bioRxiv

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SPROUT: A User-friendly, Scalable Toolkit for Multi-class Segmentation of Volumetric Images

bioRxiv Jan 1, 2025
The segmentation of fine-grained and complex structures from volumetric data, such as 3D biomedical images, is a manually intensive process, with performance hindered by limited training data and the difficulty of adapting AI models for specialised d...
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Morphologically Tunable Mycelium Chips for Physical Reservoir Computing

bioRxiv Jan 1, 2025
We introduce a neuromorphic computing substrate based on PEDOT:PSS-infused mycelium, a biofabricated, morphologically tunable material that can be engineered into electrically active components including resistors, capacitors, and non-linear elements...
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Evaluating the Effectiveness of Parameter-Efficient Fine-Tuning in Genomic Classification Tasks

bioRxiv Jan 1, 2025
Foundation models are increasingly being leveraged for biological tasks. To address the high memory requirements of fine-tuning large pre-trained language models, parameter efficient fine-tuning (PEFT) methods are also being increasingly utilized. Pr...
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EpiPred: A gene-specific machine learning model for classifying missense variants in the epilepsy-related gene STXBP1

bioRxiv Jan 1, 2025
Missense variants in the STXBP1 gene are a frequent cause of early-onset developmental and epileptic encephalopathies and related neurodevelopmental disorders, but the clinical interpretation of these variants remains a major challenge. Most reported...
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Detection of prostate cancer in 3D pathology datasets via generative immunolabeling

bioRxiv Jan 1, 2025
Recent advancements in nondestructive 3D pathology offer a complement to standard histology by enabling comprehensive volumetric analyses of intact clinical specimens (e.g. biopsies). Prior studies have demonstrated the added prognostic value of 3D p...
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Have protein-ligand cofolding methods moved beyond memorisation?

bioRxiv Jan 1, 2025
Deep learning has driven major breakthroughs in protein structure prediction, however the next critical advance is accurately predicting how proteins interact with small molecule ligands, to enable real-world applications such as drug discovery. Rece...
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Leveraging Large Language Models for Redundancy-Aware Pathway Analysis and Deep Biological Interpretation

bioRxiv Jan 1, 2025
Extracting coherent, biologically meaningful insights from vast, complex multi-omics data remains challenging. Currently, pathway enrichment analysis serves as a cornerstone for the functional interpretation of such data. However, conventional approa...
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Your Emotions, My Brain: Generalizable Neural Signatures of Emotional Memory Reactivation During Sleep

bioRxiv Jan 1, 2025
Reactivation in sleep alters the structure of memories and can potentially be used to restructure upsetting representations. Reactivation can be triggered with auditory cues and then detected using machine learning and electroencephalography (EEG), b...
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Comparative Analysis of Diffusion Models for Enhancing Alzheimer’s Disease Classification

bioRxiv Jan 1, 2025
Early and accurate detection of Alzheimer’s disease (AD) is vital for timely intervention and better patient outcomes. However, training machine learning (ML) models for this purpose is challenging due to the limited medical images available and the ...
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Hierarchical coding of local and global positions in episodic memory for naturalistic sequences

bioRxiv Jan 1, 2025
Life unfolds continuously across multiple timescales, yet how the brain encodes hierarchical event sequences remains poorly understood. Using magnetoencephalography, we investigated the neural coding of hierarchical positions in naturalistic sequence...
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