Entropy-scaling search of massive biological data

Many datasets exhibit a well-defined structure that can be exploited to design faster search tools, but it is not always clear when such acceleration is possible. Here, we introduce a framework for similarity search based on characterizing a dataset's entropy and fractal dimension. We prove that searching scales in time with metric entropy (number of covering hyperspheres), if the fractal dimension of the dataset is low, and scales in space with the sum of metric entropy and information-theoretic entropy (randomness of the data). Using these ideas, we present accelerated versions of standard tools, with no loss in specificity and little loss in sensitivity, for use in three domains---high-throughput drug screening (Ammolite, 150x speedup), metagenomics (MICA, 3.5x speedup of DIAMOND [3,700x BLASTX]), and protein structure search (esFragBag, 10x speedup of FragBag). Our framework can be used to achieve "compressive omics," and the general theory can be readily applied to data science problems outside of biology.Comment: Including supplement: 41 pages, 6 figures, 4 tables, 1 bo

SANNS: Scaling Up Secure Approximate k-Nearest Neighbors Search

The $k$-Nearest Neighbor Search ($k$-NNS) is the backbone of several cloud-based services such as recommender systems, face recognition, and database search on text and images. In these services, the client sends the query to the cloud server and receives the response in which case the query and response are revealed to the service provider. Such data disclosures are unacceptable in several scenarios due to the sensitivity of data and/or privacy laws. In this paper, we introduce SANNS, a system for secure $k$-NNS that keeps client's query and the search result confidential. SANNS comprises two protocols: an optimized linear scan and a protocol based on a novel sublinear time clustering-based algorithm. We prove the security of both protocols in the standard semi-honest model. The protocols are built upon several state-of-the-art cryptographic primitives such as lattice-based additively homomorphic encryption, distributed oblivious RAM, and garbled circuits. We provide several contributions to each of these primitives which are applicable to other secure computation tasks. Both of our protocols rely on a new circuit for the approximate top-$k$ selection from $n$ numbers that is built from $O(n + k^2)$ comparators. We have implemented our proposed system and performed extensive experimental results on four datasets in two different computation environments, demonstrating more than $18-31\times$ faster response time compared to optimally implemented protocols from the prior work. Moreover, SANNS is the first work that scales to the database of 10 million entries, pushing the limit by more than two orders of magnitude.Comment: 18 pages, to appear at USENIX Security Symposium 202

Efficient Match Pair Retrieval for Large-scale UAV Images via Graph Indexed Global Descriptor

SfM (Structure from Motion) has been extensively used for UAV (Unmanned Aerial Vehicle) image orientation. Its efficiency is directly influenced by feature matching. Although image retrieval has been extensively used for match pair selection, high computational costs are consumed due to a large number of local features and the large size of the used codebook. Thus, this paper proposes an efficient match pair retrieval method and implements an integrated workflow for parallel SfM reconstruction. First, an individual codebook is trained online by considering the redundancy of UAV images and local features, which avoids the ambiguity of training codebooks from other datasets. Second, local features of each image are aggregated into a single high-dimension global descriptor through the VLAD (Vector of Locally Aggregated Descriptors) aggregation by using the trained codebook, which remarkably reduces the number of features and the burden of nearest neighbor searching in image indexing. Third, the global descriptors are indexed via the HNSW (Hierarchical Navigable Small World) based graph structure for the nearest neighbor searching. Match pairs are then retrieved by using an adaptive threshold selection strategy and utilized to create a view graph for divide-and-conquer based parallel SfM reconstruction. Finally, the performance of the proposed solution has been verified using three large-scale UAV datasets. The test results demonstrate that the proposed solution accelerates match pair retrieval with a speedup ratio ranging from 36 to 108 and improves the efficiency of SfM reconstruction with competitive accuracy in both relative and absolute orientation

Evaluating the Differences of Gridding Techniques for Digital Elevation Models Generation and Their Influence on the Modeling of Stony Debris Flows Routing: A Case Study From Rovina di Cancia Basin (North-Eastern Italian Alps)

Debris \ufb02ows are among the most hazardous phenomena in mountain areas. To cope with debris \ufb02ow hazard, it is common to delineate the risk-prone areas through routing models. The most important input to debris \ufb02ow routing models are the topographic data, usually in the form of Digital Elevation Models (DEMs). The quality of DEMs depends on the accuracy, density, and spatial distribution of the sampled points; on the characteristics of the surface; and on the applied gridding methodology. Therefore, the choice of the interpolation method affects the realistic representation of the channel and fan morphology, and thus potentially the debris \ufb02ow routing modeling outcomes. In this paper, we initially investigate the performance of common interpolation methods (i.e., linear triangulation, natural neighbor, nearest neighbor, Inverse Distance to a Power, ANUDEM, Radial Basis Functions, and ordinary kriging) in building DEMs with the complex topography of a debris \ufb02ow channel located in the Venetian Dolomites (North-eastern Italian Alps), by using small footprint full- waveform Light Detection And Ranging (LiDAR) data. The investigation is carried out through a combination of statistical analysis of vertical accuracy, algorithm robustness, and spatial clustering of vertical errors, and multi-criteria shape reliability assessment. After that, we examine the in\ufb02uence of the tested interpolation algorithms on the performance of a Geographic Information System (GIS)-based cell model for simulating stony debris \ufb02ows routing. In detail, we investigate both the correlation between the DEMs heights uncertainty resulting from the gridding procedure and that on the corresponding simulated erosion/deposition depths, both the effect of interpolation algorithms on simulated areas, erosion and deposition volumes, solid-liquid discharges, and channel morphology after the event. The comparison among the tested interpolation methods highlights that the ANUDEM and ordinary kriging algorithms are not suitable for building DEMs with complex topography. Conversely, the linear triangulation, the natural neighbor algorithm, and the thin-plate spline plus tension and completely regularized spline functions ensure the best trade-off among accuracy and shape reliability. Anyway, the evaluation of the effects of gridding techniques on debris \ufb02ow routing modeling reveals that the choice of the interpolation algorithm does not signi\ufb01cantly affect the model outcomes