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Inspired by biology's most sophisticated computer, the brain, neural networks constitute a profound reformulation of computational principles. Remarkably, analogous high-dimensional, highly-interconnected computational architectures also…
Data storage in DNA is developing as a possible solution for archival digital data. Recently, to further increase the potential capacity of DNA-based data storage systems, the combinatorial composite DNA synthesis method was suggested. This…
Ordered nanoarrays, i.e. regular patterns of quantum structures at the nanometre scale, have recently been synthesized in a wide range of systems. Here I explore a possible route to technological exploitation: assuming a simple form of…
Generative AI systems have shown impressive capabilities in creating text, code, and images. Inspired by the rich history of research in industrial ''Design for Assembly'', we introduce a novel problem: Generative Design-for-Robot-Assembly…
We introduce staged self-assembly of Wang tiles, where tiles can be added dynamically in sequence and where intermediate constructions can be stored for later mixing. This model and its various constraints and performance measures are…
As Moore's Law continues to increase the complexity of electronic systems, Electronic Design Automation (EDA) must advance to meet global demand. An important example of an EDA technology is SKILL, a scripting language used to customize and…
RNA-seq allows detection and precise quantification of transcripts, provides comprehensive understanding of exon/intron boundaries, aids discovery of alternatively spliced isoforms and fusion transcripts along with measurement of…
The Core Imaging Library (CIL) is an open-source versatile Python framework for solving inverse problems with special emphasis on imaging applications such as computed tomography (CT), using a plug-in architecture for data and operators,…
De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…
We present a modelling framework, and basic model parameterization, for the study of DNA origami folding at the level of DNA domains. Our approach is explicitly kinetic and does not assume a specific folding pathway. The binding of each…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
Self-assembly refers to the process by which small, simple components mix and combine to form complex structures using only local interactions. Designed as a hybrid between tile assembly models and cellular automata, the Tile Automata (TA)…
Deep learning is now the gold standard in computer vision-based quality inspection systems. In order to detect defects, supervised learning is often utilized, but necessitates a large amount of annotated images, which can be costly:…
Auto-regressive sequence generative models trained by Maximum Likelihood Estimation suffer the exposure bias problem in practical finite sample scenarios. The crux is that the number of training samples for Maximum Likelihood Estimation is…
Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…
Beginning programmers struggle with the complex grammar of modern programming languages like Java, and make lot of syntax errors. The diagnostic syntax error messages from compilers and IDEs are sometimes useful, but often the messages are…
Colloidal self-assembly -- the spontaneous organization of colloids into ordered structures -- has been considered key to produce next-generation materials. However, the present-day staggering variety of colloidal building blocks and the…
Tile displacement is a newly-recognized mechanism in DNA nanotechnology that exploits principles analogous to toehold-mediated strand displacement but within the context of self-assembled DNA origami tile arrays. Here, we formulate an…
We address the problem of automatic decompilation, converting a program in low-level representation back to a higher-level human-readable programming language. The problem of decompilation is extremely important for security researchers.…
Accurate and robust disassembly of stripped binaries is challenging. The root of the difficulty is that high-level structures, such as instruction and function boundaries, are absent in stripped binaries and must be recovered based on…