bioRxiv

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spEMO: Leveraging Multi-Modal Foundation Models for Analyzing Spatial Multi-Omic and Histopathology Data

bioRxiv Jan 1, 2025
Recent advances in pathology foundation models (PFMs), which are pretrained on large-scale histopathological images, have significantly accelerated progress in disease-centered applications. In parallel, spatial multi-omic technologies collect gene a...
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Polymer-derived distance penalties improve chromatin interaction predictions from single-cell data across crop genomes

bioRxiv Jan 1, 2025
Scalable proxies of 3D genome interactions, such as from single-cell co-accessibility or Deep Learning, systematically overestimate long-range chromatin contacts. To correct this bias, we introduce a penalty function grounded in polymer physics, deri...
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Metabolomics-Guided Machine Learning Reveals Diagnostic and Mechanistic Biomarkers in CHB with MASLD

bioRxiv Jan 1, 2025
Metabolic dysfunction–associated steatotic liver disease (MASLD) often coexists with chronic hepatitis B (CHB), yet early diagnosis remains challenging, particularly in non-obese patients or those with subclinical features. This study aimed to identi...
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Trustworthy Sleep Staging from EEG: Deep Ensembles, MC Dropout, and Predictive Calibration

bioRxiv Jan 1, 2025
Reliable sleep stage classification from EEG signals is critical for the development of clinical decision support systems. However, many deep learning models lack mechanisms for estimating predictive uncertainty, which is important for trust and inte...
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The Role of Video Game Practice in Trial-by-Trial Adaptation, Consolidation, and Reinforcement Learning Biases

bioRxiv Jan 1, 2025
This study examined whether habitual video game play influences reinforcement learning dynamics, feedback adaptation, consolidation, and motivational biases. Two groups of participants (gamers and controls) completed a Probabilistic Selection Task as...
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Interleaved Replay of Novel and Familiar Memory Traces During Slow-Wave Sleep Prevents Catastrophic Forgetting

bioRxiv Jan 1, 2025
Humans and animals can learn continuously, acquiring new knowledge while integrating it into a lifelong memory pool. In contrast, artificial neural networks (ANNs) suffer from catastrophic forgetting, where new training disrupts existing memories. Th...
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Genomic constraints shape the evolution of alternative routes to drug resistance in prokaryotes

bioRxiv Jan 1, 2025
Variation within the prokaryotic pangenome is not random, and natural selection that favours particular combinations of genes appears to dominate over random drift. What is less clear is whether similar phenotypes tend to arise independently within p...
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HPInet: Interpretable prediction of Host-Pathogen protein-protein Interactions using a transformer-based neural network

bioRxiv Jan 1, 2025
Gram-negative bacteria utilize a series of secretion systems (T1SS-T10SS) to deliver secreted effector proteins (T1SE-T10SE) into host cells, leading to infections and diseases. Understanding the interactions between these effector proteins and host ...
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DeepRES: Deep learning enables reaction-based comprehensive enzyme screening

bioRxiv Jan 1, 2025
Enzymes accelerate biochemical reactions in living organisms, thus playing an important role in metabolism. Although metabolic pathway databases are growing, many metabolic reactions, termed orphan enzymes, have not been annotated to gene sequences, ...
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Enhancing Protein Binding Site Residue Prediction with Graph Neural Networks: Impacts of Cutoff Distance and Feature Selection

bioRxiv Jan 1, 2025
Identifying protein binding site residues is critical for understanding molecular interactions but challenging due to incomplete knowledge of features that determine binding. The increasing volume and accessibility of protein sequences and structures...
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