相关论文: An Algorithm for RNA Pseudoknots
We extend an hypergraph representation, introduced by Finkelstein and Roytberg, to unify dynamic programming algorithms in the context of RNA folding with pseudoknots. Classic applications of RNA dynamic programming energy minimization,…
The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the cross-over length, beyond which asymptotic scaling laws apply, depends on…
We consider a refinement of the partition function of graph homomorphisms and present a quasi-polynomial algorithm to compute it in a certain domain. As a corollary, we obtain quasi-polynomial algorithms for computing partition functions…
We investigate the possibilities to calculate vector partition functions by means of iterated partial fraction decomposition, as suggested by Beck (2004). Particularly, for an important type of families of rational functions, we describe an…
We propose an approach to determine the continual progression of algorithmic efficiency, as an alternative to standard calculations of time complexity, likely, but not exclusively, when dealing with data structures with unknown maximum…
The problem of computing functions of values at the nodes in a network in a totally distributed manner, where nodes do not have unique identities and make decisions based only on local information, has applications in sensor, peer-to-peer,…
We present a method to approximate partition functions of quantum systems using mixed-state quantum computation. For positive semi-definite Hamiltonians, our method has expected running-time that is almost linear in $(M/(\epsilon_{\rm…
We obtain two new algorithms for partial fraction decompositions; the first is over algebraically closed fields, and the second is over general fields. These algorithms takes $O(M^2)$ time, where $M$ is the degree of the denominator of the…
We establish the average-case hardness of the algorithmic problem of exact computation of the partition function associated with the Sherrington-Kirkpatrick model of spin glasses with Gaussian couplings and random external field. In…
We adapt the rectangular splitting technique of Paterson and Stockmeyer to the problem of evaluating terms in holonomic sequences that depend on a parameter. This approach allows computing the $n$-th term in a recurrent sequence of suitable…
The division operation is important for many areas of data processing. Especially considering today's demand for hardware accelerators for machine learning algorithms, there is a high demand for an efficient calculation of the division…
A new formalism for calculation of the partition function of single stranded nucleic acids is presented. Secondary structures and the topology of structure elements are the level of resolution that is used. The folding model deals with…
We present a simple and fast algorithm for computing the $N$-th term of a given linearly recurrent sequence. Our new algorithm uses $O(\mathsf{M}(d) \log N)$ arithmetic operations, where $d$ is the order of the recurrence, and…
Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA…
We present a general method for rendering representations of multi-stranded DNA complexes from textual descriptions into 2D diagrams. The complexes can be arbitrarily pseudoknotted, and if a planar rendering is possible, the method will…
We present a general setting for structure-sequence comparison in a large class of RNA structures that unifies and generalizes a number of recent works on specific families on structures. Our approach is based on tree decomposition of…
Background: We study the sparsification of dynamic programming folding algorithms of RNA structures. Sparsification applies to the mfe-folding of RNA structures and can lead to a significant reduction of time complexity. Results: We analyze…
We provide an algorithm for computing the nucleolus for an instance of a weighted voting game in pseudo-polynomial time. This resolves an open question posed by Elkind. et.al. 2007.
This paper gives an exposition of well known results on vector partition functions. The exposition is based on works of M. Brion, A. Szenes and M. Vergne and is geared toward explicit computer realizations. In particular, the paper presents…
We derive a stochastic gradient algorithm for semidefinite optimization using randomization techniques. The algorithm uses subsampling to reduce the computational cost of each iteration and the subsampling ratio explicitly controls…