bioRxiv

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Non-segmented unsupervised learning of multispectral whole slide images for robust analysis of tissue repair and regeneration

bioRxiv Jan 1, 2025
Analyzing whole tissue architecture remains challenging due to the inherent complexity of multicellular organization, variable morphology, and the limitations of conventional segmentation-based image analysis. Traditional approaches often rely on par...
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Integration of steady-state diffusion MRI with Neural Posterior Estimation (NPE) for post-mortem investigations

bioRxiv Jan 1, 2025
Post-mortem diffusion MRI plays a key role in investigative pipelines to characterise tissue microstructure, with long scan times facilitating the acquisition of datasets with improved spatial/angular resolution and reduced artefacts versus in vivo. ...
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A fully-open structure-guided RNA foundation model for robust structural and functional inference

bioRxiv Jan 1, 2025
RNA language models have achieved strong performances across diverse down-stream tasks by leveraging large-scale sequence data. However, RNA function is fundamentally shaped by its hierarchical structure, making the integration of structural informat...
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Interpretable EEG biomarkers for neurological disease models in mice using bag-of-waves classifiers

bioRxiv Jan 1, 2025
Electroencephalograms (EEGs) are time-series records of the electrical potential from collective neural activity in the brain. EEG waveform patterns—rhythmic and irregular oscillations and transient patterns of sharp waves or spikes—are potential phe...
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ChatMDV: Democratising Bioinformatics Analysis Using Large Language Models

bioRxiv Jan 1, 2025
The rapid advancement in single-cell, spatial omics, imaging, and genomic technologies requires robust analytical and visualisation platforms capable of managing complex biological data. Tools such as Multi-Dimensional Viewer (MDV) offer comprehensiv...
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Mechanistically explainable AI model for predicting synergistic cancer therapy combinations

bioRxiv Jan 1, 2025
This study introduces a Large Language Model (LLM)-based framework that combines drug combination data with a knowledge graph to predict synergistic oncology drug combinations with mechanistic insights. Using a retrieval-augmented generation (RAG) ap...
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Mesocorticolimbic reinforcement learning of reward representation and value provides an integrated mechanistic account for schizophrenia

bioRxiv Jan 1, 2025
Mesocorticolimbic dopamine projections are crucial for value learning, motivational control, and cognitive functions, but their precise neurocomputational roles remain elusive. Based on recent experimental and theoretical findings, we constructed a n...
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Latent encoding of movement in primary visual cortex

bioRxiv Jan 1, 2025
Neurons in the primary visual cortex (V1) are classically thought to encode spatial features of visual stimuli through simple population codes: each neuron exhibits a preferred orientation and preferred spatial frequency, both of which remaining inva...
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Artificial Intelligence Powered Biomarker Discovery: A Large-Scale Analysis of 236 Studies Across 19 Therapeutic Areas and 147 Diseases

bioRxiv Jan 1, 2025
Biomarkers are the molecular signatures that drive and reflect disease states and are indispensable for disease diagnosis, therapeutic target identification, and drug development. The landscape of biomarker discovery has undergone a transformative sh...
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AlphaFold-driven discovery of ORP-PIP phosphatase interactions using new generation confidence scores

bioRxiv Jan 1, 2025
Non-vesicular lipid transport contributes to the regulation of membrane composition and organelle function at membrane contact sites. OSBP-related proteins (ORPs) are central to this process, yet their interaction networks remain incompletely defined...
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