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Simulation-based inference enables learning the parameters of a model even when its likelihood cannot be computed in practice. One class of methods uses data simulated with different parameters to infer models of the likelihood-to-evidence ratio, or equivalently the posterior function. Here we frame the inference task as an estimation of an energy function parametrized with an artificial neural network. We present an intuitive approach, named MINIMALIST, in which the optimal model of the likelihood-to-evidence ratio is found by maximizing the likelihood of simulated data. Within this framework, the connection between the task of simulation-based inference and mutual information maximization is clear, and we show how several known methods of posterior estimation relate to alternative lower bounds to mutual information. These distinct objective functions aim at the same optimal energy form and therefore can be directly benchmarked. We compare their accuracy in the inference of model parameters, focusing on four dynamical systems that encompass common challenges in time series analysis: dynamics driven by multiplicative noise, nonlinear interactions, chaotic behavior, and high-dimensional parameter space.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10281432 | PMC |
http://dx.doi.org/10.1103/PhysRevE.105.055309 | DOI Listing |
J Am Chem Soc
December 2024
Nanostructured Molecular Systems and Materials group, Organic Chemistry Department, Universidad Autónoma de Madrid, Madrid 28049, Spain.
If we aim to develop efficient synthetic models of protein receptors and enzymes, we must understand the relationships of intra- and intermolecular interactions between hosts and guests and how they mutually influence their conformational energy landscape so as to adapt to each other to maximize binding energies and enhance substrate selectivities. Here, we introduce a novel design of cofacial (Zn)bisporphyrin cages based on dynamic imine bonding, which is synthetically simple, but at the same time highly robust and versatile, affording receptors composed of only -hybridized C and N atoms. The high structural rigidity of these cages renders them ideal hosts for ditopic molecules that can fit into the cavity and bind to both metal centers, leading to association constants as high as 10 M in chloroform.
View Article and Find Full Text PDFPhys Rev E
November 2024
Engineering Systems and Design, Singapore University of Technology and Design ISE, University of Illinois Urbana-Champaign, Champaign, Illinois 61820, USA.
We consider agents in a social network competing to be selected as partners in collaborative, mutually beneficial activities. We study this through a model in which an agent i can initiate a limited number k_{i}>0 of games and selects partners from its one-hop neighborhood. Each agent can accept as many games offered by its neighbors.
View Article and Find Full Text PDFBioinformatics
December 2024
Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
Motivation: Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and feature correlations in amino acid usage due to the need to maintain complementary interaction interfaces. Thus, the problem of finding interacting pairs can be formulated as searching for a pairing of sequences that maximizes a sequence similarity or a coevolution score.
View Article and Find Full Text PDFPeerJ Comput Sci
October 2024
Department of Artificial Intelligence (AI) and Data Science, Sejong University, Seoul, Republic of South Korea.
Eur J Pediatr Surg
December 2024
Department of Pediatric Surgery Unit, Giannina Gaslini Children's Hospital, Genova, Liguria, Italy.
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