Zhe Xu

Rajarshi Roy, Jean-Raphaël Gaglione, Nasim Baharisangari et al.

We consider the problem of explaining the temporal behavior of black-box systems using human-interpretable models. To this end, based on recent research trends, we rely on the fundamental yet interpretable models of deterministic finite automata (DFAs) and linear temporal logic (LTL) formulas. In contrast to most existing works for learning DFAs and LTL formulas, we rely on only positive examples. Our motivation is that negative examples are generally difficult to observe, in particular, from black-box systems. To learn meaningful models from positive examples only, we design algorithms that rely on conciseness and language minimality of models as regularizers. To this end, our algorithms adopt two approaches: a symbolic and a counterexample-guided one. While the symbolic approach exploits an efficient encoding of language minimality as a constraint satisfaction problem, the counterexample-guided one relies on generating suitable negative examples to prune the search. Both the approaches provide us with effective algorithms with theoretical guarantees on the learned models. To assess the effectiveness of our algorithms, we evaluate all of them on synthetic data.

Jiangpeng Yan, Chenghui Yu, Hanbo Chen et al.

Recently, deep neural networks have greatly advanced undersampled Magnetic Resonance Image (MRI) reconstruction, wherein most studies follow the one-anatomy-one-network fashion, i.e., each expert network is trained and evaluated for a specific anatomy. Apart from inefficiency in training multiple independent models, such convention ignores the shared de-aliasing knowledge across various anatomies which can benefit each other. To explore the shared knowledge, one naive way is to combine all the data from various anatomies to train an all-round network. Unfortunately, despite the existence of the shared de-aliasing knowledge, we reveal that the exclusive knowledge across different anatomies can deteriorate specific reconstruction targets, yielding overall performance degradation. Observing this, in this study, we present a novel deep MRI reconstruction framework with both anatomy-shared and anatomy-specific parameterized learners, aiming to "seek common ground while reserving differences" across different anatomies.Particularly, the primary anatomy-shared learners are exposed to different anatomies to model flourishing shared knowledge, while the efficient anatomy-specific learners are trained with their target anatomy for exclusive knowledge. Four different implementations of anatomy-specific learners are presented and explored on the top of our framework in two MRI reconstruction networks. Comprehensive experiments on brain, knee and cardiac MRI datasets demonstrate that three of these learners are able to enhance reconstruction performance via multiple anatomy collaborative learning.

Wentao Pan, Jiangpeng Yan, Hanbo Chen et al.

Recently, deep neural networks have greatly advanced histopathology image segmentation but usually require abundant annotated data. However, due to the gigapixel scale of whole slide images and pathologists' heavy daily workload, obtaining pixel-level labels for supervised learning in clinical practice is often infeasible. Alternatively, weakly-supervised segmentation methods have been explored with less laborious image-level labels, but their performance is unsatisfactory due to the lack of dense supervision. Inspired by the recent success of self-supervised learning methods, we present a label-efficient tissue prototype dictionary building pipeline and propose to use the obtained prototypes to guide histopathology image segmentation. Particularly, taking advantage of self-supervised contrastive learning, an encoder is trained to project the unlabeled histopathology image patches into a discriminative embedding space where these patches are clustered to identify the tissue prototypes by efficient pathologists' visual examination. Then, the encoder is used to map the images into the embedding space and generate pixel-level pseudo tissue masks by querying the tissue prototype dictionary. Finally, the pseudo masks are used to train a segmentation network with dense supervision for better performance. Experiments on two public datasets demonstrate that our human-machine interactive tissue prototype learning method can achieve comparable segmentation performance as the fully-supervised baselines with less annotation burden and outperform other weakly-supervised methods. Codes will be available upon publication.

Beidi Zhao, Boxin Du, Zhe Xu et al.

Graph Neural Networks (GNNs) have achieved tremendous success in a variety of real-world applications by relying on the fixed graph data as input. However, the initial input graph might not be optimal in terms of specific downstream tasks, because of information scarcity, noise, adversarial attacks, or discrepancies between the distribution in graph topology, features, and groundtruth labels. In this paper, we propose a bi-level optimization approach for learning the optimal graph structure via directly learning the Personalized PageRank propagation matrix as well as the downstream semi-supervised node classification simultaneously. We also explore a low-rank approximation model for further reducing the time complexity. Empirical evaluations show the superior efficacy and robustness of the proposed model over all baseline methods.

Zhe Xu, Menghai Pan, Yuzhong Chen et al.

Rationale discovery is defined as finding a subset of the input data that maximally supports the prediction of downstream tasks. In the context of graph machine learning, graph rationale is defined to locate the critical subgraph in the given graph topology. In contrast to the rationale subgraph, the remaining subgraph is named the environment subgraph. Graph rationalization can enhance the model performance as the mapping between the graph rationale and prediction label is viewed as invariant, by assumption. To ensure the discriminative power of the extracted rationale subgraphs, a key technique named "intervention" is applied whose heart is that given changing environment subgraphs, the semantics from the rationale subgraph is invariant, guaranteeing the correct prediction result. However, most, if not all, of the existing graph rationalization methods develop their intervention strategies on the graph level, which is coarse-grained. In this paper, we propose fine-grained graph rationalization (FIG). Our idea is driven by the self-attention mechanism, which provides rich interactions between input nodes. Based on that, FIG can achieve node-level and virtual node-level intervention. Our experiments involve 7 real-world datasets, and the proposed FIG shows significant performance advantages compared to 13 baseline methods.

Jueming Hu, Jean-Raphael Gaglione, Yanze Wang et al.

We investigate multi-agent reinforcement learning for stochastic games with complex tasks, where the reward functions are non-Markovian. We utilize reward machines to incorporate high-level knowledge of complex tasks. We develop an algorithm called Q-learning with reward machines for stochastic games (QRM-SG), to learn the best-response strategy at Nash equilibrium for each agent. In QRM-SG, we define the Q-function at a Nash equilibrium in augmented state space. The augmented state space integrates the state of the stochastic game and the state of reward machines. Each agent learns the Q-functions of all agents in the system. We prove that Q-functions learned in QRM-SG converge to the Q-functions at a Nash equilibrium if the stage game at each time step during learning has a global optimum point or a saddle point, and the agents update Q-functions based on the best-response strategy at this point. We use the Lemke-Howson method to derive the best-response strategy given current Q-functions. The three case studies show that QRM-SG can learn the best-response strategies effectively. QRM-SG learns the best-response strategies after around 7500 episodes in Case Study I, 1000 episodes in Case Study II, and 1500 episodes in Case Study III, while baseline methods such as Nash Q-learning and MADDPG fail to converge to the Nash equilibrium in all three case studies.

Kaize Ding, Zhe Xu, Hanghang Tong et al.

Graph neural networks, a powerful deep learning tool to model graph-structured data, have demonstrated remarkable performance on numerous graph learning tasks. To address the data noise and data scarcity issues in deep graph learning, the research on graph data augmentation has intensified lately. However, conventional data augmentation methods can hardly handle graph-structured data which is defined in non-Euclidean space with multi-modality. In this survey, we formally formulate the problem of graph data augmentation and further review the representative techniques and their applications in different deep graph learning problems. Specifically, we first propose a taxonomy for graph data augmentation techniques and then provide a structured review by categorizing the related work based on the augmented information modalities. Moreover, we summarize the applications of graph data augmentation in two representative problems in data-centric deep graph learning: (1) reliable graph learning which focuses on enhancing the utility of input graph as well as the model capacity via graph data augmentation; and (2) low-resource graph learning which targets on enlarging the labeled training data scale through graph data augmentation. For each problem, we also provide a hierarchical problem taxonomy and review the existing literature related to graph data augmentation. Finally, we point out promising research directions and the challenges in future research.

Alessa Hering, Lasse Hansen, Tony C. W. Mok et al.

Image registration is a fundamental medical image analysis task, and a wide variety of approaches have been proposed. However, only a few studies have comprehensively compared medical image registration approaches on a wide range of clinically relevant tasks. This limits the development of registration methods, the adoption of research advances into practice, and a fair benchmark across competing approaches. The Learn2Reg challenge addresses these limitations by providing a multi-task medical image registration data set for comprehensive characterisation of deformable registration algorithms. A continuous evaluation will be possible at https://learn2reg.grand-challenge.org. Learn2Reg covers a wide range of anatomies (brain, abdomen, and thorax), modalities (ultrasound, CT, MR), availability of annotations, as well as intra- and inter-patient registration evaluation. We established an easily accessible framework for training and validation of 3D registration methods, which enabled the compilation of results of over 65 individual method submissions from more than 20 unique teams. We used a complementary set of metrics, including robustness, accuracy, plausibility, and runtime, enabling unique insight into the current state-of-the-art of medical image registration. This paper describes datasets, tasks, evaluation methods and results of the challenge, as well as results of further analysis of transferability to new datasets, the importance of label supervision, and resulting bias. While no single approach worked best across all tasks, many methodological aspects could be identified that push the performance of medical image registration to new state-of-the-art performance. Furthermore, we demystified the common belief that conventional registration methods have to be much slower than deep-learning-based methods.

Nasim Baharisangari, Kazuma Hirota, Ruixuan Yan et al.

Extracting spatial-temporal knowledge from data is useful in many applications. It is important that the obtained knowledge is human-interpretable and amenable to formal analysis. In this paper, we propose a method that trains neural networks to learn spatial-temporal properties in the form of weighted graph-based signal temporal logic (wGSTL) formulas. For learning wGSTL formulas, we introduce a flexible wGSTL formula structure in which the user's preference can be applied in the inferred wGSTL formulas. In the proposed framework, each neuron of the neural networks corresponds to a subformula in a flexible wGSTL formula structure. We initially train a neural network to learn the wGSTL operators and then train a second neural network to learn the parameters in a flexible wGSTL formula structure. We use a COVID-19 dataset and a rain prediction dataset to evaluate the performance of the proposed framework and algorithms. We compare the performance of the proposed framework with three baseline classification methods including K-nearest neighbors, decision trees, support vector machine, and artificial neural networks. The classification accuracy obtained by the proposed framework is comparable with the baseline classification methods.

Yixin Wang, Zihao Lin, Zhe Xu et al.

Medical imaging plays a pivotal role in diagnosis and treatment in clinical practice. Inspired by the significant progress in automatic image captioning, various deep learning (DL)-based methods have been proposed to generate radiology reports for medical images. Despite promising results, previous works overlook the uncertainties of their models and are thus unable to provide clinicians with the reliability/confidence of the generated radiology reports to assist their decision-making. In this paper, we propose a novel method to explicitly quantify both the visual uncertainty and the textual uncertainty for DL-based radiology report generation. Such multi-modal uncertainties can sufficiently capture the model confidence degree at both the report level and the sentence level, and thus they are further leveraged to weight the losses for more comprehensive model optimization. Experimental results have demonstrated that the proposed method for model uncertainty characterization and estimation can produce more reliable confidence scores for radiology report generation, and the modified loss function, which takes into account the uncertainties, leads to better model performance on two public radiology report datasets. In addition, the quality of the automatically generated reports was manually evaluated by human raters and the results also indicate that the proposed uncertainties can reflect the variance of clinical diagnosis.

Zhe Xu, Boxin Du, Hanghang Tong

The past decades have witnessed the prosperity of graph mining, with a multitude of sophisticated models and algorithms designed for various mining tasks, such as ranking, classification, clustering and anomaly detection. Generally speaking, the vast majority of the existing works aim to answer the following question, that is, given a graph, what is the best way to mine it? In this paper, we introduce the graph sanitation problem, to answer an orthogonal question. That is, given a mining task and an initial graph, what is the best way to improve the initially provided graph? By learning a better graph as part of the input of the mining model, it is expected to benefit graph mining in a variety of settings, ranging from denoising, imputation to defense. We formulate the graph sanitation problem as a bilevel optimization problem, and further instantiate it by semi-supervised node classification, together with an effective solver named GaSoliNe. Extensive experimental results demonstrate that the proposed method is (1) broadly applicable with respect to different graph neural network models and flexible graph modification strategies, (2) effective in improving the node classification accuracy on both the original and contaminated graphs in various perturbation scenarios. In particular, it brings up to 25% performance improvement over the existing robust graph neural network methods.