Related papers: Low-density locality-sensitive hashing boosts meta…
Metagenomics characterizes microbial communities by random shotgun sequencing of DNA isolated directly from an environment of interest. An essential step in computational metagenome analysis is taxonomic sequence assignment, which allows us…
Ordinal classification has been widely applied in many high-stakes applications, e.g., medical imaging and diagnosis, where reliable uncertainty quantification (UQ) is essential for decision making. Conformal prediction (CP) is a general UQ…
We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with…
The search of binary sequences with low auto-correlations (LABS) is a discrete combinatorial optimization problem contained in the NP-hard computational complexity class. We study this problem using Warning Propagation (WP) , a message…
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional methods of characterization. Environmental shotgun sequencing…
Gene sequence search is a fundamental operation in computational genomics. Due to the petabyte scale of genome archives, most gene search systems now use hashing-based data structures such as Bloom Filters (BF). The state-of-the-art systems…
Minwise hashing is a fundamental and one of the most successful hashing algorithm in the literature. Recent advances based on the idea of densification~\cite{Proc:OneHashLSH_ICML14,Proc:Shrivastava_UAI14} have shown that it is possible to…
Once a gravitational wave signal is detected, the measurement of its source parameters is important to achieve various scientific goals. This is done through Bayesian inference, where the analysis cost increases with the model complexity…
Orthogonal time frequency space (OTFS) modulation has emerged as a robust solution for high-mobility wireless communications. However, conventional detection algorithms, such as linear equalizers and message passing (MP) methods, either…
Generative semantic hashing is a promising technique for large-scale information retrieval thanks to its fast retrieval speed and small memory footprint. For the tractability of training, existing generative-hashing methods mostly assume a…
Background: In the metagenome assembly of a microbiome community, we may think abundant species would be easier to assemble due to their deeper coverage. However, this conjucture is rarely tested. We often do not know how many abundant…
The detection of genomic structural variation (SV) has advanced tremendously in recent years due to progress in high-throughput sequencing technologies. Novel sequence insertions, insertions without similarity to a human reference genome,…
In this study, we evaluated four binarization methods. Locality-Sensitive Hashing (LSH), Iterative Quantization (ITQ), Kernel-based Supervised Hashing (KSH), and Supervised Discrete Hashing (SDH) on the ODIR dataset using deep feature…
DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
The progression of lung cancer implies the intrinsic ordinal relationship of lung nodules at different stages-from benign to unsure then to malignant. This problem can be solved by ordinal regression methods, which is between classification…
A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of set of species…
Minimizing data storage poses a significant challenge in large-scale metagenomic projects. In this paper, we present a new method for improving the encoding of FASTQ files generated by metagenomic sequencing. This method incorporates…
This paper presents a new class of sparse superposition codes for low-rates and short-packet communications over the additive white Gaussian noise channel. The new code is orthogonal sparse superposition (OSS) code. A codeword of OSS codes…
Hashing has attracted increasing research attentions in recent years due to its high efficiency of computation and storage in image retrieval. Recent works have demonstrated the superiority of simultaneous feature representations and hash…
The detection rate for compact binary mergers has grown as the sensitivity of the global network of ground based gravitational wave detectors has improved, now reaching the stage where robust automation of the analyses is essential.…