bioRxiv

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Automated Facial Landmark Analysis vs. Manual Coding: Accuracy in Dog Emotional Expression Classification

bioRxiv Jan 1, 2025
Emotional expression in dogs is central to dog-human interactions. Reliable indicators are essential for interpreting animal emotions; however, their predictive value remains debated. Fireworks, which elicit fear in many dogs, provide a real-world co...
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Data-Driven Reduced Modeling of Recurrent Neural Networks

bioRxiv Jan 1, 2025
Artificial Recurrent Neural Networks (RNNs) are widely used in neuroscience to model the collective activity of neurons during behavioral tasks. The high dimensionality of their parameter and activity spaces, however, often make it challenging to inf...
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A Single-cell Spatiotemporal Manifold of Tissue Morphology and Dynamics

bioRxiv Jan 1, 2025
Complex tissues are now characterizable at single-cell resolution, but the spatial logic underlying tissue organization remains challenging to access without effective single-cell spatial descriptors. We present a learned single-cell manifold of cell...
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Venus-MAXWELL: Efficient Learning of Protein-Mutation Stability Landscapes using Protein Language Models

bioRxiv Jan 1, 2025
In-silico prediction of protein mutant stability, measured by the difference in Gibbs free energy change (ΔΔG), is fundamental for protein engineering. Current sequence-to-label methods typically employ the two-stage pipeline: (i) encoding mutant seq...
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Computational Design of Miniprotein Binders Targeting the Viral Entry in Chikungunya and Dengue, Neglected Tropical Diseases

bioRxiv Jan 1, 2025
Neglected Tropical Diseases (NTDs) continue to be a global health concern, affecting millions worldwide. Arboviruses such as Chikungunya virus (CHIKV) and Dengue virus (DENV) are particularly threatening due to the lack of specific antiviral treatmen...
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Evidence of ecosystem process recovery across a large-scale coral reef restoration programme using AI accelerated soundscape analysis

bioRxiv Jan 1, 2025
Coral reef restoration efforts are on the increase globally. However, reporting on the ecological outcomes of these efforts is rare and typically focuses on coral related metrics. As a result, understanding of whether restoration can recover broader ...
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Performance and limitations of out-of-distribution detection for insect DNA (meta)barcoding

bioRxiv Jan 1, 2025
Successful applications of DNA barcoding/metabarcoding rely on the accurate taxonomic identification of sequence fragments. When biological surveys with DNA (meta)barcoding target underexplored biological communities, sequence-based identification is...
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The Spiking Tolman-Eichenbaum Machine: Emergent Spatial and Temporal Coding through Spiking Network Dynamics

bioRxiv Jan 1, 2025
The hippocampal–entorhinal system supports spatial navigation and memory by orchestrating the interaction between grid cells and place cells. While various models have reproduced these patterns, many rely on predefined connectivity or fixed weights a...
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IRIS: A Machine Learning-Based Pose Re-Ranking Tool for RNA-Ligand Docking

bioRxiv Jan 1, 2025
RNA-ligand docking remains challenging, due in part to intrinsic properties of RNA such as structural flexibility and a highly charged phosphate backbone. rDock, a widely used RNA docking program, can generate ligand poses close to the experimental s...
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From sequence to signature: Machine learning uncovers multiscale feature landscapes that predict AMR across ESKAPE pathogens

bioRxiv Jan 1, 2025
Since the clinical introduction of antibiotics in the 1940s, antimicrobial resistance (AMR) has become an increasingly dire threat to global public health. Pathogens acquire AMR much faster than we discover new drugs (antibiotics), warranting innovat...
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