AIMC Journal:
bioRxiv

Showing 3001 to 3010 of 4993 articles

Neural sampling from cognitive maps enables goal-directed imagination and planning

bioRxiv Jan 1, 2025
AI systems are becoming increasingly more intelligent, but at a very high cost in terms of energy consumption and training requirements. In contrast, our brains only require 20W of energy, they learn online, and they can instantly adjust to changing ...
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Default Mode Network Connectivity Predicts Individual Differences in Long-Term Forgetting: Evidence for Storage Degradation, not Retrieval Failure

bioRxiv Jan 1, 2025
Despite the importance of memories in everyday life and the progress made in understanding how they are encoded and retrieved, the neural processes by which declarative memories are maintained or forgotten remain elusive. Part of the problem is that ...
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CLM-access: A Specialized Foundation Model for High-dimensional Single-cell ATAC-seq analysis

bioRxiv Jan 1, 2025
Inspired by the success of large language models (LLMs) in natural language processing, cell language models (CLMs) have emerged as a promising paradigm for learning cell representations from high-dimensional single-cell data—particularly transcripto...
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Quantum Convolutional HLA Immunogenic Peptide Prediction (Q-CHIPP): Next-Generation Neoantigen Prediction with Quantum Neural Networks

bioRxiv Jan 1, 2025
The immune system is an intricately evolved series of cellular and protein-protein interactions, which defend the body against pathogens and abnormal cells such as cancer. A key player in the immunologic recognition of non-self is the immune synapse,...
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Inference of germinal center evolutionary dynamics via simulation-based deep learning

bioRxiv Jan 1, 2025
B cells and the antibodies they produce are vital to health and survival, motivating research on the details of the mutational and evolutionary processes in the germinal centers (GC) from which mature B cells arise. It is known that B cells with high...
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GeneSys: Generative Modeling of Developmental System

bioRxiv Jan 1, 2025
Temporal single-cell transcriptomics enables the reconstruction of dynamic gene expression changes during development. Yet, its analytical power is often limited by data sparsity, technical noise, and imbalanced representation of cell types across ti...
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DeepHalo: Deep Learning-Powered Exploration of Halogenated Metabolites Uncovering Antibacterial Depsipeptides

bioRxiv Jan 1, 2025
In the omics era, confident high-throughput analytical tools are crucial for the efficient identification of metabolites. Here, we present DeepHalo, a deep learning-integrated and hierarchically optimized workflow designed for high-throughput explora...
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Intra-DNA k-mer Conservation Patterns Encode Evolutionary Selection of Variants

bioRxiv Jan 1, 2025
Evolution shapes the structure and content of genomes, yet the contribution of local sequence composition to variant selection remains poorly understood. While traditional models emphasize protein function or cross-species conservation, we propose th...
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Powerful and accurate case-control analysis of spatial molecular data

bioRxiv Jan 1, 2025
As spatial molecular data grow in scope and resolution, there is a pressing need to identify key spatial structures associated with disease. Current approaches typically make restrictive assumptions such as representing tissue regions by local abunda...
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Explainable machine learning-assisted exploration of chromatin dynamics reveals chromosome-specific response to serum starvation

bioRxiv Jan 1, 2025
Chromatin is dynamic at all length scales, influencing chromatin-based processes, such as gene expression. Even large-scale reorganization of whole chromosome territories has been reported upon specific signals, but lack of suitable methods has preve...
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