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DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…
To search an optimal sub-network within a general deep neural network (DNN), existing neural architecture search (NAS) methods typically rely on handcrafting a search space beforehand. Such requirements make it challenging to extend them…
Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However,…
RNA co-transcriptionality is the process where RNA sequences are spliced while being transcribed from DNA templates. This process holds potential as a key tool for molecular programming. Co-transcriptional folding has been shown to be…
Three dimensional (3D) structures composed of planar surfaces can be build out of accessible materials using easier fabrication technique with shorter fabrication time. To better design 3D structures with planar surfaces, realistic models…
A simple DNA-based data storage scheme is demonstrated in which information is written using "addressing" oligonucleotides. In contrast to other methods that allow arbitrary code to be stored, the resulting DNA is suitable for downstream…
Single-cell RNA-seq (scRNA-seq) technology is a powerful tool for unraveling the complexity of biological systems. One of essential and fundamental tasks in scRNA-seq data analysis is Cell Type Annotation (CTA). In spite of tremendous…
While accurate protein structure predictions are now available for nearly every observed protein sequence, predicted structures lack much of the functional context offered by experimental structure determination. We address this gap with…
The main obstacles for the practical deployment of DNA-based data storage platforms are the prohibitively high cost of synthetic DNA and the large number of errors introduced during synthesis. In particular, synthetic DNA products contain…
Oracle bone script is the earliest-known Chinese writing system of the Shang dynasty and is precious to archeology and philology. However, real-world scanned oracle data are rare and few experts are available for annotation which make the…
Engineering system design -- whether mechatronic, control, or embedded -- often proceeds in an ad hoc manner, with requirements left implicit and traceability from intent to parameters largely absent. Existing specification-driven and…
Recent advances in algorithm-hardware co-design for deep neural networks (DNNs) have demonstrated their potential in automatically designing neural architectures and hardware designs. Nevertheless, it is still a challenging optimization…
Non-sharable sensitive data collection and analysis in large-scale consortia for genomic research is complicated. Time consuming issues in installing software arise due to different operating systems, software dependencies and running the…
We introduce an extended version of oxDNA, a coarse-grained model of DNA designed to capture the thermodynamic, structural and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves, and by…
Crafting computer-aided design (CAD) models has long been a painstaking and time-intensive task, demanding both precision and expertise from designers. With the emergence of 3D generation, this task has undergone a transformative impact,…
Previous works on font generation mainly focus on the standard print fonts where character's shape is stable and strokes are clearly separated. There is rare research on brush handwriting font generation, which involves holistic structure…
RNA plays a pivotal role in diverse biological processes, ranging from gene regulation to catalysis. Recent advances in RNA design, such as RfamGen, Ribodiffusion and RDesign, have demonstrated promising results, with successful designs of…
DNA synthesis is considered as one of the most expensive components in current DNA storage systems. In this paper, focusing on a common synthesis machine, which generates multiple DNA strands in parallel following a fixed supersequence,we…
Cognitive diagnosis plays a vital role in modern intelligent education platforms to reveal students' proficiency in knowledge concepts for subsequent adaptive tasks. However, due to the requirement of high model interpretability, existing…
Pioneering data profiling systems such as Metanome and OpenClean brought public attention to science-intensive data profiling. This type of profiling aims to extract complex patterns (primitives) such as functional dependencies, data…