Codes for Synchronization in Channels and Sources with Edits

Edit channels are a class of communication channels where the output of the channel is an edited version of the input. The edits are considered to be deletions and insertions. DNA-based data storage system is one of the motivations for this model. This thesis studies various problems related to edit channel and also edit synchronization problem. Varshamov-Tenengolts (VT) codes are first introduced. These codes can correct a single deletion or insertion and have a linear-time decoder. The problem of efficient encoding of the non-binary version of VT codes is addressed, where a simple linear-time encoding method to systematically map binary message sequences onto VT codewords is proposed. Another model that is studied is segmented edit channels, where we have the additional assumption that the channel input sequence is implicitly divided into segments such that at most one edit can occur within a segment. A code construction is proposed for this model based on subsets of VT codes chosen with pre-determined prefxes and/or sufxes. Also an upper bound is derived on the rate of any zero-error code for the segmented edit channel in terms of the segment length. This upper bound shows that the rate scaling of the proposed codes as the segment length increases is the same as that of the maximal code. Edit synchronization is another problem studied in this thesis. In this model, there are two remote nodes (encoder and decoder), each having a binary sequence. The sequence X, available at the encoder, is the updated sequence and differs from Y (available at the decoder) by a small number of edits. The goal is to construct a message M, to be sent via a one-way error-free link, such that the decoder can reconstruct X using M and Y. A coding scheme is devised for this one-way synchronization model. The scheme is based on multiple layers of VT codes combined with off-the-shelf linear error-correcting codes and uses a list decoder. Motivated by the sequence reconstruction problem from traces in DNA-based storage, the problem of designing codes for the deletion channel when multiple observations (or traces) are available to the decoder is considered. A simple binary and non-binary code is proposed that splits the codeword into blocks and employs a VT code in each block. The availability of multiple traces helps the decoder to identify deletion-free copies of a block, and to avoid mis-synchronization while decoding. The encoding complexity of the proposed scheme is linear in the codeword length; the decoding complexity is linear in the codeword length and quadratic in the number of deletions and the number of traces. The list decoding technique for the proposed code is also considered

Efficient Systematic Encoding of Non-binary VT Codes

Varshamov-Tenengolts (VT) codes are a class of codes which can correct a single deletion or insertion with a linear-time decoder. This paper addresses the problem of efficient encoding of non-binary VT codes, defined over an alphabet of size $q >2$. We propose a simple linear-time encoding method to systematically map binary message sequences onto VT codewords. The method provides a new lower bound on the size of $q$-ary VT codes of length $n$.Comment: This paper will appear in the proceedings of ISIT 201

Mu-2 ranging

The Mu-II Dual-Channel Sequential Ranging System designed as a model for future Deep Space Network ranging equipment is described. A list of design objectives is followed by a theoretical explanation of the digital demodulation techniques first employed in this machine. Hardware and software implementation are discussed, together with the details relating to the construction of the device. Two appendixes are included relating to the programming and operation of this equipment to yield the maximum scientific data

Network Processors and Next Generation Networks: Design, Applications, and Perspectives

Network Processors (NPs) are hardware platforms born as appealing solutions for packet processing devices in networking applications. Nowadays, a plethora of solutions exists, with no agreement on a common architecture. Each vendor has proposed its specific solution and no official standard still exists. The common features of all proposals are a hierarchy of processors, with a general purpose processor and several units specialized for packet processing, a series of memory devices with different sizes and latencies, a low-level programmability. The target is a platform for networking applications with low time to market and high time in market, thanks to a high flexibility and a programmability simpler than that of ASICs, for example. After about ten years since the "birth" of network processors, this research activity wants to make an analytical balance of their development and usage. Many authoritative opinions suggest that NPs have been "outdated" by multicore or manycore systems, which provide general purpose environments and some specialized cores. The main reasons of these negative opinions are the hard programmability of NPs, which often requires the knowledge of private microcode, or the excessive architectural limits, such as reduced memories and minimal instruction store. Our research shows that Network Processors can be appealing for different applications in networking area, and many interesting solutions can be obtained, which present very high performance, outscoring current solutions. However, the issues of hard programming and remarkable limits exist, and they could be alleviated only by providing almost a comprehensive programming environment and a proper design in terms of processing and memory resources. More e cient solutions can be surely provided, but the experience of network processors has produced an important legacy in developing packet processing engines. In this work, we have realized many devices for networking purposes based on NP platform, in order to understand the complexity of programming, the flexibility of design, the complexity of tasks that can be implemented, the maximum depth of packet processing, the performance of such devices, the real usefulness of NPs in network devices. All these features have been accurately analyzed and will be illustrated in this thesis. Many remarkable results have been obtained, which confirm the Network Processors as appealing solutions for network devices. Moreover, the research on NPs have lead us to analyze and solve more general issues, related for instance to multiprocessor systems or to processors with no big available memory. In particular, the latter issue lead us to design many interesting data structures for set representation and membership query, which are based on randomized techniques and allow for big memory savings

From Birds to Drug-Resistant Cancer, a novel In situ Methodology to Explore Divergent Genome Evolution

Fluorescent hybridisatio nmethodologies have not changed in principles over the past 30 years, with the increase of computational sequencing technologies causing the replacement of in situ hybridisations. Fluorescence in situ hybridisation (FISH) is in need of a refresh to be a worthwhile tool in a modern day cytogenetic laboratory to overcome short comings of these new methods. The creation of the novel multilayer FISH protocol has effectively eliminated many negative aspects of classic FISH based experiments, such as a large reduction in cost and is no longer as limited by fluorophore availability. Here presented within this thesis is the creation of this methodology and application to a wide variety of cytogenetic hypothesises. Key species from the Galliform order were investigated in order to detect previously missed intrachromosomal rearrangements within their macrochromosomes, a premise formerly overlooked. Rearrangements were found within chromosomes of the galliforme species used such as E.chinensis which displays a intrachromosomal inversion on the p-arm of chromosome 2. Furthermore, the creation of an interphase state folding prediction tool has been used to assess the arrangement of macrochromosomes during cellular growth stages within G.gallus. Here it is noted that there are particular arrangements identified which are similar across chromosomes studied. The chicken lymphoma cell line DT40 is of great importance in B-cell receptor studies along with gene disruption experiments. Presented here is an updated karyotype for the cell line. Here shows contrasting and more in-depth evidence of aberrations to further develop our understanding of the genomic arrangement of this useful cell line. The level of tumour heterogeneity in a cancer is a diagnostic tool allowing clinicians to comment on therapeutic choices and prognosis of the disease. Found to be dominant in recurrent cancers, cytotoxic resistant tumour cell populations may indeed exist within initial primary tumours at low frequency to be positively selected during chemotherapy. Within a neuroblastoma cell line,and cyto-toxic resistant derivatives lines,there has been identified a level of genomic heterogeneity which may give clues towards the generation of drug resistance mechanisms

Speech technologies for the audiovisual and multimedia interaction environments

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Quantification of network structural dissimilarities

Identifying and quantifying dissimilarities among graphs is a fundamental and challenging problem of practical importance in many fields of science. Current methods of network comparison are limited to extract only partial information or are computationally very demanding. Here we propose an efficient and precise measure for network comparison, which is based on quantifying differences among distance probability distributions extracted from the networks. Extensive experiments on synthetic and real-world networks show that this measure returns non-zero values only when the graphs are non-isomorphic. Most importantly, the measure proposed here can identify and quantify structural topological differences that have a practical impact on the information flow through the network, such as the presence or absence of critical links that connect or disconnect connected components