AIMC Journal:
bioRxiv

Showing 1811 to 1820 of 4956 articles

Back to BERT in 2026: ModernGENA as a Strong, Efficient Baseline for DNA Foundation Models

bioRxiv Apr 23, 2026
Recent advances in DNA language models have mainly come from building larger and more complex architectures, making it harder to understand the effect of changes to standard components such as the transformer layers widely used in NLP. In this work, ...
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OneGenomeRice (OGR): A Genomic Foundation Model for Rice

bioRxiv Apr 23, 2026
The transition of genomics to a predictive intelligence discipline is driven by the advent of genomic foundation models. While substantial progress has been observed in human-centric models, plant genomics, particularly for the staple crops, remains ...
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EpiRanha: Hunting for Epitope Similarity with a Structure- and Residue-Aware Graph Neural Network

bioRxiv Apr 23, 2026
Precise epitope recognition underpins the efficacy and safety of therapeutic antibodies, yet existing approaches to epitope similarity scoring rely largely on sequence identity or rigid structural superposition, limiting their ability to robustly ass...
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Machine Learning Approach for Enumeration of Circulating Cells with Diffuse in vivo Flow Cytometry

bioRxiv Apr 23, 2026
Significance: Diffuse in vivo flow cytometry (DiFC) is an emerging technique for enumerating rare, fluorescently-labeled circulating tumor cells (CTCs) in small animals without drawing blood samples. DiFC uses detection of transient fluorescent peaks...
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Cross-Attention Over RNA And Protein Sequences Enables Generalizable Interaction Prediction

bioRxiv Apr 23, 2026
Computational predictions are essential to characterize the RNA-protein interaction landscape, yet a persistent gap between benchmark performance and practical utility suggests that current models have limited generalization capabilities. To address ...
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Aiki-XP: leakage-controlled multimodal prediction of within-species relative protein expression at pan-bacterial scale

bioRxiv Apr 23, 2026
Generalizable protein-expression prediction can accelerate protein engineering, inform disease mechanisms, and help optimize heterologous recombinant protein production. Protein expression is governed by many interacting parameters that no single omi...
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An autonomous LLM agent platform for computational binder design and conjugation-aware prioritization of antibody drug conjugates

bioRxiv Apr 23, 2026
Large language model (LLM) agents have automated tool use in chemistry, but orchestrating multi step computational biology workflows spanning structure prediction, protein design, and covalent conjugation remains manually intensive. Here we present O...
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Glio-SERS: Label-Free Molecular Profiling of Plasma Extracellular Vesicles in Brain Tumors Using SERS and Artificial Intelligence

bioRxiv Apr 23, 2026
Extracellular vesicles are increasingly recognized as important carriers of disease-associated molecular information, yet robust methods for their isolation and molecular characterization from limited clinical samples remain challenging. Here, we pre...
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Machine Learning applied to MALDI-TOF data in a clinical setting: a systematic review

bioRxiv Apr 19, 2026
Bacterial identification, antimicrobial resistance prediction, and strain typification are critical tasks in clinical microbiology, essential for guiding patient treatment and controlling the spread of infectious diseases. While Machine Learning (ML)...
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Enabling the prediction of phage receptor specificity from genome data

bioRxiv Apr 19, 2026
Predicting which receptor a phage binds to from genome sequence alone has remained an intractable challenge, principally because the experimental phenotypic data required to train and validate predictive models have not been available at sufficient s...
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