AIMC Journal:
bioRxiv

Showing 2401 to 2410 of 4979 articles

ARGformer: learning on ancestral recombination graphs with transformers

bioRxiv Feb 13, 2026
Recent advances in inference of the ancestral recombination graph (ARG), which describes how segments of chromosomes trace back through recombination and shared lineages, have made it possible to reconstruct genome-wide genealogies for large cohorts,...
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A single-cell atlas and aging clock define biological age and risk-associated stem cell states in human hematopoiesis

bioRxiv Feb 13, 2026
Aging of hematopoietic stem and progenitor cells (HSPCs) impairs regenerative capacity and predisposes to hematological diseases. Here, we constructed a comprehensive single-cell transcriptomic atlas comprising 186,123 CD34+ HSPCs spanning early pren...
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Machine learning-guided spatial omics for tissue-scale discovery of cell-type-specific architectures

bioRxiv Feb 13, 2026
Multiplexed protein imaging enables spatially resolved analysis of molecular organization in tissues, but existing spatial proteomics platforms remain constrained in scalability, throughput, and integration with RNA measurements and interpretable com...
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Stimulus-Driven Thermodynamic Shifts and Geometric Reorganization in Mouse Primary Visual Cortex

bioRxiv Feb 13, 2026
Efficient coding is essential for sensory systems to extract meaningful information from the environment. Here, we investigate how stimulus-driven thermodynamic shifts and geometric reorganization enable efficient population coding. Using wide-field ...
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ChatDIA: A zero-shot large language model workflow for targeted analysis of data-independent acquisition mass spectrometry data

bioRxiv Feb 13, 2026
Data-independent acquisition (DIA) proteomics enables reproducible, large-scale protein identification and quantification but remains challenging to analyze due to highly complex MS/MS spectra and chromatographic interference, particularly in low sig...
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The scaffolding of individual variability in language processing by domain-general neural networks

bioRxiv Feb 13, 2026
Language processing is supported by distributed neural systems. Yet most research examines these systems at the population-average level, obscuring how individual cognitive differences shape language-related brain activity. In this study, we combined...
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Parameter-free representations outperform single-cell foundation models on downstream benchmarks

bioRxiv Feb 13, 2026
Single-cell RNA sequencing (scRNA-seq) data exhibit strong and reproducible statistical structure. This has motivated the development of large-scale foundation models, such as TranscriptFormer, that use transformer-based architectures to learn a gene...
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CASTLE: Cell-type Aware SpaTial domain detection via contrastive Learning Embedding

bioRxiv Feb 13, 2026
With advances in spatially resolved transcriptomics across platforms and resolutions, it is now possible to measure gene-expression profiles while preserving the tissue microenvironment. Spatial clustering is central to these analyses, and recent gra...
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Likelihood-based fine-tuning of protein language models for few-shot fitness prediction and design

bioRxiv Feb 12, 2026
Machine learning models trained on measurements of protein functional properties are widely used to accelerate laboratory-based protein design campaigns. To maximise the signal that can be extracted from limited experimental data, sequence embeddings...
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Robust machine learning for Clostridioides difficile typing from mass spectrometry via data augmentation

bioRxiv Feb 12, 2026
Machine learning (ML) approaches applied to Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) spectra have shown promise for the typing of Clostridioides difficile, yet their deployment in routine clinical se...
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