Related papers: Fast genomic optical map assembly algorithm using …
Binary embedding of high-dimensional data requires long codes to preserve the discriminative power of the input space. Traditional binary coding methods often suffer from very high computation and storage costs in such a scenario. To…
It is becoming increasingly important in the software industry, especially with the growing complexity of software ecosystems and the emphasis on security and compliance for manufacturers to inventory software used on their systems. A…
Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. It also can reliably identify barcodes and assign the reads to the original samples.…
In this paper, we propose a fast decoder algorithm for uniquely decodable (errorless) code sets for overloaded synchronous optical code-division multiple-access (O-CDMA) systems. The proposed decoder is designed in a such a way that the…
Optical endomicroscopy (OEM) is an emerging technology platform with preclinical and clinical imaging applications. Pulmonary OEM via fibre bundles has the potential to provide in vivo, in situ molecular signatures of disease such as…
Deep learning is able to functionally simulate the human brain and thus, it has attracted considerable interest. Optics-assisted deep learning is a promising approach to improve the forward-propagation speed and reduce the power…
Read mapping is a fundamental, yet computationally-expensive step in many genomics applications. It is used to identify potential matches and differences between fragments (called reads) of a sequenced genome and an already known genome…
Optical artificial neural networks (ONNs), analog computing hardware tailored for machine learning, have significant potential for ultra-high computing speed and energy efficiency. We propose a new approach to architectures for ONNs based…
Genome sequence analysis plays a pivotal role in enabling many medical and scientific advancements in personalized medicine, outbreak tracing, and forensics. However, the analysis of genome sequencing data is currently bottlenecked by the…
WebAssembly, or Wasm, is a low-level binary language that enables execution of near-native-performance code in web browsers. Wasm has proven to be useful in applications including gaming, audio and video processing, and cloud computing,…
In this article we discuss the presentation of a random binary matrix using sequence of whole nonnegative numbers. We examine some advantages and disadvantages of this presentation as an alternative of the standard presentation using…
We propose an assembly algorithm {\sc Barnacle} for sequences generated by the clone-based approach. We illustrate our approach by assembling the human genome. Our novel method abandons the original physical-mapping-first framework. As we…
Template matching is widely used for many applications in image and signal processing and usually is time-critical. Traditional methods usually focus on how to reduce the search locations by coarse-to-fine strategy or full search combined…
This paper proposes a generic formulation that significantly expedites the training and deployment of image classification models, particularly under the scenarios of many image categories and high feature dimensions. As a defining…
Optical coherence tomography (OCT) is a powerful and noninvasive method for retinal imaging. In this paper, we introduce a fast segmentation method based on a new variant of spectral graph theory named diffusion maps. The research is…
BosonSampling is a problem where a quantum computer offers a provable speedup over classical computers. Its main feature is that it can be solved with current linear optics technology, without the need for a full quantum computer. In this…
Integrated photonic convolution processors make optical neural networks (ONNs) a transformative solution for artificial intelligence applications such as machine vision. To enhance the parallelism, throughput, and energy efficiency of ONNs,…
SOM is a type of unsupervised learning where the goal is to discover some underlying structure of the data. In this paper, a new extraction method based on the main idea of Concurrent Self-Organizing Maps (CSOM), representing a…
Background Next Generation Sequencing (NGS) has dramatically enhanced our ability to sequence genomes, but not to assemble them. In practice, many published genome sequences remain in the state of a large set of contigs. Each contig…
We introduce a new concept of a subgraph class called a superbubble for analyzing assembly graphs, and propose an efficient algorithm for detecting it. Most assembly algorithms utilize assembly graphs like the de Bruijn graph or the overlap…