Related papers: Using Sequence Ensembles for Seeding Alignments of…

We propose a nested recurrent neural network (nested RNN) model for English spelling error correction and generate pseudo data based on phonetic similarity to train it. The model fuses orthographic information and context as a whole and is…

DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology…

Integrated silicon photonic devices, which manipulate light to transmit and process information on a silicon-on-insulator chip, are highly sensitive to structural variations. Minor deviations during nanofabrication-the precise process of…

Summary: We present several recent improvements to minimap2, a versatile pairwise aligner for nucleotide sequences. Now minimap2 v2.22 can more accurately map long reads to highly repetitive regions and align through insertions or deletions…

In the wake of the explosive growth in smartphones and cyberphysical systems, there has been an accelerating shift in how data is generated away from centralised data towards on-device generated data. In response, machine learning…

Biological screens are plagued by false positive hits resulting from aggregation. Thus, methods to triage small colloidally aggregating molecules (SCAMs) are in high demand. Herein, we disclose a bespoke machine-learning tool to confidently…

There are two major approaches for sequence labeling. One is the probabilistic gradient-based methods such as conditional random fields (CRF) and neural networks (e.g., RNN), which have high accuracy but drawbacks: slow training, and no…

Recently, significant improvements have been achieved in various natural language processing tasks using neural sequence-to-sequence models. While aiming for the best generation quality is important, ultimately it is also necessary to…

A seed in a word is a relaxed version of a period in which the occurrences of the repeating subword may overlap. We show a linear-time algorithm computing a linear-size representation of all the seeds of a word (the number of seeds might be…

Nanopore sequencing enables real-time long-read DNA sequencing with reads exceeding 10 kilobases, but inherent error rates of 12-15 percent present significant computational challenges for read alignment. The critical seed chaining step…

Motivation: Next-generation sequencing tools have enabled producing of huge amount of genomic information at low cost. Unfortunately, presence of sequencing errors in such data affects quality of downstream analyzes. Accuracy of them can be…

Federated learning enables collaborative model training across numerous edge devices without requiring participants to share data; however, memory and communication constraints on these edge devices may preclude their participation in…

Wideband communication is often expected to deal with a very wide spectrum, which in many environments of interest includes strong interferers. Thus receivers for the wideband communication systems often need to mitigate interferers to…

Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is…

In this paper, we propose an ensemble learning algorithm called \textit{under-bagging $k$-nearest neighbors} (\textit{under-bagging $k$-NN}) for imbalanced classification problems. On the theoretical side, by developing a new learning…

We study codes that can correct backtracking errors during nanopore sequencing. In this channel, a sequence of length $n$ over an alphabet of size $q$ is being read by a sliding window of length $\ell$, where from each window we obtain only…

Most existing set encoding algorithms operate under the implicit assumption that all the set elements are accessible, and that there are ample computational and memory resources to load the set into memory during training and inference.…

Achieving faster execution with shorter compilation time can foster further diversity and innovation in neural networks. However, the current paradigm of executing neural networks either relies on hand-optimized libraries, traditional…

Nanopore genome sequencing is the key to enabling personalized medicine, global food security, and virus surveillance. The state-of-the-art base-callers adopt deep neural networks (DNNs) to translate electrical signals generated by nanopore…

Training neural networks (NNs) using combinatorial optimization solvers has gained attention in recent years. In low-data settings, state-of-the-art mixed integer linear programming solvers can train exactly a NN, avoiding intensive…