bioRxiv

Showing 4381 to 4390 of 5016 articles

Short Excitatory Projections Promote Burst Activity and Modular Functional Organization in Neural Networks

bioRxiv Jan 1, 2025
Physical constraints in the brain favor short, distance-dependent connections. How-ever, short-range projections are not merely a compromise imposed by these constraints; they also serve essential functional roles. Here, we explore networks with bala...
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Organization of mouse prefrontal cortex subnetwork revealed by spatial single-cell multi-omic analysis of SPIDER-Seq

bioRxiv Jan 1, 2025
Deciphering the connectome, anatomy, transcriptome and spatial-omics integrated multi-modal brain atlas and the underlying organization principles remains a great challenge. We developed a Single-cell Projectome-transcriptome In situ Deciphering Sequ...
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A flaw in using pre-trained pLLMs in protein-protein interaction inference models

bioRxiv Jan 1, 2025
With the growing pervasiveness of pre-trained protein large language models (pLLMs), pLLM-based methods are increasingly being put forward for the protein-protein interaction (PPI) inference task. Here, we identify and confirm that existing pre-train...
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Specific Sensitivity to Rare and Extreme Events: Quasi-Complete Black Swan Avoidance vs Partial Jackpot Seeking in Rat Decision-Making*

bioRxiv Jan 1, 2025
Most behavioral studies in animals investigate risk using outcome probabilities larger than 10%. However, real-world Decision-Making often requires evaluating events that are both extremely unlikely and highly consequential. To address this gap, we d...
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Flexible selection of working memory representations to reduce cognitive cost

bioRxiv Jan 1, 2025
Across psychology 1–4, economics 5,6, machine learning 7, and neuroscience 8,9, it is well established that choosing a good internal representation can make complex problems easier to solve. Thus, intelligent behavior depends not only on what is stor...
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Training neural networks from scratch in a videogame leads to brittle brain encoding

bioRxiv Jan 1, 2025
Recent brain-encoding studies using videogame tasks suggest that the training objective of an artificial neural network plays a central role in how well the network’s representations align with brain activity. This study investigates the alignment of...
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Phenotypic Screening Coupled with AI-Driven Target Deconvolution Identifies α-Terthienyl as a Dual DPP-IV/HSD17β13 Modulator with Efficacy in a Mouse Model of MASLD

bioRxiv Jan 1, 2025
Metabolic dysfunction-associated steatotic liver disease (MASLD) is a highly prevalent condition characterized by fat build-up in the liver and ranges from benign steatosis to progression to metabolic dysfunction-associated steatohepatitis (MASH), fi...
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StructGuy: Data leakage free prediction of functional effects of genetic variants

bioRxiv Jan 1, 2025
The extent to which variations in protein-coding genes affect protein function has drawn the biological machine learning community’s attention to computationally model variant effect prediction tools. Multiplexed assays of variant effects (MAVE) expe...
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SigSpace: an LLM-based agent for drug response signature interpretation

bioRxiv Jan 1, 2025
Agent systems powered by large language models (LLMs) are increasingly applied in computational biology to automate analysis, integrate data, and accelerate discovery. Here, we investigate the capacity of LLM-driven agents to interpret transcriptiona...
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OmniCell: Unified Foundation Modeling of Single-Cell and Spatial Transcriptomics for Cellular and Molecular Insights

bioRxiv Jan 1, 2025
Single-cell RNA sequencing (scRNA-seq) enables characterization of cellular heterogeneity but lacks spatial context, while Spatially Transcriptomics maps gene expression in tissues with limited single-cell resolution. Integrating the complementary st...
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