Related papers: Efficient seeding techniques for protein similarit…
We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem…
We study the problem of efficiently clustering protein sequences in a limited information setting. We assume that we do not know the distances between the sequences in advance, and must query them during the execution of the algorithm. Our…
Protein structure similarity search (PSSS), which tries to search proteins with similar structures, plays a crucial role across diverse domains from drug design to protein function prediction and molecular evolution. Traditional…
Spaced seeds are important tools for similarity search in bioinformatics, and using several seeds together often significantly improves their performance. With existing approaches, however, for each seed we keep a separate linear-size data…
Working with exhaustive search on large dataset is infeasible for several reasons. Recently, developed techniques that made pattern set mining feasible by a general solver with long execution time that supports heuristic search and are…
Weakly-supervised text classification aims to induce text classifiers from only a few user-provided seed words. The vast majority of previous work assumes high-quality seed words are given. However, the expert-annotated seed words are…
Spider silks are remarkable materials characterized by superb mechanical properties such as strength, extensibility and lightweightedness. Yet, to date, limited models are available to fully explore sequence-property relationships for…
Generative deep learning techniques have demonstrated an impressive capacity for tackling biomolecular design problems in recent years. Despite their high performance, however, they still suffer from a lack of interpretability and rigorous…
Vector data is prevalent across business and scientific applications, and its popularity is growing with the proliferation of learned embeddings. Vector data collections often reach billions of vectors with thousands of dimensions, thus,…
Understanding the dietary preferences of ancient societies and their evolution across periods and regions is crucial for revealing human-environment interactions. Seeds, as important archaeological artifacts, represent a fundamental subject…
The notion of the cover is a generalization of a period of a string, and there are linear time algorithms for finding the shortest cover. The seed is a more complicated generalization of periodicity, it is a cover of a superstring of a…
Deep learning has been widely used for protein engineering. However, it is limited by the lack of sufficient experimental data to train an accurate model for predicting the functional fitness of high-order mutants. Here, we develop SESNet,…
Fuzzing is an automated application vulnerability detection method. For genetic algorithm-based fuzzing, it can mutate the seed files provided by users to obtain a number of inputs, which are then used to test the objective application in…
This report presents the implementation of a protein sequence comparison algorithm specifically designed for speeding up time consuming part on parallel hardware such as SSE instructions, multicore architectures or graphic boards. Three…
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…
The protein design problem involves finding polypeptide sequences folding into a given threedimensional structure. Its rigorous algorithmic solution is computationally demanding, involving a nested search in sequence and structure spaces.…
Spaced seeds have been recently shown to not only detect more alignments, but also to give a more accurate measure of phylogenetic distances (Boden et al., 2013, Horwege et al., 2014, Leimeister et al., 2014), and to provide a lower…
Plant breeding programs use data obtained from multi-environment selection experiments to produce improved varieties with the ultimate aim of maintaining high levels of genetic gain. Selection accuracy can be improved with the use of…
Protein retrieval, which targets the deconstruction of the relationship between sequences, structures and functions, empowers the advancing of biology. Basic Local Alignment Search Tool (BLAST), a sequence-similarity-based algorithm, has…
We consider a similarity measure between two sets $A$ and $B$ of vectors, that balances the average and maximum cosine distance between pairs of vectors, one from set $A$ and one from set $B$. As a motivation for this measure, we present…