arXiv subjects

Eric Palanques-Tost

Publications and source records attributed to Eric Palanques-Tost.

4 recordsLinked to original sources

arXiv2026

Experimental Design for Controller Selection in Synthetic Biology

Synthetic biology enables the design of genetic circuits that act as feedback controllers. These controllers are typically designed using computational models, but mismatch between model and real dynamics can lead to controllers that fail in practice. While methods to address this issue exist, synthetic biology introduces additional structural constraints. Genetic circuits are often highly constrained by experimental limitations, reducing controller design to selection among a limited set of implementable circuits rather than an optimization over a continuous space. As a result, multiple system hypotheses may lead to the same optimal controller within the implementable set. Reducing model uncertainty may therefore be irrelevant when the models lead to the same optimal controller. In this paper, we exploit this structure to develop an algorithm for controller selection in synthetic biology, formulating the problem as a decision-oriented experimental design problem over a finite controller set. We represent plant uncertainty using a set of hypotheses and select experiments to minimize the posterior controller selection risk, rather than global model uncertainty. Across three mechanistic case studies, our method reaches the stopping criterion in fewer experimental rounds than model uncertainty and random experiment selection policies, while maintaining a comparable success rate.

eess.SY↗

arXiv2026

Learning-enabled Parameter Synthesis for Nonlinear Systems from Signal Temporal Logic

Signal Temporal Logic (STL) is increasingly used to describe interpretable objectives and constraints for optimal control and learning methods, especially when no target time series data is available. In this work, we propose to synthesize parameters for nonlinear systems that robustly satisfy continuous-time STL specifications for uncertain initial conditions. To this end, we use gradient-based optimization along with set-based reachability verification to efficiently learn in high-dimensional parameter spaces while providing provable satisfaction guarantees for the optimized parameters. We demonstrate the effectiveness and scalability of our method on three systems with up to 18 parameter dimensions.

eess.SY↗

arXiv2025

STL-based Optimization of Biomolecular Neural Networks for Regression and Control

Biomolecular Neural Networks (BNNs), artificial neural networks with biologically synthesizable architectures, achieve universal function approximation capabilities beyond simple biological circuits. However, training BNNs remains challenging due to the lack of target data. To address this, we propose leveraging Signal Temporal Logic (STL) specifications to define training objectives for BNNs. We build on the quantitative semantics of STL, enabling gradient-based optimization of the BNN weights, and introduce a learning algorithm that enables BNNs to perform regression and control tasks in biological systems. Specifically, we investigate two regression problems in which we train BNNs to act as reporters of dysregulated states, and a feedback control problem in which we train the BNN in closed-loop with a chronic disease model, learning to reduce inflammation while avoiding adverse responses to external infections. Our numerical experiments demonstrate that STL-based learning can solve the investigated regression and control tasks efficiently.

cs.LG↗

arXiv2024

Learning Biomolecular Models using Signal Temporal Logic

Modeling dynamical biological systems is key for understanding, predicting, and controlling complex biological behaviors. Traditional methods for identifying governing equations, such as ordinary differential equations (ODEs), typically require extensive quantitative data, which is often scarce in biological systems due to experimental limitations. To address this challenge, we introduce an approach that determines biomolecular models from qualitative system behaviors expressed as Signal Temporal Logic (STL) statements, which are naturally suited to translate expert knowledge into computationally tractable specifications. Our method represents the biological network as a graph, where edges represent interactions between species, and uses a genetic algorithm to identify the graph. To infer the parameters of the ODEs modeling the interactions, we propose a gradient-based algorithm. On a numerical example, we evaluate two loss functions using STL robustness and analyze different initialization techniques to improve the convergence of the approach.

q-bio.MN↗