Related papers: Data Management for High-Throughput Genomics
Existing differentially private (DP) synthetic data generation mechanisms typically assume a single-source table. In practice, data is often distributed across multiple tables with relationships across tables. In this paper, we introduce…
DNA-based storage is an emerging technology that enables digital information to be archived in DNA molecules. This method enjoys major advantages over magnetic and optical storage solutions such as exceptional information density, enhanced…
Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments…
With the boom in modern software development, open-source software has become an integral part of various industries, driving progress in computer science. However, the immense complexity and diversity of the open-source ecosystem also pose…
Over the last 20 years, there has been an explosion of genomic data collected for disease association, functional analyses, and other large-scale discoveries. At the same time, there have been revolutions in cloud computing that enable…
When simulating metabolite productions with genome-scale constraint-based metabolic models, gene deletion strategies are necessary to achieve growth-coupled production, which means cell growth and target metabolite production occur…
To stay competitive in today's data driven economy, enterprises large and small are turning to stream processing platforms to process high volume, high velocity, and diverse streams of data (fast data) as they arrive. Low-level programming…
This paper presents a generic web-based database interface implemented in Prolog. We discuss the advantages of the implementation platform and demonstrate the system's applicability in providing access to integrated biochemical data. Our…
Time is one of the most difficult aspects to handle in real world applications such as database systems. Relational database management systems proposed by Codd offer very little built-in query language support for temporal data management.…
Current approaches to genomic sequence modeling often struggle to align the inductive biases of machine learning models with the evolutionarily-informed structure of biological systems. To this end, we formulate a novel application of…
High throughput sequencing is a technology that allows for the generation of millions of reads of genomic data regarding a study of interest, and data from high throughput sequencing platforms are usually count compositions. Subsequent…
This paper explores methodologies, advantages and challenges related to the use of the Information Centric Network technology for developing NoSQL distributed databases, which are expected to play a central role in the forthcoming IoT and…
Nuanced cancer patient care is needed, as the development and clinical course of cancer is multifactorial with influences from the general health status of the patient, germline and neoplastic mutations, co-morbidities, and environment. To…
We present GobyWeb, a web-based system to facilitate the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension…
Recent advances of information technology in biomedical sciences and other applied areas have created numerous large diverse data sets with a high dimensional feature space, which provide us a tremendous amount of information and new…
In the rapidly evolving AI era with large language models (LLMs) at the core, making LLMs more trustworthy and efficient, especially in output generation (inference), has gained significant attention. This is to reduce plausible but faulty…
Deploying Large Language Models (LLMs) on resource-constrained devices remains challenging due to limited memory, lack of GPUs, and the complexity of existing runtimes. In this paper, we introduce TranSQL+, a template-based code generator…
Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…
Big Data, Cloud computing, Cloud Database Management techniques, Data Science and many more are the fantasizing words which are the future of IT industry. For all the new techniques one common thing is that they deal with Data, not just…
Modern database clusters entail two levels of networks: connecting CPUs and NUMA regions inside a single server in the small and multiple servers in the large. The huge performance gap between these two types of networks used to slow down…