5,359 research outputs found
On Computing Centroids According to the p-Norms of Hamming Distance Vectors
In this paper we consider the p-Norm Hamming Centroid problem which asks to determine whether some given strings have a centroid with a bound on the p-norm of its Hamming distances to the strings. Specifically, given a set S of strings and a real k, we consider the problem of determining whether there exists a string s^* with (sum_{s in S} d^{p}(s^*,s))^(1/p) <=k, where d(,) denotes the Hamming distance metric. This problem has important applications in data clustering and multi-winner committee elections, and is a generalization of the well-known polynomial-time solvable Consensus String (p=1) problem, as well as the NP-hard Closest String (p=infty) problem.
Our main result shows that the problem is NP-hard for all fixed rational p > 1, closing the gap for all rational values of p between 1 and infty. Under standard complexity assumptions the reduction also implies that the problem has no 2^o(n+m)-time or 2^o(k^(p/(p+1)))-time algorithm, where m denotes the number of input strings and n denotes the length of each string, for any fixed p > 1. The first bound matches a straightforward brute-force algorithm. The second bound is tight in the sense that for each fixed epsilon > 0, we provide a 2^(k^(p/((p+1))+epsilon))-time algorithm. In the last part of the paper, we complement our hardness result by presenting a fixed-parameter algorithm and a factor-2 approximation algorithm for the problem
Lower bounds for approximation schemes for Closest String
In the Closest String problem one is given a family of
equal-length strings over some fixed alphabet, and the task is to find a string
that minimizes the maximum Hamming distance between and a string from
. While polynomial-time approximation schemes (PTASes) for this
problem are known for a long time [Li et al., J. ACM'02], no efficient
polynomial-time approximation scheme (EPTAS) has been proposed so far. In this
paper, we prove that the existence of an EPTAS for Closest String is in fact
unlikely, as it would imply that , a highly
unexpected collapse in the hierarchy of parameterized complexity classes. Our
proof also shows that the existence of a PTAS for Closest String with running
time , for any computable function
, would contradict the Exponential Time Hypothesis
Distributed Computing with Adaptive Heuristics
We use ideas from distributed computing to study dynamic environments in
which computational nodes, or decision makers, follow adaptive heuristics (Hart
2005), i.e., simple and unsophisticated rules of behavior, e.g., repeatedly
"best replying" to others' actions, and minimizing "regret", that have been
extensively studied in game theory and economics. We explore when convergence
of such simple dynamics to an equilibrium is guaranteed in asynchronous
computational environments, where nodes can act at any time. Our research
agenda, distributed computing with adaptive heuristics, lies on the borderline
of computer science (including distributed computing and learning) and game
theory (including game dynamics and adaptive heuristics). We exhibit a general
non-termination result for a broad class of heuristics with bounded
recall---that is, simple rules of behavior that depend only on recent history
of interaction between nodes. We consider implications of our result across a
wide variety of interesting and timely applications: game theory, circuit
design, social networks, routing and congestion control. We also study the
computational and communication complexity of asynchronous dynamics and present
some basic observations regarding the effects of asynchrony on no-regret
dynamics. We believe that our work opens a new avenue for research in both
distributed computing and game theory.Comment: 36 pages, four figures. Expands both technical results and discussion
of v1. Revised version will appear in the proceedings of Innovations in
Computer Science 201
Complexity of Combinatorial Matrix Completion With Diameter Constraints
We thoroughly study a novel and still basic combinatorial matrix completion
problem: Given a binary incomplete matrix, fill in the missing entries so that
the resulting matrix has a specified maximum diameter (that is, upper-bounding
the maximum Hamming distance between any two rows of the completed matrix) as
well as a specified minimum Hamming distance between any two of the matrix
rows. This scenario is closely related to consensus string problems as well as
to recently studied clustering problems on incomplete data.
We obtain an almost complete complexity dichotomy between polynomial-time
solvable and NP-hard cases in terms of the minimum distance lower bound and the
number of missing entries per row of the incomplete matrix. Further, we develop
polynomial-time algorithms for maximum diameter three, which are based on
Deza's theorem from extremal set theory. On the negative side we prove
NP-hardness for diameter at least four. For the parameter number of missing
entries per row, we show polynomial-time solvability when there is only one
missing entry and NP-hardness when there can be at least two missing entries.
In general, our algorithms heavily rely on Deza's theorem and the
correspondingly identified sunflower structures pave the way towards solutions
based on computing graph factors and solving 2-SAT instances
On the Complexity of the Single Individual SNP Haplotyping Problem
We present several new results pertaining to haplotyping. These results
concern the combinatorial problem of reconstructing haplotypes from incomplete
and/or imperfectly sequenced haplotype fragments. We consider the complexity of
the problems Minimum Error Correction (MEC) and Longest Haplotype
Reconstruction (LHR) for different restrictions on the input data.
Specifically, we look at the gapless case, where every row of the input
corresponds to a gapless haplotype-fragment, and the 1-gap case, where at most
one gap per fragment is allowed. We prove that MEC is APX-hard in the 1-gap
case and still NP-hard in the gapless case. In addition, we question earlier
claims that MEC is NP-hard even when the input matrix is restricted to being
completely binary. Concerning LHR, we show that this problem is NP-hard and
APX-hard in the 1-gap case (and thus also in the general case), but is
polynomial time solvable in the gapless case.Comment: 26 pages. Related to the WABI2005 paper, "On the Complexity of
Several Haplotyping Problems", but with more/different results. This papers
has just been submitted to the IEEE/ACM Transactions on Computational Biology
and Bioinformatics and we are awaiting a decision on acceptance. It differs
from the mid-August version of this paper because here we prove that 1-gap
LHR is APX-hard. (In the earlier version of the paper we could prove only
that it was NP-hard.
Pattern Matching and Consensus Problems on Weighted Sequences and Profiles
We study pattern matching problems on two major representations of uncertain
sequences used in molecular biology: weighted sequences (also known as position
weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple
version, in which only the pattern or only the text is uncertain, we obtain
efficient algorithms with theoretically-provable running times using a
variation of the lookahead scoring technique. We also consider a general
variant of the pattern matching problems in which both the pattern and the text
are uncertain. Central to our solution is a special case where the sequences
have equal length, called the consensus problem. We propose algorithms for the
consensus problem parameterized by the number of strings that match one of the
sequences. As our basic approach, a careful adaptation of the classic
meet-in-the-middle algorithm for the knapsack problem is used. On the lower
bound side, we prove that our dependence on the parameter is optimal up to
lower-order terms conditioned on the optimality of the original algorithm for
the knapsack problem.Comment: 22 page
Multivariate Fine-Grained Complexity of Longest Common Subsequence
We revisit the classic combinatorial pattern matching problem of finding a
longest common subsequence (LCS). For strings and of length , a
textbook algorithm solves LCS in time , but although much effort has
been spent, no -time algorithm is known. Recent work
indeed shows that such an algorithm would refute the Strong Exponential Time
Hypothesis (SETH) [Abboud, Backurs, Vassilevska Williams + Bringmann,
K\"unnemann FOCS'15].
Despite the quadratic-time barrier, for over 40 years an enduring scientific
interest continued to produce fast algorithms for LCS and its variations.
Particular attention was put into identifying and exploiting input parameters
that yield strongly subquadratic time algorithms for special cases of interest,
e.g., differential file comparison. This line of research was successfully
pursued until 1990, at which time significant improvements came to a halt. In
this paper, using the lens of fine-grained complexity, our goal is to (1)
justify the lack of further improvements and (2) determine whether some special
cases of LCS admit faster algorithms than currently known.
To this end, we provide a systematic study of the multivariate complexity of
LCS, taking into account all parameters previously discussed in the literature:
the input size , the length of the shorter string
, the length of an LCS of and , the numbers of
deletions and , the alphabet size, as well as
the numbers of matching pairs and dominant pairs . For any class of
instances defined by fixing each parameter individually to a polynomial in
terms of the input size, we prove a SETH-based lower bound matching one of
three known algorithms. Specifically, we determine the optimal running time for
LCS under SETH as .
[...]Comment: Presented at SODA'18. Full Version. 66 page
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