Rates of DNA Sequence Profiles for Practical Values of Read Lengths

A recent study by one of the authors has demonstrated the importance of profile vectors in DNA-based data storage. We provide exact values and lower bounds on the number of profile vectors for finite values of alphabet size $q$, read length $\ell$, and word length $n$.Consequently, we demonstrate that for $q\ge 2$ and $n\le q^{\ell/2-1}$, the number of profile vectors is at least $q^{\kappa n}$ with $\kappa$ very close to one.In addition to enumeration results, we provide a set of efficient encoding and decoding algorithms for each of two particular families of profile vectors

Turbo NOC: a framework for the design of Network On Chip based turbo decoder architectures

This work proposes a general framework for the design and simulation of network on chip based turbo decoder architectures. Several parameters in the design space are investigated, namely the network topology, the parallelism degree, the rate at which messages are sent by processing nodes over the network and the routing strategy. The main results of this analysis are: i) the most suited topologies to achieve high throughput with a limited complexity overhead are generalized de-Bruijn and generalized Kautz topologies; ii) depending on the throughput requirements different parallelism degrees, message injection rates and routing algorithms can be used to minimize the network area overhead.Comment: submitted to IEEE Trans. on Circuits and Systems I (submission date 27 may 2009

On chip interconnects for multiprocessor turbo decoding architectures

International audienc

Quickest Sequence Phase Detection

A phase detection sequence is a length-$n$ cyclic sequence, such that the location of any length-$k$ contiguous subsequence can be determined from a noisy observation of that subsequence. In this paper, we derive bounds on the minimal possible $k$ in the limit of $n\to\infty$, and describe some sequence constructions. We further consider multiple phase detection sequences, where the location of any length-$k$ contiguous subsequence of each sequence can be determined simultaneously from a noisy mixture of those subsequences. We study the optimal trade-offs between the lengths of the sequences, and describe some sequence constructions. We compare these phase detection problems to their natural channel coding counterparts, and show a strict separation between the fundamental limits in the multiple sequence case. Both adversarial and probabilistic noise models are addressed.Comment: To appear in the IEEE Transactions on Information Theor

New Algorithms and Lower Bounds for Sequential-Access Data Compression

This thesis concerns sequential-access data compression, i.e., by algorithms that read the input one or more times from beginning to end. In one chapter we consider adaptive prefix coding, for which we must read the input character by character, outputting each character's self-delimiting codeword before reading the next one. We show how to encode and decode each character in constant worst-case time while producing an encoding whose length is worst-case optimal. In another chapter we consider one-pass compression with memory bounded in terms of the alphabet size and context length, and prove a nearly tight tradeoff between the amount of memory we can use and the quality of the compression we can achieve. In a third chapter we consider compression in the read/write streams model, which allows us passes and memory both polylogarithmic in the size of the input. We first show how to achieve universal compression using only one pass over one stream. We then show that one stream is not sufficient for achieving good grammar-based compression. Finally, we show that two streams are necessary and sufficient for achieving entropy-only bounds.Comment: draft of PhD thesi