Gastroenterology

ScaleMAI: Accelerating the Development of Trusted Datasets and AI Models

Building trusted datasets is critical for transparent and responsible Medical AI (MAI) research, but creating even small, high-quality datasets can take years of effort from multidisciplinary teams. This process often delays AI benefits, as human-centric data creation and AI-centric model development are treated as separate, sequential steps. To overcome this, we propose ScaleMAI, an agent of AI...

ODFormer: a Virtual Organoid for Predicting Personalized Therapeutic Responses in Pancreatic Cancer

Pancreatic cancer (PC) patient-derived organoids (PDOs) faithfully recapitulate therapeutic responses but face clinical translation barriers, including high costs and technical complexity. To address these problems and the lack of frameworks for PDO-based drug-response assays, we developed ODFormer, a computational framework that simulates PC PDOs to predict clinically actionable, patient-specific...

Age Classification of White-tailed Deer Via Computer Vision and Deep Learning

Accurate age estimation of wild whitetail deer remains a significant challenge for wildlife management. This study presents the first application of c...

In Silico Target Identification Highlights IL12B as a Candidate for Small Molecule Drug Development

Drug discovery’s rising costs and complexities require innovative strategies to identify viable therapeutic targets. We developed a computational pipe...

RNA liquid biopsy via nanopore sequencing for novel biomarker discovery and cancer early detection

Liquid biopsies detect disease noninvasively by profiling cell-free nucleic acids that are secreted into the circulation. However, existing methods ex...

Human gut flagellome profiling using FlaPro reveals TLR5-related phenotype-specific alterations in IBD

Flagellin is the protein monomer of the bacterial flagellum, which confers motility, allowing bacteria to reach their favored niches. Flagellin is hig...

Temporal foundation model unveils ancient Hepatitis B virus evolution

Since ancient hepatitis B virus (HBV) sequencing data are scarce and incomplete, the evolutionary dynamics of HBV have long remained enigmatic. This d...

snATAC-Express infers Gene Expression from Prioritized Chromatin Accessibility Peaks using Machine Learning

Single cell multi-omic investigation opens-up new opportunities to understand mechanisms of gene regulation. Existing methods for inferring transcript...

Model-informed Deep Q-Networks to Guide Infliximab Dosing in Pediatric Crohn’s Disease

Model-informed precision dosing (MIPD) utilizes pharmacokinetic/pharmacodynamic (PK/PD) models to optimize drug therapy. However, conventional MIPD of...

Clinical and molecular characterisation of primary refractoriness to atezolizumab plus bevacizumab in patients with unresectable hepatocellular carcinoma

Despite improved outcomes with atezolizumab plus bevacizumab (A+B) in hepatocellular carcinoma (HCC), primary refractoriness (PRef), characterised by ...

MACGA: Multi-scale Adaptive Convolution with Graph Attention for LncRNA–Disease Association Prediction

Accurate prediction of lncRNA-disease associations (LDAs) is crucial for understanding complex disease mechanisms and advancing precision medicine. Ex...

Rapid and Reproducible Multimodal Biological Foundation Model Development with AIDO.ModelGenerator

Foundation models (FMs) for DNA, RNA, proteins, cells, and tissues have begun to close long-standing performance gaps in biological prediction tasks, ...

Deep-learning triage of 3D pathology datasets for comprehensive and efficient pathologist assessments

Standard-of-care slide-based 2D histopathology severely undersamples spatially heterogeneous tissue specimens, with each thin 2D section representing ...

Discovery of Prognostic Biomarkers in Gastric Cancer Through Machine Learning and Bioinformatics Analysis of Gene Expression Data

Gastric cancer (GC) often gets diagnosed in its advanced stages, resulting in poorer prognoses. To identify potential biomarkers in GC, we used fiftee...

Metabolomics-Guided Machine Learning Reveals Diagnostic and Mechanistic Biomarkers in CHB with MASLD

Metabolic dysfunction–associated steatotic liver disease (MASLD) often coexists with chronic hepatitis B (CHB), yet early diagnosis remains challengin...

Integrative Analysis of the Mouse Cecal Microbiome Across Diet, Age, and Metabolic State in the Diverse BXD Population

The gut microbiota both adapts to, and shapes, the host’s metabolic state through metabolites and gene regulatory networks, influencing multiple organ...

Machine Learning–Guided Structure–Activity Discovery of Polymer Configurations in Lipid Nanoparticles for Kiss-and-Run Endosomal Escape

Endosomal escape remains a major barrier to effective nucleic acid delivery via lipid nanoparticles (LNPs). Here, we address this challenge by incorpo...

Decoding the interconnected splicing patterns of hepatitis B virus and host using large language and deep learning models

Hepatitis B virus (HBV) infection causes approximately one million deaths annually and remains a major driver of hepatocellular carcinoma. Despite its...

Decoding Helicobacter pylori Resistance: Machine Learning–Enhanced Prediction of Antibiotic Susceptibility using Whole-Genome Sequencing

Helicobacter pylori is a significant risk factor for gastric cancer, peptic ulcers, and MALT lymphoma. Rising antibiotic resistance rates complicate t...

Extracellular Vesicle Gene Expression Enables Sensitive Detection of Colorectal Neoplasia

Extracellular vesicles (EVs), including exosomes, are emerging as promising carriers of disease-specific biomarkers due to their molecular cargo refle...