Related papers: Pairwise alignment incorporating dipeptide covaria…
This thesis surveys the research in patch-based synthesis and algorithms for finding correspondences between small local regions of images. We additionally explore a large kind of applications of this new fast randomized matching technique.…
We describe new approaches for distances between pairs of 2-dimensional surfaces (embedded in 3-dimensional space) that use local structures and global information contained in inter-structure geometric relationships. We present algorithms…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
We present an algorithm that takes an unannotated corpus as its input, and returns a ranked list of probable morphologically related pairs as its output. The algorithm tries to discover morphologically related pairs by looking for pairs…
Computational difficulty of quadratic matching and the Gromov-Wasserstein distance has led to various approximation and relaxation schemes. One of such methods, relying on the notion of distance profiles, has been widely used in practice,…
Aligning partially overlapping point sets where there is no prior information about the value of the transformation is a challenging problem in computer vision. To achieve this goal, we first reduce the objective of the robust point…
All known terrestrial proteins are coded as continuous strings of ~20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method…
Advances in deep learning have opened an era of abundant and accurate predicted protein structures; however, similar progress in protein ensembles has remained elusive. This review highlights several recent research directions towards…
The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…
Self-avoiding random walks were performed on protein residue networks. Compared with protein residue networks with randomized links, the probability of a walk being successful is lower and the length of successful walks shorter in…
The alignment of protein-protein interaction (PPI) networks has many applications, such as the detection of conserved biological network motifs, the prediction of protein interactions, and the reconstruction of phylogenetic trees [1, 2, 3].…
A protein structure is represented as a network of residues whereby edges are determined by intra-molecular contacts. We introduce inhomogeneity into these networks by assigning each edge a weight that is determined by amino-acid pair…
Comparing the internal representations of neural networks is a central goal in both neuroscience and machine learning. Standard alignment metrics operate on raw neural activations, implicitly assuming that similar representations produce…
Understanding protein-protein interactions is central to our understanding of almost all complex biological processes. Computational tools exploiting rapidly growing genomic databases to characterize protein-protein interactions are…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
Protein structure prediction based on Hydrophobic-Polar energy model essentially becomes searching for a conformation having a compact hydrophobic core at the center. The hydrophobic core minimizes the interaction energy between the amino…
Archetypal scenarios for change detection generally consider two images acquired through sensors of the same modality. However, in some specific cases such as emergency situations, the only images available may be those acquired through…
Graph alignment aims at finding the vertex correspondence between two correlated graphs, a task that frequently occurs in graph mining applications such as social network analysis. Attributed graph alignment is a variant of graph alignment,…
This paper examines the problem of ranking a collection of objects using pairwise comparisons (rankings of two objects). In general, the ranking of $n$ objects can be identified by standard sorting methods using $n log_2 n$ pairwise…
Inspired by applications in sports where the skill of players or teams competing against each other varies over time, we propose a probabilistic model of pairwise-comparison outcomes that can capture a wide range of time dynamics. We…