Related papers: Secondary structure prediction of protein construc…
Soil Organic Carbon (SOC) is a foundation of soil health and global climate resilience, yet its prediction remains difficult because of intricate physical, chemical, and biological processes. In this study, we explore a Scientific Machine…
We show that cluster expansions (CE), previously used to model solid-state materials with binary or ternary configurational disorder, can be extended to the protein design problem. We present a generalized CE framework, in which properties…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
We present TerraBind, a foundation model for protein-ligand structure and binding affinity prediction that achieves 26-fold faster inference than state-of-the-art methods while improving affinity prediction accuracy by $\sim$20\%. Current…
We introduce DiffFit, a differentiable algorithm for fitting protein atomistic structures into an experimental reconstructed Cryo-Electron Microscopy (cryo-EM) volume map. In structural biology, this process is necessary to…
Materials representation plays a key role in machine learning based prediction of materials properties and new materials discovery. Currently both graph and 3D voxel representation methods are based on the heterogeneous elements of the…
Protein secondary structure (SS) prediction is important for studying protein structure and function. When only the sequence (profile) information is used as input feature, currently the best predictors can obtain ~80% Q3 accuracy, which…
One-sided ultrasonic non-destructive evaluation (UNDE) is extensively used to characterize structures that need to be inspected and maintained from defects and flaws that could affect the performance of power plants, such as nuclear power…
The ELUCID project aims to build a series of realistic cosmological simulations that reproduce the spatial and mass distribution of the galaxies as observed in the Sloan Digital Sky Survey (SDSS). This requires powerful reconstruction…
Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…
Unsupervised Domain Adaptation (UDA) essentially trades a model's performance on a source domain for improving its performance on a target domain. To overcome this, Unsupervised Domain Expansion (UDE) has been introduced, which adapts the…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
This work presents a novel Bayesian framework for unsupervised domain adaptation (UDA) in medical image segmentation. While prior works have explored this clinically significant task using various strategies of domain alignment, they often…
Traditional reconstruction-based methods have struggled to achieve competitive performance in anomaly detection. In this paper, we introduce Denoising Diffusion Anomaly Detection (DDAD), a novel denoising process for image reconstruction…
Three-dimensional ultrasound (US) offers many clinical advantages over conventional 2D imaging, yet its widespread adoption is limited by the cost and complexity of traditional 3D systems. Sensorless 3D US, which uses deep learning to…
This work introduces Structured 3D-SVD as a practical framework for the reconstruction, compression, and analysis of biological volumetric data. Inspired by the logic of matrix singular value decomposition (SVD), the proposed approach…
Bone surface reconstruction is an essential component of computer-assisted orthopedic surgery(CAOS), forming the foundation for both preoperative planning and intraoperative guidance. Compared to traditional imaging modalities such as…
Alternative splicing of gene transcripts greatly expands the functional capacity of the genome, and certain splice isoforms may indicate specific disease states such as cancer. Splice junction microarrays interrogate thousands of splice…
The construction of uniform designs (UDs) has received much attention in computer experiments over the past decades, but most of the previous works obtain uniform designs over a U-type by lattice domain. Due to increasing demands for…
In protein structure analysis, the accurate characterization of secondary structure elements is crucial for understanding protein function and dynamics. This paper presents a software system designed for the comprehensive analysis of the…