bioRxiv

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Decoding the interconnected splicing patterns of hepatitis B virus and host using large language and deep learning models

bioRxiv Jan 1, 2025
Hepatitis B virus (HBV) infection causes approximately one million deaths annually and remains a major driver of hepatocellular carcinoma. Despite its compact 3.2-kb genome, HBV exhibits extensive alternative splicing. Functionally, HBV splice varian...
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Bridging model and experiment in systems neuroscience with Cleo: the Closed-Loop, Electrophysiology, and Optophysiology simulation testbed

bioRxiv Jan 1, 2025
Systems neuroscience has experienced an explosion of new tools for reading and writing neural activity, enabling exciting new experiments (e.g., all-optical interrogation, closed-loop control) for interrogating neural circuits. Unfortunately, these a...
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Hand Drawing Image based Causal Representation Learning for Robust Parkinson’s Disease Feature Extraction and Detection

bioRxiv Jan 1, 2025
Being an irreversible disorder regarding the human motor-system, Parkinson’s Disease(PD) has been a threat to many neurological patients, especially due to its severity in pain and muscle control restriction. As PD has no significant cure or treatmen...
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The hidden predictors of human haematopoietic clonal fate

bioRxiv Jan 1, 2025
Human haematopoietic stem and progenitor cells (HSPCs) exhibit heterogeneous lineage output, but the molecular programs underlying clonal fate remain poorly defined. To address this, we developed a human haematopoietic organoid supporting differentia...
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The development of FEDUPP: Feeding Experimentation Device Users Processing Package to Assess Learning and Cognitive Flexibility

bioRxiv Jan 1, 2025
Cognitive flexibility, the ability to adapt behavior in response to changing contingencies, is a key component of adaptive decision-making and is impaired in multiple neuropsychiatric disorders. Traditional rodent assays of cognitive flexibility are ...
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Influence of hyperparameters on the performance of deep learning-based microrobotic localization under phantom tissue

bioRxiv Jan 1, 2025
For the effective operation of medical microrobots within living organisms and precise targeting, it is imperative to employ imaging techniques closely integrated with real-time deep-tissue tracking methods. However, due to a typically low Signal-to-...
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CV.eDNA: A hybrid approach to invertebrate biomonitoring using computer vision and DNA metabarcoding

bioRxiv Jan 1, 2025
Automated invertebrate classification using computer vision has shown significant potential to improve specimen processing efficiency. However, challenges such as invertebrate diversity and morphological similarity among taxa can make it difficult to...
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A Machine Learning Approach to Predicting Dyspnea with Noninvasive Biomarkers

bioRxiv Jan 1, 2025
Dyspnea is the subjective sensation of breathing discomfort. This symptom is highly prevalent in patients with chronic and critical illness, and its presence is associated with poor clinical outcomes and long-term psychological trauma. The multidimen...
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Deep learning-based image quantification of epithelial cell shapes and its application to polycystic kidney disease

bioRxiv Jan 1, 2025
Cell shape is a fundamental determinant of tissue architecture and organ function. In epithelial tissues, cytoskeletal organization and tight junctions regulate cell geometry, shaping functional tissue units. Disruption of these mechanisms may cause ...
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FragDockRL: A Reinforcement Learning Framework for Fragment-Based Ligand Design via Building Block Assembly and Tethered Docking

bioRxiv Jan 1, 2025
We propose FragDockRL, a novel molecular design framework that combines building block-based virtual synthesis reactions with reinforcement learning. The method aims to efficiently generate synthesizable molecules by using docking scores as rewards w...
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