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We present Quip, a lossless compression algorithm for next-generation sequencing data in the FASTQ and SAM/BAM formats. In addition to implementing reference-based compression, we have developed, to our knowledge, the first assembly-based…

Quantitative Methods · Quantitative Biology 2012-07-11 Daniel C. Jones , Walter L. Ruzzo , Xinxia Peng , Michael G. Katze

Differential privacy provides the first theoretical foundation with provable privacy guarantee against adversaries with arbitrary prior knowledge. The main idea to achieve differential privacy is to inject random noise into statistical…

Data Structures and Algorithms · Computer Science 2011-11-01 Yang D. Li , Zhenjie Zhang , Marianne Winslett , Yin Yang

Any secured system can be modeled as a capability-based access control system in which each user is given a set of secret keys of the resources he is granted access to. In some large systems with resource-constrained devices, such as sensor…

Cryptography and Security · Computer Science 2021-09-21 Aldar C-F. Chan

A compression algorithm is presented that uses the set of prime numbers. Sequences of numbers are correlated with the prime numbers, and labeled with the integers. The algorithm can be iterated on data sets, generating factors of doubles on…

General Physics · Physics 2007-05-23 Gordon Chalmers

The max-relative entropy together with its smoothed version is a basic tool in quantum information theory. In this paper, we derive the exact exponent for the asymptotic decay of the small modification of the quantum state in smoothing the…

Quantum Physics · Physics 2023-06-02 Ke Li , Yongsheng Yao , Masahito Hayashi

Randomness is a critical resource of modern cryptosystems. Quantum mechanics offers the best properties of an entropy source in terms of unpredictability. However, these sources are often fragile and can fail silently. Therefore,…

Quantum Physics · Physics 2024-12-02 Rodrigo Piera , Jaideep Singh , Yury Kurochkin , James A. Grieve

Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…

Quantitative Methods · Quantitative Biology 2011-06-21 Shanika Kuruppu , Simon Puglisi , Justin Zobel

Consider the case where consecutive blocks of N letters of a semi-infinite individual sequence X over a finite-alphabet are being compressed into binary sequences by some one-to-one mapping. No a-priori information about X is available at…

Information Theory · Computer Science 2013-01-25 Jacob Ziv

In this paper, the compression of an independent and identically distributed Gaussian source sequence is studied in an unsecure network. Within a game theoretic setting for a three-party noiseless communication network (sender Alice,…

Cryptography and Security · Computer Science 2013-07-30 Eva C. Song , Paul Cuff , H. Vincent Poor

This paper studies the problem of secure communication over a K-transmitter multiple access channel in the presence of an external eavesdropper, subject to a joint secrecy constraint (i.e., information leakage rate from the collection of K…

Information Theory · Computer Science 2017-01-24 Yanling Chen , O. Ozan Koyluoglu , A. J. Han Vinck

The secrecy capacity of a network, for a given collection of permissible wiretap sets, is the maximum rate of communication such that observing links in any permissible wiretap set reveals no information about the message. This paper…

Information Theory · Computer Science 2016-11-17 Tao Cui , Tracey Ho , Joerg Kliewer

This paper investigates the benefits of the side information on the universal compression of sequences from a mixture of $K$ parametric sources. The output sequence of the mixture source is chosen from the source $i \in \{1,\ldots ,K\}$…

Information Theory · Computer Science 2014-12-01 Ahmad Beirami , Liling Huang , Mohsen Sardari , Faramarz Fekri

Lossy image compression is a many-to-one process, thus one bitstream corresponds to multiple possible original images, especially at low bit rates. However, this nature was seldom considered in previous studies on image compression, which…

Image and Video Processing · Electrical Eng. & Systems 2021-10-01 Haichuan Ma , Dong Liu , Cunhui Dong , Li Li , Feng Wu

This paper investigates the problem of variable-length lossy source coding allowing a positive excess distortion probability and an overflow probability of codeword lengths. Novel one-shot achievability and converse bounds of the optimal…

Information Theory · Computer Science 2018-12-17 Shota Saito , Hideki Yagi , Toshiyasu Matsushima

Applying encryption technology to image retrieval can ensure the security and privacy of personal images. The related researches in this field have focused on the organic combination of encryption algorithm and artificial feature…

Multimedia · Computer Science 2022-08-26 Zhixun Lu , Qihua Feng , Peiya Li

Many multivariate data such as social and biological data exhibit complex dependencies that are best characterized by graphs. Unlike sequential data, graphs are, in general, unordered structures. This means we can no longer use classic,…

Information Theory · Computer Science 2021-10-05 Mojtaba Abolfazli , Anders Host-Madsen , June Zhang , Andras Bratincsak

Fundamental rate-distortion-perception (RDP) trade-offs arise in applications requiring maintained perceptual quality of reconstructed data, such as neural image compression. When compressed data is transmitted over public communication…

Information Theory · Computer Science 2026-04-23 Gustaf Åhlgren , Onur Günlü

Motivation: Next Generation Sequencing technologies revolutionized many fields in biology by enabling the fast and cheap sequencing of large amounts of genomic data. The ever increasing sequencing capacities enabled by current sequencing…

Genomics · Quantitative Biology 2012-07-24 Himanshu Asnani , Dinesh Bharadia , Mainak Chowdhury , Idoia Ochoa , Itai Sharon , Tsachy Weissman

The information spectrum approach gives general formulae for optimal rates of various information theoretic protocols, under minimal assumptions on the nature of the sources, channels and entanglement resources involved. This paper…

Quantum Physics · Physics 2007-05-23 Garry Bowen , Nilanjana Datta

This paper studies cross-domain lossy compression through the lens of minimum entropy coupling (MEC) with rate and classification constraints. In this setting, an encoder observes samples from a degraded source domain, while the decoder is…

Information Theory · Computer Science 2026-05-12 Nam Nguyen , Hassan Tavakoli , An Vuong , Thinh Nguyen , Bella Bose