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The state of many physical, biological and socio-technical systems evolves by combining smooth local transitions and abrupt resetting events to a set of reference values. The inclusion of the resetting mechanism not only provides the…
Chimeric antigen receptor T cells (CAR T cells) are dosed similarly to donor lymphocyte infusions following hematopoietic cell transplantation. In this perspective paper a mathematical basis for personalized dosing of CAR T cells is…
This article studies the estimation of the causal effect of a time-varying treatment on time-to-an-event or on some other continuously distributed outcome. The paper applies to the situation where treatment is repeatedly adapted to…
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is implemented by the binding and unbinding…
We introduce PRISM (Predictive Reasoning in Sequential Medicine), a transformer-based architecture designed to model the sequential progression of clinical decision-making processes. Unlike traditional approaches that rely on isolated…
Cell differentiation is an important process in living organisms. Differentiation is mostly based on binary decisions with the progenitor cells choosing between two specific lineages. The differentiation dynamics have both deterministic and…
How far is neuroepithelial cell proliferation in the developing central nervous system a deterministic process? Or, to put it in a more precise way, how accurately can it be described by a deterministic mathematical model? To provide tracks…
Probabilistic cellular automata with deterministic updating are quantum systems. We employ the quantum formalism for an investigation of random probabilistic cellular automata, which start with a probability distribution over initial…
Epidemiologic studies and clinical trials with a survival outcome are often challenged by immortal time (IMT), a period of follow-up during which the survival outcome cannot occur because of the observed later treatment initiation. It has…
Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…
We study a diagnostic strategy which is based on the anticipation of the diagnostic process by simulation of the dynamical process starting from the initial findings. We show that such a strategy could result in more accurate diagnoses…
We introduce the framework of performative control, where the policy chosen by the controller affects the underlying dynamics of the control system. This results in a sequence of policy-dependent system state data with policy-dependent…
Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural…
This paper examines the concept of change in conceptual modeling. Change is inherent in the nature of things and has increasingly become a focus of much interest and investigation. Change can be modeled as a transition between two states of…
Deterministic many-body systems governed by simple interactions can self-organize into macroscopic patterns, and the determinants of long-time behavior are assumed to be encoded in the initial configuration. Here we show that predictability…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
Organisms maintain the status quo, holding key physiological variables constant to within an acceptable tolerance, and yet adapt with precision and plasticity to dynamic changes in externalities. What organizational principles ensure such…
Identifying control strategies for biological networks is paramount for practical applications that involve reprogramming a cell's fate, such as disease therapeutics and stem cell reprogramming. Here we develop a novel network control…
We study contact epidemic models for the spread of infective diseases in finite populations. The size dependence enters in the infection rate. The dynamics of such models is then analyzed within the deterministic approximation, as well as…
Many stochastic physical systems evolve smoothly over time in the sense that the distribution of states changes regularly across time steps. The transition from current state to the next state can often be modeled as the combination of a…