diffusion model

IDPForge: Deep Learning of Proteins with Global and Local Regions of Disorder

IDPForge generates all-atom ensembles of intrinsically disordered proteins and regions using a transformer diffusion model, showing good agreement with experimental data.

Computational design of metalloproteases

This paper designs de novo metalloproteases using RoseTTAFold Diffusion 2, achieving high activity and specificity for cleaving various substrates.

Large scale prospective evaluation of co-folding across hundreds of Mac1-ligand complexes and three virtual screens

On 489 evaluable new Mac1 complexes, AlphaFold3, Chai-1 and Boltz-2 placed over half of ligands within 2 Å, but on docking hit-lists AF3 and Boltz-2 added little over docking.

AlphaFold3 and Intrinsically Disordered Proteins: Reliable Monomer Prediction, Unpredictable Multimer Performance

AlphaFold3 pLDDT matches AlphaFold2 at calling disordered residues (Matthews correlation 0.693 vs 0.701); on disorder-containing complexes mean DockQ is similar, but interface features explain less variance (42% vs 58%).

DesignMaster: A Multi-Conditional Diffusion Framework for Rational PROTAC Design

DesignMaster improves PROTAC design by incorporating linker length and physicochemical constraints through a diffusion framework, achieving better validity and recovery than existing methods.

Privacy-Preserving Visualization of Brain Functional Connectivity

This paper explores privacy-preserving visualization techniques for brain functional connectivity using differential privacy to protect participant data while maintaining visual utility.

Exploring protein conformational ensembles using evolutionary conditional diffusion

This paper introduces DiffEnsemble, a diffusion-based framework for modeling protein conformational ensembles, showing improved performance over existing methods.

GDA-Pred: Generative AI-Driven Data Augmentation for Improved Prediction of IL-6 and IL-13 Inducing Peptides

GDA-Pred improves prediction of IL-6 and IL-13 inducing peptides by using generative AI to augment small datasets, enhancing classifier performance through data expansion.

Enhanced sampling of protein conformations in AlphaFold3 with repulsive bias in the diffusion generative model

This paper improves AlphaFold3's ability to predict protein conformations by introducing a repulsive bias in its diffusion model, enabling better capture of ligand-induced structural changes.

Time-dependent bistability leads to critical slowing down during floral transition in Arabidopsis

The paper shows time-dependent bistability in Arabidopsis floral transition, leading to critical slowing down and ghost attractor dynamics.

Unified Sampling and Ranking for Protein Docking with DFMDock

DFMDock is a diffusion model for protein docking that combines generative sampling and energy-based ranking, achieving higher success rates than existing methods.

Diffusion-based Representation Integration for Foundation Models Improves Spatial Transcriptomics Analysis

DRIFT improves spatial transcriptomics analysis by integrating spatial context into foundation models using diffusion on spatial graphs, outperforming specialized methods.

AFM-Fold: Rapid Reconstruction of Protein Conformations from AFM Images

AFM-Fold reconstructs 3D protein conformations from AFM images using a generative AI framework, outperforming rigid-body fitting and capturing conformational dynamics.

Counterfactual Diffusion Models for Interpretable Explanations of Artificial Intelligence Models in Pathology

MoPaDi generates counterfactual explanations for histopathology images to reveal morphological features driving classifier predictions, improving interpretability in digital pathology.

An Expert-Informed Synthetic Animal Data Generator: A Physiology-Consistent Generative Framework for High-Fidelity Animal Digital Twins

This paper introduces EICD, a framework that generates physiology-consistent synthetic animal data by embedding mechanistic biological principles, achieving high fidelity and reducing physiological hallucinations.

Chromosome X Dosage Modulates Development of Aneuploidy in Genetically Diverse Mouse Embryonic Stem Cells

The paper identifies that X chromosome dosage influences aneuploidy development in mouse embryonic stem cells, with XO and XY lines showing higher aneuploidy rates than XX lines.

In Silico Generation of Gene Expression profiles usingDiffusion Models

This paper introduces diffusion models for generating synthetic gene expression data and shows they outperform existing methods in predictive performance.

CLOP-DiT: Structured-Metadata-Conditioned Single-Cell Latent Generation via Contrastive Language-Omics Pretraining and Diffusion Transformers

CLOP-DiT generates synthetic single-cell gene expression profiles from structured biological metadata using contrastive alignment and diffusion models, achieving high steering accuracy but limited cross-dataset variability.

Distance-Restraint-Guided Diffusion Models for Sampling Protein Conformational Changes and Ligand Dissociation Pathways

This paper introduces a distance-restraint-guided diffusion model to sample protein conformational changes and ligand dissociation pathways, achieving uniform coverage and high structural quality.

InversePep: Diffusion-Driven Structure-Based Inverse Folding for Functional Peptides

InversePep generates peptides with target structural geometries using a diffusion model, outperforming existing methods in producing geometry-consistent sequences.

Cross-modal Denoising and Integration of Spatial Multi-omics data with CANDIES

CANDIES denoises and integrates spatial multi-omics data using a conditional diffusion model and contrastive learning, improving downstream analysis tasks.

Coherent Cross-modal Generation of Synthetic Biomedical Data to Advance Multimodal Precision Medicine

The paper develops a generative framework to synthesize missing modalities in multimodal datasets, validated on cancer data, showing it can maintain predictive model performance on incomplete profiles.

High-PepBinder: A pLM-Guided Latent Diffusion Framework for Affinity-Aware Target-Specific Peptide Design

High-PepBinder generates target-specific peptides using a pLM-guided diffusion model and a comprehensive dataset, producing peptides with favorable binding properties and sequence diversity.

Generative cerebral vasculature visualization using spatialtranscriptomic data

The paper uses spatial transcriptomic data and a generative model to predict brain vasculature organization from gene co-expression patterns.

Antidepressants interact with an LPA3 receptor binding site: functional and docking studies

This study investigates how antidepressants interact with LPA3 receptors through functional assays and docking simulations, revealing distinct effects on calcium and ERK 1/2 signaling.

Conditional Diffusion with Locality-Aware Modal Alignment for Generating Diverse Protein Conformational Ensembles

This paper introduces Mac-Diff, a diffusion model that generates diverse protein conformations by aligning sequence and geometry views, showing improved recovery of conformational distributions and meta-stable states.

Modelling Immune Dynamics in Locally Advanced MSI-H/dMMR Colorectal Cancer with Neoadjuvant Pembrolizumab Treatment: From Differential Equations to an Agent-Based Framework

This paper develops a differential equation model and converts it to an agent-based model to simulate immune dynamics in MSI-H/dMMR colorectal cancer under pembrolizumab treatment.

A logarithmic theory of visuomotor stabilization

This paper develops a theoretical framework showing how logarithmic coding enables adaptive visuomotor stabilization in locomotion, validated through analysis of experimental data and extension to intermittent swimming.

Improved protein binder design using -pairing targeted RFdiffusion

Conditioning RFdiffusion on edge beta-strand pairing yields specific binders to polar targets, with in silico success above 9.2% versus 0.98% for hotspot-only conditioning.

Human Messenger RNA Harbors Widespread Noncoding Splice Isoforms

The paper identifies 15,836 noncoding splice isoforms in human mRNA from 7,298 protein-coding genes, showing tissue-specific expression and association with cancer.