Non-catastrophic Encoders and Encoder Inverses for Quantum Convolutional Codes

We present an algorithm to construct quantum circuits for encoding and inverse encoding of quantum convolutional codes. We show that any quantum convolutional code contains a subcode of finite index which has a non-catastrophic encoding circuit. Our work generalizes the conditions for non-catastrophic encoders derived in a paper by Ollivier and Tillich (quant-ph/0401134) which are applicable only for a restricted class of quantum convolutional codes. We also show that the encoders and their inverses constructed by our method naturally can be applied online, i.e., qubits can be sent and received with constant delay.Comment: 6 pages, 1 figure, submitted to 2006 IEEE International Symposium on Information Theor

Optimal Haplotype Assembly from High-Throughput Mate-Pair Reads

Humans have $23$ pairs of homologous chromosomes. The homologous pairs are almost identical pairs of chromosomes. For the most part, differences in homologous chromosome occur at certain documented positions called single nucleotide polymorphisms (SNPs). A haplotype of an individual is the pair of sequences of SNPs on the two homologous chromosomes. In this paper, we study the problem of inferring haplotypes of individuals from mate-pair reads of their genome. We give a simple formula for the coverage needed for haplotype assembly, under a generative model. The analysis here leverages connections of this problem with decoding convolutional codes.Comment: 10 pages, 4 figures, Submitted to ISIT 201

Concatenation of convolutional and block codes Final report

Comparison of concatenated and sequential decoding systems and convolutional code structural propertie