DNA nanotechnology exploits the programmable specificity afforded by base-pairing to produce self-assembling macromolecular objects of custom shape. For building megadalton-scale DNA nanostructures, a long ‘scaffold’ strand can be employed to template the assembly of hundreds of oligonucleotide ‘staple’ strands into a planar antiparallel array of cross-linked helices. We recently adapted this ‘scaffolded DNA origami’ method to producing 3D shapes formed as pleated layers of double helices constrained to a honeycomb lattice. However, completing the required design steps can be cumbersome and time-consuming. Here we present caDNAno, an open-source software package with a graphical user interface that aids in the design of DNA sequences for folding 3D honeycomb-pleated shapes A series of rectangular-block motifs were designed, assembled, and analyzed to identify a well-behaved motif that could serve as a building block for future studies. The use of caDNAno significantly reduces the effort required to design 3D DNA-origami structures. The software is available at http://cadnano.org/, along with example designs and video tutorials demonstrating their construction. The source code is released under the MIT license.

Abstract-Deep neural networks are state of the art methods for many learning tasks due to their ability to extract increasingly better features at each network layer. However, the improved performance of additional layers in a deep network comes at the cost of added latency and energy usage in feedforward inference. As networks continue to get deeper and larger, these costs become more prohibitive for real-time and energy-sensitive applications. To address this issue, we present BranchyNet, a novel deep network architecture that is augmented with additional side branch classifiers. The architecture allows prediction results for a large portion of test samples to exit the network early via these branches when samples can already be inferred with high confidence. BranchyNet exploits the observation that features learned at an early layer of a network may often be sufficient for the classification of many data points. For more difficult samples, which are expected less frequently, BranchyNet will use further or all network layers to provide the best likelihood of correct prediction. We study the BranchyNet architecture using several well-known networks (LeNet, AlexNet, ResNet) and datasets (MNIST, CIFAR10) and show that it can both improve accuracy and significantly reduce the inference time of the network.

We propose distributed deep neural networks (DDNNs) over distributed computing hierarchies, consisting of the cloud, the edge (fog) and end devices. While being able to accommodate inference of a deep neural network (DNN) in the cloud, a DDNN also allows fast and localized inference using shallow portions of the neural network at the edge and end devices. When supported by a scalable distributed computing hierarchy, a DDNN can scale up in neural network size and scale out in geographical span. Due to its distributed nature, DDNNs enhance sensor fusion, system fault tolerance and data privacy for DNN applications. In implementing a DDNN, we map sections of a DNN onto a distributed computing hierarchy. By jointly training these sections, we minimize communication and resource usage for devices and maximize usefulness of extracted features which are utilized in the cloud. The resulting system has built-in support for automatic sensor fusion and fault tolerance. As a proof of concept, we show a DDNN can exploit geographical diversity of sensors to improve object recognition accuracy and reduce communication cost. In our experiment, compared with the traditional method of offloading raw sensor data to be processed in the cloud, DDNN locally processes most sensor data on end devices while achieving high accuracy and is able to reduce the communication cost by a factor of over 20x.