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Block-Sphere Vector Quantization GroupAffect-4: A Multimodal Dataset of Four-Person Collaborative Interaction CogScale: Scalable Benchmark for Sequence Processing TextAlign: Preference Alignment for Text Rendering with Hierarchical Rewards LogRouter: Adaptive Two-Level LLM Routing for Log Question Answering in Big Data Systems Agentic Cost-Aware Query Planning with Knowledge Distillation for Big Data Analytics Covariance Structure and Coordinate Heterogeneity Govern Binary Quantization of Contrastive Embeddings IVF-TQ: Calibration-Free Streaming Vector Search via a Codebook-Free Residual Layer Automatic Unsupervised Ensemble Outlier Model Selection--Extended Version A Generative AI Framework for Intelligent Utility Billing CO 2 Analytics and Sustainable Resource Optimisation Towards Foundation Models for Relational Databases with Language Models and Graph Neural Networks Gaussian Relational Graph Transformer Croissant Baker: Metadata Generation for Discoverable, Governable, and Reusable ML Datasets Reducing Hallucination in Vision-Language Models via Stage-wise Preference Optimization under Distribution Shift A Horn extension of DL-Lite with NL data complexity 3D Primitives are a Spatial Language for VLMs Enabling AI-Native Mobility in 6G: A Real-World Dataset for Handover, Beam Management, and Timing Advance A CAP-like Trilemma for Large Language Models: Correctness, Non-bias, and Utility under Semantic Underdetermination EpiCastBench: Datasets and Benchmarks for Multivariate Epidemic Forecasting FERMI: Exploiting Relations for Membership Inference Against Tabular Diffusion Models Toward Multi-Database Query Reasoning for Text2Cypher Autonomous FAIR Digital Objects: From Passive Assertions to Active Knowledge HOME-KGQA: A Benchmark Dataset for Multimodal Knowledge Graph Question Answering on Household Daily Activities Detect, Localize, and Explain: Interactive Hierarchical Log Anomaly Analytics with LLM Augmentation Open Ontologies: Tool-Augmented Ontology Engineering with Stable Matching Alignment Machine Learning-Based Pre-Test Risk Stratification for PCR-Confirmed Chlamydia Using Patient-Reported Data and Urine Biomarkers Reconciling Consistency-Based Diagnosis with Actual-Causality-Based Explanations PrepBench: How Far Are We from Natural-Language-Driven Data Preparation? Anatomy of a Query: W5H Dimensions and FAR Patterns for Text-to-SQL Evaluation Building informative materials datasets beyond targeted objectives
KmerCo: A lightweight K-mer counting technique with a tin...
Sabuzima Nayak, Ripon Patgiri · 2023-04-28 · via cs.DB updates on arXiv.org

K-mer counting is a requisite process for DNA assembly because it speeds up its overall process. The frequency of K-mers is used for estimating the parameters of DNA assembly, error correction, etc. The process also provides a list of district K-mers which assist in searching large databases and reducing the size of de Bruijn graphs. Nonetheless, K-mer counting is a data and compute-intensive process. Hence, it is crucial to implement a lightweight data structure that occupies low memory but does fast processing of K-mers. We proposed a lightweight K-mer counting technique, called KmerCo that implements a potent counting Bloom Filter variant, called countBF. KmerCo has two phases: insertion and classification. The insertion phase inserts all K-mers into countBF and determines distinct K-mers. The classification phase is responsible for the classification of distinct K-mers into trustworthy and erroneous K-mers based on a user-provided threshold value. We also proposed a novel benchmark performance metric. We used the Hadoop MapReduce program to determine the frequency of K-mers. We have conducted rigorous experiments to prove the dominion of KmerCo compared to state-of-the-art K-mer counting techniques. The experiments are conducted using DNA sequences of four organisms. The datasets are pruned to generate four different size datasets. KmerCo is compared with Squeakr, BFCounter, and Jellyfish. KmerCo took the lowest memory, highest number of insertions per second, and a positive trustworthy rate as compared with the three above-mentioned methods.