arXiv Machine Learning
Jun 30
Friend or Foe
arXiv:2509. 00123v2 Announce Type: replace-cross Abstract: A fundamental challenge in microbial ecology is determining whether bacteria compete or cooperate in different environmental conditions.
Constrained hybrid modelling to predict microbial dynamics and organic matter turnover in soil systems
arXiv:2606. 20329v1 Announce Type: new Abstract: Soil microorganisms control organic matter cycling and largely determine how soil systems can cope with and mitigate climate change and environmental threats.
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arXiv AI
Jun 9
Knowledge-Inclusive Adaptive Physics-Informed Neural Network for Microbial Interaction Modelling
arXiv:2606. 07686v1 Announce Type: cross Abstract: Physics-Informed Neural Network (PINN) is a way of including knowledge in the form of equations in Machine Learning methods.
arXiv AI
Jul 24
Leveraging Biokinetic Knowledge Priors for Data-Scarce Bioprocess Modeling
arXiv:2607. 20539v1 Announce Type: cross Abstract: While deep learning has accelerated drug discovery, its impact on biomanufacturing has been considerably more limited.
arXiv Machine Learning
Jul 24
Toward Mechanistic Interpretability of an AI Foundation Model Fine-Tuned for Atmospheric Chemistry
arXiv:2607. 20778v1 Announce Type: new Abstract: Weather forecasting foundation models (FMs) are increasingly fine-tuned to predict air quality, offering fast global pollution forecasts at lower computational cost than conventional chemical transport models.
arXiv Machine Learning
Jul 22
GEqTrain: A Configuration-Driven Framework for Retargeting Equivariant Graph Neural Networks Across 3D Scientific Tasks
arXiv:2607. 19083v1 Announce Type: new Abstract: Equivariant graph neural networks provide a powerful modeling language for three-dimensional scientific data, but their reuse is often limited by implementations tied to specific tasks, outputs, and training regimes.
arXiv AI
Jul 28
Physics-Informed Neural Networks for Predicting Nitrous Oxide Flux
arXiv:2607. 23880v1 Announce Type: cross Abstract: Nitrous oxide (N$_2$O) is the dominant ozone-depleting substance emitted in the 21st century, and the third largest contributor to anthropogenic greenhouse gases due to its high potency and long atmospheric lifetime, with more than 70% of N$_2$O emissions occurring as a result of agricultural processes.
arXiv Machine Learning
Jul 9
Trajectory Inference of Human Aging from Cross-Sectional DNA Methylation Data
arXiv:2607. 06583v1 Announce Type: cross Abstract: DNA methylation (DNAm) serves as one of the most robust molecular biomarkers of biological aging.
arXiv Machine Learning
Jul 1
ElemeNet: Multiscale Molecular Machine Learning with Uncertainty Quantification Across the Periodic Table
arXiv:2606. 30961v1 Announce Type: cross Abstract: Advances in deep learning architectures and representations have enabled ML-driven chemical property prediction, but state-of-the-art (SOTA) models have remained largely confined to independent codebases and lack support for diverse chemical species.
arXiv Machine Learning
Jun 19
SEAGAN: domain-Specific and Edge-Aware Graph Attention Network for Dynamic Plant Processes
arXiv:2606. 19623v1 Announce Type: new Abstract: Graph neural networks (GNNs) provide a flexible framework for learning from scientific data linked through physical, biological, or functional relationships.
arXiv Machine Learning
Jun 16
Multi-Modal Spatio-Temporal Graph Neural Network with Mixture of Experts for Soil Organic Carbon Prediction
arXiv:2606. 16580v1 Announce Type: new Abstract: Top-soil organic carbon (SOC) prediction is fundamental to agricultural sustainability, land use policy and fertilization planning.
arXiv Machine Learning
Jul 3
Structured Gaussian Processes for Uncertainty-Aware Classification of High-Dimensional, Small-Sampled Omics Data
arXiv:2607. 02103v1 Announce Type: cross Abstract: Classifying heterogeneous omics data remains a fundamental challenge in computational biology, particularly in high-dimensional, small-sample settings where nonlinear interactions dominate and class imbalance further complicates reliable prediction of minority phenotypes.
arXiv AI
Jul 24
Generative Artificial Intelligence in Bioinformatics: A Systematic Review of Models, Applications, and Methodological Advances
arXiv:2511. 03354v2 Announce Type: replace-cross Abstract: Generative artificial intelligence (GenAI) is transforming bioinformatics by advancing genomics, proteomics, transcriptomics, structural biology, and drug discovery.