Related papers: ConforNets: Latents-Based Conformational Control i…
Deep learning-based prediction of protein-ligand complexes has advanced significantly with the development of architectures such as AlphaFold3, Boltz-1, Chai-1, Protenix, and NeuralPlexer. Multiple sequence alignment (MSA) has been a key…
Proteins exist as a dynamic ensemble of multiple conformations, and these motions are often crucial for their functions. However, current structure prediction methods predominantly yield a single conformation, overlooking the conformational…
AlphaFold2 (AF2) has transformed protein structure prediction by harnessing co-evolutionary constraints embedded in multiple sequence alignments (MSAs). MSAs not only encode static structural information, but also hold critical details…
Convolutional networks (ConvNets) have achieved promising accuracy for various anatomical segmentation tasks. Despite the success, these methods can be sensitive to data appearance variations. Considering the large variability of scans…
This paper presents a novel approach for predicting the relative populations of protein conformations using AlphaFold 2, an AI-powered method that has revolutionized biology by enabling the accurate prediction of protein structures. While…
We present Compound Conditioned ControlNet, C3Net, a novel generative neural architecture taking conditions from multiple modalities and synthesizing multimodal contents simultaneously (e.g., image, text, audio). C3Net adapts the ControlNet…
The function of biomolecules such as proteins depends on their ability to interconvert between a wide range of structures or "conformations." Researchers have endeavored for decades to develop computational methods to predict the…
AlphaFold 3 represents a transformative advancement in computational biology, enhancing protein structure prediction through novel multi-scale transformer architectures, biologically informed cross-attention mechanisms, and geometry-aware…
AlphaFold 3 (AF3) is a powerful biomolecular structure-predicting tool based on the latest deep learning algorithms and revolutionized AI model architectures. A few of papers have already investigated its accuracy in predicting different…
Protein function relies on dynamic conformational ensembles, yet current generative models like AlphaFold3 often fail to produce ensembles that match experimental data. Recent experiment-guided generators attempt to address this by steering…
In recent years, advances in artificial intelligence (AI) have transformed structural biology, particularly protein structure prediction. Though AI-based methods, such as AlphaFold (AF), often predict single conformations of proteins with…
Transformers have attracted increasing interests in computer vision, but they still fall behind state-of-the-art convolutional networks. In this work, we show that while Transformers tend to have larger model capacity, their generalization…
Convolutional neural networks (CNNs) achieve translational invariance by using pooling operations. However, the operations do not preserve the spatial relationships in the learned representations. Hence, CNNs cannot extrapolate to various…
Foundation models are transforming machine learning across many modalities, with in-context learning replacing classical model training. Recent work on tabular data hints at a similar opportunity to build foundation models for…
AlphaFold 3 (AF3), the latest version of protein structure prediction software, goes beyond its predecessors by predicting protein-protein complexes. It could revolutionize drug discovery and protein engineering, marking a major step…
Due to the over-fitting problem caused by imbalance samples, there is still room to improve the performance of data-driven automatic modulation classification (AMC) in noisy scenarios. By fully considering the signal characteristics, an AMC…
Deep neural networks (DNN) have shown great capacity of modeling a dynamical system; nevertheless, they usually do not obey physics constraints such as conservation laws. This paper proposes a new learning framework named ConCerNet to…
Composite adaptive radial basis function neural network (RBFNN) control with a lattice distribution of hidden nodes has three inherent demerits: 1) the approximation domain of adaptive RBFNNs is difficult to be determined a priori; 2) only…
An adversarial example is a modified input image designed to cause a Machine Learning (ML) model to make a mistake; these perturbations are often invisible or subtle to human observers and highlight vulnerabilities in a model's ability to…
Designing an effective channel attention mechanism implores one to find a lossy-compression method allowing for optimal feature representation. Despite recent progress in the area, it remains an open problem. FcaNet, the current…