bioRxiv

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A Computer Vision Dataset for Pollinator Detection under Real Field Conditions

bioRxiv Jan 1, 2025
The widespread decline in biodiversity and abundance of pollinator insects is expected to provoke cascading effects on food security and jeopardize ecosystem services crucial for many crops and wild plants. Pollinator monitoring is a crucial element ...
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Hierarchical Emergence Profiles of Human-Derived Dimensions are a Fundamental Property of Deep Neural Networks

bioRxiv Jan 1, 2025
Object recognition in the human visual system is implemented within a hierarchy characterised by increasing feature complexity. Here, we investigated whether human-derived dimensions of object knowledge show a similar progressive emergence across lay...
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Deep Learning of Brain-Behavior Dimensions Identifies Transdiagnostic Biotypes in Youth with ADHD and Anxiety Disorders

bioRxiv Jan 1, 2025
Attention-deficit/hyperactivity disorder and anxiety disorders are highly prevalent in youth and are characterized by substantial heterogeneity and frequent co-occurrence. This transdiagnostic complexity challenges conventional diagnostic frameworks ...
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Natural Scene Coding Consistency in Genetically-Defined Cell Populations

bioRxiv Jan 1, 2025
Understanding how genetically-defined cell populations encode visual information remains a fundamental challenge in systems neuroscience. While extensive research has characterized individual cell responses to simple stimuli such as static gratings, ...
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Label-free biochemical imaging and timepoint analysis of neural organoids via deep learning-enhanced Raman microspectroscopy

bioRxiv Jan 1, 2025
Three-dimensional organoids have emerged as powerful models for studying human development, disease and drug response in vitro. Yet, their analysis remains constrained by standard imaging and characterisation techniques, which are invasive, require e...
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Histology-informed spatial domain identification through multi-view graph convolutional networks

bioRxiv Jan 1, 2025
Identifying spatial domains is crucial in spatial transcriptomics, yet effectively integrating gene expression, spatial location, and histology remains challenging. We present STESH, a Spatial Transcriptomics clustering method that combines Expressio...
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Benchmarking DNA Foundation Models for Genomic and Genetic Tasks

bioRxiv Jan 1, 2025
The rapid evolution of DNA foundation models promises to revolutionize genomics, yet comprehensive evaluations are lacking. Here, we present a comprehensive, unbiased benchmark of five models (DNABERT-2, Nucleotide Transformer V2, HyenaDNA, Caduceus-...
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Natural variation in IBF1 disrupts its interaction with CHS1 and affects metabolism of hulls in rice

bioRxiv Jan 1, 2025
Secondary metabolites in plants have various physiological functions, including antioxidant and antibacterial activities. Previous studies have suggested genes and associated molecular mechanisms involved in the production of diverse secondary metabo...
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Multi-scale neural networks enhance species distribution modelling across predictors and taxonomic groups

bioRxiv Jan 1, 2025
Ecological processes and patterns are scale-dependent, as reflected in how relationships between species occurrence and the environment vary across scales. In species distribution models (SDMs), spatial scale can strongly affect model predictions and...
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mosna reveals different types of cellular interactions predictive of response to immunotherapies and survival in cancer

bioRxiv Jan 1, 2025
Spatially resolved omics enable the discovery of tissue organization of biological or clinical importance. Despite the existence of several methods, performing a rational analysis including multiple algorithms while integrating different conditions s...
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