Computational Biology & Bioinformatics

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  • Authors: Kaining Peng, Zixiang Luo, Zhu Zhuo, Shengyuan Cai, Yinuo Zhang, Quanying Liu
    Abstract:

    Information communication in the brain must balance efficient functional integration with the metabolic and physical costs of long-range connectivity. How this cost–efficiency balance is implemented in large-scale communication networks, and how it adapts across cognitive states and pathology, remains poorly understood. In this study, by systematically tuning the strength of distance constraints...

    Keywords: network neuroscience; connectomics; whole-brain modeling; effective connectivity; brain network dynamics; cost–efficiency trade-off; spatial constraints; network reconfiguration
    Timeline: First Posted 2026-02-02
    Metrics: Views: 88  |  Downloads: 9  |  Favorites: 1
  • Authors: Yiping Wang, Jing Wang, Junhao Zhu, Fengyao Zhai, Hu Zhu, Ziwei Dai, Zengru Di, Da Zhou, Yu Liu
    Abstract:

    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 by the small four-letter alphabet. To address this, we adapt Ladderpath, an Algorithmic Information Theory method that identifies nested and hierarchical...

    Keywords: Tokenization; Algorithmic Information Theory; Language Model
    Timeline: First Posted 2025-12-11
    Metrics: Views: 488  |  Downloads: 105  |  Favorites: 1
  • Authors: Han Liu, Wenkang Qu, Da Liang, Xin Yu, Yuejie Lin, Haoyu Zou, Siyuan Han, Zhijun Zhao, Ying Lin, Xiaoyin Zhang, Jinyong Tao, Wenbin Li, Huiping Zhao, Yibin Zhang, Gongning Luo, Ningyi Jiang, Qiyu Peng
    Abstract: Background. Positron Emission Tomography (PET) is a vital medical imaging tool for studying in vivo metabolism. However, conventional PET systems are limited in their inability to image during free movement. Therefore, we have developed a wearable brain PET system for real-time imaging, called SmartBrain. Methods. The SmartBrain used 192 detectors and the detector consists of a 6 × 6...
    Keywords: Wearable PET; Human brain imaging; NEMA; SmartBrain
    Timeline: First Posted 2025-12-04
    Metrics: Views: 552  |  Downloads: 136  |  Favorites: 0