Related papers: Towards Reliable Automatic Protein Structure Align…
Network alignment aims to find regions of topological or functional similarities between networks. In computational biology, it can be used to transfer biological knowledge from a well-studied species to a poorly-studied species between…
Biomolecular structure comparison not only reveals evolutionary relationships, but also sheds light on biological functional properties. However, traditional definitions of structure or sequence similarity always involve superposition or…
Protein structure prediction can be shown to be an NP-hard problem; the number of conformations grows exponentially with the number of residues. The native conformations of proteins occupy a very small subset of these, hence an exploratory,…
Hierarchical clustering is a popular unsupervised data analysis method. For many real-world applications, we would like to exploit prior information about the data that imposes constraints on the clustering hierarchy, and is not captured by…
The binding complexes formed by proteins and small molecule ligands are ubiquitous and critical to life. Despite recent advancements in protein structure prediction, existing algorithms are so far unable to systematically predict the…
In recent years, learning-based methods have achieved significant advancements in multi-exposure image fusion. However, two major stumbling blocks hinder the development, including pixel misalignment and inefficient inference. Reliance on…
Homography estimation is a basic image alignment method in many applications. It is usually conducted by extracting and matching sparse feature points, which are error-prone in low-light and low-texture images. On the other hand, previous…
Topology optimization has emerged as a popular approach to refine a component's design and increase its performance. However, current state-of-the-art topology optimization frameworks are compute-intensive, mainly due to multiple finite…
In scientific and engineering scenarios, a recurring task is the detection of low-dimensional families of signals or patterns. A classic family of approaches, exemplified by template matching, aims to cover the search space with a dense…
Feature matching between image pairs is a fundamental problem in computer vision that drives many applications, such as SLAM. Recently, semi-dense matching approaches have achieved substantial performance enhancements and established a…
Many researches have been working on the protein folding problem from more than half century. Protein folding is indeed one of the major unsolved problems in science. In this work, we discuss a model for the simulation of protein…
Multimodal models have demonstrated powerful capabilities in complex tasks requiring multimodal alignment, including zero-shot classification and cross-modal retrieval. However, existing models typically rely on millions of paired…
We outline a procedure for jointly sampling substitution matrices and multiple sequence alignments, according to an approximate posterior distribution, using an MCMC-based algorithm. This procedure provides an efficient and simple method by…
CLIP retrieval is typically framed as a pointwise similarity problem in a shared embedding space. While CLIP achieves strong global cross-modal alignment, many retrieval failures arise from local geometric inconsistencies: nearby items are…
Multiple sequence alignment is a basic procedure in molecular biology, and it is often treated as being essentially a solved computational problem. However, this is not so, and here I review the evidence for this claim, and outline the…
Finding correspondences between 3D shapes is a crucial problem in computer vision and graphics, which is for example relevant for tasks like shape interpolation, pose transfer, or texture transfer. An often neglected but essential property…
We present a novel dual-head deep learning architecture for protein-protein interaction modeling that enables simultaneous prediction of binding affinity ($\Delta G$) and mutation-induced affinity changes ($\Delta\Delta G$) using only…
The tertiary structure of protein, as well as the local secondary structure organization are fully determined by the angles of the peptidic bound. The backbone dihedral angles not only determine the global fold of the protein, but also the…
The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…
Aligning protein-protein interaction (PPI) networks of different species has drawn a considerable interest recently. This problem is important to investigate evolutionary conserved pathways or protein complexes across species, and to help…