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Line Intersection Searching Amid Unit Balls in 3-Space

ALGORITHMICA 2025年第2期87卷 223-241页

作者： Agarwal, Pankaj K. Ezra, Esther Duke Univ Dept Comp Sci Box 90129 Durham NC 27708 USA Bar Ilan Univ Sch Comp Sci Ramat Gan Israel

Let B be a set of n unit balls in R-3. We present a linear-size data structure for storing B that can determine in O*(root n) time whether a query line intersects any ball of B and report all k such balls in additional O(k) time. The data structure can be constructed in O(n log n) time. (The O*(center dot) notation hides subpolynomial factors, e.g., of the form O(n(epsilon)), for arbitrarily small epsilon > 0, and their coefficients which depend on epsilon.) We also consider the dual problem: Let L be a set of n lines in R-3. We preprocess L, in O*(n(2)) time, into a data structure of size O*(n(2)) that can determine in O(log n) time whether a query unit ball intersects any line of L, or report all k such lines in additional O(k) time.

关键词： Intersection searching Range searching Test sets Shallow partition trees Union of cylinders

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Intellectual Property Protection of Deep-Learning Systems via Hardware/Software Co-Design

IEEE DESIGN & TEST

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IEEE DESIGN & TEST 2024年第2期41卷 23-31页

作者： Chen, Huili Fu, Cheng Rouhani, Bita Darvish Zhao, Jishen Koushanfar, Farinaz Univ Calif San Diego Dept Elect & Comp Engn La Jolla CA 92093 USA Univ Calif San Diego Comp Sci & Engn Dept La Jolla CA 92093 USA Microsoft Redmond WA 98052 USA Univ Calif San Diego Elect & Comp Engn La Jolla CA 92093 USA Univ Calif San Diego La Jolla CA 92093 USA

Editor’s notes: This article protects deep learning models by leveraging hardware device-specific model fingerprinting and trusted execution environment. —Gang Qu, University of Maryland, USA

关键词： Hardware Fingerprint recognition Security Watermarking IP networks Computational modeling Performance evaluation Intellectual property protection Deep learning hardware Attestation Digital fingerprinting

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On the Generic Capacity of K-User Symmetric Linear Computation Broadcast

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IEEE TRANSACTIONS ON INFORMATION THEORY 2024年第5期70卷 3693-3717页

作者： Yao, Yuhang Jafar, Syed A. Univ Calif Irvine Ctr Pervas Commun & Comp CPCC Dept Elect Engn & Comp Sci Irvine CA 92697 USA

Linear computation broadcast (LCBC) refers to a setting with d dimensional data stored at a central server, where K users, each with some prior linear side-information, wish to compute various linear combinations of the data. For each computation instance, the data is represented as ad-dimensional vector with elements in a finite field F-pn where p(n) is a power of a prime. The computation is to be performed many times, and the goal is to determine the minimum amount of information per computation instance that must be broadcast to satisfy all the users. The reciprocal of the optimal broadcast cost per computation instance is the capacity of LCBC. The capacity is known for up to K = 3users. Since LCBC includes index coding as a special case, large K settings of LCBC are at least as hard as the index coding problem. As such the general LCBC problem is beyond our reach and we do not pursue it. Instead of the general setting (all cases), by focusing on the generic setting(almost all cases) this work shows that the generic capacity of the symmetric LCBC (where every user has m ' dimensions of side-information and m dimensions of demand) for large number of users (K >= d suffices) is C-g = 1/triangle(g), where triangle(g)= min {max{0, d-m '}, dm/m+m '}, is the broadcast cost that is both achievable and unbeatable asymptotically almost surely for largen, among all LCBC instances with the given parameter sp, K, d, m, m '. Relative to baseline schemes of random coding or separate transmissions, C-g shows an extremal gain by a factor of K as a function of number of users, and by a factor of approximate to d/4 as a function of data dimensions, when optimized over remaining parameters. For arbitrary number of users, the generic capacity of the symmetric LCBC is characterized with in a factor of 2.

关键词： Encoding Indexes Costs Servers Galois fields Interference channels Wireless communication

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Valence and interactions in judicial voting

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PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES 2024年第2270期382卷 20230140页

作者： Lee, Edward D. Cantwell, George T. Complex Sci Hub Vienna Josefstaedter Str 39 Vienna Austria Univ Cambridge Dept Engn Cambridge CB2 1PZ England Santa Fe Inst 1399 Hyde Pk Rd Santa Fe NM 87501 USA

The collective statistics of voting on judicial courts present hints about their inner workings. Many approaches for studying these statistics, however, assume that judges' decisions are conditionally independent: a judge reaches a decision based on the case at hand and his or her personal views. In reality, judges interact. We develop a minimal model that accounts for judge bias, depending on the context of the case, and peer interaction. We apply the model to voting data from the US Supreme Court. We find strong evidence that interaction is an important factor across natural courts from 1946 to 2021. We also find that, after accounting for interaction, the recovered biases differ from highly cited ideological scores. Our method exemplifies how physics and complexity-inspired modelling can drive the development of theoretical models and improved measures for political *** article is part of the theme issue 'A complexity science approach to law and governance'.

关键词： maximum entropy voting US Supreme Court bias statistical inference group interactions

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Semi-quantitative group testing for efficient and accurate qPCR screening of pathogens with a wide range of loads

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BMC BIOINFORMATICS 2024年第1期25卷 1页

作者： Nambiar, Ananthan Pan, Chao Rana, Vishal Cheraghchi, Mahdi Ribeiro, Joao Maslov, Sergei Milenkovic, Olgica Univ Illinois Dept Bioengn Urbana IL 61801 USA Univ Illinois Dept Elect & Comp Engn Urbana IL 61801 USA Univ Illinois Carl R Woese Inst Genom Biol Ctr Artificial Intelligence & Modeling Urbana IL 61801 USA Univ Michigan Dept Elect Engn & Comp Sci Ann Arbor MI USA NOVA LINCS Caparica Portugal NOVA Sch Sci & Technol Caparica Portugal

Background Pathogenic infections pose a significant threat to global health, affecting millions of people every year and presenting substantial challenges to healthcare systems worldwide. Efficient and timely testing plays a critical role in disease control and transmission prevention. Group testing is a well-established method for reducing the number of tests needed to screen large populations when the disease prevalence is low. However, it does not fully utilize the quantitative information provided by qPCR methods, nor is it able to accommodate a wide range of pathogen *** To address these issues, we introduce a novel adaptive semi-quantitative group testing (SQGT) scheme to efficiently screen populations via two-stage qPCR testing. The SQGT method quantizes cycle threshold (Ct) values into multiple bins, leveraging the information from the first stage of screening to improve the detection sensitivity. Dynamic Ct threshold adjustments mitigate dilution effects and enhance test accuracy. Comparisons with traditional binary outcome GT methods show that SQGT reduces the number of tests by 24% on the only complete real-world qPCR group testing dataset from Israel, while maintaining a negligible false negative *** In conclusion, our adaptive SQGT approach, utilizing qPCR data and dynamic threshold adjustments, offers a promising solution for efficient population screening. With a reduction in the number of tests and minimal false negatives, SQGT holds potential to enhance disease control and testing strategies on a global scale.

关键词： Group testing Pooled testing Semiquantitative group testing qPCR Ct values Viral load COVID-19

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Gene syntaxes modulate gene expression and circuit behavior on plasmids

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JOURNAL OF BIOLOGICAL ENGINEERING 2025年第1期19卷 1-15页

作者： Deng, Yijie Maurais, Hannah E. Etheridge, Kai Sarpeshkar, Rahul Dartmouth Coll Thayer Sch Engn Hanover NH 03755 USA Dartmouth Coll Dept Engn Hanover NH 03755 USA Dartmouth Coll Dept Microbiol & Immunol Hanover NH 03755 USA Dartmouth Coll Dept Phys Hanover NH 03755 USA Dartmouth Coll Dept Mol & Syst Biol Hanover NH 03755 USA

Achieving consistent and predictable gene expression from plasmids remains challenging. While much attention has focused on intra-genetic elements like promoters and ribosomal binding sites, the spatial arrangement of genes within plasmids-referred to as gene syntax-also plays a crucial role in shaping gene expression dynamics. This study addresses the largely overlooked impact of gene syntaxes on gene expression variability and accuracy. Utilizing a dual-fluorescent protein system, we systematically investigated how different gene orientations and orders affect expression profiles including mean levels, relative expression ratios, and cell-to-cell variations. We found that arbitrary gene placement on a plasmid can cause significantly different expression means and ratios. Genes aligned in the same direction as a plasmid's origin of replication (Ori) typically exhibit higher expression levels;adjacent genes in the divergent orientation tend to suppress each other's expression;altering gene order without changing orientation can yield varied expression. Despite unchanged total cell-to-cell variation across different syntaxes, gene syntaxes can also influence intrinsic and extrinsic noise. Interestingly, cell-to-cell variation appears to depend on the reporter proteins, with RFP consistently showing higher variation than GFP. Moreover, the effects of gene syntax can propagate to downstream circuits, strongly affecting the performance of incoherent feedforward loops and contributing to unpredictable outcomes in genetic networks. Our findings reveal that gene syntaxes on plasmids modulate gene expression and circuit behavior, providing valuable insights for the rational design of plasmids and genetic circuits.

关键词： Plasmid design Genetic context Gene syntax Genetic circuits Gene noise Incoherent feedforward loops

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CNRein: an evolution-aware deep reinforcement learning algorithm for single-cell DNA copy number calling

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GENOME BIOLOGY 2025年第1期26卷 1-23页

作者： Ivanovic, Stefan El-Kebir, Mohammed Univ Illinois Dept Comp Sci Urbana IL 61801 USA Univ Illinois Urbana & Champaign Canc Ctr Illinois Urbana IL 61801 USA

Low-pass single-cell DNA sequencing technologies and algorithmic advancements have enabled haplotype-specific copy number calling on thousands of cells within tumors. However, measurement uncertainty may result in spurious CNAs inconsistent with realistic evolutionary constraints. We introduce evolution-aware copy number calling via deep reinforcement learning (CNRein). Our simulations demonstrate CNRein infers more accurate copy-number profiles and better recapitulates ground truth clonal structure than existing methods. On sequencing data of breast and ovarian cancer, CNRein produces more parsimonious solutions than existing methods while maintaining agreement with single-nucleotide variants. Additionally, CNRein shows consistency on a breast cancer patient sequenced with distinct low-pass technologies.

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Exploring the Interaction of RBD with Human β Defensin Type 2 Point Mutants: Insights from Molecular Dynamics Simulations

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JOURNAL OF PHYSICAL CHEMISTRY B 2025年第7期129卷 1927-1933页

作者： Jahan, Ishrat Zhang, Liqun Univ Rhode Isl Chem Engn Dept Kingston RI 02881 USA

The global health crisis triggered by the SARS-CoV-2 virus has highlighted the urgent need for effective treatments. As existing drugs are not specifically targeted at this virus, there is a growing interest in exploring natural antimicrobial peptides such as defensin as potential therapeutic options. Human beta defensin type 2 (hBD-2), which is a cationic cysteine-rich peptide, serves as the initial barrier against bacterial and fungal invaders in mammals. It can bind with Spike-RBD and occupy the same site as the ACE2 receptor, thereby hindering viral entry into cells expressing ACE2. To explore the effect of different point mutations on the binding of hBD-2 with RBD, the binding dynamics and interactions between hBD-2 point mutants with RBD were studied and compared with that of RBD&hBD-2 wild-type complex. In total, 247 hBD-2 point mutants were built with the mutation sites at the binding region of hBD-2 (RES18-30) with the RBD of CoV-2. All-atom molecular dynamics simulations were carried out on RBD binding with hBD-2 point mutants. Analysis based on root-mean-square deviation (RMSD), hydrogen bonds analysis, and binding free energy using the MM/PBSA method revealed that many point mutants of hBD-2 exhibit weaker binding with RBD compared to the wild type;however, a subset of mutants, including C20I, C20K, R22W, R23H, R23L, Y24L, K25F, K25H, G28Y, T29R, and C30K, displayed enhanced binding with RBD. The findings can offer insights designing hBD-2-based novel drugs to combat SARS-CoV-2 in the long term.

关键词： Hydrogen bonds

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Smooth connectivity in real algebraic varieties

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NUMERICAL ALGORITHMS 2024年 1-22页

作者： Cummings, Joseph Hauenstein, Jonathan D. Hong, Hoon Smyth, Clifford D. Univ Notre Dame Dept Appl & Computat Math & Stat Notre Dame IN 46556 USA North Carolina State Univ Dept Math Raleigh NC 27695 USA Univ North Carolina Greensboro Dept Math & Stat Greensboro NC 27402 USA

A standard question in real algebraic geometry is to compute the number of connected components of a real algebraic variety in affine space. This manuscript provides algorithms for computing the number of connected components, the Euler characteristic, and deciding the connectivity between two points for a smooth manifold arising as the complement of a real hypersurface of a real algebraic variety. When considering the complement of the set of singular points of a real algebraic variety, this yields an approach for determining smooth connectivity in a real algebraic variety. The method is based upon gradient ascent/descent paths on the real algebraic variety inspired by a method proposed by Hong, Rohal, Safey El Din, and Schost for complements of real hypersurfaces. Several examples are included to demonstrate the approach.

关键词： Connectivity Smooth points Real algebraic sets Polynomial systems Homotopy continuation Numerical algebraic geometry

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computing the Homology Functor on Semi-algebraic Maps and Diagrams

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DISCRETE & COMPUTATIONAL GEOMETRY 2024年第4期72卷 1437-1462页

作者： Basu, Saugata Karisani, Negin Purdue Univ Dept Math W Lafayette IN 47906 USA Purdue Univ Dept Comp Sci W Lafayette IN 47906 USA

Developing an algorithm for computing the Betti numbers of semi-algebraic sets with singly exponential complexity has been a holy grail in algorithmic semi-algebraic geometry and only partial results are known. In this paper we consider the more general problem of computing the image under the homology functor of a continuous semi-algebraic map f:X -> Y\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$f:X \rightarrow Y$$\end{document} between closed and bounded semi-algebraic sets. For every fixed l >= 0\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\ell \ge 0$$\end{document} we give an algorithm with singly exponential complexity that computes bases of the homology groups Hi(X),Hi(Y)\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\text{ H}_i(X), \text{ H}_i(Y)$$\end{document} (with rational coefficients) and a matrix with respect to these bases of the induced linear maps Hi(f):Hi(X)-> Hi(Y),0 <= i <= l\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\text{ H}_i(f):\text{ H}_i(X) \rightarrow \text{ H}_i(Y), 0 \le i \le \ell $$\end{document}. We generalize this algorithm to more general (zigzag) diagrams of continuous semi-algebraic maps between closed and bounded semi-algebraic sets and give a singly exponential algorithm for computing the homology funct

关键词： Semi-algebraic sets Simplicial complex Persistent homology Barcodes

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