Explanipedia

Compression-Based Tokenization Improves Language Modeling of Hierarchical Genomic Structure Open

Yiping Wang, Jing Wang, Junhao Zhu, Fangyi Zhai, Zhu Hu , et al. · 2025

Tokenization is a critical design choice in genomic language modeling. Widely used schemes---character-level encoding, fixed-length $k$-mers, and greedy subword algorithms such as BPE---show intrinsic limitations on DNA that are magnified …

Experimental and Numerical Study of Coupled Metronomes on a Floating Platform Open

Xiaolongzi Wu, C. Zheng, Zhao Lei, Qian Yu, Zengru Di , et al. · 2025

We investigated synchronization behavior using an experimental setup consisting of two metronomes placed on a platform floating over water. By setting the metronomes to oscillate perpendicular to the line between them, we observed three di…

Text Distance from Nested and Hierarchical Repetitions: A Compression-Based Perspective Open

Xiaojun Hu, Jing Wang, Jingwen Zhang, Fangyi Zhai, Xiao Guang Xie , et al. · 2025

We present a new method for structural sequence analysis grounded in Algorithmic Information Theory (AIT). At its core is the Ladderpath approach, which extracts nested and hierarchical relationships among repeated substructures in linguis…

Prediction of functional neural circuits in caenorhabditis elegans based on overlapping community detection Open

Xuebin Wang, Rongjun Qin, Ke Zhang, Zengru Di, Qiang Liu , et al. · 2025

The identification of functional neural circuits is crucial for understanding brain functions. However, experimental methods are often labor-intensive and resource-intensive. In this study, we modified the BIGCLAM algorithm to detect overl…

A cubic-quadratic phenomenological model explains the spiking, chaotic and bursting behaviors of neuron Open

Shuihan Qiu, Yeyuge Chen, Zengru Di · 2025

In this manuscript, we present a two-dimensional phenomenological spiking neuron model. By analyzing the bifurcation diagram and phase portraits of the two-dimensional model, Andronov-Hopf bifurcation, saddle-point bifurcation and saddle-p…

Dimorphic Neural Network Architecture Prioritizes Sexual-related Behaviors in Male C. elegans Open

Xuebin Wang, Hanli Liu, Wenjing Yang, Jingxuan Yang, Xuehong Sun , et al. · 2025

Neural network architecture determines its functional output. However, the detailed mechanisms are not well characterized. In this study, we focused on the neural network architectures of male and hermaphrodite C. elegans and the associati…

Dimorphic Neural Network Architecture Prioritizes Sexual-related Behaviors in Male C. elegans Open

Xuebin Wang, Hanli Liu, Wenjing Yang, Jingxuan Yang, Xuehong Sun , et al. · 2025

Neural network architecture determines its functional output. However, the detailed mechanisms are not well characterized. In this study, we focused on the neural network architectures of male and hermaphrodite C. elegans and the associati…

An Artificial Neural Network for Image Classification Inspired by the Aversive Olfactory Learning Neural Circuit in <i>Caenorhabditis elegans</i> (Adv. Sci. 7/2025) Open

Xuebin Wang, Chunxiuzi Liu, Meng Zhao, Ke Zhang, Zengru Di , et al. · 2025

Nematode's Brain‐Inspired AI This cover image adapts a scene from the novel Journey to the West. In this version, the Monkey King uses a high‐tech AI magic mirror to reveal the White Bone Spirit disguised among humans. The cover is linked …

Gillespie Algorithm-Based Dynamic Growth Simulation of Electrogenic Bacteria in Microbial Fuel Cells: A Theoretical Exploration to Enhance Energy Conversion Efficiency Open

Ying He, Ziyi Wang, Wei Liu, Zhipeng Li, Zengru Di · 2025

Pseudo Transitions in the Finite-Size Blume-Capel Model Open

Wei Liu, Lei Shi, Xin Zhang, Xiang Li, Fangfang Wang , et al. · 2025

Pseudo Transitions in the Finite-Size Six-State Clock Model Open

Lei Shi, Wei Liu, Kai Qi, Kezhao Xiong, Zengru Di · 2025

Competitive Exclusion Dynamics of Dual Electrogenic Bacteria in Microbial Fuel Cells: A Stochastic Modeling Under Environmental Perturbations Open

Ying He, Ziyi Wang, Wei Liu, Zhipeng Li, Zengru Di · 2025

Iterative structural coarse-graining for contagion dynamics in complex networks Open

Leyang Xue, Zengru Di, An‐Ping Zeng · 2024

Contagion dynamics in complex networks drive critical phenomena such as epidemic spread and information diffusion,but their analysis remains computationally prohibitive in large-scale, high-complexity systems. Here, we introduce the Iterat…

An Artificial Neural Network for Image Classification Inspired by the Aversive Olfactory Learning Neural Circuit in <i>Caenorhabditis elegans</i> Open

Xuebin Wang, Chunxiuzi Liu, Meng Zhao, Ke Zhang, Zengru Di , et al. · 2024

This study introduces an artificial neural network (ANN) for image classification task, inspired by the aversive olfactory learning neural circuit in Caenorhabditis elegans ( C. elegans ). Although artificial neural networks (ANNs) have de…

Dynamic multilayer networks reveal mind wandering Open

Zhongming Xu, Shaohua Tang, Zengru Di, Zheng Li · 2024

Introduction Mind-wandering is a highly dynamic phenomenon involving frequent fluctuations in cognition. However, the dynamics of functional connectivity between brain regions during mind-wandering have not been extensively studied. Method…

Pseudo Transitions in the Finite-Size Blume-Capel Model Open

Lei Shi, Wei Liu, Xing Zhang, Fangfang Wang, Kai Qi , et al. · 2024

This article investigates the pseudo transitions of the Blume-Capel model on two-dimensional finite-size lattices. By employing the Wang-Landau sampling method and microcanonical inflection point analysis, we identified the positions of ph…

Geometric properties of the additional third-order transitions in the two-dimensional Potts model Open

Xin Zhang, Wei Liu, Lei Shi, Fangfang Wang, Kai Qi , et al. · 2024

Within the canonical ensemble framework, this paper investigates the presence of higher-order transition signals in the $q$-state Potts model (for $q \geq 3$), using two geometric order parameters: isolated spins number and the average per…

The “weaken-fill-repair” model for cell budding: Linking cell wall biosynthesis with mechanics Open

Yu Liu, Chunxiuzi Liu, Shaohua Tang, Hui Xiao, Xinlin Wu , et al. · 2024

An Artificial Neural Network for Image Classification Inspired by Aversive Olfactory Learning Circuits in Caenorhabditis Elegans Open

Xuebin Wang, Chunxiuzi Liu, Meng Zhao, Ke Zhang, Zengru Di , et al. · 2024

This study introduces an artificial neural network (ANN) for image classification task, inspired by the aversive olfactory learning circuits of the nematode Caenorhabditis elegans (C. elegans). Despite the remarkable performance of ANNs in…

Uncovering multi-order Popularity and Similarity Mechanisms in Link Prediction by graphlet predictors Open

Yongjian He, Yijun Ran, Zengru Di, Tao Zhou, Xiaoke Xu · 2024

Link prediction has become a critical problem in network science and has thus attracted increasing research interest. Popularity and similarity are two primary mechanisms in the formation of real networks. However, the roles of popularity …

Learning noise-induced transitions by multi-scaling reservoir computing Open

Zequn Lin, Zhaofan Lu, Zengru Di, Ying Tang · 2024

Noise is usually regarded as adversarial to extracting effective dynamics from time series, such that conventional approaches usually aim at learning dynamics by mitigating the noisy effect. However, noise can have a functional role in dri…

Nucleation phenomena and extreme vulnerability of spatial k-core systems Open

Leyang Xue, Shengling Gao, Lazaros K. Gallos, Orr Levy, Bnaya Gross , et al. · 2024

K-core percolation is a fundamental dynamical process in complex networks with applications that span numerous real-world systems. Earlier studies focus primarily on random networks without spatial constraints and reveal intriguing mixed-o…

Out of randomness: How evolution benefits from modularity Open

Chunxiuzi Liu, Shaohua Tang, Linjie Que, Zecheng Zhang, Lü Peng , et al. · 2024

Brute force random search, effective in exploring solution spaces, often becomes inefficient or infeasible in real-world scenarios with vast solution spaces. A more effective method, akin to natural evolution, involves recombining existing…

Evolutionary tinkering enriches the hierarchical and nested structures in amino acid sequences Open

Zecheng Zhang, Chunxiuzi Liu, Yingjun Zhu, Lü Peng, Weiyi Qiu , et al. · 2024

Genetic information often exhibits hierarchical and nested relationships, achieved through the reuse of repetitive subsequences such as duplicons and transposable elements, a concept termed “evolutionary tinkering” by François Jacob. Curre…

Motif-based community detection in heterogeneous multilayer networks Open

Yafang Liu, Aiwen Li, An Zeng, Jianlin Zhou, Ying Fan , et al. · 2024

Dynamic functional connectivity correlates of mental workload Open

Zhongming Xu, Jing Huang, Chuancai Liu, Qiankun Zhang, Heng Gu , et al. · 2024

Evolutionary Tinkering Enriches the Hierarchical and Nested Structures in Amino Acid Sequences Open

Zecheng Zhang, Chunxiuzi Liu, Yingjun Zhu, Lü Peng, Weiyi Qiu , et al. · 2024

Genetic information often exhibits hierarchical and nested relationships, achieved through the reuse of repetitive subsequences such as duplicons and transposable elements, a concept termed ``evolutionary tinkering'' by Fran\c{c}ois Jacob.…

Weakening and Disappearance of the Jaming Behaviour in Systems of Self-Propelled Particles Open

Zerun Li, Wei Liu, Jincheng Wang, Kezhao Xiong, Zengru Di · 2024

Temporal segmentation of EEG based on functional connectivity network structure Open

Zhongming Xu, Shaohua Tang, Chuancai Liu, Qiankun Zhang, Heng Gu , et al. · 2023

Theoretical perspective on synthetic man‐made life: Learning from the origin of life Open

Lü Peng, Zecheng Zhang, Xianyi Wang, Weiyi Qiu, Liqian Zhou , et al. · 2023

Creating a man‐made life in the laboratory is one of life science’s most intriguing yet challenging problems. Advances in synthetic biology and related theories, particularly those related to the origin of life, have laid the groundwork fo…

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