Related papers: A Process Calculus for Molecular Interaction Maps

We propose PALPS, a Process Algebra with Locations for Population Systems. PALPS allows us to produce spatially-explicit, individual-based models and to reason about their behavior. Our calculus has two levels: at the first level we may…

We present Gradient Activation Maps (GAM) - a machinery for explaining predictions made by visual similarity and classification models. By gleaning localized gradient and activation information from multiple network layers, GAM offers…

We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…

Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation…

We give a geometry of interaction model for a typed lambda-calculus endowed with operators for sampling from a continuous uniform distribution and soft conditioning, namely a paradigmatic calculus for higher-order Bayesian programming. The…

Recently, symbolic computation and computer algebra systems have been successfully applied in systems biology, especially in chemical reaction network theory. One advantage of symbolic computation is its potential for qualitative answers to…

Molecular activity prediction is critical in drug design. Machine learning techniques such as kernel methods and random forests have been successful for this task. These models require fixed-size feature vectors as input while the molecules…

Local interactions among biomolecules, and the role played by their environment, have gained increasing attention in modelling biochemical reactions. By defining the automaton of molecular perceptions, we explore an agent-based…

In this paper we present a formal computational framework for modeling manipulation actions. The introduced formalism leads to semantics of manipulation action and has applications to both observing and understanding human manipulation…

Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…

Biological cells rely on precise spatiotemporal coordination of biochemical reactions to control their many functions. Such cell signaling networks have been a common focus for mathematical models, but they remain challenging to simulate,…

Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…

Efforts toward a comprehensive description of behavior have indeed facilitated the development of representation-based approaches that utilize deep learning to capture behavioral information. As behavior complexity increases, the expressive…

Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made…

The goal of our Macro Lambda Calculus project (MLC) is to encode lambda terms into interaction nets. Its software implementation will accept input in the notation similar to lambda calculus allowing macro definitions. Output is similar to…

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…

The extracellular matrix (ECM) is a highly complex structure through which biochemical and mechanical signals are transmitted. In processes of cell migration, the ECM also acts as a scaffold, providing structural support to cells as well as…

We present a new approach to the simulation and analysis of immune system behavior. The simulations that can be done with our software package called SIMMUNE are based on immunological data that describe the behavior of immune system agents…

A discrete time model that is capable of replicating the basic features of cardiac cell action potentials is suggested. The paper shows how the map-based approaches can be used to design highly efficient computational models (algorithms)…

Graph rewrite formalisms are a powerful approach to modeling complex molecular systems. They capture the intrinsic concurrency of molecular interactions, thereby enabling a formal notion of mechanism (a partially ordered set of events) that…