bioRxiv

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TopoTome: Topology-informed unsupervised segmentation and analysis of 3D images

bioRxiv Jan 1, 2025
Biological systems are three-dimensional and complex. Today, images of biological structures can be acquired using different imaging technologies and at increasing resolutions. However, identifying relevant structural features in three-dimensional (3...
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SoluProtMut: Siamese Deep Learning for Predicting Solubility Effects of Protein Mutations with Experimental Validation

bioRxiv Jan 1, 2025
Protein solubility is an attractive engineering target because it is a critical property influencing the scalability of protein production and the success of therapeutic proteins in biomedical applications. However, predicting solubility changes upon...
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Comparative Computational Modeling of Approach–Avoidance Biases in Suicidal Populations via Hierarchical Bayesian Inference

bioRxiv Jan 1, 2025
Pavlovian “approach or avoid” impulses are critical behavioral biases that, in excess, are linked to multiple psychiatric conditions. To investigate how such biases contribute to suicidal thoughts and behaviors, we analyzed data from two clinical pop...
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A human spiking computational model to explore sound localization

bioRxiv Jan 1, 2025
Sound localization relies on precise processing of binaural cues in medial (MSO) and lateral superior olive (LSO). However, key questions remain on how these two nuclei perform their specific computations depending on sound frequency, the relative co...
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Natural language processing captures memory content associated with shared neural patterns at encoding

bioRxiv Jan 1, 2025
People can experience the same event yet form distinct memories shaped by individual interpretations. Prior research shows that multivariate activity patterns in the Default Mode Network (DMN) are correlated across individuals during shared experienc...
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A plastic attractor model of flexible rule-based selective attention

bioRxiv Jan 1, 2025
A defining feature of human cognition is the ability to select and respond to stimuli flexibly in different circumstances. Here we show that a recently proposed class of small associative neural network, plastic attractors, can perform such flexible ...
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Botanic Spectrum Analyser: A Deep Learning GUI for Plant Image Segmentation in Hyperspectral and RGB Phenotyping

bioRxiv Jan 1, 2025
Plant phenotyping systematically quantifies plant traits such as growth, morphology, physiology, or yield, assessing genetic and environmental influences on plant performance. The integration of advanced phenotyping technologies, including imaging se...
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QuantaMind MD enables protein modeling with ab initio accuracy

bioRxiv Jan 1, 2025
Accurate biomolecular simulations are essential for understanding chemical processes and advancing applications such as protein engineering and drug design. While quantum mechanical (QM) methods can provide chemical accuracy, their computational cost...
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Population analyses reveal heterogenous encoding in the medial prefrontal cortex during naturalistic foraging

bioRxiv Jan 1, 2025
Foraging in the wild requires coordinated switching of critical functions, including goal-oriented navigation and context-appropriate action selection. Nevertheless, few studies have examined how different functions are represented in the brain durin...
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A multimodal learning approach for automated detection of wildlife trade on social media

bioRxiv Jan 1, 2025
Social media data and machine learning methods for automated content analysis are increasingly being used in ecology and conservation science. A current limitation is the lack of methods for automated multimodal analysis of textual and visual content...
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