相关论文: Some Remarks on Input Choices for Biochemical Syst…
Information transmission in biological signaling circuits has often been described using the metaphor of a noise filter. Cellular systems need accurate, real-time data about their environmental conditions, but the biochemical reaction…
Humans and animals exhibit a range of interesting behaviors in dynamic environments, and it is unclear how our brains actively reformat this dense sensory information to enable these behaviors. Experimental neuroscience is undergoing a…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
In this note, we focus on a selection model problem: a mono-exponential model versus a bi-exponential one. This is done in the biological context of living cells, where small data are available. Classical statistics are revisited to improve…
The advent of advanced AI underscores the urgent need for comprehensive safety evaluations, necessitating collaboration across communities (i.e., AI, software engineering, and governance). However, divergent practices and terminologies…
This paper is a first step to chase the ambitious objective of developing a mathmatical theory of living systems. The contents refer modeling large systems of interacting living entities with the aim of describing their collective behaviors…
This technical report presents an evaluation of the ontology annotations in the metadata of a subset of entries of MetaboLights, a database for Metabolomics experiments and derived information. The work includes a manual analysis of the…
In this paper, we view a policy or plan as a transition system over a space of information states that reflect a robot's or other observer's perspective based on limited sensing, memory, computation, and actuation. Regardless of whether…
Receptor-induced apoptosis is a complex signal transduction pathway involving numerous protein/protein interactions and post-transcriptional modifications. The response to death receptor stimulation varies significantly from one cell line…
Physical limit of molecular sensing has been extensively studied in biological systems. Biosensors are engineered equivalents of molecular sensors in living systems and play critical role in disease diagnosis and management. Investigation…
Mathematical models are increasingly a part of microbiological research. Here, we share our perspective on how modeling advances the discipline by: (i) enforcing logical consistency, (ii) enabling quantitative prediction, (iii) extracting…
Insufficient performance of optimization approaches for fitting of mathematical models is still a major bottleneck in systems biology. In this manuscript, the reasons and methodological challenges are summarized as well as their impact in…
Monotone systems constitute one of the most important classes of dynamical systems used in mathematical biology modeling. The objective of this paper is to extend the notion of monotonicity to systems with inputs and outputs, a necessary…
Biomolecular logic systems processing biochemical input signals and producing "digital" outputs in the form of YES/NO were developed for analysis of physiological conditions characteristic of liver injury, soft tissue injury and abdominal…
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…
It is widely believed that theory is useful in physics because it describes simple systems and that strictly empirical phenomenological approaches are necessary for complex biological and social systems. Here we prove based upon an analysis…
Networked systems are systems of interconnected components, in which the dynamics of each component are influenced by the behavior of neighboring components. Examples of networked systems include biological networks, critical…
In this paper I consider the necessity and the possibilities of engineering bio-inspired political systems. Systems capable of harnessing the complexity of the human social systems and their increasingly growing and diversifying…
We define some notions of the decentralization of a deterministic input-output machine. This opens the possibility for introducing game-theoretic elements -- such as strategic players -- inside the machine, as part of its design.
There exists a theory of a single general-purpose learning algorithm which could explain the principles its operation. It assumes the initial rough architecture, a small library of simple innate circuits which are prewired at birth. and…