22 papers · ranked by Valyu relevance
Son K. Hoang, Laurent Voisin, Asieh Salehi Fathabadi, Michael Butler + 2 more
'Toby Wilkinson' 'Nicolas Beauger'] Abstract. The Theory plug-in enables modellers to extend the mathematical modelling notation for Event-B, with accompanying support for reasoning about the extended language. Previous version of the Theory plug-in has been implemented based on Rodin 2.x. This presentation outline the…
Hongxiao Li, Wanling Gao, Lei Wang, Jianfeng Zhan
LARA is a key-value algebra that aims at unifying linear and relational algebra with three types of operation abstraction. The study of LARA's expressive ability reports that it can represent relational algebra and most linear algebra operations. However, several essential computations, such as matrix inversion and…
Masahito Hasegawa
We argue that operads provide a general framework for dealing with polynomials and combinatory completeness of combinatory algebras, including the classical SK-algebras, linear BCI-algebras, planar BI( ) • -algebras as well as the braided BC±Ialgebras. We show that every extensional combinatory algebra gives rise to a…
Stefan Mengel, Sebastian Skritek
We study the complexity of evaluating well-designed pattern trees, a query language extending conjunctive queries with the possibility to define parts of the query to be optional. This possibility of optional parts is important for obtaining meaningful results over incomplete data sources as it is common in semantic…
Wenxuan Xu, Yan Yan, Irina Artsimovitch, Nicolas Sunday + 2 more
During elongation, RNA polymerase (RNAP) must navigate through proteins that decorate genomic DNA. Several of these mediate long-distance interactions via structures, such as loops, that alter DNA topology and create torsional barriers. We used the tethered particle motion (TPM) technique and magnetic tweezers to…
Zhihua Zhang
For a smooth bivariate function defined on a general domain with arbitrary shape, it is difficult to do Fourier approximation or wavelet approximation. In order to solve these problems, in this paper, we give an extension of the bivariate function on a general domain with arbitrary shape to a smooth, periodic function…
Carsten Schneider
A summation framework is developed that enhances Karr's difference field approach. It covers not only indefinite nested sums and products in terms of transcendental extensions, but it can treat, e.g., nested products defined over roots of unity. The theory of the so-called $RΠΣ⁎$-extensions is supplemented by…
Boris Yamrom, Yoon-ha Lee, Steven Marks, Lubomir Chorbadjiev + 2 more
Snakemake is one of the most popular workflow management systems, particularly in biological sciences. Snakemake workflows are highly portable, scalable, and transparent. Moreover, they enable the painless reproduction of published results and adaption to similar data processing and analysis projects. Here we present…
Ding-Hong Peng, Tie-Dan Wang, Chang-Yuan Gao, Hua Wang
Interval-valued hesitant fuzzy set (IVHFS), which is the further generalization of hesitant fuzzy set, can overcome the barrier that the precise membership degrees are sometimes hard to be specified and permit the membership degrees of an element to a set to have a few different interval values. To efficiently and…
Hend Dawood, Nefertiti Megahed, Nicholas Higham
Acquiring reliable knowledge amidst uncertainty is a topical issue of modern science. Interval mathematics has proved to be of central importance in coping with uncertainty and imprecision. Algorithmic differentiation, being superior to both numeric and symbolic differentiation, is nowadays one of the most celebrated…
Rémi Segretain, Sergiu Ivanov, Laurent Trilling, Nicolas Glade
Formal interaction networks are well suited for representing complex biological systems and have been used to model signalling pathways, gene regulatory networks, interaction within ecosystems, etc. In this paper, we introduce Sign Boolean Networks (SBNs), which are a uniform variant of Threshold Boolean Networks…
Authors not listed
Genetic Algorithms are a powerful method to solve optimization problems with complex cost functions over vast search spaces that rely in particular on recombining parts of previous solutions. Crossover operators play a crucial role in this context. Here, we describe a large class of these operators designed for…
Chris J. Mungall
In order to take full advantage of next generation genomics data, I need informatics methods to be based on agreed upon formally specified standards that can be implemented easily in a uniform fashion without ambiguity. These standards should be encoded as logical formulae, so that provably correct and efficient…
Arnaud Poret, Claudio Monteiro Sousa, Jean-Pierre Boissel
Due to the scarcity of quantitative details about biological phenomena, quantitative modeling in systems biology can be compromised, especially at the subcellular scale. One way to get around this is qualitative modeling because it requires few to no quantitative information. One of the most popular qualitative…
Authors not listed
We present a graph-based proof of the size-extensivity of the first-order exchange energy in symmetry-adapted perturbation theory (SAPT). The connectedness of the exchange energy expression can be established via derivatives of chromatic polynomials $\chi'_G(x)$ evaluated at $x=0$. The proof holds to all orders of the…
Samira Attou, Ludovic Mignot, Clément Miklarz, Florent Nicart
We propose another interpretation of well-known derivatives computations from regular expressions, due to Brzozowski, Antimirov or Lombardy and Sakarovitch, in order to abstract the underlying data structures (e.g. sets or linear combinations) using the notion of monad. As an example of this generalization advantage…
J.A. Bergstra, Alban Ponse
| 1 | Introduction | | 2 | | --- | --- | --- | --- | | | 1.1 | Notation and axioms for poly-infix operator families | 2 | | | 1.2 | Poly-infix notation | 3 | | 2 | | Six examples of poly-infix operator kernels | 3 | | | 2.1 | Three pre-arithmetical poly-infix operator kernels | 4 | | | 2.2 | Two intra-arithmetical…
Authors not listed
Real-world datasets in chemical engineering and bioengineering processes--such as those from catalytic reactors, multiphase flows, polymerization reactors, bioreactors, and clinical trials--can often be unlabelled or disorganized, rendering the training of existing supervised learning models ineffective at learning the…
Rahul Varki, Christina Boucher
Relative Lempel–Ziv (RLZ) is an effective compression method for large, repetitive collections; however, the fundamental primitives required to elevate it from a passive archival format to a tractable representation for compressed construction have yet to be fully established. In this paper, we introduce an algorithmic…
S. Boukraa, S. Hassani, J-M Maillard, J-A Weil
We first revisit an order-six linear differential operator, already introduced in a previous paper, having a solution which is a diagonal of a rational function of three variables. This linear differential operator is such that its exterior square has a rational solution, indicating that it has a selected differential…
Yue Lu, Gustavo Borias, Zsuzsanna Voros, Christine Henderson + 3 more
Many DNA-binding proteins induce topological structures such as loops or wraps through binding to two or more sites along the DNA. Such topologies may regulate transcription initiation and may also be roadblocks for elongating RNA polymerase (RNAP). Remarkably, a lac repressor protein bound to a weak binding site (O2)…
Zuan Liu, Philippe Malbos
– This paper introduces the structure of operated polygraphs as a categorical model for rewriting in operated algebras, generalizing Gröbner-Shirshov bases with non-monomial termination orders. We provide a combinatorial description of critical branchings of operated polygraphs using the structure of polyautomata that…