Related papers: scadnano: A browser-based, scriptable tool for des…
As neuroimaging databases grow in size and complexity, the time researchers spend investigating and managing the data increases to the expense of data analysis. As a result, investigators rely more and more heavily on scripting using…
In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…
To model deformation of anatomical shapes, non-linear statistics are required to take into account the non-linear structure of the data space. Computer implementations of non-linear statistics and differential geometry algorithms often lead…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
User interface design is a complex task that involves designers examining a wide range of options. We present Spacewalker, a tool that allows designers to rapidly search a large design space for an optimal web UI with integrated support.…
The rapidly evolving field of Artificial Intelligence necessitates automated approaches to co-design neural network architecture and neural accelerators to maximize system efficiency and address productivity challenges. To enable joint…
Brain MRI underpins a wide range of neuroscientific and clinical applications, yet most learning-based methods remain task-specific and require substantial labeled data. Here we show that a single self-supervised representation can…
Neural Architecture Search (NAS) has shown promising capability in learning text representation. However, existing text-based NAS neither performs a learnable fusion of neural operations to optimize the architecture, nor encodes the latent…
Online handwriting generation (OHG) enhances handwriting recognition models by synthesizing diverse, human-like samples. However, existing OHG methods struggle to generate unseen characters, particularly in glyph-based languages like…
Single-cell RNA sequencing (scRNA-seq) has transformed our ability to explore biological systems. Nevertheless, proficient expertise is essential for handling and interpreting the data. In this paper, we present scX, an R package built on…
This chapter introduces how to run molecular dynamics simulations for DNA origami using the oxDNA coarse-grained model.
Computer-aided design (CAD) has become a critical element in the creation of nanopatterned structures and devices. In particular, with the increased adoption of easy-to-learn programming languages like Python there has been a significant…
SnadiOpt is a package that supports the use of the automatic differentiation package ADIFOR with the optimization package Snopt. Snopt is a general-purpose system for solving optimization problems with many variables and constraints. It…
RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…
Training a state-of-the-art deep neural network (DNN) is a computationally-expensive and time-consuming process, which incentivizes deep learning developers to debug their DNNs for computational performance. However, effectively performing…
The exponentially increasing demand for data storage has been facing more and more challenges during the past years. The energy costs that it represents are also increasing, and the availability of the storage hardware is not able to follow…
We describe the first DNA-based storage architecture that enables random access to data blocks and rewriting of information stored at arbitrary locations within the blocks. The newly developed architecture overcomes drawbacks of existing…
We propose generative neural network methods to generate DNA sequences and tune them to have desired properties. We present three approaches: creating synthetic DNA sequences using a generative adversarial network; a DNA-based variant of…
Processing high-throughput DNA sequencing data of individuals or populations requires stringing together independent software tools with many parameters, often leading to non-reproducible pipelines and datasets. We developed grenepipe to…
Multi-arm designs provide an effective means of evaluating several treatments within the same clinical trial. Given the large number of treatments now available for testing in many disease areas, it has been argued that their utilisation…