Output-Constrained Lossy Source Coding With Application to Rate-Distortion-Perception Theory

The distortion-rate function of output-constrained lossy source coding with limited common randomness is analyzed for the special case of squared error distortion measure. An explicit expression is obtained when both source and reconstruction distributions are Gaussian. This further leads to a partial characterization of the information-theoretic limit of quadratic Gaussian rate-distortion-perception coding with the perception measure given by Kullback-Leibler divergence or squared quadratic Wasserstein distance.

Learning Universal and Robust 3D Molecular Representations with Graph Convolutional Networks

To learn accurate representations of molecules, it is essential to consider both chemical and geometric features. To encode geometric information, many descriptors have been proposed in constrained circumstances for specific types of molecules and do not have the properties to be ``robust": 1. Invariant to rotations and translations; 2. Injective when embedding molecular structures. In this work, we propose a universal and robust Directional Node Pair (DNP) descriptor based on the graph representations of 3D molecules. Our DNP descriptor is robust compared to previous ones and can be applied to multiple molecular types. To combine the DNP descriptor and chemical features in molecules, we construct the Robust Molecular Graph Convolutional Network (RoM-GCN) which is capable to take both node and edge features into consideration when generating molecule representations. We evaluate our model on protein and small molecule datasets. Our results validate the superiority of the DNP descriptor in incorporating 3D geometric information of molecules. RoM-GCN outperforms all compared baselines.

Exploration of Dark Chemical Genomics Space via Portal Learning: Applied to Targeting the Undruggable Genome and COVID-19 Anti-Infective Polypharmacology

Advances in biomedicine are largely fueled by exploring uncharted territories of human biology. Machine learning can both enable and accelerate discovery, but faces a fundamental hurdle when applied to unseen data with distributions that differ from previously observed ones -- a common dilemma in scientific inquiry. We have developed a new deep learning framework, called {\textit{Portal Learning}}, to explore dark chemical and biological space. Three key, novel components of our approach include: (i) end-to-end, step-wise transfer learning, in recognition of biology's sequence-structure-function paradigm, (ii) out-of-cluster meta-learning, and (iii) stress model selection. Portal Learning provides a practical solution to the out-of-distribution (OOD) problem in statistical machine learning. Here, we have implemented Portal Learning to predict chemical-protein interactions on a genome-wide scale. Systematic studies demonstrate that Portal Learning can effectively assign ligands to unexplored gene families (unknown functions), versus existing state-of-the-art methods, thereby allowing us to target previously "undruggable" proteins and design novel polypharmacological agents for disrupting interactions between SARS-CoV-2 and human proteins. Portal Learning is general-purpose and can be further applied to other areas of scientific inquiry.

A multi-center prospective evaluation of THEIA to detect diabetic retinopathy (DR) and diabetic macular edema (DME) in the New Zealand screening program

Purpose: to assess the efficacy of THEIA, an artificial intelligence for screening diabetic retinopathy in a multi-center prospective study. To validate the potential application of THEIA as clinical decision making assistant in a national screening program. Methods: 902 patients were recruited from either an urban large eye hospital, or a semi-rural optometrist led screening provider, as they were attending their appointment as part of New Zealand Diabetic Screening programme. These clinics used a variety of retinal cameras and a range of operators. The de-identified images were then graded independently by three senior retinal specialists, and final results were aggregated using New Zealand grading scheme, which is then converted to referable\non-referable and Healthy\mild\more than mild\vision threatening categories. Results: compared to ground truth, THEIA achieved 100% sensitivity and [95.35%-97.44%] specificity, and negative predictive value of 100%. THEIA also did not miss any patients with more than mild or vision threatening disease. The level of agreement between the clinicians and the aggregated results was (k value: 0.9881, 0.9557, and 0.9175), and the level of agreement between THEIA and the aggregated labels was (k value: 0.9515). Conclusion: Our multi-centre prospective trial showed that THEIA does not miss referable disease when screening for diabetic retinopathy and maculopathy. It also has a very high level of granularity in reporting the disease level. Since THEIA is being tested on a variety of cameras, operating in a range of clinics (rural\urban, ophthalmologist-led\optometrist-led), we believe that it will be a suitable addition to a public diabetic screening program.

Real-world plant species identification based on deep convolutional neural networks and visual attention

This paper investigates the issue of real-world identification to fulfill better species protection. We focus on plant species identification as it is a classic and hot issue. In tradition plant species identification the samples are scanned specimen and the background is simple. However, real-world species recognition is more challenging. We first systematically investigate what is realistic species recognition and the difference from tradition plant species recognition. To deal with the challenging task, an interdisciplinary collaboration is presented based on the latest advances in computer science and technology. We propose a novel framework and an effective data augmentation method for deep learning in this paper. We first crop the image in terms with visual attention before general recognition. Besides, we apply it as a data augmentation method. We call the novel data augmentation approach attention cropping (AC). Deep convolutional neural networks are trained to predict species from a large amount of data. Extensive experiments on traditional dataset and specific dataset for real-world recognition are conducted to evaluate the performance of our approach. Experiments first demonstrate that our approach achieves state-of-the-art results on different types of datasets. Besides, we also evaluate the performance of data augmentation method AC. Results show that AC provides superior performance. Compared with the precision of methods without AC, the results with AC achieve substantial improvement.