Lifu Zhang

Donglai Wei, Kisuk Lee, Hanyu Li et al.

Electron microscopy (EM) enables the reconstruction of neural circuits at the level of individual synapses, which has been transformative for scientific discoveries. However, due to the complex morphology, an accurate reconstruction of cortical axons has become a major challenge. Worse still, there is no publicly available large-scale EM dataset from the cortex that provides dense ground truth segmentation for axons, making it difficult to develop and evaluate large-scale axon reconstruction methods. To address this, we introduce the AxonEM dataset, which consists of two 30x30x30 um^3 EM image volumes from the human and mouse cortex, respectively. We thoroughly proofread over 18,000 axon instances to provide dense 3D axon instance segmentation, enabling large-scale evaluation of axon reconstruction methods. In addition, we densely annotate nine ground truth subvolumes for training, per each data volume. With this, we reproduce two published state-of-the-art methods and provide their evaluation results as a baseline. We publicly release our code and data at https://connectomics-bazaar.github.io/proj/AxonEM/index.html to foster the development of advanced methods.

Lifu Zhang, Tarek S. Abdelrahman

The growth in the complexity of Convolutional Neural Networks (CNNs) is increasing interest in partitioning a network across multiple accelerators during training and pipelining the backpropagation computations over the accelerators. Existing approaches avoid or limit the use of stale weights through techniques such as micro-batching or weight stashing. These techniques either underutilize of accelerators or increase memory footprint. We explore the impact of stale weights on the statistical efficiency and performance in a pipelined backpropagation scheme that maximizes accelerator utilization and keeps memory overhead modest. We use 4 CNNs (LeNet-5, AlexNet, VGG and ResNet) and show that when pipelining is limited to early layers in a network, training with stale weights converges and results in models with comparable inference accuracies to those resulting from non-pipelined training on MNIST and CIFAR-10 datasets; a drop in accuracy of 0.4%, 4%, 0.83% and 1.45% for the 4 networks, respectively. However, when pipelining is deeper in the network, inference accuracies drop significantly. We propose combining pipelined and non-pipelined training in a hybrid scheme to address this drop. We demonstrate the implementation and performance of our pipelined backpropagation in PyTorch on 2 GPUs using ResNet, achieving speedups of up to 1.8X over a 1-GPU baseline, with a small drop in inference accuracy.