Related papers: Multicriteria global optimization for biocircuit d…
Biotechnology offers many opportunities for the sustainable manufacturing of valuable products. The toolbox to optimize bioprocesses includes \textit{extracellular} process elements such as the bioreactor design and mode of operation,…
Molecular design and synthesis planning are two critical steps in the process of molecular discovery that we propose to formulate as a single shared task of conditional synthetic pathway generation. We report an amortized approach to…
Studies have shown that multi-objective optimization problems are hard problems. Such problems either require longer time to converge to an optimum solution, or may not converge at all. Recently some researchers have claimed that real…
Optimization of expensive computer models with the help of Gaussian process emulators in now commonplace. However, when several (competing) objectives are considered, choosing an appropriate sampling strategy remains an open question. We…
The buildings and construction sector is a significant source of greenhouse gas emissions, with cement production alone contributing 7~\% of global emissions and the industry as a whole accounting for approximately 37~\%. Reducing emissions…
Understanding how biochemical systems settle into stable states, such as how protein concentrations reach equilibrium, is central to explaining cellular behavior and designing synthetic biological circuits. However, existing analytical…
Multiobjective feature selection seeks to determine the most discriminative feature subset by simultaneously optimizing two conflicting objectives: minimizing the number of selected features and the classification error rate. The goal is to…
Although many of works have been done in multivalued quantum logic synthesis, the question whether multivalued quantum circuits are more efficient than the conventional binary quantum circuits is still open. In this article we devote to the…
Rule-based modeling is a powerful way to model kinetic interactions in biochemical systems. Rules enable a precise encoding of biochemical interactions at the resolution of sites within molecules, but obtaining an integrated global view…
We describe a light-weight yet performant system for hyper-parameter optimization that approximately minimizes an overall scalar cost function that is obtained by combining multiple performance objectives using a target-priority-limit…
We develop a new interior-point algorithm for solving multiconic optimization problems using the parabolic target space approach. The feasible cone in these problems is composed as a direct product of many small-dimensional cones. Our…
Scientists are attempting to use models of ever increasing complexity, especially in medicine, where gene-based diseases such as cancer require better modeling of cell regulation. Complex models suffer from uncertainty and experiments are…
The design and engineering of molecular communication (MC) components capable of processing chemical concentration signals is the key to unleashing the potential of MC for interdisciplinary applications. By controlling the signaling pathway…
Synthesizability in generative molecular design remains a pressing challenge. Existing methods to assess synthesizability span heuristics-based methods, retrosynthesis models, and synthesizability-constrained molecular generation. The…
This paper gives a concise overview of evolutionary algorithms for multiobjective optimization. A substantial number of evolutionary computation methods for multiobjective problem solving has been proposed so far, and an attempt of unifying…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
We propose a model-based, automated, bottom-up approach for design, which is applicable to various physical domains, but in this work we focus on the electrical domain. This bottom-up approach is based on a meta-topology in which each link…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
State-of-the-art aeronautic Low Pressure gas Turbines (LPTs) are already characterized by high quality standards, thus they offer very narrow margins of improvement. Typical design process starts with a Concept Design (CD) phase, defined…
Bayesian optimal design is considered for experiments where the response distribution depends on the solution to a system of non-linear ordinary differential equations. The motivation is an experiment to estimate parameters in the equations…