bioRxiv

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Learning a chemistry-aware latent space for molecular encoding and generation with a large-scale Transformer Variational Autoencoder

bioRxiv Jan 1, 2025
Searching for molecules optimizing certain properties remains a key challenge due to the vastness of the chemical space, its discrete nature, and the limited availability of bioactivity data. One way to address these issues is to build a mapping from...
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Genome-Level Hierarchical Attention Transformer with Multi-Head Attention Weighted Sum for Broad-Spectrum Antimicrobial Resistance Prediction and Discovery of Resistance-Related Genomic Contexts

bioRxiv Jan 1, 2025
Antimicrobial resistance is a growing global health concern, requiring reliable tools for predicting resistance across a wide range of bacteria and antibiotics. In this study, we introduce a genome-level hierarchical attention transformer (GL-HAT) th...
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MAYOCTransformer: Masked-Attention for Yielding Comprehensive Semantic Segmentation of Retinal Optical Coherence Tomography Images using Transformer-based Neural Networks

bioRxiv Jan 1, 2025
Optical coherence tomography (OCT) is a widely used imaging modality in ophthalmology. Accurate semantic segmentation of these images is critical for both clinical and research applications, yet existing convolutional neural network (CNN)-based metho...
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CRISPR-based neuromorphic computing for solving regression and classification

bioRxiv Jan 1, 2025
The CRISPR-dCas9 system has emerged as a versatile platform for programmable gene regulation, offering unique advantages in modularity and orthogonality for constructing synthetic genetic circuits. Here, we present a novel architecture for biomolecul...
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MS4MS: LLMs-driven Multi-agent System for Small-molecule Identification via LC-MS/MS

bioRxiv Jan 1, 2025
Small molecule identification is central to research fields such as drug discovery, but in complex systems like Traditional Chinese Medicine (TCM), traditional mass spectrometry analysis methods remain constrained by bottlenecks including insufficien...
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Neural categorization of visual words of alphabetic and non-alphabetic languages

bioRxiv Jan 1, 2025
Languages provide social-category markers that tag people as one or another social group. How does the brain sort words into different language categories as a basis of the social-categorization function of language? We addressed this issue by testin...
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Comprehensive perturbation of transcription factors in human cardiomyocytes reveals the regulatory architecture of congenital heart disease

bioRxiv Jan 1, 2025
Over 100 genes have been implicated in congenital heart disease (CHD), yet the genetic basis for >50% of CHD remains unexplained. A key challenge is to define the regulatory architecture of CHD genes. Here, we systematically perturb 1983 transcriptio...
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Motion sequencing reveals hidden patterns of repetitive behavior in a mouse model of epilepsy

bioRxiv Jan 1, 2025
Epilepsy is the 4th most prevalent neurological condition with 50 million cases worldwide. Patients with epilepsy bare a disproportionate burden of cognitive decline and psychiatric disorders which remain poorly understood and go underdressed by curr...
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Successful Predictive Modeling of Pollen Fitness Phenotypes Is Enabled by Measures of Expression Specificity

bioRxiv Jan 1, 2025
The ability to predict phenotypes from genotypes in multicellular organisms remains limited despite rapid advances in genotyping and phenotyping methods. Machine learning offers a promising way to model phenotype from genotype, but requires sizable d...
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SNooPy: a statistical framework for long-read metagenomic variant calling

bioRxiv Jan 1, 2025
Current long-read single-nucleotide variant callers were designed primarily for genomic data—particularly human genomes. While some have been used on metagenomic data, their underlying assumptions and training procedures fail to account for the inher...
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