AIMC Journal:
bioRxiv

Showing 131 to 140 of 4935 articles

A biological-response compound representation allows chemical perturbation prediction across cell lines

bioRxiv Sep 29, 2026
Accurately predicting cellular responses to drugs remains a challenge with the potential to reduce experimental screening costs and accelerate drug discovery. Current computational approaches represent compounds through chemical structures, which car...
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EpiZoo: a DNA sequence-aware foundation model for cross-species single-cell epigenomics

bioRxiv Sep 29, 2026
Large-scale single-cell epigenomic atlases characterize chromatin regulatory landscapes across diverse biological contexts, spanning cell types, tissues, individuals and species. Foundation models provide an opportunity to capture the full spectrum o...
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Evaluating the Transferability of Pathology Foundation Models Across Cancer-related H&E Neurodegeneration-related Immunohistochemical Classification Tasks

bioRxiv Sep 29, 2026
Foundation models (FMs) have rapidly become dominant in artificial intelligence and are increasingly being adopted in computational pathology. Numerous pathology-specific FMs have been developed and evaluated for a variety of downstream tasks, most c...
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Cellular and Network Effects of Introducing Connexin-36 Expression in an Uncoupled Neuronal Population in the Mouse Hypothalamus

bioRxiv Sep 29, 2026
Electrical synapses are prevalent throughout nervous systems, including the mammalian brain. Several lines of evidence implicate these gap junction connections in several important roles in neural networks. Yet, progress has been hampered by a shorta...
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Neural networks as decision trees: an analytical framework for learning and neural selectivity

bioRxiv Sep 29, 2026
Nonlinear neural networks develop structured internal representations, yet how their geometry is determined by the tasks being learned remains poorly understood. Here, we develop an analytical framework for piecewise-linear feedforward and recurrent ...
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SpatialTRACE predicts anatomical axes and regions in spatial transcriptomics and microscopy

bioRxiv Sep 29, 2026
Spatial transcriptomics measures gene expression in tissue sections. However, interpretation requires anatomical maps that link gene expression and cellular composition to tissue structure. Annotating entire sections often requires extensive manual l...
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An agentic AI environment to support biomedical research in collaborative academic environments

bioRxiv Sep 29, 2026
Agentic artificial intelligence (AAI) is increasingly used by biomedical scientists, where it has substantially lowered the difficulty of integrating computational, statistical and data-science approaches into day-to-day research activities, assistin...
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Millisecond-scale detection of mouse ultrasonic vocalizations enables closed-loop experiments

bioRxiv Sep 29, 2026
Mouse ultrasonic vocalizations (USVs) provide a rapidly evolving readout of social interaction but are typically analysed only after acquisition. Here we introduce DeepFisFis, a waveform-based neural network that detects USVs while they are being pro...
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Sum-h2, enabling genetic discovery for deep learning-derived phenotypes through a fast evaluation framework and arena of performance

bioRxiv Sep 29, 2026
In the recent growing interest of AI research toward biology, genetic association studies of AI- derived phenotypes from high-content modalities such as images emerges as a powerful means for biological discovery. However, such AI-phenotyping methods...
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A low-annotation-budget PubMedBERT classifier for chondrogenesis regulator discovery via active learning

bioRxiv Sep 29, 2026
Motivation: Biomedical natural language processing (Bio-NLP) classification tasks are often limited by the cost of manual annotation, especially for specialised extraction problems where labelled corpora are scarce. Active learning can reduce this co...
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