AIMC Journal:
bioRxiv

Showing 2931 to 2940 of 4993 articles

Neural and computational evidence for a predictive learning account of the testing effect

bioRxiv Jan 1, 2025
Testing enhances memory more than studying. Although numerous studies have demonstrated the robustness of this classic effect, its neural and computational origin remains debated. Predictive learning is a potential mechanism behind this phenomenon: B...
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Recon8D: A metabolic regulome network from oct-omics and machine learning

bioRxiv Jan 1, 2025
To explore multiomic regulation of the metabolome, we used machine learning to predict metabolomic variation across ∼1000 different cancer cell lines with matched omics data from 8 biomolecular classes: genomics (copy-number and mutations), epigenomi...
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RNA liquid biopsy via nanopore sequencing for novel biomarker discovery and cancer early detection

bioRxiv Jan 1, 2025
Liquid biopsies detect disease noninvasively by profiling cell-free nucleic acids that are secreted into the circulation. However, existing methods exhibit low sensitivity for detecting early stages of diseases such as cancer. Here we show that long-...
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When word order matters: human brains represent sentence meaning differently from large language models

bioRxiv Jan 1, 2025
Large language models based on the transformer architecture are now capable of producing human-like language. But do they encode and process linguistic meaning in a human-like way? Here, we address this question by analysing 7T fMRI data from 30 part...
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SIMPLICITY: an agent-based, multi-scale mathematical model to study SARS-CoV-2 intra- and between-host evolution

bioRxiv Jan 1, 2025
Computational tools are frequently used to describe pathogen evolutionary dynamics either within infected hosts or at the population level. However, there is a lack of models that capture the complex interplay between within-host and between-host evo...
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ProtoBind-Diff: A Structure-Free Diffusion Language Model for Protein Sequence-Conditioned Ligand Design

bioRxiv Jan 1, 2025
Designing small molecules that selectively bind to protein targets remains a central challenge in drug discovery. While recent generative models leverage 3D structural data to guide ligand generation, their applicability is limited by the sparsity an...
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Cell-free DNA fragmentomic characteristics in transposon elements inform molecular regulators and enhance cancer diagnosis

bioRxiv Jan 1, 2025
Fragmentomics of plasma cell-free DNA (cfDNA) are emerging diagnostic biomarkers in cancer liquid biopsy, while the molecular regulations of cfDNA fragmentation remain elusive. In this study, we investigated the cfDNA fragmentomics in transposon elem...
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The Fengshu Large Model for Wugu Fengdeng: An Innovation Engine for Knowledge Integration in the Soybean Field

bioRxiv Jan 1, 2025
Against the backdrop of global population growth and the continuous escalation of food demand, the acceleration of agricultural modernization has emerged as the core pathway to safeguard food security. As the world’s fourth-largest food crop, soybean...
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KIMMDY: a biomolecular reaction emulator

bioRxiv Jan 1, 2025
Molecular simulations have become indispensable in biological research. Their accuracy continues to improve, but directly modelling biochemical reactions – central to all life processes – remains computationally challenging. Here, we present a biomol...
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Biological Database Mining for LLM-Driven Alzheimer’s Disease Drug Repurposing

bioRxiv Jan 1, 2025
This study presents a software pipeline that leverages LLMs to apply knowledge stored in natural language (such as in pharmacological texts) and ontologies in a transparent Drug Repurposing (DR) information structure. Alzheimer’s Disease (AD) related...
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