Related papers: Producing a Set of Models for the Iron Homeostasis…
Homeostasis is concerned with regulatory mechanisms, present in biological systems, where some specific variable is kept close to a set value as some external disturbance affects the system. Mathematically, the notion of homeostasis can be…
Gene expression analysis aims at identifying the genes able to accurately predict biological parameters like, for example, disease subtyping or progression. While accurate prediction can be achieved by means of many different techniques,…
This paper addresses the planning and control problem for nonlinear systems under Signal Temporal Logic (STL) specifications. We first decompose an STL task into finite local tasks. A sampling-based method generates sequences of local…
From biological systems to cyber-physical systems, monitoring the behavior of such dynamical systems often requires to reason about complex spatio-temporal properties of physical and/or computational entities that are dynamically…
Table reasoning with large language models (LLMs) plays a critical role in building intelligent systems capable of understanding and analyzing tabular data. Despite recent progress, existing methods still face key limitations: their…
Network inference approaches are now widely used in biological applications to probe regulatory relationships between molecular components such as genes or proteins. Many methods have been proposed for this setting, but the connections and…
In this paper we propose an existence and uniqueness theory for the solutions of a system of non-linear hyperbolic conservation laws, structured in age and maturity variables, representing a tissue environment. In particular we are…
Mathematical modeling is now used commonly in the analysis of signaling networks. With advances in high resolution microscopy, the spatial location of different signaling molecules and the spatio-temporal dynamics of signaling microdomains…
We consider the problem of mining signal temporal logical requirements from a dataset of regular (good) and anomalous (bad) trajectories of a dynamical system. We assume the training set to be labeled by human experts and that we have…
To express temporal properties of dense-time real-valued signals, the Signal Temporal Logic (STL) has been defined by Maler et al. The work presented a monitoring algorithm deciding the satisfiability of STL formulae on finite discrete…
Investigating the relation between the structure and behavior of complex biological networks often involves posing the following two questions: Is a hypothesized structure of a regulatory network consistent with the observed behavior? And…
A biological system achieve homeostasis when there is a regulated quantity that is maintained within a narrow range of values. Here we consider homeostasis as a phenomenon of network dynamics. In this context, we improve a general theory…
The main difficulty when modelling gene networks is the identification of the parameters that govern their dynamics. It is particularly difficult for models in which time is continuous: parameters have real values which cannot be…
A new Bayesian approach to linear system identification has been proposed in a series of recent papers. The main idea is to frame linear system identification as predictor estimation in an infinite dimensional space, with the aid of…
We present a new average-based robustness score for Signal Temporal Logic (STL) and a framework for optimal control of a dynamical system under STL constraints. By averaging the scores of different specifications or subformulae at different…
Stochastic modelling provides an indispensable tool for understanding how random events at the molecular level influence cellular functions. In practice, the common challenge is to calibrate a large number of model parameters against the…
Cell injection is an approach used for the delivery of small sample substances into a biological cell and is widely used in drug development, gene injection, intracytoplasmic sperm injection (ICSI) and in-virto fertilization (IVF). Robotic…
We introduce a simple method to estimate the system parameters in continuous dynamical systems from the time series. In this method, we construct a modified system by introducing some constants (controlling constants) into the given…
To model biological systems using networks, it is desirable to allow more than two levels of expression for the nodes and to allow the introduction of parameters. Various modeling and simulation methods addressing these needs using Boolean…
We present a robust control framework for time-critical systems in which satisfying real-time constraints robustly is of utmost importance for the safety of the system. Signal Temporal Logic (STL) provides a formal means to express a large…