Multi-View Graph Neural Networks for Molecular Property Prediction

The crux of molecular property prediction is to generate meaningful representations of the molecules. One promising route is to exploit the molecular graph structure through Graph Neural Networks (GNNs). It is well known that both atoms and bonds significantly affect the chemical properties of a molecule, so an expressive model shall be able to exploit both node (atom) and edge (bond) information simultaneously. Guided by this observation, we present Multi-View Graph Neural Network (MV-GNN), a multi-view message passing architecture to enable more accurate predictions of molecular properties. In MV-GNN, we introduce a shared self-attentive readout component and disagreement loss to stabilize the training process. This readout component also renders the whole architecture interpretable. We further boost the expressive power of MV-GNN by proposing a cross-dependent message passing scheme that enhances information communication of the two views, which results in the MV-GNN^cross variant. Lastly, we theoretically justify the expressiveness of the two proposed models in terms of distinguishing non-isomorphism graphs. Extensive experiments demonstrate that MV-GNN models achieve remarkably superior performance over the state-of-the-art models on a variety of challenging benchmarks. Meanwhile, visualization results of the node importance are consistent with prior knowledge, which confirms the interpretability power of MV-GNN models.

Co-Heterogeneous and Adaptive Segmentation from Multi-Source and Multi-Phase CT Imaging Data: A Study on Pathological Liver and Lesion Segmentation

In medical imaging, organ/pathology segmentation models trained on current publicly available and fully-annotated datasets usually do not well-represent the heterogeneous modalities, phases, pathologies, and clinical scenarios encountered in real environments. On the other hand, there are tremendous amounts of unlabelled patient imaging scans stored by many modern clinical centers. In this work, we present a novel segmentation strategy, co-heterogenous and adaptive segmentation (CHASe), which only requires a small labeled cohort of single phase imaging data to adapt to any unlabeled cohort of heterogenous multi-phase data with possibly new clinical scenarios and pathologies. To do this, we propose a versatile framework that fuses appearance based semi-supervision, mask based adversarial domain adaptation, and pseudo-labeling. We also introduce co-heterogeneous training, which is a novel integration of co-training and hetero modality learning. We have evaluated CHASe using a clinically comprehensive and challenging dataset of multi-phase computed tomography (CT) imaging studies (1147 patients and 4577 3D volumes). Compared to previous state-of-the-art baselines, CHASe can further improve pathological liver mask Dice-Sorensen coefficients by ranges of $4.2\% \sim 9.4\%$, depending on the phase combinations: e.g., from $84.6\%$ to $94.0\%$ on non-contrast CTs.

Dual Message Passing Neural Network for Molecular Property Prediction

The crux of molecular property prediction is to conduct meaningful and informative representations of molecules. One promising way of doing this is exploiting the molecular graph structure, which leads to several graph-based deep learning models, such as Graph Neural Networks (GNN), Message Passing Networks (MPN), etc. However, current deep graph learning models generally focus on either node embedding or edge embedding. Since both atoms and chemical bonds play important roles in chemical reactions and reflect the property of molecules, existing methods fail to exploit both node (atom) and edge (bond) features simultaneously to make property prediction. In this paper, we propose Dual Message Passing Neural Network (DualMPNN), a multi-view message passing architecture with a two-tier constraint, to make more accurate molecular property prediction. DualMPNN consists of two sub-models: one model as NodeMPN for atom-oriented modeling and the other as EdgeMPN for bond-oriented modeling. We design a shared self-attentive readout and disagreement loss to stabilize the training process and enhance the interactions between two sub-models. On the other hand, the designed self-attentive readout also provides the interpretability for molecular property prediction, which is crucial for real applications like molecular design and drug discovery. Our extensive experimental evaluations demonstrate that DualMPNN achieves remarkably superior improvement over the state-of-the-art approaches on a variety of challenging benchmarks. Meanwhile, the visualization of the self-attention demonstrates how different atoms affect the prediction performance, which brings in the interpretability of deep learning models out of the black-box.

COVID-DA: Deep Domain Adaptation from Typical Pneumonia to COVID-19

The outbreak of novel coronavirus disease 2019 (COVID-19) has already infected millions of people and is still rapidly spreading all over the globe. Most COVID-19 patients suffer from lung infection, so one important diagnostic method is to screen chest radiography images, e.g., X-Ray or CT images. However, such examinations are time-consuming and labor-intensive, leading to limited diagnostic efficiency. To solve this issue, AI-based technologies, such as deep learning, have been used recently as effective computer-aided means to improve diagnostic efficiency. However, one practical and critical difficulty is the limited availability of annotated COVID-19 data, due to the prohibitive annotation costs and urgent work of doctors to fight against the pandemic. This makes the learning of deep diagnosis models very challenging. To address this, motivated by that typical pneumonia has similar characteristics with COVID-19 and many pneumonia datasets are publicly available, we propose to conduct domain knowledge adaptation from typical pneumonia to COVID-19. There are two main challenges: 1) the discrepancy of data distributions between domains; 2) the task difference between the diagnosis of typical pneumonia and COVID-19. To address them, we propose a new deep domain adaptation method for COVID-19 diagnosis, namely COVID-DA. Specifically, we alleviate the domain discrepancy via feature adversarial adaptation and handle the task difference issue via a novel classifier separation scheme. In this way, COVID-DA is able to diagnose COVID-19 effectively with only a small number of COVID-19 annotations. Extensive experiments verify the effectiveness of COVID-DA and its great potential for real-world applications.

Real-Time Semantic Segmentation via Auto Depth, Downsampling Joint Decision and Feature Aggregation

To satisfy the stringent requirements on computational resources in the field of real-time semantic segmentation, most approaches focus on the hand-crafted design of light-weight segmentation networks. Recently, Neural Architecture Search (NAS) has been used to search for the optimal building blocks of networks automatically, but the network depth, downsampling strategy, and feature aggregation way are still set in advance by trial and error. In this paper, we propose a joint search framework, called AutoRTNet, to automate the design of these strategies. Specifically, we propose hyper-cells to jointly decide the network depth and downsampling strategy, and an aggregation cell to achieve automatic multi-scale feature aggregation. Experimental results show that AutoRTNet achieves 73.9% mIoU on the Cityscapes test set and 110.0 FPS on an NVIDIA TitanXP GPU card with 768x1536 input images.

Disturbance-immune Weight Sharing for Neural Architecture Search

Neural architecture search (NAS) has gained increasing attention in the community of architecture design. One of the key factors behind the success lies in the training efficiency created by the weight sharing (WS) technique. However, WS-based NAS methods often suffer from a performance disturbance (PD) issue. That is, the training of subsequent architectures inevitably disturbs the performance of previously trained architectures due to the partially shared weights. This leads to inaccurate performance estimation for the previous architectures, which makes it hard to learn a good search strategy. To alleviate the performance disturbance issue, we propose a new disturbance-immune update strategy for model updating. Specifically, to preserve the knowledge learned by previous architectures, we constrain the training of subsequent architectures in an orthogonal space via orthogonal gradient descent. Equipped with this strategy, we propose a novel disturbance-immune training scheme for NAS. We theoretically analyze the effectiveness of our strategy in alleviating the PD risk. Extensive experiments on CIFAR-10 and ImageNet verify the superiority of our method.

Spectral Graph Attention Network

Variants of Graph Neural Networks (GNNs) for representation learning have been proposed recently and achieved fruitful results in various fields. Among them, graph attention networks (GATs) first employ a self-attention strategy to learn attention weights for each edge in the spatial domain. However, learning the attentions over edges only pays attention to the local information of graphs and greatly increases the number of parameters. In this paper, we first introduce attentions in the spectral domain of graphs. Accordingly, we present Spectral Graph Attention Network (SpGAT) that learn representations for different frequency components regarding weighted filters and graph wavelets bases. In this way, SpGAT can better capture global patterns of graphs in an efficient manner with much fewer learned parameters than that of GAT. We thoroughly evaluate the performance of SpGAT in the semi-supervised node classification task and verified the effectiveness of the learned attentions in the spectral domain.

Label-Driven Reconstruction for Domain Adaptation in Semantic Segmentation

Unsupervised domain adaptation enables to alleviate the need for pixel-wise annotation in the semantic segmentation. One of the most common strategies is to translate images from the source domain to the target domain and then align their marginal distributions in the feature space using adversarial learning. However, source-to-target translation enlarges the bias in translated images, owing to the dominant data size of the source domain. Furthermore, consistency of the joint distribution in source and target domains cannot be guaranteed through global feature alignment. Here, we present an innovative framework, designed to mitigate the image translation bias and align cross-domain features with the same category. This is achieved by 1) performing the target-to-source translation and 2) reconstructing both source and target images from their predicted labels. Extensive experiments on adapting from synthetic to real urban scene understanding demonstrate that our framework competes favorably against existing state-of-the-art methods.