bioRxiv

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From movement to cognitive maps: recurrent neural networks reveal how locomotor development shapes hippocampal spatial coding

bioRxiv Jan 1, 2025
The hippocampus contains neurons whose firing correlates with an animal’s location and orientation in space. Collectively, these neurons are held to support a cognitive map of the environment, enabling the recall of and navigation to specific locatio...
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A Generalizable Machine Learning Framework for cfDNA based Early Detection of Hepatocellular Carcinoma: a Feasibility Study with Preclinical Validation

bioRxiv Jan 1, 2025
Early detection of hepatocellular carcinoma (HCC) is critical for improving patient outcomes, yet current screening tools lack sensitivity and specificity. We demonstrate a flexible machine learning framework for HCC detection using methylation profi...
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SiaRNA: A Siamese Neural Network with Bidirectional Cross-Attention for Pairwise siRNA-mRNA Efficacy Prediction

bioRxiv Jan 1, 2025
Small interfering RNA (siRNA) therapeutics have extraordinary potential for targeted gene silencing. They mediate post-transcriptional gene regulation by binding to complementary messenger RNA (mRNA) sequences and degrading them, thereby preventing t...
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An Empirical Analysis of Fine-Tuning Large Language Models on Bioinformatics Literature: PRSGPT and BioStarsGPT

bioRxiv Jan 1, 2025
Large language models (LLMs) often lack specialized knowledge for complex bioinformatics applications. We present a reproducible pipeline for fine-tuning LLMs on specialized bioinformatics data, demonstrated through two use cases: PRSGPT, focused on ...
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GDA-Pred: Generative AI-Driven Data Augmentation for Improved Prediction of IL-6 and IL-13 Inducing Peptides

bioRxiv Jan 1, 2025
The identification of interleukin-6 (IL-6) and interleukin-13 (IL-13) inducing peptides is crucial for accelerating drug discovery targeting cancer, immune disorders, and infectious diseases. However, experimental screening methods remain time-consum...
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Microenvironment-Inferred Genotyping: An Exclusionary Classifier for EGFR Amplification When DNA Testing Fails

bioRxiv Jan 1, 2025
EGFR amplification occurs in approximately 40-50% of glioblastoma (GBM) cases and is critical for treatment selection [1]. However, GBM tissue samples frequently yield insufficient material for comprehensive molecular testing due to extensive necrosi...
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BrainBridge Characterizes Key Factors affecting Alzheimer’s Disease and Associated Phenotypes

bioRxiv Jan 1, 2025
Single-cell RNA sequencing (scRNA-seq) has significantly advanced our understanding of Alzheimer’s disease and aging by revealing cellular heterogeneity and shifts in cell-type composition between diseased/old and healthy/young individuals. However, ...
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Dual-feature selectivity enables bidirectional coding in visual cortical neurons

bioRxiv Jan 1, 2025
Sensory neurons are traditionally viewed as feature detectors that respond with an increase in firing rate to preferred stimuli while remaining unresponsive to others. Here, we identify a dual-feature encoding strategy in macaque visual cortex, where...
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Biophysically Grounded Deep Learning Improves Protein–Protein ΔΔG Prediction

bioRxiv Jan 1, 2025
Predicting how mutations alter protein–protein binding affinity (ΔΔG) is central to protein engineering and therapeutic design, yet current deep learning models often fail to generalize beyond narrow benchmarks. We show that SKEMPI2, the field’s domi...
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Deep learning inference of universal dormancy pseudotime reveals the cellular targets of anti-cancer therapies

bioRxiv Jan 1, 2025
Controlled exit from and re-entry into the cell cycle is essential for multi-cellular life, while aberrant quiescent and senescent cell states have been implicated in age-related diseases and cancer treatment evasion. Recent molecular and imaging stu...
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