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: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: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:2509.23552v2 Announce Type: replace-cross Abstract: Antimicrobial Resistance (AMR) is a rapidly escalating global health crisis. While genomic sequencing enables rapid prediction of resistance...
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:2605.28868v2 Announce Type: replace-cross Abstract: Metagenomic taxonomic annotation is essential for interpreting complex microbial communities, yet reliable annotation remains challenging und...
arXiv:2607. 20539v1 Announce Type: cross Abstract: While deep learning has accelerated drug discovery, its impact on biomanufacturing has been considerably more limited.
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. 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. 19376v1 Announce Type: cross Abstract: Machine learning models trained on biochemical data are routinely evaluated using splits that fail to account for relational structure, causing information leakage and over-optimistic performance estimates.
arXiv:2602. 22822v3 Announce Type: replace Abstract: Tandem mass spectrometry (MS/MS) is central to small molecule identification, but current deep learning systems for spectrum prediction still remain difficult to evaluate and deploy in practice.
arXiv:2607. 06224v1 Announce Type: new Abstract: Designing microbial strains that produce high-value chemicals at commercially viable titers remains a central challenge in metabolic engineering.
This paper introduces a hierarchical Bayesian multitask learning model that assumes a shared sparsity structure across different binary classification tasks. The authors develop a variational inference algorithm for efficient posterior approximation and evaluate the method on synthetic data and pooled microbiome studies. Results show superior support recovery in synthetic experiments and robust, well‑calibrated predictions with informative taxa selection in microbiome classification.