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The current biochemical information processing systems behave in a predetermined manner because all features are defined during the design phase. To make such unconventional computing systems reusable and programmable for biomedical…
Biochemical processes in cells are governed by complex networks of many chemical species interacting stochastically in diverse ways and on different time scales. Constructing microscopically accurate models of such networks is often…
The control of manufacturing processes must satisfy high quality and efficiency requirements while meeting safety requirements. A broad spectrum of monitoring and control strategies, such as model- and optimization-based controllers, are…
Human decisional processes result from the employment of selected quantities of relevant information, generally synthesized from environmental incoming data and stored memories. Their main goal is the production of an appropriate and…
Gene expression is a stochastic process in which cells produce biomolecules essential to the function of life. Modern experimental methods allow for the measurement of biomolecules at single-cell and single-molecule resolution over time.…
How do organisms recognize their environment by acquiring knowledge about the world, and what actions do they take based on this knowledge? This article examines hypotheses about organisms' adaptation to the environment from machine…
Biomolecules stochastically occupy different possible configurations with probabilities given by non-equilibrium steady-state distributions. These distributions are determined by the transition rate constants between different…
In computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology, Nevertheless, I argue that Shannon's concept…
Signaling in enzymatic networks is typically triggered by environmental fluctuations, resulting in a series of stochastic chemical reactions, leading to corruption of the signal by noise. For example, information flow is initiated by…
Our brain consists of biological neurons encoding information through accurate spike timing, yet both the architecture and learning rules of our brain remain largely unknown. Comparing to the recent development of backpropagation-based…
Although it has been notoriously difficult to pin down precisely what it is that makes life so distinctive and remarkable, there is general agreement that its informational aspect is one key property, perhaps the key property. The unique…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
A biochemical network can be simulated by a set of ordinary differential equations (ODE) under well stirred reactor conditions, for large numbers of molecules, and frequent reactions. This is no longer a robust representation when some…
Information access systems are getting complex, and our understanding of user behavior during information seeking processes is mainly drawn from qualitative methods, such as observational studies or surveys. Leveraging the advances in…
We must recognize that natural language is a way of information encoding, and it encodes not only the information but also the procedures for how information is processed. To understand natural language, the same as we conceive and design…
There are significant analogies between the issues related to real-time event selection in HEP, and the issues faced by the human visual system. In fact, the visual system needs to extract rapidly the most important elements of the external…
Living systems continuously sense, integrate, and act on chemical information using multiscale biochemical networks whose dynamics are inherently nonlinear, adaptive, and energy-efficient. Yet, most attempts to harness such "wetware" for…
The vast amount of biological knowledge accumulated over the years has allowed researchers to identify various biochemical interactions and define different families of pathways. There is an increased interest in identifying pathways and…
Process discovery aims to learn process models from observed behaviors, i.e., event logs, in the information systems.The discovered models serve as the starting point for process mining techniques that are used to address performance and…
Biochemical reaction networks frequently consist of species evolving on multiple timescales. Stochastic simulations of such networks are often computationally challenging and therefore various methods have been developed to obtain sensible…