Related papers: A universal framework to efficiently share materia…
Obtaining a relevant dataset is central to conducting empirical studies in software engineering. However, in the context of mining software repositories, the lack of appropriate tooling for large scale mining tasks hinders the creation of…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
We provide an overview of current approaches to DNA-based storage system design and accompanying synthesis, sequencing and editing methods. We also introduce and analyze a suite of new constrained coding schemes for both archival and random…
Because of DNA appealing features as perfect material, including minuscule size, defined structural repeat and rigidity, programmable DNA-mediated processing is a promising computing paradigm, which employs DNAs as information storing and…
Reference-guided DNA sequencing and alignment is an important process in computational molecular biology. The amount of DNA data grows very fast, and many new genomes are waiting to be sequenced while millions of private genomes need to be…
Model documentation plays a crucial role in promoting transparency and responsible development of AI systems. With the rise of Generative AI (GenAI), open-source platforms have increasingly become hubs for hosting and distributing these…
The design of novel protein sequences with targeted functionalities underpins a central theme in protein engineering, impacting diverse fields such as drug discovery and enzymatic engineering. However, navigating this vast combinatorial…
In this paper, we motivate the need for a publicly available, generic software framework for question-answering (QA) systems. We present an open-source QA framework QANUS which researchers can leverage on to build new QA systems easily and…
With the rapid development of classical and quantum machine learning, a large number of machine learning frameworks have been proposed. However, existing machine learning frameworks usually only focus on classical or quantum, rather than…
DNA sequence analysis is fundamental to life science research. The rapid development of next generation sequencing (NGS) technologies, and the richness and diversity of applications it makes feasible, have created an enormous gulf between…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…
Data sharing efforts increasingly contribute to the acceleration of scientific discovery. Neuroimaging data is accumulating in distributed domain-specific databases and there is currently no integrated access mechanism nor an accepted…
Recent advances in DNA sequencing open prospects to make whole-genome analysis rapid and reliable, which is promising for various applications including personalized medicine. However, existing techniques for {\it de novo} genome assembly,…
Generative AI and large language models (LLMs) have shown strong capabilities in code understanding, but their use in cybersecurity, particularly for malware detection and analysis, remains limited. Existing detection systems often fail to…
Generative modeling has become a central paradigm in protein research, extending machine learning beyond structure prediction toward sequence design, backbone generation, inverse folding, and biomolecular interaction modeling. However, the…
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…
Nanopore sequencing technologies continue to advance rapidly, offering critical benefits such as real-time analysis, the ability to sequence extremely long DNA fragments (up to millions of bases in a single read), and the option to…
Diagrams are crucial for communicating complex information, yet creating and modifying them remains a labor-intensive task. We present GenAI-DrawIO-Creator, a novel framework that leverages Large Language Models (LLMs) to automate diagram…
Genomic data has become increasingly accessible to the general public with the advent of companies offering whole genome sequencing at a relatively low cost. However, their reports are not verifiable due to a lack of crucial details and…
The design of quantum circuits is often still done manually, for instance by following certain patterns or rule of thumb. While this approach may work well for some problems, it can be a tedious task and present quite the challenge in other…