Related papers: Probabilistic pairwise sequence alignment
Motivation: Revealing structural variations across sequences of closely related individuals or species is crucial for understanding their diversification mechanisms and roles. Results: We developed PatchWorkPlot, a tool for visualization of…
We describe a new global multiple alignment program capable of aligning a large number of genomic regions. Our progressive alignment approach incorporates the following ideas: maximum-likelihood inference of ancestral sequences, automatic…
Multiple sequence alignment is a key process in today's biology, and finding a relevant alignment of several sequences is much more challenging than just optimizing some improbable evaluation functions. Our approach for addressing multiple…
Predicting and understanding human motion dynamics has many applications, such as motion synthesis, augmented reality, security, and autonomous vehicles. Due to the recent success of generative adversarial networks (GAN), there has been…
Two of the most popular modelling paradigms in computer vision are feed-forward neural networks (FFNs) and probabilistic graphical models (GMs). Various connections between the two have been studied in recent works, such as e.g. expressing…
In this paper, we proposed a novel Probabilistic Attribute Tree-CNN (PAT-CNN) to explicitly deal with the large intra-class variations caused by identity-related attributes, e.g., age, race, and gender. Specifically, a novel PAT module with…
Stochastic reaction networks are mathematical models with a wide range of applications in biochemistry, ecology, and epidemiology, and are often complex to analyze. Except for some special cases, it is generally difficult to predict how the…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
This work proposes a multi-image matching method to estimate semantic correspondences across multiple images. In contrast to the previous methods that optimize all pairwise correspondences, the proposed method identifies and matches only a…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
Dominant sentence ordering models can be classified into pairwise ordering models and set-to-sequence models. However, there is little attempt to combine these two types of models, which inituitively possess complementary advantages. In…
We proposed a probabilistic algorithm to solve the Multiple Sequence Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits the representation of the Multiple Alignment between $D$ sequences as a directed polymer in…
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…
We propose a novel approach to image classification inspired by complex nonlinear biological visual processing, whereby classical convolutional neural networks (CNNs) are equipped with learnable higher-order convolutions. Our model…
Multiple Sequence Alignment (MSA) is one of the most computationally intensive tasks in Computational Biology. Existing best known solutions for multiple sequence alignment take several hours (in some cases days) of computation time to…
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…
A hybrid evolutionary algorithm with importance sampling method is proposed for multi-dimensional optimization problems in this paper. In order to make use of the information provided in the search process, a set of visited solutions is…
Frameshift translation is an important phenomenon that contributes to the appearance of novel Coding DNA Sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of genes coding regions. Frameshift…
We consider the problem of aligning a pair of databases with jointly Gaussian features. We consider two algorithms, complete database alignment via MAP estimation among all possible database alignments, and partial alignment via a…
Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. A standard approach to speed up this task is to compute "sketches" of the DNA reads (typically via…