bioRxiv

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Benchmarking the Impact of Data Leakage on the Performance of Knowledge Graph Embedding Models for Biomedical Link Prediction

bioRxiv Jan 1, 2025
In recent years, Knowledge Graphs (KGs) have received increasing attention for their ability to organize complex biomedical knowledge into structured representations of entities and relations. Knowledge Graph Embedding (KGE) models facilitate efficie...
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Decoding pathogen ecological memory from chemical-stress phenotypes

bioRxiv Jan 1, 2025
Can standardized chemical stress reveal an ecological “memory” of host origin in plant pathogens? We profiled six coffee-associated Colletotrichum isolates using four phenolic-branched compounds and compared them with a previously characterized cacao...
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Cross-task, explainable, and real-time decoding of human emotion states by integrating grey and white matter intracranial neural activity

bioRxiv Jan 1, 2025
Decoding human emotion states from neural activity has significant applications in human-computer interfaces, psychiatric diagnostics, and neuromodulation therapies. Intracranial electroencephalogram (iEEG) provides a promising modality for decoding ...
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Behavioral age-detection in individuals reconstructs minute-scale developmental transcriptomics

bioRxiv Jan 1, 2025
Capturing rapid changes in gene-expression across development time is crucial for uncovering the molecular pathways that organize dynamic developmental processes. Here, we introduce ‘BehaveSeq’, a method that enables time reconstruction of minute-res...
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Adaptive resampling for improved machine learning in imbalanced single-cell datasets

bioRxiv Jan 1, 2025
While machine learning models trained on single-cell transcriptomics data have shown great promise in providing biological insights, existing tools struggle to effectively model underrepresented and out-of-distribution cellular features or states. We...
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The influence of power-training and aging on endomysium content and fiber cross-sectional area in the human soleus muscle

bioRxiv Jan 1, 2025
The Master Athletic Laboratory Study of Intramuscular Connective Tissue (MALICoT, DRKS00015764) set out to analyze the endomysium content of the human soleus muscle in response to athletic exercise and aging. Forty-three healthy male study participan...
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Tractography-based transcranial magnetic stimulation prediction using machine learning

bioRxiv Jan 1, 2025
Identifying the stimulation brain target is fundamental for transcranial magnetic stimulation (TMS). Currently, this process is time-consuming and heavily dependent on the operator’s expertise. This study evaluated a deep learning–based approach to s...
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Interpretable and Brain-Inspired Recurrent Model of Hierarchical Decision-Making Capturing Trial-by-Trial Variability

bioRxiv Jan 1, 2025
Humans often make decisions in hierarchical environments, where low-level perceptual judgments inform high-level strategies. Understanding how the brain computationally navigates such multi-level decisions remains an open challenge. While existing mo...
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Multimodal AI Decodes Extreme Environment Functional Dark Matter Beyond Homology

bioRxiv Jan 1, 2025
Functional annotation of proteins from extreme environments represents a major bottleneck for bioresource discovery, as a vast reservoir of functional dark matter defies existing homology-based methods. We demonstrate that environmental pressures imp...
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Combining artificial intelligence and local ecological knowledge to document the largest ever-counted Cape buffalo mega-herd

bioRxiv Jan 1, 2025
Large aggregations of wild mammals are declining globally, sometimes before they can be scientifically documented and their ecological value understood, although non-scientists may be aware of these phenomena. Video recording of wildlife by non-acade...
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