| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Kumar, Siddhartha, 1991, et al.
(författare)
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Achieving Maximum Distance Separable Private Information Retrieval Capacity With Linear Codes
- 2019
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Ingår i: IEEE Transactions on Information Theory. - 0018-9448 .- 1557-9654. ; 65:7, s. 4243-4273
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Tidskriftsartikel (refereegranskat)abstract
- We propose three private information retrieval (PIR) protocols for distributed storage systems (DSSs) where data is stored using an arbitrary linear code. The first two protocols, named Protocol 1 and Protocol 2, achieve privacy for the scenario with noncolluding nodes. Protocol 1 requires a file size that is exponential in the number of files in the system, while Protocol 2 requires a file size that is independent of the number of files and is hence simpler. We prove that, for certain linear codes, Protocol 1 achieves the maximum distance separable (MDS) PIR capacity, i.e., the maximum PIR rate (the ratio of the amount of retrieved stored data per unit of downloaded data) for a DSS that uses an MDS code to store any given (finite and infinite) number of files, and Protocol 2 achieves the asymptotic MDS-PIR capacity (with infinitely large number of files in the DSS). In particular, we provide a necessary and a sufficient condition for a code to achieve the MDS-PIR capacity with Protocols 1 and 2 and prove that cyclic codes, Reed-Muller (RM) codes, and a class of distance-optimal local reconstruction codes achieve both the finite MDS-PIR capacity (i.e., with any given number of files) and the asymptotic MDS-PIR capacity with Protocols 1 and 2, respectively. Furthermore, we present a third protocol, Protocol 3, for the scenario with multiple colluding nodes, which can be seen as an improvement of a protocol recently introduced by Freij-Hollanti et al.. Similar to the noncolluding case, we provide a necessary and a sufficient condition to achieve the maximum possible PIR rate of Protocol 3. Moreover, we provide a particular class of codes that is suitable for this protocol and show that RM codes achieve the maximum possible PIR rate for the protocol. For all three protocols, we present an algorithm to optimize their PIR rates.
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| 3. |
- Kumar, Siddhartha, 1991, et al.
(författare)
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Local Reconstruction Codes: A Class of MDS-PIR Capacity-Achieving Codes
- 2018
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Ingår i: 2018 IEEE Information Theory Workshop, ITW 2018.
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Konferensbidrag (refereegranskat)abstract
- We prove that a class of distance-optimal local reconstruction codes (LRCs), an important family of repair-efficient codes for distributed storage systems, achieve the maximum distance separable private information retrieval capacity for the case of noncolluding nodes. This particular class of codes includes Pyramid codes and other LRCs proposed in the literature.
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| 4. |
- Lin, Hsuan-Yin, et al.
(författare)
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An MDS-PIR Capacity-Achieving Protocol for Distributed Storage Using Non-MDS Linear Codes
- 2018
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Ingår i: IEEE International Symposium on Information Theory - Proceedings. - 2157-8095. ; 2018-June, s. 966-970
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Konferensbidrag (refereegranskat)abstract
- We propose a private information retrieval (PIR) protocol for distributed storage systems (DSSs) with noncolluding nodes where data is stored using an arbitrary linear code. An expression for the PIR rate, i.e., the ratio of the amount of retrieved stored data per unit of downloaded data, is derived, and a necessary and a sufficient condition for codes to achieve the PIR capacity are given. The necessary condition is based on the generalized Hamming weights of the storage code, while the sufficient condition is based on code automorphisms. We show that cyclic codes and Reed-Muller codes satisfy the sufficient condition and are thus PIR capacity-achieving.
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| 5. |
- Lin, Hsuan-Yin, et al.
(författare)
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Asymmetry Helps: Improved Private Information Retrieval Protocols for Distributed Storage
- 2018
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Ingår i: 2018 IEEE Information Theory Workshop, ITW 2018.
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Konferensbidrag (refereegranskat)abstract
- We consider private information retrieval (PIR) for distributed storage systems (DSSs) with noncolluding nodes where data is stored using a non maximum distance separable (MDS) linear code. It was recently shown that if data is stored using a particular class of non-MDS linear codes, the MDS-PIR capacity, i.e., the maximum possible PIR rate for MDS-coded DSSs, can be achieved. For this class of codes, we prove that the PIR capacity is indeed equal to the MDS-PIR capacity, giving the first family of non-MDS codes for which the PIR capacity is known. For other codes, we provide asymmetric PIR protocols that achieve a strictly larger PIR rate compared to existing symmetric PIR protocols.
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| 6. |
- Lin, Hsuan Yin, et al.
(författare)
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Multi-Server Weakly-Private Information Retrieval
- 2022
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Ingår i: IEEE Transactions on Information Theory. - 0018-9448 .- 1557-9654. ; 68:2, s. 1197-1219
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Tidskriftsartikel (refereegranskat)abstract
- Private information retrieval (PIR) protocols ensure that a user can download a file from a database without revealing any information on the identity of the requested file to the servers storing the database. While existing protocols strictly impose that no information is leaked on the file’s identity, this work initiates the study of the tradeoffs that can be achieved by relaxing the perfect privacy requirement. We refer to such protocols as weakly-private information retrieval (WPIR) protocols. In particular, for the case of multiple noncolluding replicated servers, we study how the download rate, the upload cost, and the access complexity can be improved when relaxing the perfect privacy constraint. To quantify the information leakage on the requested file’s identity we consider mutual information (MI), worst-case information leakage, and maximal leakage (MaxL). We present two WPIR schemes, denoted by Scheme A and Scheme B, based on two recent PIR protocols and show that the download rate of the former can be optimized by solving a convex optimization problem. We also show that Scheme A achieves an improved download rate compared to the recently proposed scheme by Samy et al. under the so-called ϵ-privacy metric. Additionally, a family of schemes based on partitioning is presented. Moreover, we provide an information-theoretic converse bound for the maximum possible download rate for the MI and MaxL privacy metrics under a practical restriction on the alphabet size of queries and answers. For two servers and two files, the bound is tight under the MaxL metric, which settles the WPIR capacity in this particular case. Finally, we compare the performance of the proposed schemes and their gap to the converse bound.
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| 7. |
- Lin, Hsuan Yin, et al.
(författare)
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The Capacity of Single-Server Weakly-Private Information Retrieval
- 2020
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Ingår i: IEEE International Symposium on Information Theory - Proceedings. - 2157-8095. ; 2020-June, s. 1053-1058
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Konferensbidrag (refereegranskat)abstract
- Weakly-private information retrieval (WPIR) is a variant of the private information retrieval problem in which a user wants to efficiently retrieve a file stored across a set of servers while tolerating some information leakage on the identity of the requested file to the servers. In this paper, we consider WPIR from a single-server database where the information leakage is measured in terms of the mutual information (MI) or maximal leakage (MaxL) privacy metrics. In particular, we establish a connection between the WPIR problem and rate-distortion theory, and fully characterize the optimal tradeoff between the download cost and the allowed information leakage under the MI and MaxL metrics, settling the single-server WPIR capacity.
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| 8. |
- Lin, Hsuan Yin, et al.
(författare)
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The Capacity of Single-Server Weakly-Private Information Retrieval
- 2021
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Ingår i: IEEE Journal on Selected Areas in Information Theory. - 2641-8770. ; 2:1, s. 415-427
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Tidskriftsartikel (refereegranskat)abstract
- A private information retrieval (PIR) protocol guar- antees that a user can privately retrieve files stored in a database without revealing any information about the identity of the requested file. Existing information-theoretic PIR proto- cols ensure perfect privacy, i.e., zero information leakage to the servers storing the database, but at the cost of high download. In this work, we present weakly-private information retrieval (WPIR) schemes that trade off perfect privacy to improve the download cost when the database is stored on a single server. We study the tradeoff between the download cost and information leakage in terms of mutual information (MI) and maximal leak- age (MaxL) privacy metrics. By relating the WPIR problem to rate-distortion theory, the download-leakage function, which is defined as the minimum required download cost of all single- server WPIR schemes for a given level of information leakage and a fixed file size, is introduced. By characterizing the download- leakage function for the MI and MaxL metrics, the capacity of single-server WPIR is fully described.
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