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Motivation: The topic of this paper is the estimation of alignments and mutation rates based on stochastic sequence-evolution models that allow insertions and deletions of subsequences ("fragments") and not just single bases. The model we propose is a variant of a model introduced by Thorne, Kishino, and Felsenstein (1992). The computational tractability of the model depends on certain restrictions in the insertion/deletion process; possible effects we discuss.
Results: The process of fragment insertion and deletion in the sequence-evolution model induces a hidden Markov structure at the level of alignments and thus makes possible efficient statistical alignment algorithms. As an example we apply a sampling procedure to assess the variability in alignment and mutation parameter estimates for HVR1 sequences of human and orangutan, improving results of previous work. Simulation studies give evidence that estimation methods based on the proposed model also give satisfactory results when applied to data for which the restrictions in the insertion/deletion process do not hold.
Availability: The source code of the software for sampling alignments and mutation rates for a pair of DNA sequences according to the fragment insertion and deletion model is freely available from www.math.uni-frankfurt.de/~stoch/software/mcmcsalut under the terms of the GNU public license (GPL, 2000).
Pseudorandom function tribe ensembles based on one-way permutations: improvements and applications
(1999)
Pseudorandom function tribe ensembles are pseudorandom function ensembles that have an additional collision resistance property: almost all functions have disjoint ranges. We present an alternative to the construction of pseudorandom function tribe ensembles based on oneway permutations given by Canetti, Micciancio and Reingold [CMR98]. Our approach yields two different but related solutions: One construction is somewhat theoretic, but conceptually simple and therefore gives an easier proof that one-way permutations suffice to construct pseudorandom function tribe ensembles. The other, slightly more complicated solution provides a practical construction; it starts with an arbitrary pseudorandom function ensemble and assimilates the one-way permutation to this ensemble. Therefore, the second solution inherits important characteristics of the underlying pseudorandom function ensemble: it is almost as effcient and if the starting pseudorandom function ensemble is efficiently invertible (given the secret key) then so is the derived tribe ensemble. We also show that the latter solution yields so-called committing private-key encryption schemes. i.e., where each ciphertext corresponds to exactly one plaintext independently of the choice of the secret key or the random bits used in the encryption process.
We introduce the relationship between incremental cryptography and memory checkers. We present an incremental message authentication scheme based on the XOR MACs which supports insertion, deletion and other single block operations. Our scheme takes only a constant number of pseudorandom function evaluations for each update step and produces smaller authentication codes than the tree scheme presented in [BGG95]. Furthermore, it is secure against message substitution attacks, where the adversary is allowed to tamper messages before update steps, making it applicable to virus protection. From this scheme we derive memory checkers for data structures based on lists. Conversely, we use a lower bound for memory checkers to show that so-called message substitution detecting schemes produce signatures or authentication codes with size proportional to the message length.
We present efficient non-malleable commitment schemes based on standard assumptions such as RSA and Discrete-Log, and under the condition that the network provides publicly available RSA or Discrete-Log parameters generated by a trusted party. Our protocols require only three rounds and a few modular exponentiations. We also discuss the difference between the notion of non-malleable commitment schemes used by Dolev, Dwork and Naor [DDN00] and the one given by Di Crescenzo, Ishai and Ostrovsky [DIO98].
Based on the quadratic residuosity assumption we present a non-interactive crypto-computing protocol for the greater-than function, i.e., a non-interactive procedure between two parties such that only the relation of the parties' inputs is revealed. In comparison to previous solutions our protocol reduces the number of modular multiplications significantly. We also discuss applications to conditional oblivious transfer, private bidding and the millionaires' problem.
We propose a new security measure for commitment protocols, called Universally Composable (UC) Commitment. The measure guarantees that commitment protocols behave like an \ideal commitment service," even when concurrently composed with an arbitrary set of protocols. This is a strong guarantee: it implies that security is maintained even when an unbounded number of copies of the scheme are running concurrently, it implies non-malleability (not only with respect to other copies of the same protocol but even with respect to other protocols), it provides resilience to selective decommitment, and more. Unfortunately two-party uc commitment protocols do not exist in the plain model. However, we construct two-party uc commitment protocols, based on general complexity assumptions, in the common reference string model where all parties have access to a common string taken from a predetermined distribution. The protocols are non-interactive, in the sense that both the commitment and the opening phases consist of a single message from the committer to the receiver.
We review the representation problem based on factoring and show that this problem gives rise to alternative solutions to a lot of cryptographic protocols in the literature. And, while the solutions so far usually either rely on the RSA problem or the intractability of factoring integers of a special form (e.g., Blum integers), the solutions here work with the most general factoring assumption. Protocols we discuss include identification schemes secure against parallel attacks, secure signatures, blind signatures and (non-malleable) commitments.
We show that non-interactive statistically-secret bit commitment cannot be constructed from arbitrary black-box one-to-one trapdoor functions and thus from general public-key cryptosystems. Reducing the problems of non-interactive crypto-computing, rerandomizable encryption, and non-interactive statistically-sender-private oblivious transfer and low-communication private information retrieval to such commitment schemes, it follows that these primitives are neither constructible from one-to-one trapdoor functions and public-key encryption in general. Furthermore, our separation sheds some light on statistical zeroknowledge proofs. There is an oracle relative to which one-to-one trapdoor functions and one-way permutations exist, while the class of promise problems with statistical zero-knowledge proofs collapses in P. This indicates that nontrivial problems with statistical zero-knowledge proofs require more than (trapdoor) one-wayness.
We show lower bounds for the signature size of incremental schemes which are secure against substitution attacks and support single block replacement. We prove that for documents of n blocks such schemes produce signatures of \Omega(n^(1/(2+c))) bits for any constant c>0. For schemes accessing only a single block resp. a constant number of blocks for each replacement this bound can be raised to \Omega(n) resp. \Omega(sqrt(n)). Additionally, we show that our technique yields a new lower bound for memory checkers.
We propose a fast variant of the Gaussian algorithm for the reduction of two dimensional lattices for the l1-, l2- and l-infinite- norm. The algorithm runs in at most O(nM(B) logB) bit operations for the l-infinite- norm and in O(n log n M(B) logB) bit operations for the l1 and l2 norm on input vectors a, b 2 ZZn with norm at most 2B where M(B) is a time bound for B-bit integer multiplication. This generalizes Schönhages monotone Algorithm [Sch91] to the centered case and to various norms.
We introduce algorithms for lattice basis reduction that are improvements of the famous L3-algorithm. If a random L3-reduced lattice basis b1,b2,...,bn is given such that the vector of reduced Gram-Schmidt coefficients ({µi,j} 1<= j< i<= n) is uniformly distributed in [0,1)n(n-1)/2, then the pruned enumeration finds with positive probability a shortest lattice vector. We demonstrate the power of these algorithms by solving random subset sum problems of arbitrary density with 74 and 82 many weights, by breaking the Chor-Rivest cryptoscheme in dimensions 103 and 151 and by breaking Damgard's hash function.
We call a vector x/spl isin/R/sup n/ highly regular if it satisfies =0 for some short, non-zero integer vector m where <...> is the inner product. We present an algorithm which given x/spl isin/R/sup n/ and /spl alpha//spl isin/N finds a highly regular nearby point x' and a short integer relation m for x'. The nearby point x' is 'good' in the sense that no short relation m~ of length less than /spl alpha//2 exists for points x~ within half the x'-distance from x. The integer relation m for x' is for random x up to an average factor 2/sup /spl alpha//2/ a shortest integer relation for x'. Our algorithm uses, for arbitrary real input x, at most O(n/sup 4/(n+log A)) many arithmetical operations on real numbers. If a is rational the algorithm operates on integers having at most O(n/sup 5/+n/sup 3/(log /spl alpha/)/sup 2/+log(/spl par/qx/spl par//sup 2/)) many bits where q is the common denominator for x.
We report on improved practical algorithms for lattice basis reduction. We propose a practical floating point version of theL3-algorithm of Lenstra, Lenstra, Lovász (1982). We present a variant of theL3-algorithm with "deep insertions" and a practical algorithm for block Korkin—Zolotarev reduction, a concept introduced by Schnorr (1987). Empirical tests show that the strongest of these algorithms solves almost all subset sum problems with up to 66 random weights of arbitrary bit length within at most a few hours on a UNISYS 6000/70 or within a couple of minutes on a SPARC1 + computer.
We call a distribution on n bit strings (", e) locally random, if for every choice of e · n positions the induced distribution on e bit strings is in the L1 norm at most " away from the uniform distribution on e bit strings. We establish local randomness in polynomial random number generators (RNG) that are candidate one way functions. Let N be a squarefree integer and let f1, . . . , f be polynomials with coe±- cients in ZZN = ZZ/NZZ. We study the RNG that stretches a random x 2 ZZN into the sequence of least significant bits of f1(x), . . . , f(x). We show that this RNG provides local randomness if for every prime divisor p of N the polynomials f1, . . . , f are linearly independent modulo the subspace of polynomials of degree · 1 in ZZp[x]. We also establish local randomness in polynomial random function generators. This yields candidates for cryptographic hash functions. The concept of local randomness in families of functions extends the concept of universal families of hash functions by Carter and Wegman (1979). The proofs of our results rely on upper bounds for exponential sums.
We propose two improvements to the Fiat Shamir authentication and signature scheme. We reduce the communication of the Fiat Shamir authentication scheme to a single round while preserving the e±ciency of the scheme. This also reduces the length of Fiat Shamir signatures. Using secret keys consisting of small integers we reduce the time for signature generation by a factor 3 to 4. We propose a variation of our scheme using class groups that may be secure even if factoring large integers becomes easy.
Assuming a cryptographically strong cyclic group G of prime order q and a random hash function H, we show that ElGamal encryption with an added Schnorr signature is secure against the adaptive chosen ciphertext attack, in which an attacker can freely use a decryption oracle except for the target ciphertext. We also prove security against the novel one-more-decyption attack. Our security proofs are in a new model, corresponding to a combination of two previously introduced models, the Random Oracle model and the Generic model. The security extends to the distributed threshold version of the scheme. Moreover, we propose a very practical scheme for private information retrieval that is based on blind decryption of ElGamal ciphertexts.
We enhance the security of Schnorr blind signatures against the novel one-more-forgery of Schnorr [Sc01] andWagner [W02] which is possible even if the discrete logarithm is hard to compute. We show two limitations of this attack. Firstly, replacing the group G by the s-fold direct product G exp(×s) increases the work of the attack, for a given number of signer interactions, to the s-power while increasing the work of the blind signature protocol merely by a factor s. Secondly, we bound the number of additional signatures per signer interaction that can be forged effectively. That fraction of the additional forged signatures can be made arbitrarily small.