Related papers: Ultra-large alignments using Phylogeny-aware Profi…
Rapid development of modern sequencing platforms enabled an unprecedented growth of protein families databases. The abundance of sets composed of hundreds of thousands sequences is a great challenge for multiple sequence alignment…
Protein language models have excelled in a variety of tasks, ranging from structure prediction to protein engineering. However, proteins are highly diverse in functions and structures, and current state-of-the-art models including the…
The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata…
We theorize that phylogenetic profiles provide a quantitative method that can relate the structural and functional properties of proteins, as well as their evolutionary relationships. A key feature of phylogenetic profiles is the…
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…
Protein contacts contain important information for protein structure and functional study, but contact prediction from sequence information remains very challenging. Recently evolutionary coupling (EC) analysis, which predicts contacts by…
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…
As in many other scientific domains, we face a fundamental problem when using machine learning to identify proteins from mass spectrometry data: large ground truth datasets mapping inputs to correct outputs are extremely difficult to…
Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for…
Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental role in drug design.…
Depth map super-resolution technology aims to improve the spatial resolution of low-resolution depth maps and effectively restore high-frequency detail information. Traditional convolutional neural network has limitations in dealing with…
Accurate pathloss prediction is essential for the design and optimization of UAV-assisted millimeter-wave (mmWave) networks. While deep learning approaches have shown strong potential, their generalization across diverse environments,…
We describe an new algorithm for visualizing an alignment of biological sequences according to a probabilistic model of evolution. The resulting data array is readily interpreted by the human eye and amenable to digital image techniques. We…
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…
Generating crisp, i.e., one-pixel-wide, edge maps remains one of the fundamental challenges in edge detection, affecting both traditional and learning-based methods. To obtain crisp edges, most existing approaches rely on two hand-crafted…
Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applications, such as the prediction of protein function, detection of…
Uniform Manifold Approximation and Projection (UMAP) is a widely used manifold learning technique for dimensionality reduction. This paper studies UMAP, supervised UMAP, and several competing dimensionality reduction methods, including…
Advances in bio-technology have made available massive amounts of functional, structural and genomic data for many biological sequences. This increased availability of heterogeneous biological data has resulted in biological applications…
Signal peptide (SP) is a short peptide located in the N-terminus of proteins. It is essential to target and transfer transmembrane and secreted proteins to correct positions. Compared with traditional experimental methods to identify signal…
Acquiring plausible pathways on high-dimensional structural distributions is beneficial in several domains. For example, in the drug discovery field, a protein conformational pathway, i.e. a highly probable sequence of protein structural…