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This paper describes a method to efficiently retrieve protein database sequences similar to a query sequence, while allowing for significant numbers of mutations. We call this method SEQR for SEQuence Retrieval. This approach increases the…

Genomics · Quantitative Biology 2018-11-05 David I. Hurwitz , Lianyi Han , Lewis Y. Geer

Approximate nearest neighbor (ANN) search is a performance-critical component of many machine learning pipelines. Rigorous benchmarking is essential for evaluating the performance of vector indexes for ANN search. However, the datasets of…

Machine Learning · Computer Science 2025-05-26 Elias Jääsaari , Ville Hyvönen , Matteo Ceccarello , Teemu Roos , Martin Aumüller

Large-scale vector databases for approximate nearest neighbor (ANN) search typically store a quantized dataset in main memory for fast access, and full precision data on remote disk. State-of-the-art ANN quantization methods are highly…

Data Structures and Algorithms · Computer Science 2025-12-23 Ishaq Aden-Ali , Hakan Ferhatosmanoglu , Alexander Greaves-Tunnell , Nina Mishra , Tal Wagner

Embedding-based dense retrieval has become the cornerstone of many critical applications, where approximate nearest neighbor search (ANNS) queries are often combined with filters on labels such as dates and price ranges. Graph-based indexes…

Databases · Computer Science 2026-01-13 Yicheng Jin , Yongji Wu , Wenjun Hu , Bruce M. Maggs , Jun Yang , Xiao Zhang , Danyang Zhuo

Question-answering (QA) is an important application of Information Retrieval (IR) and language models, and the latest trend is toward pre-trained large neural networks with embedding parameters. Augmenting QA performances with these LLMs…

Information Retrieval · Computer Science 2024-11-05 Lixiao Yang , Mengyang Xu , Weimao Ke

Approximate Nearest Neighbor Search (ANNS), as the core of vector databases (VectorDBs), has become widely used in modern AI and ML systems, powering applications from information retrieval to bio-informatics. While graph-based ANNS methods…

Machine Learning · Computer Science 2025-10-07 Dingyi Kang , Dongming Jiang , Hanshen Yang , Hang Liu , Bingzhe Li

Vector databases typically rely on approximate nearest neighbor (ANN) search to retrieve the top-k closest vectors to a query in embedding space. While effective, this approach often yields semantically redundant results, missing the…

Machine Learning · Computer Science 2025-07-29 Rahul Raja , Arpita Vats

Vector similarity search presents significant challenges in terms of scalability for large and high-dimensional datasets, as well as in providing native support for hybrid queries. Serverless computing and cloud functions offer attractive…

Distributed, Parallel, and Cluster Computing · Computer Science 2025-02-04 Joe Oakley , Hakan Ferhatosmanoglu

Embedding-based vector search underpins many important applications, such as recommendation and retrieval-augmented generation (RAG). It relies on vector indices to enable efficient search. However, these indices require storing…

We present a new approach for efficient approximate nearest neighbor (ANN) search in high dimensional spaces, extending the idea of Product Quantization. We propose a two-level product and vector quantization tree that reduces the number of…

Computer Vision and Pattern Recognition · Computer Science 2017-02-21 Patrick Wieschollek , Oliver Wang , Alexander Sorkine-Hornung , Hendrik P. A. Lensch

Approximate nearest neighbor (ANN) search in high dimensions is an integral part of several computer vision systems and gains importance in deep learning with explicit memory representations. Since PQT, FAISS, and SONG started to leverage…

Computer Vision and Pattern Recognition · Computer Science 2022-04-08 Fabian Groh , Lukas Ruppert , Patrick Wieschollek , Hendrik P. A. Lensch

Quantization methods have been introduced to perform large scale approximate nearest search tasks. Residual Vector Quantization (RVQ) is one of the effective quantization methods. RVQ uses a multi-stage codebook learning scheme to lower the…

Computer Vision and Pattern Recognition · Computer Science 2015-09-18 Shicong Liu , Hongtao Lu , Junru Shao

In embedding-based retrieval, Approximate Nearest Neighbor (ANN) search enables efficient retrieval of similar items from large-scale datasets. While maximizing recall of relevant items is usually the goal of retrieval systems, a low…

Information Retrieval · Computer Science 2024-08-12 Nicholas Rossi , Juexin Lin , Feng Liu , Zhen Yang , Tony Lee , Alessandro Magnani , Ciya Liao

Nearest neighbour search over dense vector collections has important applications in information retrieval, retrieval augmented generation (RAG), and content ranking. Performing efficient search over large vector collections is a well…

Approximate nearest neighbor search (ANNS) has become vital to modern AI infrastructure, particularly in retrieval-augmented generation (RAG) applications. Numerous in-browser ANNS engines have emerged to seamlessly integrate with popular…

Information Retrieval · Computer Science 2025-07-03 Mugeng Liu , Siqi Zhong , Qi Yang , Yudong Han , Xuanzhe Liu , Yun Ma

Retrieval Augmented Generation (RAG) uses vector databases to expand the expertise of an LLM model without having to retrain it. The idea can be applied over data lakes, leading to the notion of embedding data lakes, i.e., a pool of vector…

Databases · Computer Science 2026-03-09 Vasilis Mageirakos , Bowen Wu , Gustavo Alonso

Filtered ANN search is an increasingly important problem in vector retrieval, yet systems face a difficult trade-off due to the execution order: Pre-filtering (filtering first, then ANN over the passing subset) requires expensive…

Databases · Computer Science 2026-02-23 Zhuocheng Gan , Yifan Wang

Sparse embeddings of data form an attractive class due to their inherent interpretability: Every dimension is tied to a term in some vocabulary, making it easy to visually decipher the latent space. Sparsity, however, poses unique…

Data Structures and Algorithms · Computer Science 2025-09-30 Sebastian Bruch , Franco Maria Nardini , Cosimo Rulli , Rossano Venturini

Similarity search based on a distance function in metric spaces is a fundamental problem for many applications. Queries for similar objects lead to the well-known machine learning task of nearest-neighbours identification. Many data…

Information Retrieval · Computer Science 2022-08-05 Felipe Ortega , Maria Jesus Algar , Isaac Martín de Diego , Javier M. Moguerza

Cross-encoder models, which jointly encode and score a query-item pair, are prohibitively expensive for direct k-nearest neighbor (k-NN) search. Consequently, k-NN search typically employs a fast approximate retrieval (e.g. using BM25 or…

Information Retrieval · Computer Science 2023-10-24 Nishant Yadav , Nicholas Monath , Manzil Zaheer , Andrew McCallum