Algorithms for extracting motifs from biological weighted sequences

In this paper we present three algorithms for the Motif Identification Problem in Biological Weighted Sequences. The first algorithm extracts repeated motifs from a biological weighted sequence. The motifs correspond to repetitive words which are approximately equal, under a Hamming distance, with probability of occurrence 1/k, where k is a small constant. The second algorithm extracts common motifs from a set of N2 weighted sequences. In this case, the motifs consists of words that must occur with probability 1/k, in 1qN distinct sequences of the set. The third algorithm extracts maximal pairs from a biological weighted sequence. A pair in a sequence is the occurrence of the same word twice. In addition, the algorithms presented in this paper improve previous work on these problems.     

Existence of HSOLSSOMs of type

In this paper we investigate the existence of holey self-orthogonal Latin squares with a symmetric orthogonal mate of type 2ⁿu¹ (HSOLSSOM(2ⁿu¹)). For u2, necessary conditions for existence of such an HSOLSSOM are that u must be even and n3u/2+1. Xu Yunqing and Hu Yuwang have shown that these HSOLSSOMs exist whenever either (1) n9 and n3u/2+1 or (2) n263 and n2(u-2). In this paper we show that in (1) the condition n9 can be extended to n30 and that in (2), the condition n263 can be improved to n4, except possibly for 19 pairs (n,u), the largest of which is (53,28).     

Continued fractions with multiple limits

For integers m2, we study divergent continued fractions whose numerators and denominators in each of the m arithmetic progressions modulo m converge. Special cases give, among other things, an infinite sequence of divergence theorems, the first of which is the classical Stern–Stolz theorem.We give a theorem on a class of Poincaré-type recurrences which shows that they tend to limits when the limits are taken in residue classes and the roots of their characteristic polynomials are distinct roots of unity.We also generalize a curious q-continued fraction of Ramanujan's with three limits to a continued fraction with k distinct limit points, k2. The k limits are evaluated in terms of ratios of certain q-series.Finally, we show how to use Daniel Bernoulli's continued fraction in an elementary way to create analytic continued fractions with m limit points, for any positive integer m2.     

disjoint cycles containing specified independent vertices

Let k1 be an integer and G be a graph of order n3k satisfying the condition that σ₂(G)n+k-1. Let v₁,…,v_k be k independent vertices of G, and suppose that G has k vertex-disjoint triangles C₁,…,C_k with v_iV(C_i) for all 1ik.Then G has k vertex-disjoint cycles such that

(i) for all 1ik.

(ii) , and

(iii) At least k-1 of the k cycles are triangles.

The condition of degree sum σ₂(G)n+k-1 is sharp.

Arithmetic progressions consisting of unlike powers

In this paper we present some new results about unlike powers in arithmetic progression. We prove among other things that for given k 4 and L 3 there are only finitely many arithmetic progressions of the form with x_i , gcd(x₀, x_l) = 1 and 2 l_i L for i = 0, 1, …, k − 1. Furthermore, we show that, for L = 3, the progression (1, 1,…, 1) is the only such progression up to sign. Our proofs involve some well-known theorems of Faltings [9], Darmon and Granville [6] as well as Chabauty's method applied to superelliptic curves.     

On the structure of semi-invariant polynomials in Ore extensions

Let D be an X-outer S-derivation of a prime ring R, where S is an automorphism of R. The following is proved among other things: The degree of the minimal semi-invariant polynomial of the Ore extension R[X;S,D] is ν if charR=0, and is p^kν for some k0 if charR=p2, where ν is the least integer ν1 such that S^νDS^−ν−D is X-inner. A similar result holds for cv-polynomials. These are done by introducing the new notion of k-basic polynomials for each integer k0, which enable us to analyze semi-invariant polynomials inductively.     

Hilbert's Tenth Problem for function fields of varieties over number fields and p-adic fields

Let k be a subfield of a p-adic field of odd residue characteristic, and let be the function field of a variety of dimension n1 over k. Then Hilbert's Tenth Problem for is undecidable. In particular, Hilbert's Tenth Problem for function fields of varieties over number fields of dimension 1 is undecidable.     

On shredders and vertex connectivity augmentation

We consider the following problem: given a k-(node) connected graph G find a smallest set F of new edges so that the graph G+F is (k+1)-connected. The complexity status of this problem is an open question. The problem admits a 2-approximation algorithm. Another algorithm due to Jordán computes an augmenting edge set with at most (k−1)/2 edges over the optimum. CV(G) is a k-separator (k-shredder) of G if |C|=k and the number b(C) of connected components of G−C is at least two (at least three). We will show that the problem is polynomially solvable for graphs that have a k-separator C with b(C)k+1. This leads to a new splitting-off theorem for node connectivity. We also prove that in a k-connected graph G on n nodes the number of k-shredders with at least p components (p3) is less than 2n/(2p−3), and that this bound is asymptotically tight.     

On the code generated by the incidence matrix of points and k-spaces in and its dual

In this paper, we study the p-ary linear code C_k(n,q), q=p^h, p prime, h1, generated by the incidence matrix of points and k-dimensional spaces in PG(n,q). For kn/2, we link codewords of C_k(n,q)C_k(n,q) of weight smaller than 2q^k to k-blocking sets. We first prove that such a k-blocking set is uniquely reducible to a minimal k-blocking set, and exclude all codewords arising from small linear k-blocking sets. For k<n/2, we present counterexamples to lemmas valid for kn/2. Next, we study the dual code of C_k(n,q) and present a lower bound on the weight of the codewords, hence extending the results of Sachar [H. Sachar, The F_p span of the incidence matrix of a finite projective plane, Geom. Dedicata 8 (1979) 407–415] to general dimension.     

The union of minimal hitting sets: Parameterized combinatorial bounds and counting

A k-hitting set in a hypergraph is a set of at most k vertices that intersects all hyperedges. We study the union of all inclusion-minimal k-hitting sets in hypergraphs of rank r (where the rank is the maximum size of hyperedges). We show that this union is relevant for certain combinatorial inference problems and give worst-case bounds on its size, depending on r and k. For r=2 our result is tight, and for each r3 we have an asymptotically optimal bound and make progress regarding the constant factor. The exact worst-case size for r3 remains an open problem. We also propose an algorithm for counting all k-hitting sets in hypergraphs of rank r. Its asymptotic runtime matches the best one known for the much more special problem of finding one k-hitting set. The results are used for efficient counting of k-hitting sets that contain any particular vertex.     

On the number of independent chorded cycles in a graph

Hajnal and Corrádi proved that any simple graph on at least 3k vertices with minimal degree at least 2k contains k independent cycles. We prove the analogous result for chorded cycles. Let G be a simple graph with |V(G)|4k and minimal degree δ(G)3k. Then G contains k independent chorded cycles. This result is sharp.     

Viscosity approximation to common fixed points of a nonexpansive semigroup with a generalized contraction mapping

The purpose of this paper is to introduce and construct the implicit and explicit viscosity iterative processes by a generalized contraction mapping f and a nonexpansive semigroup {T(t):t0}, and to prove that under suitable conditions these iterative processes converge strongly to a unique common fixed point of {T(t):t0} in reflexive Banach spaces which admits a weakly sequentially continuous duality mapping.     

Uniform Kazhdan constant for some families of linear groups

Let R be a ring generated by l elements with stable range r. Assume that the group EL_d(R) has Kazhdan constant ₀>0 for some dr+1. We prove that there exist (₀,l)>0 and , s.t. for every nd, EL_n(R) has a generating set of order k and a Kazhdan constant larger than . As a consequence, we obtain for where n3, a Kazhdan constant which is independent of n w.r.t. generating set of a fixed size.     

Eigenvalue estimates for non-normal matrices and the zeros of random orthogonal polynomials on the unit circle

We prove that for any n×n matrix, A, and z with |z|A, we have that . We apply this result to the study of random orthogonal polynomials on the unit circle.     

An iterative approximation procedure for the distribution of the maximum of a random walk

Let I(F) be the distribution function (d.f.) of the maximum of a random walk whose i.i.d. increments have the common d.f. F and a negative mean. We derive a recursive sequence of embedded random walks whose underlying d.f.'s F_k converge to the d.f. of the first ladder variable and satisfy FF₁F₂ on [0,∞) and I(F)=I(F₁)=I(F₂)=. Using these random walks we obtain improved upper bounds for the difference of I(F) and the d.f. of the maximum of the random walk after finitely many steps.     

Point spectra of partially power-bounded operators

Let T be an operator on a separable Banach space, and denote by σ_p(T) its point spectrum. We answer a question left open in (Israel J. Math. 146 (2005) 93–110) by showing that it is possible that be uncountable, yet Tⁿ∞. We further investigate the relationship between the growth of sequences (n_k) such that sup_kT^n_k<∞ and the possible size of .Analogous results are also derived for continuous operator semigroups (T_t)_t0.     

Perfect codes in direct products of cycles—a complete characterization

Let be a direct product of cycles. It is known that for any r1, and any n2, each connected component of G contains a so-called canonical r-perfect code provided that each ℓ_i is a multiple of rⁿ+(r+1)ⁿ. Here we prove that up to a reasonably defined equivalence, these are the only perfect codes that exist.     

On Mean Convergence of Lagrange Interpolation for General Arrays

For n1, let {x_jn}ⁿ_j=1 be n distinct points in a compact set K and letL_n[·] denote the corresponding Lagrange interpolation operator. Let v be a suitably restricted function on K. What conditions on the array {x_jn}_1jn, n1 ensure the existence of p>0 such that lim_n→∞ (f−L_n[f]) v_Lp(K)=0 for very continuous f: K→ ? We show that it is necessary and sufficient that there exists r>0 with sup_n1 π_nv_Lr(K) ∑ⁿ_j=1 (1/|π′_n| (x_jn))<∞. Here for n1, π_n is a polynomial of degree n having {x_jn}ⁿ_j=1 as zeros. The necessity of this condition is due to Ying Guang Shi.     

Hankel determinants and orthogonal polynomials

We develop a general context for the computation of the determinant of a Hankel matrix H_n = (α_i+j)0i,jn, assuming some suitable conditions for the exponential (or ordinary) generating function of the sequence (α_n)_n0. Several well-known particular cases are thus derived in a unified way.