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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…
The emergence of foundational models and generative artificial intelligence (GenAI) is poised to transform productivity in scientific computing, especially in code development, refactoring, and translating from one programming language to…
The recent progress of artificial intelligence(AI) has shown great potentials for alleviating human burden in various complex tasks. From the view of software engineering, AI techniques can be seen in many fundamental aspects of…
Driven by the recent advances in deep learning methods and, in particular, by the development of modern self-supervised learning algorithms, increased interest and efforts have been devoted to build foundation models (FMs) for medical…
DeepLog is an operational neurosymbolic framework that unifies logic and deep learning within standard PyTorch workflows. While existing neurosymbolic systems focus on a particular paradigm and semantics, DeepLog serves as a universal…
Programmers often reuse code from source code repositories to reduce the development effort. Code clones are candidates for reuse in exploratory or rapid development, as they represent often repeated functionality in software systems. To…
Magnetic resonance imaging (MRI) is a powerful and versatile imaging technique, offering a wide spectrum of information about the anatomy by employing different acquisition modalities. However, in the clinical workflow, it is impractical to…
Object-Oriented Programming (OOP) has become a crucial paradigm for managing the growing complexity of modern software systems, particularly in fields like machine learning, deep learning, large language models (LLM), and data analytics.…
Despite advancements in robotic-assisted surgery, automating complex tasks like suturing remain challenging due to the need for adaptability and precision. Learning-based approaches, particularly reinforcement learning (RL) and imitation…
Magnetic Resonance Imaging (MRI) is a non-invasive diagnostic and radiotherapy (RT) planning tool, offering detailed insights into the anatomy of the human body. The extensive scan time is stressful for patients, who must remain motionless…
Software optimization refines programs for resource efficiency while preserving functionality. Traditionally, it is a process done by developers and compilers. This paper introduces a third option, automated optimization at the source code…
The number and complexity of artificial intelligence (AI) applications is growing relentlessly. As a result, even with the many algorithmic and mathematical advances experienced over past decades as well as the impressive energy efficiency…
As large language models (LLMs) like OpenAI's GPT series continue to make strides, we witness the emergence of artificial intelligence applications in an ever-expanding range of fields. In medicine, these LLMs hold considerable promise for…
Recent advances in language and vision have demonstrated that scaling up model capacity consistently improves performance across diverse tasks. In 3D visual geometry reconstruction, large-scale training has likewise proven effective for…
We present the Open MatSci ML Toolkit: a flexible, self-contained, and scalable Python-based framework to apply deep learning models and methods on scientific data with a specific focus on materials science and the OpenCatalyst Dataset. Our…
This dissertation is devoted to provide advanced nonconvex nonsmooth variational models of (Magnetic Resonance Image) MRI reconstruction, efficient learnable image reconstruction algorithms and parameter training algorithms that improve the…
Large Language Models (LLMs) excel in code generation yet struggle with modern AI software engineering tasks. Unlike traditional function-level or file-level coding tasks, AI software engineering requires not only basic coding proficiency…
Deep learning-based Magnetic Resonance (MR) reconstruction methods have focused on generating high-quality images but often overlook the impact on downstream tasks (e.g., segmentation) that utilize the reconstructed images. Cascading…
This retrospective-prospective study evaluated whether a deep learning-based MRI reconstruction algorithm can preserve diagnostic quality in brain MRI scans accelerated up to fourfold, using both public and prospective clinical data. The…
MRI-based medical imaging has become indispensable in modern clinical diagnosis, particularly for brain tumor detection. However, the rapid growth in data volume poses challenges for conventional diagnostic approaches. Although deep…