定量生物学
Deep learning has advanced fMRI analysis, yet it remains unclear which architectural inductive biases are most effective at capturing functional patterns in human brain activity. This issue is particularly important in small-sample…
Topological Data Analysis (TDA) has emerged as a powerful framework for extracting robust, multiscale, and interpretable features from complex molecular data for artificial intelligence (AI) modeling and topological deep learning (TDL).…
Antibiotic resistance presents a growing global health threat by diminishing the effectiveness of treatments and allowing once-manageable bacterial infections to persist. This study develops and analyzes an optimization-based mathematical…
Antibiotics are a vital class of drugs closely associated with the prevention and treatment of bacterial infections. Accurate prediction of molecular antimicrobial activity remains a key challenge in the pursuit of novel antibiotic…
There are a number of errors in "mbtransfer: Microbiome intervention analysis using transfer functions and mirror statistics" PLOS Comp Bio (2024) spanning multiple aspects of the paper. The wrong inputs were provided to comparator methods…
Recently, a new vector encoding, Ordered Leaf Attachment (OLA), was introduced that represents $n$-leaf phylogenetic trees as $n-1$ length integer vectors by recording the placement location of each leaf. Both encoding and decoding of trees…
We show that a simple mechanistic model of spatial dispersal for settling organisms, subject to parameter variability, can generate heavy-tailed radial probability density functions. The movement of organisms in the model consists of a…
Reconciling increasing food production with biodiversity conservation is critical yet challenging, particularly given global declines in beneficial insects driven by monoculture intensification. Intercropping, the simultaneous or sequential…
Lung cancer continues to be the predominant cause of cancer-related mortality globally. This review analyzes various approaches, including advanced image processing methods, focusing on their efficacy in interpreting CT scans, chest…
State-of-the-art (SOTA) Convolutional Neural Networks (CNNs) are criticized for their extensive computational power, long training times, and large datasets. To overcome this limitation, we propose a reasonable network (R-Net), a…
Early and accurate detection through Pap smear analysis is critical to improving patient outcomes and reducing mortality of Cervical cancer. State-of-the-art (SOTA) Convolutional Neural Networks (CNNs) require substantial computational…
Network analysis of human brain connectivity indicates that individual differences in cognitive abilities arise from neurobiological mechanisms inherent in structural and functional brain networks. Existing studies routinely treat…
Emotions play a crucial role in human life. The research community has proposed many theories on emotions without reaching much consensus. The situation is similar for emotions in cognitive architectures and autonomous agents. I propose in…
The article introduces an accessible pathway into neuroscience using the MicroBCI device, which leverages the STM32 Nucleo-55RG development board as the core platform. MicroBCI enables the STM32 board to function as a brain-computer…
Brain atlases are essential for reducing the dimensionality of neuroimaging data and enabling interpretable analysis. However, most existing atlases are predefined, group-level templates with limited flexibility and resolution. We present…
Several international agreements have called for the rapid expansion of protected areas to halt biodiversity declines. However, recent research has shown that expanding protected areas may be less cost-effective than redirecting resources…
Background: While benchmarks on short-read variant calling suggest low error rate below 0.5%, they are only applicable to predefined confident regions. For a human sample without such regions, the error rate could be 10 times higher.…
Motivation: Spliced alignment refers to the alignment of messenger RNA (mRNA) or protein sequences to eukaryotic genomes. It plays a critical role in gene annotation and the study of gene functions. Accurate spliced alignment demands…
When formulating a model there is a trade-off between model complexity and (biological) realism. In the present paper we demonstrate how model reduction from a precise mechanistic "super model" to simpler conceptual models using…
Despite the critical role of functional diversity (FD) in understanding ecological systems and processes, its robust quantification remains a significant challenge. A long-held view in the field is that it is not possible to capture its…