arXiv:2608. 08182v1 Announce Type: cross Abstract: Machine learning models for MALDI-TOF mass spectrometry have shown considerable promise for clinical microbiology tasks such as microbial identification and antimicrobial resistance prediction.
arXiv:2607. 14070v1 Announce Type: cross Abstract: Genomic foundation models such as Evo 2 learn rich sequence representations, but their value for biosecurity screening is largely unexplored.
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.
arXiv:2608.07632v2 Announce Type: replace-cross Abstract: Image-based profiling captures rich phenotypic signatures for drug discovery and functional genomics. Large public datasets like JUMP Cell Pa...
arXiv:2508. 07345v2 Announce Type: replace-cross Abstract: \textbf{Introduction:} Accurate prediction of Phage Virion Proteins (PVP) is essential for genomic studies due to their crucial role as structural elements in bacteriophages.
Antimicrobial peptides (AMPs) often act against multiple pathogen classes, making multi-label activity prediction a more realistic screening target than binary antimicrobial classification. The ESCAPE...
arXiv:2603. 02221v2 Announce Type: replace-cross Abstract: In clinical tabular prediction, classical machine learning models with feature engineering often outperform neural methods.
The study demonstrates that a simple, sequence-only approach using 330 interpretable descriptors and the TabPFN tabular foundation model can outperform complex multimodal deep learning methods for multi-label antimicrobial peptide activity prediction. On the ESCAPE benchmark (82,359 peptides, five labels), a label‑powerset TabPFN model achieved a mean average precision of 77.8%, surpassing the previous best of 72.1%. The approach also shows that predicted structure is unnecessary, that a small set of global physicochemical scalars can recover most performance, and that modeling label dependence benefits rare activities and informs assay prioritization.
arXiv:2608. 01924v2 Announce Type: replace-cross Abstract: Personalized neoantigen prediction is challenging due to the scarcity of positive samples, the noise of the experimental data, the severe class imbalance trait and the complex of immunogenicity features.
MODIS is a semi‑supervised framework for integrating multi‑omics data that are often unpaired, partially labeled, and scarce, such as in rare disease studies. It trains on a large reference database and a small target dataset simultaneously, using diagonal integration and class‑label alignment to handle class imbalance. The architecture combines variational auto‑encoders, a class classifier, and an adversarially trained modality classifier, with a regularized relativistic GAN loss for stable training, and demonstrates high accuracy on synthetic data and the TCGA cancer dataset.
arXiv:2607. 15774v1 Announce Type: cross Abstract: Explainable AI (XAI) for time series has seen significant algorithmic growth, but its utility in providing measurable performance gains for downstream tasks remains under-explored.
arXiv:2607. 16681v1 Announce Type: new Abstract: Early sepsis prediction from electronic health records is challenged by irregular sampling, high missingness, and class imbalance.