21 papers · ranked by Valyu relevance
David S White, Marcel P Goldschen-Ohm, Randall H Goldsmith, Baron Chanda + 2 more
'Baron Chanda' 'Olga Boudker' 'Leon D Islas'] Single-molecule approaches provide enormous insight into the dynamics of biomolecules, but adequately sampling distributions of states and events often requires extensive sampling. Although emerging experimental techniques can generate such large datasets, existing analysis…
Alireza Mohammadidoost, Matin Hashemi
—This paper describes a parallel implementation of Viterbi decoding algorithm. Viterbi decoder is widely used in many state-of-the-art wireless systems. The proposed solution optimizes both throughput and memory usage by applying optimizations such as unified kernel implementation and parallel traceback. Experimental…
Alireza Mohammadidoost, Matin Hashemi
—Many research works have been performed on implementation of Vitrerbi decoding algorithm on GPU instead of FPGA because this platform provides considerable flexibility in addition to great performance. Recently, the recently-introduced Tensor cores in modern GPU architectures provide incredible computing capability.…
T. Kalavathi Devi, Sakthivel Palaniappan
Convolutional codes are comprehensively used as Forward Error Correction (FEC) codes in digital communication systems. For decoding of convolutional codes at the receiver end, Viterbi decoder is often used to have high priority. This decoder meets the demand of high speed and low power. At present, the design of a…
Alexander Churbanov, Stephen Winters-Hilt
Background The Baum-Welch learning procedure for Hidden Markov Models (HMMs) provides a powerful tool for tailoring HMM topologies to data for use in knowledge discovery and clustering. A linear memory procedure recently proposed by Miklós, I. and Meyer, I.M. describes a memory sparse version of the Baum-Welch…
Tin Y Lam, Irmtraud M Meyer
Background Hidden Markov models are widely employed by numerous bioinformatics programs used today. Applications range widely from comparative gene prediction to time-series analyses of micro-array data. The parameters of the underlying models need to be adjusted for specific data sets, for example the genome of a…
H. Mertens, Marc Van Droogenbroeck
The Viterbi algorithm, presented in 1967, allows a maximum likelihood decoding of partial response codes. This study focuses on the duobinary code which is the first member of this family and has been specified for the digital part of television systems recommended by International Organizations. Up to now the…
Waqar Ahmad, Imran Hafeez Abbassi, Usman Sanwal, Hasan Mahmood
—In recent years, the decoding algorithms in communication networks are becoming increasingly complex aiming to achieve high reliability in correctly decoding received messages. These decoding algorithms involve computationally complex operations requiring high performance computing hardware, which are generally…
Leah Spontaneo, Nick Cercone
Background CpG islands are important regions in DNA. They usually appear at the 5’ end of genes containing GC-rich dinucleotides. When DNA methylation occurs, gene regulation is affected and it sometimes leads to carcinogenesis. We propose a new detection program using a hidden-markov model alongside the Viterbi…
Martin Steinegger, Markus Meier, Milot Mirdita, Harald Vöhringer + 2 more
HH-suite is a widely used open source software suite for sensitive sequence similarity searches and protein fold recognition. It is based on pairwise alignment of profile Hidden Markov models (HMMs), which represent multiple sequence alignments of homologous sequences. We developed a single-instruction multiple-data…
Piero Fariselli, Pier Luigi Martelli, Rita Casadio
Background Structure prediction of membrane proteins is still a challenging computational problem. Hidden Markov models (HMM) have been successfully applied to the problem of predicting membrane protein topology. In a predictive task, the HMM is endowed with a decoding algorithm in order to assign the most probable…
Hassan Kilavo, Michael Kisangiri, Salehe I. Mrutu
Viterbi Algorithm Decoder Enhanced with Non-transmittable Codewords is one of the best decoding algorithm which effectively improves forward error correction performance. HoweverViterbi decoder enhanced with NTCs is not yet designed to work in storage media devices. Currently Reed Solomon (RS) Algorithm is almost the…
Tim Anderson, Travis J. Wheeler
Sequence alignment lies at the heart of genome sequence annotation. While the BLAST suite of alignment tools has long held an important role in alignment-based sequence database search, greater sensitivity is achieved through the use of profile hidden Markov models (pHMMs). The Forward algorithm that provides much of…
Minhyuk Park, Tandy Warnow
Despite advances in method development for multiple sequence alignment over the last several decades, the alignment of datasets exhibiting substantial sequence length heterogeneity, especially when the input sequences include very short sequences (either as a result of sequencing technologies or of large deletions…
Tianyu Song, Pooi‐Yuen Kam
Since atmospheric turbulence and pointing errors cause fluctuations in the intensity of the received signal, the photoncounting free space optical (FSO) system with intensity modulation requires the channel state information(CSI), i.e., the instantaneous value of the channel gain h, to adjust the detection threshold.…
Kentaro Tomii, Shravan Kumar, Degui Zhi, Steven E. Brenner
Insertion and deletion sequencing errors are relatively common in next-generation sequencing data and produce long stretches of mistranslated sequence. These frameshifting errors can cause very serious damages to downstream data analysis of reads. However, it is possible to obtain more precise alignment of DNA…
Jorge Ortín, Paloma García, F. Gutierrez, Antonio Valdovinos
—The A algorithm is a graph search algorithm which has shown good results in terms of computational complexity for Maximum Likelihood (ML) decoding of tailbiting convolutional codes. The decoding of tailbiting codes with this algorithm is performed in two phases. In the first phase, a typical Viterbi decoding is…
Jorge Ortín, Paloma García, F. Gutierrez, Antonio Valdovinos
—In this work we propose a novel decoding algorithm for tailbiting convolutional codes and evaluate its performance over different channels. The proposed method consists on a fixed two-step Viterbi decoding of the received data. In the first step, an estimation of the most likely state is performed based on a SOVA…
Gerton Lunter
The Li and Stephens model, which approximates the coalescent describing the pattern of variation in a population, underpins a range of key tools and results in genetics. Although highly efficient compared to the coalescent, standard implemen-tations of this model still cannot deal with the very large reference cohorts…
Zhihao Lan, WanZhen Liang
The variational quantum eigensolver (VQE) algorithm can simulate the chemical systems such as molecules in the noisy intermediate-scale quantum devices and shows promising applications in quantum chemistry simulations. The accuracy and computational cost of the VQE simulations are determined by the underlying Ansätze.…
Benson Chen, Xiang Fu, Tommi Jaakkola, Regina Barzilay
Searching for novel molecular compounds with desired properties is an important problem in drug discovery. Many existing frameworks generate molecules one atom at a time. We instead propose a flexible editing paradigm that generates molecules using learned molecular fragments---meaningful substructures of molecules. To…