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A reaction-coordinate--resolved information-theoretic analysis of chemical reactivity is developed using mutual information and partial information decomposition (PID). Along an intrinsic reaction coordinate (IRC), a local empirical…
Classification models are a fundamental component of physical-asset management technologies such as structural health monitoring (SHM) systems and digital twins. Previous work introduced risk-based active learning, an online approach for…
In this Chapter, we ask questions (1) What is the right way to measure the quality of information processing in a biological system? and (2) What can real-life organisms do in order to improve their performance in information-processing…
Inputs to signaling pathways can have complex statistics that depend on the environment and on the behavioral response to previous stimuli. Such behavioral feedback is particularly important in navigation. Successful navigation relies on…
Brownian Dynamics algorithms are widely used for simulating soft-matter and biochemical systems. In recent times, their application has been extended to the simulation of coarse-grained models of cellular networks in simple organisms. In…
We present a computational method for performing structural translation, which has been studied recently in the context of analyzing the steady states and dynamical behavior of mass-action systems derived from biochemical reaction networks.…
We evaluate the benefits of combining different offline and online data assimilation methodologies to improve personalized blood glucose prediction with type 2 diabetes self-monitoring data. We collect self-monitoring data (nutritional…
Biological organisms are open, adaptve systems that can respond to changes in environment in specific ways. Adaptation and response can be posed as an optimization problem, with a tradeoff between the benefit obtained from a response and…
Active perception systems maximizing information gain to support both monitoring and decision making have seen considerable application in recent work. In this paper, we propose and demonstrate a method of acquiring and extrapolating…
In clinical practice, there is significant interest in integrating novel biomarkers with existing clinical data to construct interpretable and robust decision rules. Motivated by the need to improve decision-making for early disease…
Motivated by the pressing challenges in the digital twin development for biomanufacturing systems, we introduce an adjoint sensitivity analysis (SA) approach to expedite the learning of mechanistic model parameters. In this paper, we…
Bacterial sensor systems can be used for the detection and measurement of molecular signal concentrations. The dynamics of the sensor directly depend on the biological properties of the bacterial sensor cells; manipulation of these features…
Existing methods in estimating the mean outcome under a given dynamic treatment regime rely on intention-to-treat analyses which estimate the effect of following a certain dynamic treatment regime regardless of compliance behavior of…
Biological systems sense and extract information from fluctuating signals while operating under energetic constraints and limited resolution. We introduce a general chemical model in which a sensor, coupled to a signaling pathway activated…
Flux balance analysis has proven an effective tool for analyzing metabolic networks. In flux balance analysis, reaction rates and optimal pathways are ascertained by solving a linear program, in which the growth rate is maximized subject to…
The notion of entropy is shared between statistics and thermodynamics, and is fundamental to both disciplines. This makes statistical problems particularly suitable for reaction network implementations. In this paper we show how to perform…
In this paper we present the results of unstructured data clustering in this case a textual data from Reuters 21578 corpus with a new biomimetic approach using immune system. Before experimenting our immune system, we digitalized textual…
The process of dynamic state estimation (filtering) based on point process observations is in general intractable. Numerical sampling techniques are often practically useful, but lead to limited conceptual insight about optimal…
Statistical mechanics provides an effective framework to investigate information processing in biochemical reactions. Within such framework far-reaching analogies are established among (anti-) cooperative collective behaviors in chemical…
Distributed computation in artificial life and complex systems is often described in terms of component operations on information: information storage, transfer and modification. Information modification remains poorly described however,…