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In the post-deep learning era, the Transformer architecture has demonstrated its powerful performance across pre-trained big models and various downstream tasks. However, the enormous computational demands of this architecture have deterred many researchers. To further reduce the complexity of attention models, numerous efforts have been made to design more efficient methods. Among them, the State Space Model (SSM), as a possible replacement for the self-attention based Transformer model, has drawn more and more attention in recent years. In this paper, we give the first comprehensive review of these works and also provide experimental comparisons and analysis to better demonstrate the features and advantages of SSM. Specifically, we first give a detailed description of principles to help the readers quickly capture the key ideas of SSM. After that, we dive into the reviews of existing SSMs and their various applications, including natural language processing, computer vision, graph, multi-modal and multi-media, point cloud/event stream, time series data, and other domains. In addition, we give statistical comparisons and analysis of these models and hope it helps the readers to understand the effectiveness of different structures on various tasks. Then, we propose possible research points in this direction to better promote the development of the theoretical model and application of SSM. More related works will be continuously updated on the following GitHub: //github.com/Event-AHU/Mamba_State_Space_Model_Paper_List.

The fusion of causal models with deep learning introducing increasingly intricate data sets, such as the causal associations within images or between textual components, has surfaced as a focal research area. Nonetheless, the broadening of original causal concepts and theories to such complex, non-statistical data has been met with serious challenges. In response, our study proposes redefinitions of causal data into three distinct categories from the standpoint of causal structure and representation: definite data, semi-definite data, and indefinite data. Definite data chiefly pertains to statistical data used in conventional causal scenarios, while semi-definite data refers to a spectrum of data formats germane to deep learning, including time-series, images, text, and others. Indefinite data is an emergent research sphere inferred from the progression of data forms by us. To comprehensively present these three data paradigms, we elaborate on their formal definitions, differences manifested in datasets, resolution pathways, and development of research. We summarize key tasks and achievements pertaining to definite and semi-definite data from myriad research undertakings, present a roadmap for indefinite data, beginning with its current research conundrums. Lastly, we classify and scrutinize the key datasets presently utilized within these three paradigms.

Over the past few years, the rapid development of deep learning technologies for computer vision has greatly promoted the performance of medical image segmentation (MedISeg). However, the recent MedISeg publications usually focus on presentations of the major contributions (e.g., network architectures, training strategies, and loss functions) while unwittingly ignoring some marginal implementation details (also known as "tricks"), leading to a potential problem of the unfair experimental result comparisons. In this paper, we collect a series of MedISeg tricks for different model implementation phases (i.e., pre-training model, data pre-processing, data augmentation, model implementation, model inference, and result post-processing), and experimentally explore the effectiveness of these tricks on the consistent baseline models. Compared to paper-driven surveys that only blandly focus on the advantages and limitation analyses of segmentation models, our work provides a large number of solid experiments and is more technically operable. With the extensive experimental results on both the representative 2D and 3D medical image datasets, we explicitly clarify the effect of these tricks. Moreover, based on the surveyed tricks, we also open-sourced a strong MedISeg repository, where each of its components has the advantage of plug-and-play. We believe that this milestone work not only completes a comprehensive and complementary survey of the state-of-the-art MedISeg approaches, but also offers a practical guide for addressing the future medical image processing challenges including but not limited to small dataset learning, class imbalance learning, multi-modality learning, and domain adaptation. The code has been released at: //github.com/hust-linyi/MedISeg

The rapid development of deep learning has made a great progress in segmentation, one of the fundamental tasks of computer vision. However, the current segmentation algorithms mostly rely on the availability of pixel-level annotations, which are often expensive, tedious, and laborious. To alleviate this burden, the past years have witnessed an increasing attention in building label-efficient, deep-learning-based segmentation algorithms. This paper offers a comprehensive review on label-efficient segmentation methods. To this end, we first develop a taxonomy to organize these methods according to the supervision provided by different types of weak labels (including no supervision, coarse supervision, incomplete supervision and noisy supervision) and supplemented by the types of segmentation problems (including semantic segmentation, instance segmentation and panoptic segmentation). Next, we summarize the existing label-efficient segmentation methods from a unified perspective that discusses an important question: how to bridge the gap between weak supervision and dense prediction -- the current methods are mostly based on heuristic priors, such as cross-pixel similarity, cross-label constraint, cross-view consistency, cross-image relation, etc. Finally, we share our opinions about the future research directions for label-efficient deep segmentation.

The incredible development of federated learning (FL) has benefited various tasks in the domains of computer vision and natural language processing, and the existing frameworks such as TFF and FATE has made the deployment easy in real-world applications. However, federated graph learning (FGL), even though graph data are prevalent, has not been well supported due to its unique characteristics and requirements. The lack of FGL-related framework increases the efforts for accomplishing reproducible research and deploying in real-world applications. Motivated by such strong demand, in this paper, we first discuss the challenges in creating an easy-to-use FGL package and accordingly present our implemented package FederatedScope-GNN (FS-G), which provides (1) a unified view for modularizing and expressing FGL algorithms; (2) comprehensive DataZoo and ModelZoo for out-of-the-box FGL capability; (3) an efficient model auto-tuning component; and (4) off-the-shelf privacy attack and defense abilities. We validate the effectiveness of FS-G by conducting extensive experiments, which simultaneously gains many valuable insights about FGL for the community. Moreover, we employ FS-G to serve the FGL application in real-world E-commerce scenarios, where the attained improvements indicate great potential business benefits. We publicly release FS-G, as submodules of FederatedScope, at //github.com/alibaba/FederatedScope to promote FGL's research and enable broad applications that would otherwise be infeasible due to the lack of a dedicated package.

Despite the recent progress in deep learning, most approaches still go for a silo-like solution, focusing on learning each task in isolation: training a separate neural network for each individual task. Many real-world problems, however, call for a multi-modal approach and, therefore, for multi-tasking models. Multi-task learning (MTL) aims to leverage useful information across tasks to improve the generalization capability of a model. This thesis is concerned with multi-task learning in the context of computer vision. First, we review existing approaches for MTL. Next, we propose several methods that tackle important aspects of multi-task learning. The proposed methods are evaluated on various benchmarks. The results show several advances in the state-of-the-art of multi-task learning. Finally, we discuss several possibilities for future work.

Molecular design and synthesis planning are two critical steps in the process of molecular discovery that we propose to formulate as a single shared task of conditional synthetic pathway generation. We report an amortized approach to generate synthetic pathways as a Markov decision process conditioned on a target molecular embedding. This approach allows us to conduct synthesis planning in a bottom-up manner and design synthesizable molecules by decoding from optimized conditional codes, demonstrating the potential to solve both problems of design and synthesis simultaneously. The approach leverages neural networks to probabilistically model the synthetic trees, one reaction step at a time, according to reactivity rules encoded in a discrete action space of reaction templates. We train these networks on hundreds of thousands of artificial pathways generated from a pool of purchasable compounds and a list of expert-curated templates. We validate our method with (a) the recovery of molecules using conditional generation, (b) the identification of synthesizable structural analogs, and (c) the optimization of molecular structures given oracle functions relevant to drug discovery.

With the advances of data-driven machine learning research, a wide variety of prediction problems have been tackled. It has become critical to explore how machine learning and specifically deep learning methods can be exploited to analyse healthcare data. A major limitation of existing methods has been the focus on grid-like data; however, the structure of physiological recordings are often irregular and unordered which makes it difficult to conceptualise them as a matrix. As such, graph neural networks have attracted significant attention by exploiting implicit information that resides in a biological system, with interactive nodes connected by edges whose weights can be either temporal associations or anatomical junctions. In this survey, we thoroughly review the different types of graph architectures and their applications in healthcare. We provide an overview of these methods in a systematic manner, organized by their domain of application including functional connectivity, anatomical structure and electrical-based analysis. We also outline the limitations of existing techniques and discuss potential directions for future research.

Small data challenges have emerged in many learning problems, since the success of deep neural networks often relies on the availability of a huge amount of labeled data that is expensive to collect. To address it, many efforts have been made on training complex models with small data in an unsupervised and semi-supervised fashion. In this paper, we will review the recent progresses on these two major categories of methods. A wide spectrum of small data models will be categorized in a big picture, where we will show how they interplay with each other to motivate explorations of new ideas. We will review the criteria of learning the transformation equivariant, disentangled, self-supervised and semi-supervised representations, which underpin the foundations of recent developments. Many instantiations of unsupervised and semi-supervised generative models have been developed on the basis of these criteria, greatly expanding the territory of existing autoencoders, generative adversarial nets (GANs) and other deep networks by exploring the distribution of unlabeled data for more powerful representations. While we focus on the unsupervised and semi-supervised methods, we will also provide a broader review of other emerging topics, from unsupervised and semi-supervised domain adaptation to the fundamental roles of transformation equivariance and invariance in training a wide spectrum of deep networks. It is impossible for us to write an exclusive encyclopedia to include all related works. Instead, we aim at exploring the main ideas, principles and methods in this area to reveal where we are heading on the journey towards addressing the small data challenges in this big data era.

In this paper, we propose the joint learning attention and recurrent neural network (RNN) models for multi-label classification. While approaches based on the use of either model exist (e.g., for the task of image captioning), training such existing network architectures typically require pre-defined label sequences. For multi-label classification, it would be desirable to have a robust inference process, so that the prediction error would not propagate and thus affect the performance. Our proposed model uniquely integrates attention and Long Short Term Memory (LSTM) models, which not only addresses the above problem but also allows one to identify visual objects of interests with varying sizes without the prior knowledge of particular label ordering. More importantly, label co-occurrence information can be jointly exploited by our LSTM model. Finally, by advancing the technique of beam search, prediction of multiple labels can be efficiently achieved by our proposed network model.