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Integration of multiple sensor modalities and deep learning into Simultaneous Localization And Mapping (SLAM) systems are areas of significant interest in current research. Multi-modality is a stepping stone towards achieving robustness in…
As computing systems become increasingly advanced and as users increasingly engage themselves in technology, security has never been a greater concern. In malware detection, static analysis, the method of analyzing potentially malicious…
Motivation: The visualization and analysis of high-dimensional data are essential in biomedical research. There is a need for secure, scalable, and reproducible tools to facilitate data exploration and interpretation. Results: We introduce…
Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data becomes more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and…
The remarkable success of foundation models has sparked growing interest in their application to single-cell biology. Models like Geneformer and scGPT promise to serve as versatile tools in this specialized field. However, representing a…
DNA has been considered a promising medium for storing digital information. As an essential step in the DNA-based data storage workflow, coding algorithms are responsible to implement functions including bit-to-base transcoding, error…
Motivation: Second generation sequencing technology makes it feasible for many researches to obtain enough sequence reads to attempt the de novo assembly of higher eukaryotes (including mammals). De novo assembly not only provides a tool…
Single-cell RNA-seq (scRNA-seq) enables atlas-scale profiling of complex tissues, revealing rare lineages and transient states. Yet, assigning biologically valid cell identities remains a bottleneck because markers are tissue- and…
The proliferation of new types of drugs necessitates the urgent development of faster and more accurate detection methods. Traditional detection methods have high requirements for instruments and environments, making the operation complex.…
Deep generative models have gained significant advancements to accelerate drug discovery by generating bioactive chemicals against desired targets. Nevertheless, most generated compounds that have been validated for potent bioactivity often…
There is extensive literature on perceiving road structures by fusing various sensor inputs such as lidar point clouds and camera images using deep neural nets. Leveraging the latest advance of neural architects (such as transformers) and…
Genome analysis fundamentally starts with a process known as read mapping, where sequenced fragments of an organism's genome are compared against a reference genome. Read mapping is currently a major bottleneck in the entire genome analysis…
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
Breeding by introgressive hybridization is a pivotal strategy to broaden the genetic basis of crops. Usually, the desired traits are monitored in consecutive crossing generations by marker-assisted selection, but their analyses fail in…
Users often have to integrate information about entities from multiple data sources. This task is challenging as each data source may represent information about the same entity in a distinct form, e.g., each data source may use a different…
Genome sequence analysis is a powerful tool in medical and scientific research. Considering the inevitable sequencing errors and genetic variations, approximate string matching (ASM) has been adopted in practice for genome sequencing.…
PhyloFrame is a Python library for phylogenetic computation targeting the gap between specialist, compiler-optimized operations and flexible, script-based workflows -- with emphasis on fast, memory-efficient operations for very large tree…
Hiring processes often involve the manual screening of hundreds of resumes for each job, a task that is time and effort consuming, error-prone, and subject to human bias. This paper presents Smart-Hiring, an end-to-end Natural Language…
The advent of high-throughput sequencing technologies constituted a major advance in genomic studies, offering new prospects in a wide range of applications. We propose a rigorous and flexible algorithmic solution to mapping SOLiD…