Related papers: CLePAPS: Fast Pair Alignment of Protein Structures…
The Automated Protein Structure Analysis (APSA) method is used for the classification of supersecondary structures. Basis for the classification is the encoding of three-dimensional (3D) residue conformations into a 16-letter code (3D-1D…
Cross-lingual plagiarism (CLP) occurs when texts written in one language are translated into a different language and used without acknowledging the original sources. One of the most common methods for detecting CLP requires online machine…
Aligning multiple protein structures can yield valuable information about structural similarities among related proteins, as well as provide insight into evolutionary relationships between proteins in a family. We have developed an…
Protein structure prediction is one of the most important problems in computational biology. The most successful computational approach, also called template-based modeling, identifies templates with solved crystal structures for the query…
The closest pair of points problem or closest pair problem (CPP) is an important problem in computational geometry where we have to find a pair of points from a set of points in metric space with the smallest distance between them. This…
Superpixels have become very popular in many computer vision applications. Nevertheless, they remain underexploited since the superpixel decomposition may produce irregular and non stable segmentation results due to the dependency to the…
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…
Previous partial permutation synchronization (PPS) algorithms, which are commonly used for multi-object matching, often involve computation-intensive and memory-demanding matrix operations. These operations become intractable for large…
Recent advances in geometric deep learning and generative modeling have enabled the design of novel proteins with a wide range of desired properties. However, current state-of-the-art approaches are typically restricted to generating…
In this paper we report on an algorithm for aligning multiple protein structures. The algorithm has been tested on a variety of inputs and it performs well in comparison to well-known algorithms for this problem.
Protein retrieval, which targets the deconstruction of the relationship between sequences, structures and functions, empowers the advancing of biology. Basic Local Alignment Search Tool (BLAST), a sequence-similarity-based algorithm, has…
A similarity join aims to find all similar pairs between two collections of records. Established approaches usually deal with synthetic differences like typos and abbreviations, but neglect the semantic relations between words. Such…
Correlation clustering is a widely studied framework for clustering based on pairwise similarity and dissimilarity scores, but its best approximation algorithms rely on impractical linear programming relaxations. We present faster…
Vision-language models (VLMs) such as CLIP are trained via contrastive learning between text and image pairs, resulting in aligned image and text embeddings that are useful for many downstream tasks. A notable drawback of CLIP, however, is…
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…
Modeling fine-grained speaking styles remains challenging for language-speech representation pre-training, as existing speech-text models are typically trained with coarse captions or task-specific supervision, and scalable fine-grained…
Feature selection has been proven a powerful preprocessing step for high-dimensional data analysis. However, most state-of-the-art methods tend to overlook the structural correlation information between pairwise samples, which may…
Contrastive Language and Image Pairing (CLIP), a transformative method in multimedia retrieval, typically trains two neural networks concurrently to generate joint embeddings for text and image pairs. However, when applied directly, these…
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…
Referring image segmentation aims at localizing all pixels of the visual objects described by a natural language sentence. Previous works learn to straightforwardly align the sentence embedding and pixel-level embedding for highlighting the…