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Index-based, High-dimensional, Cosine Threshold Querying with Optimality Guarantees

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Abstract

Given a database of vectors, a cosine threshold query returns all vectors in the database having cosine similarity to a query vector above a given threshold θ. These queries arise naturally in many applications, such as document retrieval, image search, and mass spectrometry. The paper considers the efficient evaluation of such queries, as well as of the closely related top-k cosine similarity queries. It provides novel optimality guarantees that exhibit good performance on real datasets. We take as a starting point Fagin’s well-known Threshold Algorithm (TA), which can be used to answer cosine threshold queries as follows: an inverted index is first built from the database vectors during pre-processing; at query time, the algorithm traverses the index partially to gather a set of candidate vectors to be later verified for θ-similarity. However, directly applying TA in its raw form misses significant optimization opportunities. Indeed, we first show that one can take advantage of the fact that the vectors can be assumed to be normalized, to obtain an improved, tight stopping condition for index traversal and to efficiently compute it incrementally. Then we show that multiple real-world data sets from mass spectrometry, natural language process, and computer vision exhibit a certain form of data skewness and we exploit this property to obtain better traversal strategies. We show that under the skewness assumption, the new traversal strategy has a strong, near-optimal performance guarantee. The techniques developed in the paper are quite general since they can be applied to a large class of similarity functions beyond cosine.

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Notes

  1. There is no need to include pairs with zero values in the list.

  2. This optimization is equally applicable to the TA’s problem: Scan only the lists that correspond to dimensions that actually affect the function F.

  3. Notice, the unit vector constraint enables inference about the collective weight of the unseen coordinates of a vector.

  4. The inner product threshold problem is the special case where fi(s[i]) = qi ⋅s[i].

  5. [d] is the set \(\{1, \dots , d\}\)

  6. Recall that Li[0] = 1.

  7. We denote by fi(Li) the list \([f_{i}(L_{i}[0]), f_{i}(L_{i}[1]), \dots ]\) for every Li.

  8. where each fi of the decomposable function F is the identity function

  9. https://proteomics2.ucsd.edu/ProteoSAFe/index.jsp

  10. The linear scan is feasible for join because the naive approach of join is quadratic.

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Acknowledgments

We thank the anonymous reviewers of ICDT and ToCS for the very constructive and helpful comments. We are also grateful to Victor Vianu who helped us improve the presentation of the paper. This work was supported in part by the National Science Foundation (NSF) under awards BIGDATA 1447943 and ABI 1759980, and by the National Institutes of Health (NIH) under awards P41GM103484 and R24GM127667.

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Authors and Affiliations

  1. Megagon Labs, 444 Castro Street Suite 720, Mountain View, CA, 94041, USA

    Yuliang Li

  2. Department of Computer Science, Purdue University, 610 Purdue Mall, West Lafayette, IN, 47907, USA

    Jianguo Wang

  3. UC San Diego, 9500 Gilman Drive, San Diego, CA, 92093, USA

    Benjamin Pullman, Nuno Bandeira & Yannis Papakonstantinou

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Li, Y., Wang, J., Pullman, B. et al. Index-based, High-dimensional, Cosine Threshold Querying with Optimality Guarantees. Theory Comput Syst 65, 42–83 (2021). https://doi.org/10.1007/s00224-020-10009-6

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