Related papers: Evaluating protein binding interfaces with PUMBA

The goal of multimodal image fusion is to integrate complementary information from infrared and visible images, generating multimodal fused images for downstream tasks. Existing downstream pre-training models are typically trained on…

Mamba, based on state space model (SSM) with its linear complexity and great success in classification provide its superiority in 3D point cloud analysis. Prior to that, Transformer has emerged as one of the most prominent and successful…

Predicting protein complex structures is essential for protein function analysis, protein design, and drug discovery. While AI methods like AlphaFold can predict accurate structural models for many protein complexes, reliably estimating the…

Temporal video grounding (TVG) is a critical task in video content understanding, requiring precise alignment between video content and natural language instructions. Despite significant advancements, existing methods face challenges in…

Protein-protein interactions (PPIs) govern nearly all cellular processes, yet computational methods for identifying binding partners typically produce ranked predictions without mechanistic justification. This creates a fundamental barrier…

Neuron segmentation is the cornerstone of reconstructing comprehensive neuronal connectomes, which is essential for deciphering the functional organization of the brain. The irregular morphology and densely intertwined structures of neurons…

As one of the most representative DL techniques, Transformer architecture has empowered numerous advanced models, especially the large language models (LLMs) that comprise billions of parameters, becoming a cornerstone in deep learning.…

Many real-world computer vision tasks, such as depth completion, must handle inputs with arbitrarily shaped regions of missing or invalid data. For Convolutional Neural Networks (CNNs), Partial Convolutions solved this by a mask-aware…

Multimodal aspect-based sentiment analysis (MABSA) aims to understand opinions in a granular manner, advancing human-computer interaction and other fields. Traditionally, MABSA methods use a joint prediction approach to identify aspects and…

Abnormality detection in medical imaging is a critical task requiring both high efficiency and accuracy to support effective diagnosis. While convolutional neural networks (CNNs) and Transformer-based models are widely used, both face…

Low-resolution fine-grained image classification has recently made significant progress, largely thanks to the super-resolution techniques and knowledge distillation methods. However, these approaches lead to an exponential increase in the…

Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…

Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…

Linear RNN architectures, like Mamba, can be competitive with Transformer models in language modeling while having advantageous deployment characteristics. Given the focus on training large-scale Transformer models, we consider the…

An ecosystem of Transformer-based models has been established by building large models with extensive data. Parameter-efficient fine-tuning (PEFT) is a crucial technology for deploying these models to downstream tasks with minimal cost…

Recent 2D CNN-based domain adaptation approaches struggle with long-range dependencies due to limited receptive fields, making it difficult to adapt to target domains with significant spatial distribution changes. While transformer-based…

PPI network alignment aims to find topological and functional similarities between networks of different species. Several alignment approaches have been proposed. Each of these approaches relies on a different alignment method and uses…

Computational docking is the core process of computer-aided drug design; it aims at predicting the best orientation and conformation of a small drug molecule when bound to a target large protein receptor. The docking quality is typically…

Visual Mamba is an approach that extends the selective space state model, Mamba, to vision tasks. It processes image tokens sequentially in a fixed order, accumulating information to generate outputs. Despite its growing popularity for…

Protein-Protein Interactions (PPIs) are fundamental in various biological processes and play a key role in life activities. The growing demand and cost of experimental PPI assays require computational methods for efficient PPI prediction.…