Designing effective architectures is one of the key factors behind the success of deep neural networks. Existing deep architectures are either manually designed or automatically searched by some Neural Architecture Search (NAS) methods. However, even a well-designed/searched architecture may still contain many nonsignificant or redundant modules/operations. Thus, it is necessary to optimize the operations inside an architecture to improve the performance without introducing extra computational cost. To this end, we have proposed a Neural Architecture Transformer (NAT) method which casts the optimization problem into a Markov Decision Process (MDP) and seeks to replace the redundant operations with more efficient operations, such as skip or null connection. Note that NAT only considers a small number of possible transitions and thus comes with a limited search/transition space. As a result, such a small search space may hamper the performance of architecture optimization. To address this issue, we propose a Neural Architecture Transformer++ (NAT++) method which further enlarges the set of candidate transitions to improve the performance of architecture optimization. Specifically, we present a two-level transition rule to obtain valid transitions, i.e., allowing operations to have more efficient types (e.g., convolution->separable convolution) or smaller kernel sizes (e.g., 5x5->3x3). Note that different operations may have different valid transitions. We further propose a Binary-Masked Softmax (BMSoftmax) layer to omit the possible invalid transitions. Extensive experiments on several benchmark datasets show that the transformed architecture significantly outperforms both its original counterpart and the architectures optimized by existing methods.
In adversarial training (AT), the main focus has been the objective and optimizer while the model has been less studied, so that the models being used are still those classic ones in standard training (ST). Classic network architectures (NAs) are generally worse than searched NAs in ST, which should be the same in AT. In this paper, we argue that NA and AT cannot be handled independently, since given a dataset, the optimal NA in ST would be no longer optimal in AT. That being said, AT is time-consuming itself; if we directly search NAs in AT over large search spaces, the computation will be practically infeasible. Thus, we propose a diverse-structured network (DS-Net), to significantly reduce the size of the search space: instead of low-level operations, we only consider predefined atomic blocks, where an atomic block is a time-tested building block like the residual block. There are only a few atomic blocks and thus we can weight all atomic blocks rather than find the best one in a searched block of DS-Net, which is an essential trade-off between exploring diverse structures and exploiting the best structures. Empirical results demonstrate the advantages of DS-Net, i.e., weighting the atomic blocks.
Graph Neural Networks (GNNs) draw their strength from explicitly modeling the topological information of structured data. However, existing GNNs suffer from limited capability in capturing the hierarchical graph representation which plays an important role in graph classification. In this paper, we innovatively propose hierarchical graph capsule network (HGCN) that can jointly learn node embeddings and extract graph hierarchies. Specifically, disentangled graph capsules are established by identifying heterogeneous factors underlying each node, such that their instantiation parameters represent different properties of the same entity. To learn the hierarchical representation, HGCN characterizes the part-whole relationship between lower-level capsules (part) and higher-level capsules (whole) by explicitly considering the structure information among the parts. Experimental studies demonstrate the effectiveness of HGCN and the contribution of each component.
Deep multimodal fusion by using multiple sources of data for classification or regression has exhibited a clear advantage over the unimodal counterpart on various applications. Yet, current methods including aggregation-based and alignment-based fusion are still inadequate in balancing the trade-off between inter-modal fusion and intra-modal processing, incurring a bottleneck of performance improvement. To this end, this paper proposes Channel-Exchanging-Network (CEN), a parameter-free multimodal fusion framework that dynamically exchanges channels between sub-networks of different modalities. Specifically, the channel exchanging process is self-guided by individual channel importance that is measured by the magnitude of Batch-Normalization (BN) scaling factor during training. The validity of such exchanging process is also guaranteed by sharing convolutional filters yet keeping separate BN layers across modalities, which, as an add-on benefit, allows our multimodal architecture to be almost as compact as a unimodal network. Extensive experiments on semantic segmentation via RGB-D data and image translation through multi-domain input verify the effectiveness of our CEN compared to current state-of-the-art methods. Detailed ablation studies have also been carried out, which provably affirm the advantage of each component we propose. Our code is available at https://github.com/yikaiw/CEN.
Recently, the teacher-student knowledge distillation framework has demonstrated its potential in training Graph Neural Networks (GNNs). However, due to the difficulty of training deep and wide GNN models, one can not always obtain a satisfactory teacher model for distillation. Furthermore, the inefficient training process of teacher-student knowledge distillation also impedes its applications in GNN models. In this paper, we propose the first teacher-free knowledge distillation framework for GNNs, termed GNN Self-Distillation (GNN-SD), that serves as a drop-in replacement for improving the training process of GNNs.We design three knowledge sources for GNN-SD: neighborhood discrepancy rate (NDR), compact graph embedding and intermediate logits. Notably, serving as a metric of the non-smoothness of the embedded graph, NDR empowers the transferability of knowledge that maintains high neighborhood discrepancy by enforcing consistency between consecutive GNN layers. We conduct exploring analysis to verify that our framework could improve the training dynamics and embedding quality of GNNs. Extensive experiments on various popular GNN models and datasets demonstrate that our approach obtains consistent and considerable performance enhancement, proving its effectiveness and generalization ability.
Retrosynthesis is the process of recursively decomposing target molecules into available building blocks. It plays an important role in solving problems in organic synthesis planning. To automate or assist in the retrosynthesis analysis, various retrosynthesis prediction algorithms have been proposed. However, most of them are cumbersome and lack interpretability about their predictions. In this paper, we devise a novel template-free algorithm for automatic retrosynthetic expansion inspired by how chemists approach retrosynthesis prediction. Our method disassembles retrosynthesis into two steps: i) identify the potential reaction center of the target molecule through a novel graph neural network and generate intermediate synthons, and ii) generate the reactants associated with synthons via a robust reactant generation model. While outperforming the state-of-the-art baselines by a significant margin, our model also provides chemically reasonable interpretation.
Given the input graph and its label/property, several key problems of graph learning, such as finding interpretable subgraphs, graph denoising and graph compression, can be attributed to the fundamental problem of recognizing a subgraph of the original one. This subgraph shall be as informative as possible, yet contains less redundant and noisy structure. This problem setting is closely related to the well-known information bottleneck (IB) principle, which, however, has less been studied for the irregular graph data and graph neural networks (GNNs). In this paper, we propose a framework of Graph Information Bottleneck (GIB) for the subgraph recognition problem in deep graph learning. Under this framework, one can recognize the maximally informative yet compressive subgraph, named IB-subgraph. However, the GIB objective is notoriously hard to optimize, mostly due to the intractability of the mutual information of irregular graph data and the unstable optimization process. In order to tackle these challenges, we propose: i) a GIB objective based-on a mutual information estimator for the irregular graph data; ii) a bi-level optimization scheme to maximize the GIB objective; iii) a connectivity loss to stabilize the optimization process. We evaluate the properties of the IB-subgraph in three application scenarios: improvement of graph classification, graph interpretation and graph denoising. Extensive experiments demonstrate that the information-theoretic IB-subgraph enjoys superior graph properties.
Traditional image-based survival prediction models rely on discriminative patch labeling which make those methods not scalable to extend to large datasets. Recent studies have shown Multiple Instance Learning (MIL) framework is useful for histopathological images when no annotations are available in classification task. Different to the current image-based survival models that limit to key patches or clusters derived from Whole Slide Images (WSIs), we propose Deep Attention Multiple Instance Survival Learning (DeepAttnMISL) by introducing both siamese MI-FCN and attention-based MIL pooling to efficiently learn imaging features from the WSI and then aggregate WSI-level information to patient-level. Attention-based aggregation is more flexible and adaptive than aggregation techniques in recent survival models. We evaluated our methods on two large cancer whole slide images datasets and our results suggest that the proposed approach is more effective and suitable for large datasets and has better interpretability in locating important patterns and features that contribute to accurate cancer survival predictions. The proposed framework can also be used to assess individual patient's risk and thus assisting in delivering personalized medicine. Codes are available at https://github.com/uta-smile/DeepAttnMISL_MEDIA.
The overexpression of human epidermal growth factor receptor 2 (HER2) has been established as a therapeutic target in multiple types of cancers, such as breast and gastric cancers. Immunohistochemistry (IHC) is employed as a basic HER2 test to identify the HER2-positive, borderline, and HER2-negative patients. However, the reliability and accuracy of HER2 scoring are affected by many factors, such as pathologists' experience. Recently, artificial intelligence (AI) has been used in various disease diagnosis to improve diagnostic accuracy and reliability, but the interpretation of diagnosis results is still an open problem. In this paper, we propose a real-time HER2 scoring system, which follows the HER2 scoring guidelines to complete the diagnosis, and thus each step is explainable. Unlike the previous scoring systems based on whole-slide imaging, our HER2 scoring system is integrated into an augmented reality (AR) microscope that can feedback AI results to the pathologists while reading the slide. The pathologists can help select informative fields of view (FOVs), avoiding the confounding regions, such as DCIS. Importantly, we illustrate the intermediate results with membrane staining condition and cell classification results, making it possible to evaluate the reliability of the diagnostic results. Also, we support the interactive modification of selecting regions-of-interest, making our system more flexible in clinical practice. The collaboration of AI and pathologists can significantly improve the robustness of our system. We evaluate our system with 285 breast IHC HER2 slides, and the classification accuracy of 95\% shows the effectiveness of our HER2 scoring system.