Smoothness Analysis for Probabilistic Programs with Application to Optimised Variational Inference

We present a static analysis for discovering differentiable or more generally smooth parts of a given probabilistic program, and show how the analysis can be used to improve the pathwise gradient estimator, one of the most popular methods for posterior inference and model learning. Our improvement increases the scope of the estimator from differentiable models to non-differentiable ones without requiring manual intervention of the user; the improved estimator automatically identifies differentiable parts of a given probabilistic program using our static analysis, and applies the pathwise gradient estimator to the identified parts while using a more general but less efficient estimator, called score estimator, for the rest of the program. Our analysis has a surprisingly subtle soundness argument, partly due to the misbehaviours of some target smoothness properties when viewed from the perspective of program analysis designers. For instance, some smoothness properties are not preserved by function composition, and this makes it difficult to analyse sequential composition soundly without heavily sacrificing precision. We formulate five assumptions on a target smoothness property, prove the soundness of our analysis under those assumptions, and show that our leading examples satisfy these assumptions. We also show that by using information from our analysis, our improved gradient estimator satisfies an important differentiability requirement and thus, under a mild regularity condition, computes the correct estimate on average, i.e., it returns an unbiased estimate. Our experiments with representative probabilistic programs in the Pyro language show that our static analysis is capable of identifying smooth parts of those programs accurately, and making our improved pathwise gradient estimator exploit all the opportunities for high performance in those programs.

tBDFS: Temporal Graph Neural Network Leveraging DFS

Temporal graph neural networks (temporal GNNs) have been widely researched, reaching state-of-the-art results on multiple prediction tasks. A common approach employed by most previous works is to apply a layer that aggregates information from the historical neighbors of a node. Taking a different research direction, in this work, we propose tBDFS -- a novel temporal GNN architecture. tBDFS applies a layer that efficiently aggregates information from temporal paths to a given (target) node in the graph. For each given node, the aggregation is applied in two stages: (1) A single representation is learned for each temporal path ending in that node, and (2) all path representations are aggregated into a final node representation. Overall, our goal is not to add new information to a node, but rather observe the same exact information in a new perspective. This allows our model to directly observe patterns that are path-oriented rather than neighborhood-oriented. This can be thought as a Depth-First Search (DFS) traversal over the temporal graph, compared to the popular Breath-First Search (BFS) traversal that is applied in previous works. We evaluate tBDFS over multiple link prediction tasks and show its favorable performance compared to state-of-the-art baselines. To the best of our knowledge, we are the first to apply a temporal-DFS neural network.

Polarized Color Image Denoising using Pocoformer

Polarized color photography provides both visual textures and object surficial information in one single snapshot. However, the use of the directional polarizing filter array causes extremely lower photon count and SNR compared to conventional color imaging. Thus, the feature essentially leads to unpleasant noisy images and destroys polarization analysis performance. It is a challenge for traditional image processing pipelines owing to the fact that the physical constraints exerted implicitly in the channels are excessively complicated. To address this issue, we propose a learning-based approach to simultaneously restore clean signals and precise polarization information. A real-world polarized color image dataset of paired raw short-exposed noisy and long-exposed reference images are captured to support the learning-based pipeline. Moreover, we embrace the development of vision Transformer and propose a hybrid transformer model for the Polarized Color image denoising, namely PoCoformer, for a better restoration performance. Abundant experiments demonstrate the effectiveness of proposed method and key factors that affect results are analyzed.

Adaptive GLCM sampling for transformer-based COVID-19 detection on CT

The world has suffered from COVID-19 (SARS-CoV-2) for the last two years, causing much damage and change in people's daily lives. Thus, automated detection of COVID-19 utilizing deep learning on chest computed tomography (CT) scans became promising, which helps correct diagnosis efficiently. Recently, transformer-based COVID-19 detection method on CT is proposed to utilize 3D information in CT volume. However, its sampling method for selecting slices is not optimal. To leverage rich 3D information in CT volume, we propose a transformer-based COVID-19 detection using a novel data curation and adaptive sampling method using gray level co-occurrence matrices (GLCM). To train the model which consists of CNN layer, followed by transformer architecture, we first executed data curation based on lung segmentation and utilized the entropy of GLCM value of every slice in CT volumes to select important slices for the prediction. The experimental results show that the proposed method improve the detection performance with large margin without much difficult modification to the model.

PalQuant: Accelerating High-precision Networks on Low-precision Accelerators

Recently low-precision deep learning accelerators (DLAs) have become popular due to their advantages in chip area and energy consumption, yet the low-precision quantized models on these DLAs bring in severe accuracy degradation. One way to achieve both high accuracy and efficient inference is to deploy high-precision neural networks on low-precision DLAs, which is rarely studied. In this paper, we propose the PArallel Low-precision Quantization (PalQuant) method that approximates high-precision computations via learning parallel low-precision representations from scratch. In addition, we present a novel cyclic shuffle module to boost the cross-group information communication between parallel low-precision groups. Extensive experiments demonstrate that PalQuant has superior performance to state-of-the-art quantization methods in both accuracy and inference speed, e.g., for ResNet-18 network quantization, PalQuant can obtain 0.52\% higher accuracy and 1.78$\times$ speedup simultaneously over their 4-bit counter-part on a state-of-the-art 2-bit accelerator. Code is available at \url{https://github.com/huqinghao/PalQuant}.

ChrSNet: Chromosome Straightening using Self-attention Guided Networks

Karyotyping is an important procedure to assess the possible existence of chromosomal abnormalities. However, because of the non-rigid nature, chromosomes are usually heavily curved in microscopic images and such deformed shapes hinder the chromosome analysis for cytogeneticists. In this paper, we present a self-attention guided framework to erase the curvature of chromosomes. The proposed framework extracts spatial information and local textures to preserve banding patterns in a regression module. With complementary information from the bent chromosome, a refinement module is designed to further improve fine details. In addition, we propose two dedicated geometric constraints to maintain the length and restore the distortion of chromosomes. To train our framework, we create a synthetic dataset where curved chromosomes are generated from the real-world straight chromosomes by grid-deformation. Quantitative and qualitative experiments are conducted on synthetic and real-world data. Experimental results show that our proposed method can effectively straighten bent chromosomes while keeping banding details and length.

Highlight Specular Reflection Separation based on Tensor Low-rank and Sparse Decomposition Using Polarimetric Cues

This paper is concerned with specular reflection removal based on tensor low-rank decomposition framework with the help of polarization information. Our method is motivated by the observation that the specular highlight of an image is sparsely distributed while the remaining diffuse reflection can be well approximated by a linear combination of several distinct colors using a low-rank and sparse decomposition framework. Unlike current solutions, our tensor low-rank decomposition keeps the spatial structure of specular and diffuse information which enables us to recover the diffuse image under strong specular reflection or in saturated regions. We further define and impose a new polarization regularization term as constraint on color channels. This regularization boosts the performance of the method to recover an accurate diffuse image by handling the color distortion, a common problem of chromaticity-based methods, especially in case of strong specular reflection. Through comprehensive experiments on both synthetic and real polarization images, we demonstrate that our method is able to significantly improve the accuracy of highlight specular removal, and outperform the competitive methods to recover the diffuse image, especially in regions of strong specular reflection or in saturated areas.

One-shot Generative Prior Learned from Hankel-k-space for Parallel Imaging Reconstruction

Magnetic resonance imaging serves as an essential tool for clinical diagnosis. However, it suffers from a long acquisition time. The utilization of deep learning, especially the deep generative models, offers aggressive acceleration and better reconstruction in magnetic resonance imaging. Nevertheless, learning the data distribution as prior knowledge and reconstructing the image from limited data remains challenging. In this work, we propose a novel Hankel-k-space generative model (HKGM), which can generate samples from a training set of as little as one k-space data. At the prior learning stage, we first construct a large Hankel matrix from k-space data, then extract multiple structured k-space patches from the large Hankel matrix to capture the internal distribution among different patches. Extracting patches from a Hankel matrix enables the generative model to be learned from redundant and low-rank data space. At the iterative reconstruction stage, it is observed that the desired solution obeys the learned prior knowledge. The intermediate reconstruction solution is updated by taking it as the input of the generative model. The updated result is then alternatively operated by imposing low-rank penalty on its Hankel matrix and data consistency con-strain on the measurement data. Experimental results confirmed that the internal statistics of patches within a single k-space data carry enough information for learning a powerful generative model and provide state-of-the-art reconstruction.

Developing an NLP-based Recommender System for the Ethical, Legal, and Social Implications of Synthetic Biology

Synthetic biology is an emerging field that involves the engineering and re-design of organisms for purposes such as food security, health, and environmental protection. As such, it poses numerous ethical, legal, and social implications (ELSI) for researchers and policy makers. Various efforts to ensure socially responsible synthetic biology are underway. Policy making is one regulatory avenue, and other initiatives have sought to embed social scientists and ethicists on synthetic biology projects. However, given the nascency of synthetic biology, the number of heterogeneous domains it spans, and the open nature of many ethical questions, it has proven challenging to establish widespread concrete policies, and including social scientists and ethicists on synthetic biology teams has met with mixed success. This text proposes a different approach, asking instead is it possible to develop a well-performing recommender model based upon natural language processing (NLP) to connect synthetic biologists with information on the ELSI of their specific research? This recommender was developed as part of a larger project building a Synthetic Biology Knowledge System (SBKS) to accelerate discovery and exploration of the synthetic biology design space. Our approach aims to distill for synthetic biologists relevant ethical and social scientific information and embed it into synthetic biology research workflows.

TFCNs: A CNN-Transformer Hybrid Network for Medical Image Segmentation

Medical image segmentation is one of the most fundamental tasks concerning medical information analysis. Various solutions have been proposed so far, including many deep learning-based techniques, such as U-Net, FC-DenseNet, etc. However, high-precision medical image segmentation remains a highly challenging task due to the existence of inherent magnification and distortion in medical images as well as the presence of lesions with similar density to normal tissues. In this paper, we propose TFCNs (Transformers for Fully Convolutional denseNets) to tackle the problem by introducing ResLinear-Transformer (RL-Transformer) and Convolutional Linear Attention Block (CLAB) to FC-DenseNet. TFCNs is not only able to utilize more latent information from the CT images for feature extraction, but also can capture and disseminate semantic features and filter non-semantic features more effectively through the CLAB module. Our experimental results show that TFCNs can achieve state-of-the-art performance with dice scores of 83.72\% on the Synapse dataset. In addition, we evaluate the robustness of TFCNs for lesion area effects on the COVID-19 public datasets. The Python code will be made publicly available on https://github.com/HUANGLIZI/TFCNs.