Related papers: A Bigraph Relational Model
Graph-based reaction systems were recently introduced as a generalization of the intensely studied set-based reaction systems. They deal with simple edge-labeled directed graphs, and dynamic semantics of graph-based reaction systems is…
Formation of a molecular network from multifunctional precursors is modelled with a random graph process. The random graph model favours reactivity for monomers that are positioned close in the network topology, and disfavours reactivity…
The ability to reason beyond established knowledge allows Organic Chemists to solve synthetic problems and to invent novel transformations. Here, we propose a model which mimics chemical reasoning and formalises reaction prediction as…
Over the past decade, a number of researchers in systems biology have sought to relate the function of biological systems to their network-level descriptions -- lists of the most important players and the pairwise interactions between them.…
We present the MIM calculus, a modeling formalism with a strong biological basis, which provides biologically-meaningful operators for representing the interaction capabilities of molecular species. The operators of the calculus are…
Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations…
This technical report relates Biochemical Space Language (BCSL) to Multiset rewriting systems (MRS). For a BCSL model, the semantics are defined in terms of transition systems, while for an MRS, they are defined in terms of a set of runs.…
The relational model is the most commonly used data model for storing large datasets, perhaps due to the simplicity of the tabular format which had revolutionized database management systems. However, many real world objects are recursive…
We advocate the use of qualitative models in the analysis of large biological systems. We show how qualitative models are linked to theoretical differential models and practical graphical models of biological networks. A new technique for…
We introduce the BioBeta Framework, a meta-model for both protein-level and membrane-level interactions of living cells. This formalism aims to provide a formal setting where to encode, compare and merge models at different abstraction…
Graphical interaction models have become an important tool for analysing multivariate time series. In these models, the interrelationships among the components of a time series are described by undirected graphs in which the vertices depict…
Reaction systems are a formal model that has been introduced to investigate the interactive behaviors of biochemical reactions. Based on the formal framework of reaction systems, we propose new computing models called reaction automata that…
The mathematical models used to capture features of complex, biological systems are typically non-linear, meaning that there are no generally valid simple relationships between their outputs and the data that might be used to validate them.…
Temporal information extraction plays a critical role in natural language understanding. Previous systems have incorporated advanced neural language models and have successfully enhanced the accuracy of temporal information extraction…
This article deals with OLAP systems based on multidimensional model. The conceptual model we provide, represents data through a constellation (multi-facts) composed of several multi-hierarchy dimensions. In this model, data are displayed…
We develop a query answering system, where at the core of the work there is an idea of query answering by rewriting. For this purpose we extend the DL DL-Lite with the ability to support n-ary relations, obtaining the DL DLR-Lite, which is…
Social relation defines the association, e.g, warm, friendliness, and dominance, between two or more people. Motivated by psychological studies, we investigate if such fine-grained and high-level relation traits can be characterised and…
Binary multirelations generalise binary relations by associating elements of a set to its subsets. We study the structure and algebra of multirelations under the operations of union, intersection, sequential and parallel composition, as…
An important problem in the field of bioinformatics is to identify interactive effects among profiled variables for outcome prediction. In this paper, a logistic regression model with pairwise interactions among a set of binary covariates…
It is fundamental for science and technology to be able to predict chemical reactions and their properties. To achieve such skills, it is important to develop good representations of chemical reactions, or good deep learning architectures…