_1$ wedge-based Stokes--energy discretisation is verified against the Zhong et al.(2008) spherical-shell convection benchmark suite. We showcase TERRA-NG through strong- and weak-scaling on the JUWELS Booster (NVIDIA A100), MareNostrum 5 (NVIDIA H100), LUMI-G (AMD MI250X), Hunter (AMD MI300A APU), and SuperMUC-NG Phase 2 (Intel PVC) supercomputers. Coupled mantle convection simulations at $\sim\!11$ km and $\sim\!5.6$ km radial spacing ($\sim 2.8$ B and $\sim 22$ B DoFs) can be run routinely on standard node partitions of all considered systems. Global $\sim\!1$ km-per-gridpoint mantle convection ($\sim 1.4$ T DoFs) is feasible on an extreme-scale allocation, and a sub-km hero-run at $\sim\!0.7$ km grid spacing scaling up to $\sim 11,000$ GPUs of LUMI-G ($\sim 11$ T DoFs) shows the potential of the code on future, larger machines.

cs.CE↗
arXiv2026

FireDataForge: A Unified Framework for Multi-Source Wildfire Data Retrieval and Integration

Wildfire research, modeling, and education require geospatial data from multiple sources that vary in formats, coordinate systems, spatial resolutions, and temporal cadences. This preprocessing burden limits reproducible reuse. We present FireDataForge, an open-source Python framework that automates retrieval and harmonization of 11 wildfire-related sources spanning fire behavior, weather, land cover, vegetation, elevation, built environment, wildland-urban interface, fire history, and satellite imagery. Given an MTBS Event ID, FireDataForge retrieves relevant datasets, aligns them to a common grid, and outputs analysis-ready NumPy arrays with embedded metadata. Batch processing of historical fires demonstrates support for fire behavior simulation, educational visualization, machine learning, and AI-assisted wildfire analysis.

cs.CE↗