Computational Biology Simulation, Agent-Based Modelling and AI

A special issue of Biomimetics (ISSN 2313-7673).

Deadline for manuscript submissions: 31 August 2025 | Viewed by 1094

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Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
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Dear Colleagues,

This Special Collection aims to explore the innovative applications of simulation techniques, artificial intelligence (AI), and agent-based models in the field of computational biology. By assembling a diverse array of research articles, reviews, and case studies, this Collection seeks to provide a comprehensive overview of how these advanced computational methodologies are transforming our understanding of biological systems. The objective is to highlight the synergy between AI, simulations, and agent-based modelling, demonstrating their potential to address complex biological questions and to inspire future research in this interdisciplinary domain. This Special Collection invites contributions from computational biologists, AI researchers, simulation experts, and interdisciplinary teams working at the interface of biology and computational sciences. By fostering knowledge exchange and highlighting pioneering research, this Collection aims to advance the field of computational biology and enhance our understanding of complex biological systems through innovative computational approaches. Potential topics include the following:

  • simulation and modelling of biological systems;
  • artificial intelligence in computational biology;
  • agent-based models (ABMs) to simulate biological systems;
  • hybrid approaches such as AI and ABMs to model biological systems; computational approaches for biomedical research;
  • ecological and evolutionary models;
  • challenges and limitations of computational biology models; and emerging trends in simulations,
  • AI, and agent-based modelling in biology.

Dr. Neil Vaughan
Guest Editor

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Keywords

  • computational biology simulation
  • agent-based modelling
  • AI

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Published Papers (1 paper)

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Research

28 pages, 39604 KiB  
Article
A Bio-Inspired Visual Neural Model for Robustly and Steadily Detecting Motion Directions of Translating Objects Against Variable Contrast in the Figure-Ground and Noise Interference
by Sheng Zhang, Ke Li, Zhonghua Luo, Mengxi Xu and Shengnan Zheng
Biomimetics 2025, 10(1), 51; https://doi.org/10.3390/biomimetics10010051 - 14 Jan 2025
Viewed by 571
Abstract
(1) Background: At present, the bio-inspired visual neural models have made significant achievements in detecting the motion direction of the translating object. Variable contrast in the figure-ground and environmental noise interference, however, have a strong influence on the existing model. The responses of [...] Read more.
(1) Background: At present, the bio-inspired visual neural models have made significant achievements in detecting the motion direction of the translating object. Variable contrast in the figure-ground and environmental noise interference, however, have a strong influence on the existing model. The responses of the lobula plate tangential cell (LPTC) neurons of Drosophila are robust and stable in the face of variable contrast in the figure-ground and environmental noise interference, which provides an excellent paradigm for addressing these challenges. (2) Methods: To resolve these challenges, we propose a bio-inspired visual neural model, which consists of four stages. Firstly, the photoreceptors (R1–R6) are utilized to perceive the change in luminance. Secondly, the change in luminance is divided into parallel ON and OFF pathways based on the lamina monopolar cell (LMC), and the spatial denoising and the spatio-temporal lateral inhibition (LI) mechanisms can suppress environmental noise and improve motion boundaries, respectively. Thirdly, the non-linear instantaneous feedback mechanism in divisive contrast normalization is adopted to reduce local contrast sensitivity; further, the parallel ON and OFF contrast pathways are activated. Finally, the parallel motion and contrast pathways converge on the LPTC in the lobula complex. (3) Results: By comparing numerous experimental simulations with state-of-the-art (SotA) bio-inspired models, we can draw four conclusions. Firstly, the effectiveness of the contrast neural computation and the spatial denoising mechanism is verified by the ablation study. Secondly, this model can robustly detect the motion direction of the translating object against variable contrast in the figure-ground and environmental noise interference. Specifically, the average detection success rate of the proposed bio-inspired model under the pure and real-world complex noise datasets was increased by 5.38% and 5.30%. Thirdly, this model can effectively reduce the fluctuation in this model response against variable contrast in the figure-ground and environmental noise interference, which shows the stability of this model; specifically, the average inter-quartile range of the coefficient of variation in the proposed bio-inspired model under the pure and real-world complex noise datasets was reduced by 38.77% and 47.84%, respectively. The average decline ratio of the sum of the coefficient of variation in the proposed bio-inspired model under the pure and real-world complex noise datasets was 57.03% and 67.47%, respectively. Finally, the robustness and stability of this model are further verified by comparing other early visual pre-processing mechanisms and engineering denoising methods. (4) Conclusions: This model can robustly and steadily detect the motion direction of the translating object under variable contrast in the figure-ground and environmental noise interference. Full article
(This article belongs to the Special Issue Computational Biology Simulation, Agent-Based Modelling and AI)
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