bioRxiv

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SpatialFuser: A Unified Deep Learning Framework for Spatial Multi-Omics Data Integrative Analysis

bioRxiv Jan 1, 2025
Recent advances in spatial multi-omics technologies provide unprecedented opportunities to integrate and interpret molecular features within the tissue microenvironment. Here we present SpatialFuser, the first unified deep learning framework for deta...
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Study on Early pregnancy diagnosis in sows based on joint analysis of vaginal secretion metabolomics and machine learning

bioRxiv Jan 1, 2025
Metabolic transformations in female mammals throughout gestation manifest in the metabolite profiles of bodily fluids, potentially serving as biomarkers for the diagnosis of pregnancy. This investigation concentrated on sows 18 days post-mating, with...
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Soft Metropolis-Hastings Correction for Generative Model Sampling

bioRxiv Jan 1, 2025
Molecular diffusion models suffer from systematic sampling biases that prevent optimal structure formation, resulting in chemically suboptimal molecules with metastable conformations trapped in local energy minima. We introduce Metropolis-Hastings (M...
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Automated generation of personalized trajectories of aging phenotypes with DyViA-GAN

bioRxiv Jan 1, 2025
With a general increase in human lifespan, the need for technological advances to develop strategies for healthy aging has assumed great importance. In the present study, our goal is to predict the progression of selected aging phenotypes in a given ...
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PRIME: A Multi-Agent Environment for Orchestrating Dynamic Computational Workflows in Protein Engineerings

bioRxiv Jan 1, 2025
Artificial intelligence (AI) is revolutionizing protein engineering, yet its practical application is often hindered by a fragmented toolchain and the specialized expertise required to orchestrate complex computational workflows. To address these cha...
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Disease-specific variant pathogenicity prediction using multimodal biomedical language models

bioRxiv Jan 1, 2025
Missense variants play a key role in the diagnosis of genetic disorders and in disease risk prediction. Existing methods focus primarily on the prediction of variant effects in terms of their deleteriousness, without taking into account the disease-s...
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The inevitability and superfluousness of cell types in spatial cognition

bioRxiv Jan 1, 2025
Discoveries of functional cell types, exemplified by the cataloging of spatial cells in the hippocampal formation, are heralded as scientific breakthroughs. We question whether the identification of cell types based on human intuitions has scientific...
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Behavioral Decoding Reveals Cortical Endocannabinoid Potentiation during Δ9-THC Impairment

bioRxiv Jan 1, 2025
How Δ9-tetrahydrocannabinol (THC) impairs natural behaviors in mice remains unknown. We developed a video-monitored behavioral platform with machine learning classifiers to unravel discrete changes in natural mouse behaviors. THC infusion into the me...
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Modulation of specific interactions within a viral fusion protein predicted from machine learning blocks membrane fusion

bioRxiv Jan 1, 2025
Enveloped viruses must enter host cells to initiate infections through a fusion process, during which the fusion proteins undergo significant and complex structural changes from pre-fusion to post-fusion conformations. Understanding of the fusion pro...
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Evaluating Multiomics Integration Architectures for Training With Structured Missingness

bioRxiv Jan 1, 2025
Multimodal bioinformatics datasets are increasingly common in biomedical research, for tasks such as cancer subtyping and outcome prediction. It is feasible that data from a given patient, or even all data from a given institution, does not have cove...
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