AIMC Journal:
bioRxiv

Showing 3041 to 3050 of 4993 articles

Functional immune state classification of unlabeled live human monocytes using holotomography and machine learning

bioRxiv Jan 1, 2025
Precise evaluation of immune status is critical for managing diseases such as sepsis, in which the immune system transitions between hyper-inflammatory and immune-suppressed states. However, current biomarkers are limited by low specificity and time-...
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Associative synaptic plasticity creates dynamic persistent activity

bioRxiv Jan 1, 2025
In biological neural circuits, the dynamics of neurons and synapses are tightly coupled. We study the consequences of this coupling and show that it enables a novel form of working memory. In recurrent neural network models with ongoing Hebbian plast...
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DeepADR: Multi-modal Prediction of Adverse Drug Reaction Frequency by Integrating Early-Stage Drug Discovery Information via Kolmogorov-Arnold Networks

bioRxiv Jan 1, 2025
Adverse drug reactions (ADRs) are a major cause of clinical trial failure and post-market withdrawal, posing significant risks to public health and impeding drug development. While computational methods offer an alternative to costly preclinical test...
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Accurate detection and quantification of single-base m6A RNA modification using nanopore signals with multi-view deep learning

bioRxiv Jan 1, 2025
N6-methyladenosine (m6A) is a crucial epitranscriptomic mark. While Nanopore Direct RNA Sequencing (DRS) enables transcriptome-wide detection, most existing methods neglect or lack the capacity to effectively process the intrinsically variable-length...
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Pretraining Improves Prediction of Genomic Datasets Across Species

bioRxiv Jan 1, 2025
Recent studies suggest that deep neural network models trained on thousands of human genomic datasets can accurately predict genomic features, including gene expression and chromatin accessibility. However, training these models is computation- and t...
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Machine Learning Enables Rapid Assessment of Disease Vulnerability in a Threatened Cetacean Population

bioRxiv Jan 1, 2025
Cetaceans (whales and dolphins) are important ecosystem sentinels but face growing threats from major disease-related mortality events expected to intensify under climate change. Because both environmental factors (temperature, salinity) and demograp...
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Learning sequence-function relationships with scalable, interpretable Gaussian processes

bioRxiv Jan 1, 2025
Understanding the relationship between biological sequences, such as DNA, RNA or protein sequences, and their resulting phenotypes is one of the central goals of genetics. This task is complicated by epistasis, i.e., the context dependence of mutatio...
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Exposing the Molecular Reaction Blind Spots of LLMs with PathwayQA

bioRxiv Jan 1, 2025
Proteins mediate a large portion of cellular activity, and understanding protein pathways can yield novel biological insights. Large language models (LLMs) have become increasingly adept at performing inference tasks across different fields of scienc...
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Transcriptomic profiling and machine learning uncover gene signatures of psoriasis endotypes and disease severity

bioRxiv Jan 1, 2025
Despite increased understanding of psoriasis pathogenesis, molecular classification of clinical phenotypes and disease severity is poorly defined. Knowledge gaps include whether molecular endotypes of psoriasis underlie distinct clinical phenotypes a...
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Squidiff: Predicting cellular development and responses to perturbations using a diffusion model

bioRxiv Jan 1, 2025
Single-cell sequencing has revolutionized our understanding of cellular heterogeneity and responses to environmental stimuli. However, mapping transcriptomic changes across diverse cell types in response to various stimuli and elucidating underlying ...
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