Related papers: A Minimal OO Calculus for Modelling Biological Sys…
A biologically plausible low-order model (LOM) of biological neural networks is a recurrent hierarchical network of dendritic nodes/trees, spiking/nonspiking neurons, unsupervised/ supervised covariance/accumulative learning mechanisms,…
Just because some purely recurrent models suffer from being hard to optimize and inefficient on today's hardware, they are not necessarily bad models of language. We demonstrate this by the extent to which these models can still be improved…
The mathematical modeling of generics in Java and other similar nominally-typed object-oriented programming languages is a challenge. In this short paper we present the outline of a novel order-theoretic approach to modeling generics, in…
Applied process calculi include advanced programming constructs such as type systems, communication with pattern matching, encryption primitives, concurrent constraints, nondeterminism, process creation, and dynamic connection topologies.…
The formal system lambda-delta is a typed lambda calculus that pursues the unification of terms, types, environments and contexts as the main goal. lambda-delta takes some features from the Automath-related lambda calculi and some from the…
Several authors devised type-based termination criteria for ML-like languages allowing non-structural recursive calls. We extend these works to general rewriting and dependent types, hence providing a powerful termination criterion for the…
Single-cell omics technologies have transformed our understanding of cellular diversity by enabling high-resolution profiling of individual cells. However, the unprecedented scale and heterogeneity of these datasets demand robust frameworks…
In this work, we propose a novel optimization model termed "sum-of-minimum" optimization. This model seeks to minimize the sum or average of $N$ objective functions over $k$ parameters, where each objective takes the minimum value of a…
Object-oriented programming (OOP) is one of the most popular paradigms used for building software systems. However, despite its industrial and academic popularity, OOP is still missing a formal apparatus similar to \(\lambda\)-calculus,…
The increasing relevance of areas such as real-time and embedded systems, pervasive computing, hybrid systems control, and biological and social systems modeling is bringing a growing attention to the temporal aspects of computing, not only…
This is a short note with some (very elementary) remarks concerning realization theory and the choice of inputs for identifying systems. Its goal is to bring some of these facts to the attention of the systems biology community.
Biological systems are generally complicated and/or complex. In the former approach, one sets up a model with a large number of parameters to describe the system in detail. The latter approach focuses on understanding the universal aspects…
We describe recent progress in developing practical ab initio methods for which the computer effort is proportional to the number of atoms: linear scaling or O(N) methods. It is shown that the locality property of the density matrix gives a…
In the former article "Formal mathematical systems including a structural induction principle" we have presented a unified theory for formal mathematical systems including recursive systems closely related to formal grammars, including the…
We present a method for extracting general modules for ontologies formulated in the description logic ALC. A module for an ontology is an ideally substantially smaller ontology that preserves all entailments for a user-specified set of…
The paper explores the nature of risk, providing a characterization using the categories of the Basic Formal Ontology (BFO). It argues that the category Risk is a subclass of BFO:Role, contrasting it with a similar view classifying Risk as…
We propose active object languages as a development tool for formal system models of distributed systems. Additionally to a formalization based on a term rewriting system, we use established Software Engineering concepts, including software…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
This paper studies the role that ontologies can play in establishing conceptual data models during the process of information systems development. A mapping algorithm has been proposed and embedded in a special purpose Transformation-Engine…
Bigraphs are a versatile modelling formalism that allows easy expression of placement and connectivity relations in a graphical format. System evolution is user defined as a set of rewrite rules. This paper presents a practical, yet…