Related papers: Experimental Biological Protocols with Formal Sema…
Bioprocess mechanistic modeling is essential for advancing intelligent digital twin representation of biomanufacturing, yet challenges persist due to complex intracellular regulation, stochastic system behavior, and limited experimental…
Over the past decade, the automated generation of test inputs has made significant advances. Modern fuzzers and test generators easily produce complex input formats that do systematically cover the input and execution space. Testing…
We develop Process Execution Graphs (PEG), a document-level representation of real-world wet lab biochemistry protocols, addressing challenges such as cross-sentence relations, long-range coreference, grounding, and implicit arguments. We…
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…
Building machines that can understand text like humans is an AI-complete problem. A great deal of research has already gone into this, with astounding results, allowing everyday people to discuss with their telephones, or have their reading…
Background. It is assumed that the introduction of stochastic in mathematical model makes it more adequate. But there is virtually no methods of coordinated (depended on structure of the system) stochastic introduction into deterministic…
We develop a novel method to analyze the dynamics of stochastic rewriting systems evolving over finitary adhesive, extensive categories. Our formalism is based on the so-called rule algebra framework and exhibits an intimate relationship…
Context: The complexity of modern safety-critical systems in industries keep on increasing due to the rising number of features and functionalities. This calls for formal methods in order to entrust confidence in such systems. Nevertheless,…
We propose a theoretical formalism, molecular finite automata (MFA), to describe individual proteins as rule-based computing machines. The MFA formalism provides a framework for modeling individual protein behaviors and systems-level…
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…
Stochastic dynamics govern many important processes in cellular biology, and an underlying theoretical approach describing these dynamics is desirable to address a wealth of questions in biology and medicine. Mathematical tools exist for…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
Probabilistic bisimulation is a fundamental notion of process equivalence for probabilistic systems. Among others, it has important applications including formalizing the anonymity property of several communication protocols. There is a lot…
Formal methods refer to rigorous, mathematical approaches to system development and have played a key role in establishing the correctness of safety-critical systems. The main building blocks of formal methods are models and specifications,…
In programming models with a reversible semantics, computational steps can be undone. This paper addresses the integration of reversible semantics into process languages for communication-centric systems equipped with behavioral types. In…
Probabilistic programming is related to a compositional approach to stochastic modeling by switching from discrete to continuous time dynamics. In continuous time, an operator-algebra semantics is available in which processes proceeding in…
We formalize synthesis of shared control protocols with correctness guarantees for temporal logic specifications. More specifically, we introduce a modeling formalism in which both a human and an autonomy protocol can issue commands to a…
The stochastic simulation of large-scale biochemical reaction networks is of great importance for systems biology since it enables the study of inherently stochastic biological mechanisms at the whole cell scale. Stochastic Simulation…
The focus of these lecture notes is on abstract models and basic ideas and results that relate to the operational semantics of programming languages largely conceived. The approach is to start with an abstract description of the computation…
Scenario-based development and test processes are a promising approach for verifying and validating automated driving functions. For this purpose, scenarios have to be generated during the development process in a traceable manner. In early…