AIMC Journal:
bioRxiv

Showing 1581 to 1590 of 4956 articles

Decoding the Sequence Requirements for Translation Initiation

bioRxiv May 12, 2026
Accurate selection of start codons by ribosomes is a fundamental determinant of proteome composition. Although the 'Kozak sequence'--an 8-nucleotide sequence flanking the start codon--has long been viewed as the primary determinant of initiation in e...
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Detecting and quantifying overparametrization in RNA language models with REDIAL

bioRxiv May 12, 2026
While RNA language models (LMs) have served as foundation models (FMs) to advanced structural prediction, their evaluation relies heavily on supervised downstream tasks. Such tasks can often mask FM inefficiencies and reflect downstream training set ...
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Unified sampling framework and experimental benchmarking of sequence- and structure-based protein models

bioRxiv May 12, 2026
Generative models are increasingly used for protein design, but the lack of standardized evaluation frameworks limits comparison across model classes and hinders translation to experimental success. Here, we introduce a unified sampling and benchmark...
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Corpus-wide causality: Algorithm design & application for aggregating gene-disease causal evidence

bioRxiv May 12, 2026
Identifying causal relationships, rather than mere associations, is essential for applications such as finding genes driving diseases and guiding drug discovery towards disease mechanisms rather than symptom management. Although many studies extract ...
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Cyst-type epithelial heterogeneity shapes therapeutic responsiveness in ADPKD

bioRxiv May 12, 2026
Autosomal dominant polycystic kidney disease (ADPKD) exhibits substantial interpatient variability in disease course and therapeutic response, but the cellular basis for this variability remains poorly understood. Here, we combine single-nucleus RNA ...
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ClaroAI-Bench: Evaluating Agentic Scientific Reproducibility on Real Biomedical Papers

bioRxiv May 12, 2026
We introduce ClaroAI-Bench, an evaluation suite for measuring AI agents' ability to reproduce computational findings from published biomedical research. The benchmark comprises 35 real NIH-funded papers spanning five modalities (genomics, imaging, cl...
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Integrating Diffusion and Liquid AI Models for Predicting Peptide Affinity from mRNA Display Selections

bioRxiv May 11, 2026
In vitro selection and directed evolution technologies such as mRNA display, explore large libraries (10^14 variants) and generate thousands to millions of functional polypeptide ligands to a variety of targets. Denoising diffusion implicit machine l...
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Simulation-conditioned generative modeling for biologically realistic pattern prediction

bioRxiv May 11, 2026
Pattern formation underlies biological organization across scales, but predicting experimentally observed patterns remains difficult because mechanistic models and data-driven generative models fail in complementary ways. Coarse-grained mechanistic m...
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InterScale reveals multi-scale cellular interaction programs in spatial transcriptomics

bioRxiv May 11, 2026
Tissue homeostasis and disease emerge from cell-cell interactions operating across spatial scales: from autocrine and juxtacrine signals within micrometers to paracrine gradients coordinating responses across tissues. While these can be read out from...
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Learning activator-inhibitor dynamics at the cell cortex with neural likelihood ratio estimation

bioRxiv May 11, 2026
A key question in cell biology is how cell-scale organization emerges from a given set of molecular players and rules of interaction. Given its multiscale nature, addressing this question requires a combination of experimental perturbation, mathemati...
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