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.
Studies involving subsequences and supersequences encompass a wide variety of problems that arise in various contexts such as formal languages, coding theory, computer intrusion detection and DNA sequencing to name a few. Despite their prevalence in such a wide range of disciplines, they remain largely unexplored and still present a considerable wealth of unanswered questions. In the realm of stringology and formal languages, the problem of determining the number of distinct subsequences obtainable from a fixed number of deletions, and closely related problems, have been studied extensively in @cite_26 @cite_24 @cite_5 @cite_15 . Perhaps it is worth noting that the same entropy minimizing and maximizing strings conjectured in @cite_22 and characterized in the present work, have been shown to lead to the minimum and maximum number of distinct subsequences, respectively. The problems of finding shortest common supersequences (SCS) and longest common subsequences (LCS) represent two well-known NP-hard problems @cite_6 @cite_9 @cite_0 that involve subproblems similar to our work. Finally, devising efficient algorithms for subsequence combinatorics based on dynamic programming for counting the number of occurrences of a subsequence in DNA sequencing is yet another important and closely related line of research @cite_3 @cite_19 .
@cite_26 @cite_22 @cite_9 @cite_6 @cite_3 @cite_24 @cite_0 @cite_19 @cite_5 @cite_15
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Abstract In this paper we investigate the complexity of finding various kinds of common super- and subsequences with respect to one or two given sets of strings. We show that Longest Minimal Common Supersequence, Shortest Maximal Common Subsequence, and Shortest Maximal Common Non-Supersequence are MAX SNP-hard over a binary alphabet. Moreover, we show that Shortest Common Supersequence, Longest Common Subsequence, Longest Common Non-Supersequence, Shortest Common Non-Subsequence, and Longest Minimal Common Non-Supersequence are MAX SNP-hard over a binary alphabet if the number of zeros is fixed (by the instance). We show how these problems can be related to finding sequences consistent with respect to two given sets of strings. This leads to a unified approach for characterizing the complexity of such problems. 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]. The longest common subsequence problem is examined from the point of view of parameterized computational complexity. There are several different ways in which parameters enter the problem, such as the number of sequences to be analyzed, the length of the common subsequence, and the size of the alphabet. Lower bounds on the complexity of this basic problem imply lower bounds on a number of other sequence alignment and consensus problems. An issue in the theory of parameterized complexity is whether a problem which takes input (x, k) can be solved in time ƒ(k) · nα where α is independent of k (termed fixed-parameter tractability). It can be argued that this is the appropriate asymptotic model of feasible computability for problems for which a small range of parameter values covers important applications — a situation which certainly holds for many problems in biological sequence analysis. Our main results show that: 1. (1) The longest common subsequence (LCS) parameterized by the number of sequences to be analyzed is hard for W[t] for all t. 2. (2) The LCS problem, parameterized by the length of the common subsequence, belongs to W[P] and is hard for W[2]. 3. (3) The LCS problem parameterized both by the number of sequences and the length of the common subsequence, is complete for W[1]. All of the above results are obtained for unrestricted alphabet sizes. For alphabets of a fixed size, problems (2) and (3) are fixed-parameter tractable. We conjecture that (1) remains hard. We investigate combinatorial enumeration problems related to subsequences of strings; in contrast to substrings, subsequences need not be contiguous. For a finite alphabet E, the following three problems are solved. (1) Number of distinct subsequences: Given a sequence s ∈ Σ n and a nonnegative integer k ≤ n, how many distinct subsequences of length k does s contain? A previous result by Chase states that this number is maximized by choosing s as a repeated permutation of the alphabet. This has applications in DNA microarray production. (2) Number of ρ-restricted p-generated sequences: Given s ∈ Σ n and integers k ≥ 1 and p > 1, how many distinct sequences in Σ k contain no single nucleotide repeat longer than p and can be written as s[ r1 1 ... s rn n with 0 1, determine the number of sequences in E whose longest strictly increasing subsequence has length k, where 0 < k < K. This has applications to significance computations for chaining algorithms. In the paper two combinatorial problems for the set Fnq of sequences of length n over the alphabet Fq= 0, 1, ?, q?1 are considered. The maximum size N?q(n, t) of the set of common subsequences of length n?t and the maximum size N+q(n, t) of the set of common supersequences of length n+t of two different sequences of Fnq are found for any nonnegative integers n and t. The number N?q(n, t)+1 (respectively, N+q(n, t)+1) is equal to the minimum number N of different subsequences of length n?t (supersequences of length n+t) of an unknown sequence X?Fnq which are sufficient for its reconstruction. Simple algorithms to recover X?Fnq from N?q(n, t)+1 of its subsequences of length n?t and from N+q(n, t)+1 of its supersequences of length n+t are given. Super- substring problems and super- subsequence problems are well-known problems in stringology that have applications in a variety of areas, such as manufacturing systems design and molecular biology. Here we investigate the complexity of a new type of such problem that forms a combination of a super- substring and a super- subsequence problem. Moreover we introduce different types of minimal superstring and maximal substring problems. In particular, we consider the following problems: given a set L of strings and a string S, (i) find a minimal superstring (or maximal substring) of L that is also a supersequence (or a subsequence) of S, (ii) find a minimal supersequence (or maximal subsequence) of L that is also a superstring (or a substring) of S. In addition some non-super- non-substring and non-super- nonsubsequence variants are studied. We obtain several NP-hardness or even MAX SNP-hardness results and also identify types of "weak minimal" superstrings and "weak maximal" substrings for which (i) is polynomial-time solvable. The problem of finding a longest common subsequence of two strings is discussed. This problem arises in data processing applications such as comparing two files and in genetic applications such as studying molecular evolution. The difficulty of computing a longest common subsequence of two strings is examined using the decision tree model of computation, in which vertices represent “equal - unequal” comparisons. It is shown that unless a bound on the total number of distinct symbols is assumed, every solution to the problem can consume an amount of time that is proportional to the product of the lengths of the two strings. A general lower bound as a function of the ratio of alphabet size to string length is derived. The case where comparisons between symbols of the same string are forbidden is also considered and it is shown that this problem is of linear complexity for a two-symbol alphabet and quadratic for an alphabet of three or more symbols. A subsequence is obtained from a string by deleting any number of characters; thus in contrast to a substring, a subsequence is not necessarily a contiguous part of the string. Counting subsequences under various constraints has become relevant to biological sequence analysis, to machine learning, to coding theory, to the analysis of categorical time series in the social sciences, and to the theory of word complexity. We present theorems that lead to efficient dynamic programming algorithms to count (1) distinct subsequences in a string, (2) distinct common subsequences of two strings, (3) matching joint embeddings in two strings, (4) distinct subsequences with a given minimum span, and (5) sequences generated by a string allowing characters to come in runs of a length that is bounded from above. We study a problem of mining frequently occurring periodic patterns with a gap requirement from sequences. Given a character sequence S of length L and a pattern P of length l, we consider P a frequently occurring pattern in S if the probability of observing P given a randomly picked length-l subsequence of S exceeds a certain threshold. In many applications, particularly those related to bioinformatics, interesting patterns are periodic with a gap requirement. That is to say, the characters in P should match subsequences of S in such a way that the matching characters in S are separated by gaps of more or less the same size. We show the complexity of the mining problem and discuss why traditional mining algorithms are computationally infeasible. We propose practical algorithms for solving the problem, and study their characteristics. We also present a case study in which we apply our algorithms on some DNA sequences. We discuss some interesting patterns obtained from the case study. The nearestor near-neighbor query problems arise in a large variety of database applications, usually in the context of similarity searching. Of late, there has been increasing interest in building search index structures for performing similarity search over high-dimensional data, e.g., image databases, document collections, time-series databases, and genome databases. Unfortunately, all known techniques for solving this problem fall prey to the of dimensionality." That is, the data structures scale poorly with data dimensionality; in fact, if the number of dimensions exceeds 10 to 20, searching in k-d trees and related structures involves the inspection of a large fraction of the database, thereby doing no better than brute-force linear search. It has been suggested that since the selection of features and the choice of a distance metric in typical applications is rather heuristic, determining an approximate nearest neighbor should su ce for most practical purposes. In this paper, we examine a novel scheme for approximate similarity search based on hashing. The basic idea is to hash the points Supported by NAVY N00014-96-1-1221 grant and NSF Grant IIS-9811904. Supported by Stanford Graduate Fellowship and NSF NYI Award CCR-9357849. Supported by ARO MURI Grant DAAH04-96-1-0007, NSF Grant IIS-9811904, and NSF Young Investigator Award CCR9357849, with matching funds from IBM, Mitsubishi, Schlumberger Foundation, Shell Foundation, and Xerox Corporation. Permission to copy without fee all or part of this material is granted provided that the copies are not made or distributed for direct commercial advantage, the VLDB copyright notice and the title of the publication and its date appear, and notice is given that copying is by permission of the Very Large Data Base Endowment. To copy otherwise, or to republish, requires a fee and or special permission from the Endowment. Proceedings of the 25th VLDB Conference, Edinburgh, Scotland, 1999. from the database so as to ensure that the probability of collision is much higher for objects that are close to each other than for those that are far apart. We provide experimental evidence that our method gives signi cant improvement in running time over other methods for searching in highdimensional spaces based on hierarchical tree decomposition. Experimental results also indicate that our scheme scales well even for a relatively large number of dimensions (more than 50). Several important time series data mining problems reduce to the core task of finding approximately repeated subsequences in a longer time series. In an earlier work, we formalized the idea of approximately repeated subsequences by introducing the notion of time series motifs. Two limitations of this work were the poor scalability of the motif discovery algorithm, and the inability to discover motifs in the presence of noise.Here we address these limitations by introducing a novel algorithm inspired by recent advances in the problem of pattern discovery in biosequences. Our algorithm is probabilistic in nature, but as we show empirically and theoretically, it can find time series motifs with very high probability even in the presence of noise or "don't care" symbols. Not only is the algorithm fast, but it is an anytime algorithm, producing likely candidate motifs almost immediately, and gradually improving the quality of results over time. A natural problem in extremal combinatorics is to maximize the number of distinct subsequences for any length- @math string over a finite alphabet @math ; this value grows exponentially, but slower than @math . We use the probabilistic method to determine the maximizing string, which is a cyclically repeating string. The number of distinct subsequences is exactly enumerated by a generating function, from which we also derive asymptotic estimates. For the alphabet @math , @math has the maximum number of distinct subsequences, namely @math . We also consider the same problem with sub strings in lieu of sub sequences . Here, we show that an appropriately truncated de Bruijn word attains the maximum. For both problems, we compare the performance of random strings with that of the optimal ones. Polar codes, as the first provable capacity-achieving error-correcting codes, have received much attention in recent years. However, the decoding performance of polar codes with traditional successive-cancellation (SC) algorithm cannot match that of the low-density parity-check or Turbo codes. Because SC list (SCL) decoding algorithm can significantly improve the error-correcting performance of polar codes, design of SCL decoders is important for polar codes to be deployed in practical applications. However, because the prior latency reduction approaches for SC decoders are not applicable for SCL decoders, these list decoders suffer from the long-latency bottleneck. In this paper, we propose a multibit-decision approach that can significantly reduce latency of SCL decoders. First, we present a reformulated SCL algorithm that can perform intermediate decoding of 2 b together. The proposed approach, referred as 2-bit reformulated SCL ( 2b-rSCL ) algorithm , can reduce the latency of SCL decoder from ( @math ) to ( @math ) clock cycles without any performance loss. Then, we extend the idea of 2-b-decision to general case, and propose a general decoding scheme that can perform intermediate decoding of any @math bits simultaneously. This general approach, referred as @math -bit reformulated SCL ( @math b-rSCL ) algorithm , can reduce the overall decoding latency to as short as @math cycles. Furthermore, on the basis of the proposed algorithms, very large-scale integration architectures for 2b-rSCL and 4b-rSCL decoders are synthesized. Compared with a prior SCL decoder, the proposed (1024, 512) 2b-rSCL and 4b-rSCL decoders can achieve 21 and 60 reduction in latency, 1.66 and 2.77 times increase in coded throughput with list size 2, and 2.11 and 3.23 times increase in coded throughput with list size 4, respectively. Most existing work on sequence databases use correlation (e.g., Euclidean distance and Pearson correlation) as a core function for various analytical tasks. Typically, it requires users to set a length for the similarity queries. However, there is no steady way to define the proper length on different application needs. In this work we focus on discovering longest-lasting highly correlated subsequences in sequence databases, which is particularly useful in helping those analyses without prior knowledge about the query length. Surprisingly, there has been limited work on this problem. A baseline solution is to calculate the correlations for every possible subsequence combination. Obviously, the brute force solution is not scalable for large datasets. In this work we study a space-constrained index that gives a tight correlation bound for subsequences of similar length and offset by intra-object grouping and inter-object grouping techniques. To the best of our knowledge, this is the first index to support normalized distance metric of arbitrary length subsequences. Extensive experimental evaluation on both real and synthetic sequence datasets verifies the efficiency and effectiveness of our proposed methods. Topic models, such as Latent Dirichlet Allocation (LDA), posit that documents are drawn from admixtures of distributions over words, known as topics. The inference problem of recovering topics from admixtures, is NP-hard. Assuming separability, a strong assumption, [4] gave the first provable algorithm for inference. For LDA model, [6] gave a provable algorithm using tensor-methods. But [4,6] do not learn topic vectors with bounded @math error (a natural measure for probability vectors). Our aim is to develop a model which makes intuitive and empirically supported assumptions and to design an algorithm with natural, simple components such as SVD, which provably solves the inference problem for the model with bounded @math error. A topic in LDA and other models is essentially characterized by a group of co-occurring words. Motivated by this, we introduce topic specific Catchwords, group of words which occur with strictly greater frequency in a topic than any other topic individually and are required to have high frequency together rather than individually. A major contribution of the paper is to show that under this more realistic assumption, which is empirically verified on real corpora, a singular value decomposition (SVD) based algorithm with a crucial pre-processing step of thresholding, can provably recover the topics from a collection of documents drawn from Dominant admixtures. Dominant admixtures are convex combination of distributions in which one distribution has a significantly higher contribution than others. Apart from the simplicity of the algorithm, the sample complexity has near optimal dependence on @math , the lowest probability that a topic is dominant, and is better than [4]. Empirical evidence shows that on several real world corpora, both Catchwords and Dominant admixture assumptions hold and the proposed algorithm substantially outperforms the state of the art [5]. The problem considered is that of determining the number of subsequences obtainable by deleting t symbols from a string of length n over an alphabet of size s. Recurrences are proven and solved for the maximum and average case values, and bounds on these values are exhibited. The problem considered is that of determining the number of subsequences obtain- able by deleting symbols from a string of length over an alphabet of size . Recurrences are proven and solved for the maximum and average case values, and bounds on these values are exhibited. We investigate techniques for analysis and retrieval of object trajectories in two or three dimensional space. Such data usually contain a large amount of noise, that has made previously used metrics fail. Therefore, we formalize non-metric similarity functions based on the longest common subsequence (LCSS), which are very robust to noise and furthermore provide an intuitive notion of similarity between trajectories by giving more weight to similar portions of the sequences. Stretching of sequences in time is allowed, as well as global translation of the sequences in space. Efficient approximate algorithms that compute these similarity measures are also provided. We compare these new methods to the widely used Euclidean and time warping distance functions (for real and synthetic data) and show the superiority of our approach, especially in the strong presence of noise. We prove a weaker version of the triangle inequality and employ it in an indexing structure to answer nearest neighbor queries. Finally, we present experimental results that validate the accuracy and efficiency of our approach. By using a run-length representation of sequences, ways to determine suband supersequences are discussed. This is then used in determining the number of sub- and supersequences of a sequence after double insertions or deletions. It is also used in creating subsequence supersequence books that are searched to find new double insertion deletion correcting code books with higher cardinalities than those already known. Given a set @math of @math strings of total length @math , our task is to report the "most relevant"strings for a given query pattern @math . This involves somewhat more advanced query functionality than the usual pattern matching, as some notion of "most relevant" is involved. In information retrieval literature, this task is best achieved by using inverted indexes. However, inverted indexes work only for some predefined set of patterns. In the pattern matching community, the most popular pattern-matching data structures are suffix trees and suffix arrays. However, a typical suffix tree search involves going through all the occurrences of the pattern over the entire string collection, which might be a lot more than the required relevant documents. The first formal framework to study such kind of retrieval problems was given by [Muthukrishnan, 2002]. He considered two metrics for relevance: frequency and proximity. He took a threshold-based approach on these metrics and gave data structures taking @math words of space. We study this problem in a slightly different framework of reporting the top @math most relevant documents (in sorted order) under similar and more general relevance metrics. Our framework gives linear space data structure with optimal query times for arbitrary score functions. As a corollary, it improves the space utilization for the problems in [Muthukrishnan, 2002] while maintaining optimal query performance. We also develop compressed variants of these data structures for several specific relevance metrics.