A binary string transmitted via a memoryless i.i.d. deletion channel is received as a subsequence of the original input. From this, one obtains a posterior distribution on the channel input, corresponding to a set of candidate supersequences weighted by the number of times the received subsequence can be embedded in them. In a previous work it is conjectured on the basis of experimental data that the entropy of the posterior is minimized and maximized by the constant and the alternating strings, respectively. In this work, we present an algorithm for counting the number of subsequence embeddings using a run-length encoding of strings. We then describe two different ways of clustering the space of supersequences and prove that their cardinality depends only on the length of the received subsequence and its Hamming weight, but not its exact form. Then, we consider supersequences that contain a single embedding of a fixed subsequence, referred to as singletons, and provide a closed form expression for enumerating them using the same run-length encoding. We prove an analogous result for the minimization and maximization of the number of singletons, by the alternating and the uniform strings, respectively. Next, we prove the original minimal entropy conjecture for the special cases of single and double deletions using similar clustering techniques and the same run-length encoding, which allow us to characterize the distribution of the number of subsequence embeddings in the space of compatible supersequences to demonstrate the effect of an entropy decreasing operation.
Perhaps rather surprisingly, the problem of determining the number of occurrences of a fixed subsequence in random sequences has not received the same amount and level of attention from the various communities. The state-of-the-art in the finite-length regime remains rather limited in scope. More precisely, the distribution of the number of occurrences constitutes a central problem in coding theory, with a maximum likelihood decoding argument, which represents the holy grail in the study of deletion channels. A comprehensive survey, which among other things, outlines the significance of figuring out this particular distribution is given by Mitzenmacher in @cite_13 .
@cite_13
2963712885 2170484108 2010260400 2949560198
This paper studies problems in data reconstruction, an important area with numerous applications. In particular, we examine the reconstruction of binary and nonbinary sequences from synchronization (insertion deletion-correcting) codes. These sequences have been corrupted by a fixed number of symbol insertions (larger than the minimum edit distance of the code), yielding a number of distinct traces to be used for reconstruction. We wish to know the minimum number of traces needed for exact reconstruction. This is a general version of a problem tackled by Levenshtein for uncoded sequences. We introduce an exact formula for the maximum number of common supersequences shared by sequences at a certain edit distance, yielding an upper bound on the number of distinct traces necessary to guarantee exact reconstruction. Without specific knowledge of the code words, this upper bound is tight. We apply our results to the famous single deletion insertion-correcting Varshamov–Tenengolts (VT) codes and show that a significant number of VT code word pairs achieve the worst case number of outputs needed for exact reconstruction. We also consider extensions to other channels, such as adversarial deletion and insertion deletion channels and probabilistic channels. We introduce and solve some new problems of efficient reconstruction of an unknown sequence from its versions distorted by errors of a certain type. These erroneous versions are considered as outputs of repeated transmissions over a channel, either a combinatorial channel defined by the maximum number of permissible errors of a given type, or a discrete memoryless channel. We are interested in the smallest N such that N erroneous versions always suffice to reconstruct a sequence of length n, either exactly or with a preset accuracy and or with a given probability. We are also interested in simple reconstruction algorithms. Complete solutions for combinatorial channels with some types of errors of interest in coding theory, namely, substitutions, transpositions, deletions, and insertions of symbols are given. For these cases, simple reconstruction algorithms based on majority and threshold principles and their nontrivial combination are found. In general, for combinatorial channels the considered problem is reduced to a new problem of reconstructing a vertex of an arbitrary graph with the help of the minimum number of vertices in its metrical ball of a given radius. A certain sufficient condition for solution of this problem is presented. For a discrete memoryless channel, the asymptotic behavior of the minimum number of repeated transmissions which are sufficient to reconstruct any sequence of length n within Hamming distance d with error probability spl epsiv is found when d n and spl epsiv tend to 0 as n spl rarr spl infin . A similar result for the continuous channel with discrete time and additive Gaussian noise is also obtained. The problems of finding shortest common supersequences (SCS) and longest common subsequences (LCS) are two well-known NP -hard problems that have applications in many areas including computational molecular biology, data compression, robot motion planning and scheduling, text editing, etc. A lot of fruitless effort has been spent in searching for good approximation algorithms for these problems. In this paper, we show that these problems are inherently hard to approximate in the worst case. In particular, we prove that (i) SCS does not have a polynomial time linear approximation algorithm, unless P = NP ; (ii) There exists a constant @math such that, if SCS has a polynomial time approximation algorithm with ratio @math , where @math is the number of input sequences, then NP is contained in DTIME @math ; (iii) There exists a constant @math such that, if LCS has a polynomial time approximation algorithm with performance ratio @math , then P = NP . The proofs utilize the recent results of [Proc. 23rd IEEE Symposium on Foundations of Computer Science, 1992, pp. 14-23] on the complexity of approximation problems. In the second part of the paper, we introduce a new method for analyzing the average-case performance of algorithms for sequences, based on Kolmogorov complexity. Despite the above nonapproximability results, we show that near optimal solutions for both SCS and LCS can be found on the average. More precisely, consider a fixed alphabet @math and suppose that the input sequences are generated randomly according to the uniform probability distribution and are of the same length @math . Moreover, assume that the number of input sequences is polynomial in @math . Then, there are simple greedy algorithms which approximate SCS and LCS with expected additive errors @math and @math for any @math , respectively. Incidentally, our analyses also provide tight upper and lower bounds on the expected LCS and SCS lengths for a set of random sequences, solving a generalization of another well-known open question on the expected LCS length for two random sequences [K. Alexander, The rate of convergence of the mean length of the longest common subsequence, 1992, manuscript],[V. Chvatal and D. Sankoff, J. Appl. Probab., 12 (1975), pp. 306-315], [D. Sankoff and J. Kruskall, eds., Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison, Addison-Wesley, Reading, MA, 1983]. We initiate the probabilistic analysis of linear programming (LP) decoding of low-density parity-check (LDPC) codes. Specifically, we show that for a random LDPC code ensemble, the linear programming decoder of Feldman succeeds in correcting a constant fraction of errors with high probability. The fraction of correctable errors guaranteed by our analysis surpasses previous nonasymptotic results for LDPC codes, and in particular, exceeds the best previous finite-length result on LP decoding by a factor greater than ten. This improvement stems in part from our analysis of probabilistic bit-flipping channels, as opposed to adversarial channels. At the core of our analysis is a novel combinatorial characterization of LP decoding success, based on the notion of a flow on the Tanner graph of the code. An interesting by-product of our analysis is to establish the existence of ldquoprobabilistic expansionrdquo in random bipartite graphs, in which one requires only that almost every (as opposed to every) set of a certain size expands, for sets much larger than in the classical worst case setting.