Related papers: CLeFAPS: Fast Flexible Alignment of Protein Struct…

Crystal Structure Prediction (CSP) of molecular crystals plays a central role in applications, such as pharmaceuticals and organic electronics. CSP is challenging and computationally expensive due to the need to explore a large search space…

Motivation: Assessing the match between two biomolecular structures is at the heart of structural analyses such as superposition, alignment and docking. These tasks are typically solved with specialized structure-matching techniques…

Fragment-based shape signature techniques have proven to be powerful tools for computer-aided drug design. They allow scientists to search for target molecules with some similarity to a known active compound. They do not require reference…

Due to the increased availability of large datasets of biological sequences, the tools for sequence comparison are now relying on efficient alignment-free approaches to a greater extent. Most of the alignment-free approaches require the…

Network Pruning is a promising way to address the huge computing resource demands of the deployment and inference of Large Language Models (LLMs). Retraining-free is important for LLMs' pruning methods. However, almost all of the existing…

Speculative decoding (SD) is a promising method for accelerating the decoding process of Large Language Models (LLMs). The efficiency of SD primarily hinges on the consistency between the draft model and the verify model. However, existing…

In consensus clustering, a clustering algorithm is used in combination with a subsampling procedure to detect stable clusters. Previous studies on both simulated and real data suggest that consensus clustering outperforms native algorithms.…

As the rapid development of computer vision and the emergence of powerful network backbones and architectures, the application of deep learning in medical imaging has become increasingly significant. Unlike natural images, medical images…

Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…

Assembling a gene from candidate exons is an important problem in computational biology. Among the most successful approaches to this problem is \emph{spliced alignment}, proposed by Gelfand et al., which scores different candidate exon…

Computational protein design is experiencing a transformation driven by AI/ML. However, the range of potential protein sequences and structures is astronomically vast, even for moderately sized proteins. Hence, achieving convergence between…

Proteins move and deform to ensure their biological functions. Despite significant progress in protein structure prediction, approximating conformational ensembles at physiological conditions remains a fundamental open problem. This paper…

Motivation: Protein function prediction is a challenging task and an open problem in computational biology. The Critical Assessment of protein Function Annotation (CAFA) is a triennial, community-driven initiative that provides an…

Background: Coevolution within a protein family is often predicted using statistics that measure the degree of covariation between positions in the protein sequence. Mutual Information is a measure of dependence between two random variables…

Accurate and stable feature matching is critical for computer vision tasks, particularly in applications such as Simultaneous Localization and Mapping (SLAM). While recent learning-based feature matching methods have demonstrated promising…

We consider the constrained Linear Inverse Problem (LIP), where a certain atomic norm (like the $\ell_1 $ norm) is minimized subject to a quadratic constraint. Typically, such cost functions are non-differentiable, which makes them not…

Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…

Inherent structures, derived by eliminating thermal fluctuations from complex trajectories, illuminate fundamental mechanisms underlying structural relaxation and dynamic heterogeneity in dense glassy systems. However, determining these…

Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid…

We introduce a new type of foundational model for parsing human anatomy in medical images that works for different modalities. It supports supervised or unsupervised training and can perform matching, registration, classification, or…