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In the emerging field of DNA storage, data is encoded as DNA sequences and stored. The data is read out again by sequencing the stored DNA. Nanopore sequencing is a new sequencing technology that has many advantages over other methods; in…
The ever-increasing quantity of multivariate process data is driving a need for skilled engineers to analyze, interpret, and build models from such data. Multivariate data analytics relies heavily on linear algebra, optimization, and…
Nanopore sequencing is an emerging new technology for sequencing DNA, which can read long fragments of DNA (~50,000 bases) in contrast to most current short-read sequencing technologies which can only read hundreds of bases. While nanopore…
Molecular carriers represent an increasingly common strategy in the field of nanopore sensing to use secondary molecules to selectively report on the presence of target analytes in solution, allowing for sensitive assays of otherwise…
DNA has many valuable characteristics that make it suitable for a long-term storage medium, in particular its durability and high information density. DNA can be stored safely for hundreds of years with virtually no degradation, in contrast…
Nanopore protein sequencing produces long, noisy ionic current traces in which key molecular phases, such as protein capture and translocation, are embedded. Capture phases mark the successful entry of a protein into the pore and serve as…
Purpose Nanopore-based molecular sensing and measurement, specifically Deoxyribonucleic acid (DNA) sequencing, is advancing at a fast pace. Some embodiments have matured from coarse particle counters to enabling full human genome assembly.…
Variational autoencoders (VAEs) have been used extensively to discover low-dimensional latent factors governing neural activity and animal behavior. However, without careful model selection, the uncovered latent factors may reflect noise in…
Computer simulations have become a popular tool of assessing complex skills such as problem-solving skills. Log files of computer-based items record the entire human-computer interactive processes for each respondent. The response processes…
Domain adaption (DA) allows machine learning methods trained on data sampled from one distribution to be applied to data sampled from another. It is thus of great practical importance to the application of such methods. Despite the fact…
We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…
The adaptation of foundation models has significantly advanced environmental audio deepfake detection (EADD), a rapidly growing area of research. These models are typically fine-tuned or utilized in their frozen states for downstream tasks.…
DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA…
Variational autoencoders (VAEs), that are built upon deep neural networks have emerged as popular generative models in computer vision. Most of the work towards improving variational autoencoders has focused mainly on making the…
DNA nanotechnology uses predictable interactions of nucleic acids to precisely engineer complex nanostructures. Characterizing these self-assembled structures at the single-structure level is crucial for validating their design and…
Detectors in next-generation high-energy physics experiments face several daunting requirements, such as high data rates, damaging radiation exposure, and stringent constraints on power, space, and latency. To address these challenges,…
Understanding the structure of complex, nonstationary, high-dimensional time-evolving signals is a central challenge in scientific data analysis. In many domains, such as speech and biomedical signal processing, the ability to learn…
Model reduction for fluid flow simulation continues to be of great interest across a number of scientific and engineering fields. In a previous work [arXiv:2104.13962], we explored the use of Neural Ordinary Differential Equations (NODE) as…
Computer simulations are indispensable for analyzing complex systems, yet high-fidelity models often incur prohibitive computational costs. Multi-fidelity frameworks address this challenge by combining inexpensive low-fidelity simulations…
As deep Variational Auto-Encoder (VAE) frameworks become more widely used for modeling biomolecular simulation data, we emphasize the capability of the VAE architecture to concurrently maximize the timescale of the latent space while…