bioRxiv

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Impact of variation in tissue staining and scanning devices on performance of pan-cancer AI models: a study of sarcoma and their mimics

bioRxiv Jan 1, 2025
Histopathological analysis is considered the gold standard for the diagnosis and prognostication of cancer. Recent advances in AI, driven by large-scale digitisation and pan-cancer foundation models, are opening new opportunities for clinical integra...
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Interpretable Machine Learning on Soybean Multi Omics Data Reveals Drought-Driven Shifts of Plant-Microbe Interactions

bioRxiv Jan 1, 2025
Plant-microbe interactions in the rhizosphere are central to plant growth, nutrient acquisition, and stress resilience. Multi-omics approaches enable comprehensive profiling of different biological layers, yet integrating these data to understand the...
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Microbial Named Entity Recognition and Normalisation for AI-assisted Literature Review and Meta-Analysis

bioRxiv Jan 1, 2025
Manual curation of biomedical literature is slow and error-prone and while large language models (LLMs) trained on general texts have shown to be useful for text summarisation, these methods lack the domain-specific expertise required to perform this...
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Efficient Double Helix Detection with Steerable Filters

bioRxiv Jan 1, 2025
We present an efficient detection scheme for localization of Double Helix point-spread functions for 3D single-molecule localization microscopy or tracking. Using steerable filters, we extract both 2D position and lobe orientation (axial position) es...
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TISCalling: Leveraging Machine Learning to Identify Translational Initiation Sites in Plants and Viruses

bioRxiv Jan 1, 2025
The recognition of translational initiation sites (TISs) offers complementary insights into identifying genes encoding novel proteins or small peptides. Conventional computational methods primarily identify Ribo-seq-supported TISs and lack the capaci...
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Taguchi–Machine Learning Hybrid Framework for Optimization of Particulate Drug Delivery Systems

bioRxiv Jan 1, 2025
Optimizing particulate drug carrier systems requires balancing multiple formulation parameters to achieve target physicochemical properties while minimizing experimental burden. Here, we implement a hybrid optimization framework integrating a Taguchi...
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Drosophila Video-assisted Activity Monitor (DrosoVAM): a versatile method for behavior monitoring

bioRxiv Jan 1, 2025
Drosophila melanogaster has been a pioneering model system for investigations into the genetic bases of behavior. Studies of circadian activity were some of the first behaviors investigated in flies. The DAM system by TriKinetics played a key role in...
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The role of active mRNA-ribosome dynamics and closing constriction in daughter chromosome separation in Escherichia coli

bioRxiv Jan 1, 2025
The mechanisms by which two sister chromosomes separate and partition into daughter cells in bacteria remain poorly understood. A recent theoretical model has proposed that out-of-equilibrium central dogma reactions involving mRNA and ribosomes play ...
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Imagined Speech Reconstruction with 3D Neural Metabolism and Large Language Model Integration

bioRxiv Jan 1, 2025
Cognitive linguistics posits that language underpins human thought, and this principle has influenced the study and development of large language models (LLMs). In particular, several studies have investigated the metabolic costs of sentence formatio...
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A Deep Learning Pipeline for Mapping in situ Network-level Neurovascular Coupling in Multi-photon Fluorescence Microscopy

bioRxiv Jan 1, 2025
Functional hyperaemia is a well-established hallmark of healthy brain function, whereby local brain blood flow adjusts in response to a change in the activity of the surrounding neurons. Although functional hyperemia has been extensively studied at t...
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