Related papers: A comparative analysis of progressive multiple seq…

We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is…

The protein-ligand binding affinity (PLA) prediction goal is to predict whether or not the ligand could bind to a protein sequence. Recently, in PLA prediction, deep learning has received much attention. Two steps are involved in deep…

We propose an approach for multiple sequence alignment (MSA) derived from the dynamic time warping viewpoint and recent techniques of curve synchronization developed in the context of functional data analysis. Starting from pairwise…

Pyro-Align is a multiple alignment program specifically designed for pyrosequencing reads of huge number. Multiple sequence alignment is shown to be NP-hard and heuristics are designed for approximate solutions. Multiple sequence alignment…

Increasing size of sequence databases caused by the development of high throughput sequencing, poses multiple alignment algorithms to face one of the greatest challenges yet. As we show, well-established techniques employed for increasing…

The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…

Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed…

Similarity join finds all pairs of close points within a given distance threshold. Many similarity join methods have been proposed, but they are usually not efficient on high-dimensional space due to the curse of dimensionality and…

Cross-modal alignment is crucial for multimodal representation fusion due to the inherent heterogeneity between modalities. While Transformer-based methods have shown promising results in modeling inter-modal relationships, their quadratic…

Regrasp planning is often required when one pick-and-place cannot transfer an object from an initial pose to a goal pose while maintaining grasp feasibility. The main challenge is to reason about shared-grasp connectivity across…

Exact structured inference with neural network scoring functions is computationally challenging but several methods have been proposed for approximating inference. One approach is to perform gradient descent with respect to the output…

The way for performing multiple sequence alignment is based on the criterion of the maximum scored information content computed from a weight matrix, but it is possible to have two or more alignments to have the same highest score leading…

This paper focuses on the alignment of flow matching models with human preferences. A promising way is fine-tuning by directly backpropagating reward gradients through the differentiable generation process of flow matching. However,…

Sound correspondence patterns form the basis of cognate detection and phonological reconstruction in historical language comparison. Methods for the automatic inference of correspondence patterns from phonetically aligned cognate sets have…

Edit distances between merge trees of scalar fields have many applications in scientific visualization, such as ensemble analysis, feature tracking or symmetry detection. In this paper, we propose branch mappings, a novel approach to the…

While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…

Geometric matching is a key step in computer vision tasks. Previous learning-based methods for geometric matching concentrate more on improving alignment quality, while we argue the importance of naturalness issue simultaneously. To deal…

Millimeter-wave communication has the potential to deliver orders of magnitude increases in mobile data rates. A key design challenge is to enable rapid beam alignment with phased arrays. Traditional millimeter-wave systems require a high…

The structure of a protein is crucial in determining its functionality, and is much more conserved than sequence during evolution. A key task in structural biology is to compare protein structures in order to determine evolutionary…

In many clinical and epidemiological studies, collecting longitudinal measurements together with time-to-event outcomes is essential. Accurately estimating the association between longitudinal markers and event risks, as well as identifying…