AIMC Journal:
bioRxiv

Showing 2611 to 2620 of 4979 articles

PIMO: Pathway-based Interpretable Multi-Omics interactions for multi-omics integration

bioRxiv Jan 28, 2026
Motivation: Modeling inter-omics interactions across multiple molecular levels is critical for deciphering the mechanisms underlying complex diseases. Epigenomic and structural alterations, such as DNA methylation and copy number alterations, modulat...
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Knowledge-Guided Learning with Curated Prior Genetic Biomarkers for Robust Model Interpretation

bioRxiv Jan 28, 2026
Motivation: Knowledge-guided learning offers effective and robust model training strategies in data-scarce settings by incorporating established domain knowledge, thereby enhancing generalization, robustness, and interpretability. By contrast, conven...
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Global mRNA 3'UTR lengthening in small-cell neuroendocrine carcinoma

bioRxiv Jan 28, 2026
Small-cell neuroendocrine carcinoma (SCNC) is a rare but highly malignant tumor subtype that primarily arises in the lung, also rarely in other organs, and as a consequence of treatment induced lineage transdifferentiation of prostate adenocarcinomas...
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Semantic axes in the brain support analogical representations

bioRxiv Jan 28, 2026
In vectorial embeddings of word meaning, semantic features often reflect consistent directions, or axes, within a representational space. A classic example is gender: the vector spanning boy to girl can be added to the embedding for king to predict q...
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scChat: A Large Language Model-Powered Co-Pilot for Contextualized Single-Cell RNA Sequencing Analysis

bioRxiv Jan 27, 2026
Single-cell RNA sequencing (scRNA-seq) has transformed biomedical research by enabling transcriptomic analysis at single-cell resolution. Yet, existing computational approaches remain primarily data-driven and lack the ability to integrate research c...
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Experimental evaluation of AI-driven protein design risks using safe biological proxies

bioRxiv Jan 27, 2026
Advances in machine learning are providing leaps forward for beneficial applications of protein engineering, while also raising concerns about biosecurity. Recently, Wittmann et al. described an in silico pipeline of generative AI tools to reformulat...
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A systematic delineation of 3' UTR regulatory elements and their contextual associations

bioRxiv Jan 27, 2026
The 3'UTR encodes regulatory information that shapes transcript abundance and subcellular distribution, yet the underlying sequence rules remain incompletely defined. Using SEERS, we quantified the effects of ~2 million synthetic 3'UTR inserts in A54...
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Prioritizing DNA methylation biomarkers using graph neural networks and explainable AI

bioRxiv Jan 27, 2026
DNA methylation is a significant epigenetic modification involving the addition of a methyl group to the position 5' of the cytosine residues. The modification is responsible for disease progression, immune response, and outcomes in diseases such as ...
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Electrophysiological Correlates of Reinforcement Learning in the Human Ventral Tegmental Area

bioRxiv Jan 27, 2026
The ventral tegmental area is the primary source of dopaminergic input to the human prefrontal cortex and plays a central role in reinforcement learning. Although animal studies have established that dopaminergic neurons encode reward prediction erro...
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An enzyme-level benchmark based on environmental bacterial laccases for predicting contaminant fate in water

bioRxiv Jan 27, 2026
Bacterial laccases are widespread multicopper oxidases whose roles in the fate of anthropogenic chemicals in aquatic environments remain poorly understood. Here, we integrate metagenomic analysis, a miniaturized high-throughput assay and machine lear...
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