Related papers: A Process Calculus for Molecular Interaction Maps
This paper presents Networks of Influence Diagrams (NID), a compact, natural and highly expressive language for reasoning about agents beliefs and decision-making processes. NIDs are graphical structures in which agents mental models are…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
In this paper, we study a functional programming approach to natural language semantics, allowing us to increase the expressiveness of a more traditional denotation style. We will formalize a category based type and effect system to…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
Living cells encode and transmit information in the temporal dynamics of biochemical components. Gaining a detailed understanding of the input-output relationship in biological systems therefore requires quantitative measures that capture…
Concurrent pattern calculus (CPC) drives interaction between processes by comparing data structures, just as sequential pattern calculus drives computation. By generalising from pattern matching to pattern unification, interaction becomes…
Molecular biology and biochemistry interpret microscopic processes in the living world in terms of molecular structures and their interactions, which are quantum mechanical by their very nature. Whereas the theoretical foundations of these…
The Calculus of Wrapped Compartments (CWC) is a recently proposed modelling language for the representation and simulation of biological systems behaviour. Although CWC has no explicit structure modelling a spatial geometry, its compartment…
Cells process external and internal signals through chemical interactions. Cells that constitute the immune system (e.g., antigen presenting cell, T-cell, B-cell, mast cell) can have different functions (e.g., adaptive memory, inflammatory…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
In this paper, we propose novel mixed-integer linear programming (MIP) formulations to model decision problems posed as influence diagrams. We also present a novel heuristic that can be employed to warm start the MIP solver, as well as…
Quantum machine learning (QML) has recently made significant advancements in various topics. Despite the successes, the safety and interpretability of QML applications have not been thoroughly investigated. This work proposes using…
The ability of a cell to communicate with its environment is essential for key cellular functions like replication, metabolism, or cell fate decisions. The involved molecular mechanisms are highly dynamic and difficult to capture…
The BioAmbients calculus is a process algebra suitable for representing compartmentalization, molecular localization and movements between compartments. In this paper we enrich this calculus with a static type system classifying each…
We introduce a Geometry of Interaction model for higher-order quantum computation, and prove its adequacy for a full quantum programming language in which entanglement, duplication, and recursion are all available. Our model comes with a…
Simultaneously optimizing multiple, frequently conflicting, molecular properties is a key bottleneck in the development of novel therapeutics. Although a promising approach, the efficacy of multi-task learning is often compromised by…
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
Multi-agent systems have been studied in various contexts of both application and theory. We take Dynamic Epistemic Logic (DEL), one of the formalisms designed to reason about such systems, as the foundation of the language we will build.…
Membrane systems are a biologically-inspired computational model based on the structure of biological cells and the way chemicals interact and traverse their membranes. Although their dynamics are described by rules, encoding membrane…
Activity coefficients, which are a measure of the non-ideality of liquid mixtures, are a key property in chemical engineering with relevance to modeling chemical and phase equilibria as well as transport processes. Although experimental…