Augmented Equivariant Attention Networks for Microscopy Image Reconstruction

It is time-consuming and expensive to take high-quality or high-resolution electron microscopy (EM) and fluorescence microscopy (FM) images. Taking these images could be even invasive to samples and may damage certain subtleties in the samples after long or intense exposures, often necessary for achieving high-quality or high resolution in the first place. Advances in deep learning enable us to perform image-to-image transformation tasks for various types of microscopy image reconstruction, computationally producing high-quality images from the physically acquired low-quality ones. When training image-to-image transformation models on pairs of experimentally acquired microscopy images, prior models suffer from performance loss due to their inability to capture inter-image dependencies and common features shared among images. Existing methods that take advantage of shared features in image classification tasks cannot be properly applied to image reconstruction tasks because they fail to preserve the equivariance property under spatial permutations, something essential in image-to-image transformation. To address these limitations, we propose the augmented equivariant attention networks (AEANets) with better capability to capture inter-image dependencies, while preserving the equivariance property. The proposed AEANets captures inter-image dependencies and shared features via two augmentations on the attention mechanism, which are the shared references and the batch-aware attention during training. We theoretically derive the equivariance property of the proposed augmented attention model and experimentally demonstrate its consistent superiority in both quantitative and visual results over the baseline methods.Comment: 11 pages, 8 figure

PatDNN: Achieving Real-Time DNN Execution on Mobile Devices with Pattern-based Weight Pruning

With the emergence of a spectrum of high-end mobile devices, many applications that formerly required desktop-level computation capability are being transferred to these devices. However, executing the inference of Deep Neural Networks (DNNs) is still challenging considering high computation and storage demands, specifically, if real-time performance with high accuracy is needed. Weight pruning of DNNs is proposed, but existing schemes represent two extremes in the design space: non-structured pruning is fine-grained, accurate, but not hardware friendly; structured pruning is coarse-grained, hardware-efficient, but with higher accuracy loss. In this paper, we introduce a new dimension, fine-grained pruning patterns inside the coarse-grained structures, revealing a previously unknown point in design space. With the higher accuracy enabled by fine-grained pruning patterns, the unique insight is to use the compiler to re-gain and guarantee high hardware efficiency. In other words, our method achieves the best of both worlds, and is desirable across theory/algorithm, compiler, and hardware levels. The proposed PatDNN is an end-to-end framework to efficiently execute DNN on mobile devices with the help of a novel model compression technique (pattern-based pruning based on extended ADMM solution framework) and a set of thorough architecture-aware compiler- and code generation-based optimizations (filter kernel reordering, compressed weight storage, register load redundancy elimination, and parameter auto-tuning). Evaluation results demonstrate that PatDNN outperforms three state-of-the-art end-to-end DNN frameworks, TensorFlow Lite, TVM, and Alibaba Mobile Neural Network with speedup up to 44.5x, 11.4x, and 7.1x, respectively, with no accuracy compromise. Real-time inference of representative large-scale DNNs (e.g., VGG-16, ResNet-50) can be achieved using mobile devices.Comment: To be published in the Proceedings of Twenty-Fifth International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS 20

Tuning the Performance of a Computational Persistent Homology Package

In recent years, persistent homology has become an attractive method for data analysis. It captures topological features, such as connected components, holes, and voids from point cloud data and summarizes the way in which these features appear and disappear in a filtration sequence. In this project, we focus on improving the performanceof Eirene, a computational package for persistent homology. Eirene is a 5000-line open-source software library implemented in the dynamic programming language Julia. We use the Julia profiling tools to identify performance bottlenecks and develop novel methods to manage them, including the parallelization of some time-consuming functions on multicore/manycore hardware. Empirical results show that performance can be greatly improved

Continuous-Flow Matrix Transposition Using Memories

In this paper, we analyze how to calculate the matrix transposition in continuous flow by using a memory or group of memories. The proposed approach studies this problem for specific conditions such as square and non-square matrices, use of limited access memories and use of several memories in parallel. Contrary to previous approaches, which are based on specific cases or examples, the proposed approach derives the fundamental theory involved in the problem of matrix transposition in a continuous flow. This allows for obtaining the exact equations for the read and write addresses of the memories and other control signals in the circuits. Furthermore, the cases that involve non-square matrices, which have not been studied in detail in the literature, are analyzed in depth in this paper. Experimental results show that the proposed approach is capable of transposing matrices of 8192 times 8192 32-bit data received in series at a rate of 200 mega samples per second, which doubles the throughput of previous approaches. © 2004-2012 IEEE