AIMC Journal:
bioRxiv

Showing 281 to 290 of 4935 articles

CellART: a unified framework for extracting single-cell information from high-resolution spatial transcriptomics

bioRxiv Sep 8, 2026
Understanding how different cell types assemble into tissues and organs, as well as how they interact to transmit and receive biological signals, is essential for advancing biomedical and biological research. Recent advancements in spatial transcript...
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Biologically grounded locality priors close the data gap for vision transformers in neural prediction

bioRxiv Sep 8, 2026
For datasets with thousands of neurons and images, vision transformers have proven successful at predicting neural responses to stimuli. However, they are expected to underperform in low-data regimes, where CNNs and Gaussian processes are considered ...
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EukaUTR: a foundation model for functional modelling and design of eukaryotic 3' UTRs

bioRxiv Sep 8, 2026
Eukaryotic mRNA 3' UTRs encode regulatory signals that shape post-transcriptional regulation, RNA fate and gene expression. However, a foundation model that spans broad eukaryotic 3' UTR sequence space while unifying prediction, interpretation and de...
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Deep-layer cortical tracking abruptly collapses in the absence of language comprehension

bioRxiv Sep 8, 2026
The brain builds meaning from speech in stages, transforming acoustic input into linguistic comprehension. Yet where comprehension separates from general acoustic processing has been difficult to localize, because the two are tightly entangled in con...
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Machine learning prediction of eukaryotic hosts for giant viruses

bioRxiv Sep 8, 2026
Giant viruses (GVs; Nucleocytoviricota) infect diverse eukaryotes and are ecologically important across ecosystems. Although cultivation-independent sequencing has recovered tens of thousands of GV genomes from environmental samples, eukaryotic hosts...
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bioq: a unified, agent-native command-line interface to a fleet of AI drug-discovery methods

bioRxiv Sep 8, 2026
Artificial intelligence methods now span the drug-discovery pipeline --structure prediction, de novo design, docking, affinity estimation, and ADMET -- yet each tool ships with its own, often incompatible, GPU software stack, so chaining several into...
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End-to-end plaque counting and virus titration from laboratory plate images with deep learning

bioRxiv Sep 8, 2026
Plaque assays are the gold standard for quantifying infectious virus, yet plaque enumeration is still routinely performed manually, making virus titration labor-intensive, subjective, and difficult to standardize across analysts and laboratories. Exi...
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Agent-driven Model Development for RNA 3D Structure Prediction

bioRxiv Sep 8, 2026
Large language model (LLM) agents have shown promise in driving scientific discovery, but their effectiveness in complex, real-world biological problems remains underexplored. We ask whether a general-purpose LLM agent can drive semi-autonomous devel...
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PharmCast: rapid generation of three-dimensional pharmacophore fingerprints from two-dimensional structure without conformer generation

bioRxiv Sep 7, 2026
A three-dimensional pharmacophore fingerprint records the binding features a molecule can present. It is a description of a hand in search of a glove. Because it is defined by presented features instead of two-dimensional structure, it can identify p...
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Benchmark validity in graph neural network scoring of metabolic reaction activity on Recon3D: detecting label leakage, memorized noise and input-invariant models

bioRxiv Sep 7, 2026
Context-specific genome-scale metabolic modeling begins with scoring which of the approximately 10,600 human reactions are active in a patient's tumor. Methods in this literature are routinely benchmarked against activity labels obtained by threshold...
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