Related papers: Multiple sequence alignment based on set covers
We present an adaptation of RNN sequence models to the problem of multi-label classification for text, where the target is a set of labels, not a sequence. Previous such RNN models define probabilities for sequences but not for sets;…
The automatic assignment of species information to the corresponding genes in a research article is a critically important step in the gene normalization task, whereby a gene mention is normalized and linked to a database record or…
Multiple sequence alignment (MSA) is a ubiquitous problem in computational biology. Although it is NP-hard to find an optimal solution for an arbitrary number of sequences, due to the importance of this problem researchers are trying to…
We present a general setting for structure-sequence comparison in a large class of RNA structures that unifies and generalizes a number of recent works on specific families on structures. Our approach is based on tree decomposition of…
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…
To mimic human vision with the way of recognizing the diverse and open world, foundation vision models are much critical. While recent techniques of self-supervised learning show the promising potentiality of this mission, we argue that…
Humans process visual scenes selectively and sequentially using attention. Central to models of human visual attention is the saliency map. We propose a hierarchical visual architecture that operates on a saliency map and uses a novel…
In this paper, we deal with the task of building a dynamic ensemble of chain classifiers for multi-label classification. To do so, we proposed two concepts of classifier chains algorithms that are able to change label order of the chain…
We propose a metric for the space of multiple sequence alignments that can be used to compare two alignments to each other. In the case where one of the alignments is a reference alignment, the resulting accuracy measure improves upon…
We define a mapping from transition-based parsing algorithms that read sentences from left to right to sequence labeling encodings of syntactic trees. This not only establishes a theoretical relation between transition-based parsing and…
An important component of any generation system is the mapping dictionary, a lexicon of elementary semantic expressions and corresponding natural language realizations. Typically, labor-intensive knowledge-based methods are used to…
Sentence ordering aims at arranging a list of sentences in the correct order. Based on the observation that sentence order at different distances may rely on different types of information, we devise a new approach based on multi-granular…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…
The identification of syllables within phonetic sequences is known as syllabification. This task is thought to play an important role in natural language understanding, speech production, and the development of speech recognition systems.…
Multi-label text classification involves extracting all relevant labels from a sentence. Given the unordered nature of these labels, we propose approaching the problem as a set prediction task. To address the correlation between labels, we…
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…
When reasoning about formal objects whose structures involve binding, it is often necessary to analyze expressions relative to a context that associates types, values, and other related attributes with variables that appear free in the…
Sequence alignment supports numerous tasks in bioinformatics, natural language processing, pattern recognition, social sciences, and others fields. While the alignment of two sequences may be performed swiftly in many applications, the…
Real world deployments of word alignment are almost certain to cover both high and low resource languages. However, the state-of-the-art for this task recommends a different model class depending on the availability of gold alignment…