Related papers: Fast and Exact Sequence Alignment with the Smith-W…
We study the problem of local alignment, which is finding pairs of similar subsequences with gaps. The problem exists in biosequence databases. BLAST is a typical software for finding local alignment based on heuristic, but could miss…
Summary: The Smith Waterman (SW) algorithm, which produces the optimal pairwise alignment between two sequences, is frequently used as a key component of fast heuristic read mapping and variation detection tools, but current implementations…
We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer errors) and 10-100x faster than state-of-the-art tools such as BWA. Unlike recent…
We present SentAlign, an accurate sentence alignment tool designed to handle very large parallel document pairs. Given user-defined parameters, the alignment algorithm evaluates all possible alignment paths in fairly large documents of…
In this paper, we present the RISE-SLAM algorithm for performing visual-inertial simultaneous localization and mapping (SLAM), while improving estimation consistency. Specifically, in order to achieve real-time operation, existing…
This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
The maximal sensitivity of the Smith-Waterman (SW) algorithm has enabled its wide use in biological sequence database search. Unfortunately, the high sensitivity comes at the expense of quadratic time complexity, which makes the algorithm…
Permutation symmetries of deep networks make basic operations like model merging and similarity estimation challenging. In many cases, aligning the weights of the networks, i.e., finding optimal permutations between their weights, is…
The well-known Smith-Waterman (SW) algorithm is the most commonly used method for local sequence alignments. However, SW is very computationally demanding for large protein databases. There exist several implementations that take advantage…
Recent empirical evidence suggests that the Weston-Watkins support vector machine is among the best performing multiclass extensions of the binary SVM. Current state-of-the-art solvers repeatedly solve a particular subproblem approximately…
Sequence-to-sequence models with soft attention had significant success in machine translation, speech recognition, and question answering. Though capable and easy to use, they require that the entirety of the input sequence is available at…
We introduce string2string, an open-source library that offers a comprehensive suite of efficient algorithms for a broad range of string-to-string problems. It includes traditional algorithmic solutions as well as recent advanced neural…
We consider the Maximum-weight Matching (MWM) problem in the streaming sliding window model of computation. In this model, the input consists of a sequence of weighted edges on a given vertex set $V$ of size $n$. The objective is to…
Nonparametric correlations such as Spearman's rank correlation and Kendall's tau correlation are widely applied in scientific and engineering fields. This paper investigates the problem of computing nonparametric correlations on the fly for…
A novel processing-in-storage (PRinS) architecture based on Resistive CAM (ReCAM) is described and proposed for Smith-Waterman (S-W) sequence alignment. The ReCAM massively-parallel compare operation finds matching base-pairs in a fixed…
This paper presents an algorithm for the efficient approximation of the saddle-extremum persistence diagram of a scalar field. Vidal et al. introduced recently a fast algorithm for such an approximation (by interrupting a progressive…
Many robotics applications require alignment and fusion of observations obtained at multiple views to form a global model of the environment. Multi-way data association methods provide a mechanism to improve alignment accuracy of pairwise…
Online augmentation of an oblique aerial image sequence with structural information is an essential aspect in the process of 3D scene interpretation and analysis. One key aspect in this is the efficient dense image matching and depth…
Neural architecture search (NAS) in expressive search spaces is a computationally hard problem, but it also holds the potential to automatically discover completely novel and performant architectures. To achieve this we need effective…
Summary: Longer sequencing reads, with at least 200 bases per template are now common. While traditional aligners have adopted new strategies to improve the mapping of longer reads, aligners specific to bisulfite-sequencing were optimized…