AIMC Journal:
bioRxiv

Showing 961 to 970 of 4938 articles

Noradrenergic administration improves cognitive flexibility even after glutamatergic damage in rat mediodorsal thalamus or thalamic nucleus reuniens

bioRxiv Jun 28, 2026
Cognitive flexibility, switching behaviour responses to changing task demands, is classically attributed to the prefrontal cortex. Prefrontal thalamocortical circuits from mediodorsal thalamus (MD) or thalamic nucleus reuniens (RE) are altered in neu...
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Desktop-Scale Hit-Point Discovery for Intrinsically Disordered α-Synuclein Using State-Space Compression and a Discrete Phase-Interference Search Operator

bioRxiv Jun 28, 2026
The accessible chemical space dwarfs any tractable screening budget, and most artificial intelligence drug discovery pipelines respond by docking and ranking a small sublibrary. The resulting hit list is agnostic to selectivity, brain penetration, to...
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EvoSeq-ML: Advancing Data-Centric Machine Learning with Evolutionary-Informed Protein Sequence Representation and Generation

bioRxiv Jun 27, 2026
From protein structure prediction to novel protein generation, challenging protein engineering tasks have been made possible by advancements in machine learning (ML). While largely driven by ML architecture refinements, these advancements in ML-based...
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Real Science Is Harder Than Benchmarks: Evaluating Advanced AI Frameworks on Published Studies. I. Uncertainty Quantification, ML on Therapeutic Data Commons, and Agent-Based Modeling

bioRxiv Jun 27, 2026
Artificial Intelligence (AI) frameworks for automating scientific research have shown strong performance on benchmarks, but their capacity to routinely reproduce results from multiple real-life published studies remains largely untested. We evaluated...
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Glitch genes: embedding geometry predicts functional fragility in single-cell foundation models

bioRxiv Jun 27, 2026
Background: Single-cell foundation models are increasingly used for perturbation prediction and gene network inference, but their learned gene representations are rarely audited directly. In natural language processing, geometric analyses of token em...
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eRNAformer enables genome-wide de novo mapping of enhancer-derived RNA loci

bioRxiv Jun 27, 2026
Enhancer-derived RNAs (eRNAs) are critical regulators of gene transcription, yet their genome-wide annotation remains challenging. Here, we present eRNAformer, a multi-modal deep learning framework that integrates convolutional neural networks with t...
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Computational reconstruction of hierarchical cis-regulatory networks reveals synergistic transcription control and disease-associated rewiring

bioRxiv Jun 26, 2026
Gene regulation emerges from coordinated interactions among dispersed cis-regulatory elements, yet how these elements integrate into functional regulatory networks and collectively regulate gene transcription remains poorly understood. Here, we prese...
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Multi-Omics Clustering Differentiates the Total and Intact HIV Reservoirs and Related Host Immune Mechanisms

bioRxiv Jun 26, 2026
HIV reservoirs are heterogeneous across individuals, yet host determinants of this variability remain unclear. Applying multi-omics clustering to 1,230 people with HIV, integrating omics and functional data from circulating immune cells (transcriptom...
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PlantGeneAnn: a strand-specific genome foundation model for ab initio gene structure annotation of plant genomes

bioRxiv Jun 26, 2026
High-quality plant genome assemblies are rapidly increasing, but accurate structural annotation remains reliant on transcript and homology evidence, limiting applications in newly sequenced and non-model species. Here, we present PlantGeneAnn, a plan...
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PhenoXtract: combining Large Language Model and Knowledge Graph embedding to extract phenotypes from clinical descriptions

bioRxiv Jun 26, 2026
Motivation: Standardized phenotypic descriptions are essential for accurate diagnosis, yet clinicians and researchers face challenges in manually extracting and mapping phenotypes from scientific literature or patient clinical records to the Human Ph...
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