2022 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB 2022)
Biosystems. 2024 Jan 25:105129. doi: 10.1016/j.biosystems.2024.105129. Online ahead of print.NO ABSTRACTPMID:38280445 | DOI:10.1016/j.biosystems.2024.105129 (Source: Biosystems)
Source: Biosystems - January 27, 2024 Category: Biotechnology Authors: Joseph A Brown Sheridan Houghten Gary B Fogel Source Type: research
Using steady-state formula to estimate time-dependent parameters of stochastic gene transcription models
In this study, we developed a method to estimate time-dependent parameters in a classical two-state model without prior assumptions regarding the system parameters. At each measured time point, the method fitted the dynamic distribution data using a steady-state distribution formula, in which the estimated constant parameters were approximated as time-dependent parameter values at the measured time point. The accuracy of this method can be guaranteed for RNA molecules with relatively high degradation rates and genes with relatively slow responses to induction. We quantify the accuracy of the method and implemented this met...
Source: Biosystems - January 27, 2024 Category: Biotechnology Authors: Congrun Zhang Feng Jiao Source Type: research
A Data-Distribution and Successive Spline Points based discretization approach for evolving gene regulatory networks from scRNA-Seq time-series data using Cartesian Genetic Programming
Biosystems. 2024 Feb;236:105126. doi: 10.1016/j.biosystems.2024.105126. Epub 2024 Jan 24.ABSTRACTThe inference of gene regulatory networks (GRNs) is a widely addressed problem in Systems Biology. GRNs can be modeled as Boolean networks, which is the simplest approach for this task. However, Boolean models need binarized data. Several approaches have been developed for the discretization of gene expression data (GED). Also, the advance of data extraction technologies, such as single-cell RNA-Sequencing (scRNA-Seq), provides a new vision of gene expression and brings new challenges for dealing with its specificities, such as...
Source: Biosystems - January 26, 2024 Category: Biotechnology Authors: Jos é Eduardo H da Silva Patrick C de Carvalho Jos é J Camata Itamar L de Oliveira Heder S Bernardino Source Type: research
Natural gradient ascent in evolutionary games
Biosystems. 2024 Feb;236:105127. doi: 10.1016/j.biosystems.2024.105127. Epub 2024 Jan 23.ABSTRACTWe consider evolutionary games with a continuous trait space where the replicator dynamics are restricted to the manifold of multivariate Gaussian distributions. We demonstrate that replicator dynamics are gradient flows with respect to the Fisher information metric. The potential function for these gradient flows is closely related to the mean fitness. Our findings extend previous results on natural gradient ascent in evolutionary games with a finite strategy set. Throughout the paper we pursue an information-geometric point o...
Source: Biosystems - January 25, 2024 Category: Biotechnology Authors: Vladimir Ja ćimović Source Type: research
Systems theory, thermodynamics and life: Integrated thinking across ecology, organization and biological evolution
Biosystems. 2024 Feb;236:105123. doi: 10.1016/j.biosystems.2024.105123. Epub 2024 Jan 19.ABSTRACTIn this paper we explore the relevance and integration of system theory and thermodynamics in terms of the Earth system. It is proposed that together, these fields explain the evolution, organization, functionality and directionality of life on Earth. We begin by summarizing historical and current thinking on the definition of life itself. We then investigate the evidence for a single unit of life. Given that any definition of life and its levels of organization are intertwined, we explore how the Earth system is structured and...
Source: Biosystems - January 20, 2024 Category: Biotechnology Authors: Keith R Skene Source Type: research
Influence analysis of network evolution on Parrondo effect
Biosystems. 2024 Feb;236:105124. doi: 10.1016/j.biosystems.2024.105124. Epub 2024 Jan 18.ABSTRACTParrondo's paradox is a scheme used to describe an interesting paradoxical situation that a losing Game A and a losing Game B played randomly or periodically will produce a winning result. Here, a dynamic process of network evolution of Link A + Game B is proposed to yield the Parrondo effect. Game B with two asymmetric branches depends on the relative comparison between the capital of the network node and the average capital of all its neighbors. Simulation results demonstrate that network structure evolution make the losing G...
Source: Biosystems - January 20, 2024 Category: Biotechnology Authors: Ye Ye Zhuo-Yuan Zhai Xiao-Rong Hang Neng-Gang Xie Source Type: research
Network-based identification of diagnosis-specific trans-omic biomarkers via integration of multiple omics data
Biosystems. 2024 Feb;236:105122. doi: 10.1016/j.biosystems.2024.105122. Epub 2024 Jan 8.ABSTRACTThe integration of multiple omics data promises to reveal new insights into the pathogenic mechanisms of complex human diseases, with the potential to identify avenues for the development of targeted therapies for disease subtypes. However, the extraction of diagnostic/disease-specific biomarkers from multiple omics data with biological pathway knowledge is a challenging issue in precision medicine. In this paper, we present a novel computational method to identify diagnosis-specific trans-omic biomarkers from multiple omics dat...
Source: Biosystems - January 10, 2024 Category: Biotechnology Authors: Md Mamunur Rashid Momoko Hamano Midori Iida Michio Iwata Toshiyuki Ko Seitaro Nomura Issei Komuro Yoshihiro Yamanishi Source Type: research
Neural networks from biological to artificial and vice versa
Biosystems. 2024 Jan;235:105110. doi: 10.1016/j.biosystems.2023.105110. Epub 2024 Jan 2.ABSTRACTIn this paper, we examine how deep learning can be utilized to investigate neural health and the difficulties in interpreting neurological analyses within algorithmic models. The key contribution of this paper is the investigation of the impact of a dead neuron on the performance of artificial neural networks (ANNs). Therefore, we conduct several tests using different training algorithms and activation functions to identify the precise influence of the training process on neighboring neurons and the overall performance of the AN...
Source: Biosystems - January 4, 2024 Category: Biotechnology Authors: Abdullatif Baba Source Type: research
Effect of the electromagnetic induction in the electrical activity of the Kazantsev model of inferior Olive Neuron model
Biosystems. 2024 Feb;236:105114. doi: 10.1016/j.biosystems.2023.105114. Epub 2024 Jan 2.ABSTRACTIn this paper, based on the four variables Kazantsev et al. inferior olive neuron (ION) dynamic equations, a five variables neuron model is designed to describe the effect of electromagnetic induction in ION activities. Within the new ION model, the effect of magnetic flow on membrane potential is described by imposing additive memristive current in the master block of the Kasantsev et al. neuron model. The impact of magnetic flux on the stability of equilibrium point is studied. Hopf bifurcation and bifurcation diagram indicate...
Source: Biosystems - January 4, 2024 Category: Biotechnology Authors: M R Tchuisseuh A C Chamgou é F M Moukam Kakmeni Source Type: research
Neural networks from biological to artificial and vice versa
Biosystems. 2024 Jan 2;235:105110. doi: 10.1016/j.biosystems.2023.105110. Online ahead of print.ABSTRACTIn this paper, we examine how deep learning can be utilized to investigate neural health and the difficulties in interpreting neurological analyses within algorithmic models. The key contribution of this paper is the investigation of the impact of a dead neuron on the performance of artificial neural networks (ANNs). Therefore, we conduct several tests using different training algorithms and activation functions to identify the precise influence of the training process on neighboring neurons and the overall performance o...
Source: Biosystems - January 4, 2024 Category: Biotechnology Authors: Abdullatif Baba Source Type: research
Effect of the electromagnetic induction in the electrical activity of the Kazantsev model of inferior Olive Neuron model
Biosystems. 2024 Jan 2:105114. doi: 10.1016/j.biosystems.2023.105114. Online ahead of print.ABSTRACTIn this paper, based on the four variables Kasantsev et al. inferior olive neuron (ION) dynamic equations, a five variables neuron model is designed to describe the effect of electromagnetic induction in ION activities. Within the new ION model, the effect of magnetic flow on membrane potential is described by imposing additive memristive current in the master block of the Kasantsev et al. neuron model. The impact of magnetic flux on the stability of equilibrium point is studied. Hopf bifurcation and bifurcation diagram indi...
Source: Biosystems - January 4, 2024 Category: Biotechnology Authors: M R Tchuisseuh A C Chamgou é F M M Kakmeni Source Type: research
Neural networks from biological to artificial and vice versa
Biosystems. 2024 Jan 2;235:105110. doi: 10.1016/j.biosystems.2023.105110. Online ahead of print.ABSTRACTIn this paper, we examine how deep learning can be utilized to investigate neural health and the difficulties in interpreting neurological analyses within algorithmic models. The key contribution of this paper is the investigation of the impact of a dead neuron on the performance of artificial neural networks (ANNs). Therefore, we conduct several tests using different training algorithms and activation functions to identify the precise influence of the training process on neighboring neurons and the overall performance o...
Source: Biosystems - January 4, 2024 Category: Biotechnology Authors: Abdullatif Baba Source Type: research
Effect of the electromagnetic induction in the electrical activity of the Kazantsev model of inferior Olive Neuron model
Biosystems. 2024 Jan 2:105114. doi: 10.1016/j.biosystems.2023.105114. Online ahead of print.ABSTRACTIn this paper, based on the four variables Kasantsev et al. inferior olive neuron (ION) dynamic equations, a five variables neuron model is designed to describe the effect of electromagnetic induction in ION activities. Within the new ION model, the effect of magnetic flow on membrane potential is described by imposing additive memristive current in the master block of the Kasantsev et al. neuron model. The impact of magnetic flux on the stability of equilibrium point is studied. Hopf bifurcation and bifurcation diagram indi...
Source: Biosystems - January 4, 2024 Category: Biotechnology Authors: M R Tchuisseuh A C Chamgou é F M M Kakmeni Source Type: research
Neural networks from biological to artificial and vice versa
Biosystems. 2024 Jan 2;235:105110. doi: 10.1016/j.biosystems.2023.105110. Online ahead of print.ABSTRACTIn this paper, we examine how deep learning can be utilized to investigate neural health and the difficulties in interpreting neurological analyses within algorithmic models. The key contribution of this paper is the investigation of the impact of a dead neuron on the performance of artificial neural networks (ANNs). Therefore, we conduct several tests using different training algorithms and activation functions to identify the precise influence of the training process on neighboring neurons and the overall performance o...
Source: Biosystems - January 4, 2024 Category: Biotechnology Authors: Abdullatif Baba Source Type: research
Effect of the electromagnetic induction in the electrical activity of the Kazantsev model of inferior Olive Neuron model
Biosystems. 2024 Jan 2:105114. doi: 10.1016/j.biosystems.2023.105114. Online ahead of print.ABSTRACTIn this paper, based on the four variables Kasantsev et al. inferior olive neuron (ION) dynamic equations, a five variables neuron model is designed to describe the effect of electromagnetic induction in ION activities. Within the new ION model, the effect of magnetic flow on membrane potential is described by imposing additive memristive current in the master block of the Kasantsev et al. neuron model. The impact of magnetic flux on the stability of equilibrium point is studied. Hopf bifurcation and bifurcation diagram indi...
Source: Biosystems - January 4, 2024 Category: Biotechnology Authors: M R Tchuisseuh A C Chamgou é F M M Kakmeni Source Type: research
