Infectious Disease

PhageTAILor leverages machine learning for phage tail-like elements detection and classification in plant-associated bacteria

Phage tail-like elements (PTEs) -- tailocins, bacterial type VI secretion systems (T6SS), and extracellular contractile injection systems (eCIS) -- are contractile nanomachines that bacteria use to kill their neighbors and compete within their micro-ecosystems. PTEs help shape microbial community composition. Most PTE detection tools only detect a single PTE class. Moreover, most tailocin detectio...

MiNER: Fine-Tuned Biomedical Natural Language Processing for Malaria Disease Entity Recognition in Clinical Texts

Malaria remains a significant global health burden, necessitating continuous research efforts to understand its complex molecular mechanisms, epidemiology, and potential therapeutic interventions. Extracting essential biomedical information from the vast and constantly growing malaria literature is a challenging task that demands innovative approaches. Recently, pre-trained language models have re...

Novel Entropy-Based Framework for Quantifying Dynamic Epistemic Uncertainty in Clinical Medicine

The widespread adoption of clinical large language models (LLMs) introduces significant risks of automation bias, premature closure, and clinician des...

Clinical evaluation of artificial intelligence for diagnostics of antibiotic-resistant bacteria

Antimicrobial resistance is a public health challenge, driving the need for rapid, cost-effective diagnostic support tools. Artificial intelligence (A...

Primary Care Quality and Inappropriate Community Antibiotic Use: A Double Machine Learning Instrumental Variable Approach

Inappropriate antibiotic use presents a major global health challenge, particularly in low-resource settings where access to quality care is limited b...

Genome-scale label-free imaging reveals cellular physiology encoded in bacterial collective architecture

DNA sequencing unified microbial genotyping into a single, comprehensive readout, yet phenotyping remains a slow and fragmented endeavor. Here, we int...

Tc17-driven antibody-independent mucosal immunity is critical for protection against extracellular bacterial pneumonia

Klebsiella pneumoniae (Kp) is a WHO high-priority pathogen for vaccine development, yet previous efforts failed largely because key protective immune ...

Coarse composition suffices: tabular in-context learning for multi-activity antimicrobial peptide profiling

Antimicrobial peptides (AMPs) often act against multiple pathogen classes, making multi-label activity prediction a more realistic screening target th...

Beyond Accuracy: Quantifying Pulmonary Attribution in Anatomy-Guided Chest X-Ray Classification Under Domain Shift

Deep-learning models can achieve strong chest X-ray (CXR) classification performance without establishing whether their predictions predominantly rely...

PhageTransformer - scalable and accurate host assignments for bacteriophages

Bacteriophages can only be understood through their interactions with bacterial hosts. As environmental sequencing efforts expanded, the number of ava...

Towards a ML-powered Multiscale Computational Platform Based on QSP and PBPK Modeling to Support the Development of mRNA-based Therapies

mRNA-based therapeutics have emerged as a transformative class of medicines, yet their translation beyond infectious disease vaccines remains challeng...

Coarse composition suffices: tabular in-context learning for multi-activity antimicrobial peptide profiling

Antimicrobial peptides (AMPs) often act against multiple pathogen classes, making multi-label activity prediction a more realistic screening target th...

Organelle interdependencies underlie the collapse of eukaryotic intracellular organization during cell death and aging

Complex intracellular organization is a defining feature of eukaryotic cells, and the loss of its integrity is a hallmark of aging and disease. We com...

Adaptive forecasting of antiretroviral therapy demand using machine learning in India's national HIV programme

Antiretroviral therapy (ART) stock-outs interrupt treatment, increase the risk of virologic failure and drug resistance, and erode the population-leve...

DISRUPTION OF A DNA REPAIR PROTEIN PROMOTES ANTIBIOTIC RESISTANCE IN ACINETOBACTER BAUMANNII

Acinetobacter baumannii is a high priority Gram negative opportunistic pathogen known for its high rates of multidrug resistance (MDR). Minocycline (M...

Molecular Determinants of Functional Bacterial sRNA-mRNA Interactions Revealed by Integrating RNA Interactomes and Interpretable Machine Learning

Bacterial small RNAs (sRNAs) regulate gene expression by base pairing with target mRNAs, yet transcriptome-wide interactome mapping has shown that man...

Learning a Continuous Sepsis Severity Score Without Hour-by-Hour Supervision: A Two-Site Retrospective Study

Currently used sepsis severity indices rely on fixed variables and weights established decades ago, which are coarsely discretized and calibrated to a...

Why ML-based cough models do not generalize: a systematic cross-dataset evaluation for tuberculosis screening

Cough acoustics are promising for non-invasive tuberculosis (TB) screening, yet whether machine learning (ML) models capture disease-related acoustics...

Cell Cycle Phases, Spindle Dynamics and Kinesin-5 Motor LocalizationCharacterized by Deep Learning, Dual Segmentation and Decision-Tree Pipeline

Three-dimensional live-cell fluorescence imaging of yeast cells is crucial for studying cell-cycle mechanics and regulation. However, extracting multi...

Offline Reinforcement Learning for Out-of-Distribution ICU Sepsis Decision Support

Offline reinforcement learning (RL) provides a promising framework for learning and evaluating treatment policies from logged clinical data, particula...