SurvReLU: Inherently Interpretable Survival Analysis via Deep ReLU Networks

Survival analysis models time-to-event distributions with censorship. Recently, deep survival models using neural networks have dominated due to their representational power and state-of-the-art performance. However, their "black-box" nature hinders interpretability, which is crucial in real-world applications. In contrast, "white-box" tree-based survival models offer better interpretability but struggle to converge to global optima due to greedy expansion. In this paper, we bridge the gap between previous deep survival models and traditional tree-based survival models through deep rectified linear unit (ReLU) networks. We show that a deliberately constructed deep ReLU network (SurvReLU) can harness the interpretability of tree-based structures with the representational power of deep survival models. Empirical studies on both simulated and real survival benchmark datasets show the effectiveness of the proposed SurvReLU in terms of performance and interoperability. The code is available at \href{https://github.com/xs018/SurvReLU}{\color{magenta}{ https://github.com/xs018/SurvReLU}}.

RBAD: A Dataset and Benchmark for Retinal Vessels Branching Angle Detection

Detecting retinal image analysis, particularly the geometrical features of branching points, plays an essential role in diagnosing eye diseases. However, existing methods used for this purpose often are coarse-level and lack fine-grained analysis for efficient annotation. To mitigate these issues, this paper proposes a novel method for detecting retinal branching angles using a self-configured image processing technique. Additionally, we offer an open-source annotation tool and a benchmark dataset comprising 40 images annotated with retinal branching angles. Our methodology for retinal branching angle detection and calculation is detailed, followed by a benchmark analysis comparing our method with previous approaches. The results indicate that our method is robust under various conditions with high accuracy and efficiency, which offers a valuable instrument for ophthalmic research and clinical applications.

DGR-MIL: Exploring Diverse Global Representation in Multiple Instance Learning for Whole Slide Image Classification

Multiple instance learning (MIL) stands as a powerful approach in weakly supervised learning, regularly employed in histological whole slide image (WSI) classification for detecting tumorous lesions. However, existing mainstream MIL methods focus on modeling correlation between instances while overlooking the inherent diversity among instances. However, few MIL methods have aimed at diversity modeling, which empirically show inferior performance but with a high computational cost. To bridge this gap, we propose a novel MIL aggregation method based on diverse global representation (DGR-MIL), by modeling diversity among instances through a set of global vectors that serve as a summary of all instances. First, we turn the instance correlation into the similarity between instance embeddings and the predefined global vectors through a cross-attention mechanism. This stems from the fact that similar instance embeddings typically would result in a higher correlation with a certain global vector. Second, we propose two mechanisms to enforce the diversity among the global vectors to be more descriptive of the entire bag: (i) positive instance alignment and (ii) a novel, efficient, and theoretically guaranteed diversification learning paradigm. Specifically, the positive instance alignment module encourages the global vectors to align with the center of positive instances (e.g., instances containing tumors in WSI). To further diversify the global representations, we propose a novel diversification learning paradigm leveraging the determinantal point process. The proposed model outperforms the state-of-the-art MIL aggregation models by a substantial margin on the CAMELYON-16 and the TCGA-lung cancer datasets. The code is available at \url{https://github.com/ChongQingNoSubway/DGR-MIL}.

SelfReg-UNet: Self-Regularized UNet for Medical Image Segmentation

Since its introduction, UNet has been leading a variety of medical image segmentation tasks. Although numerous follow-up studies have also been dedicated to improving the performance of standard UNet, few have conducted in-depth analyses of the underlying interest pattern of UNet in medical image segmentation. In this paper, we explore the patterns learned in a UNet and observe two important factors that potentially affect its performance: (i) irrelative feature learned caused by asymmetric supervision; (ii) feature redundancy in the feature map. To this end, we propose to balance the supervision between encoder and decoder and reduce the redundant information in the UNet. Specifically, we use the feature map that contains the most semantic information (i.e., the last layer of the decoder) to provide additional supervision to other blocks to provide additional supervision and reduce feature redundancy by leveraging feature distillation. The proposed method can be easily integrated into existing UNet architecture in a plug-and-play fashion with negligible computational cost. The experimental results suggest that the proposed method consistently improves the performance of standard UNets on four medical image segmentation datasets. The code is available at \url{https://github.com/ChongQingNoSubway/SelfReg-UNet}

TimeMIL: Advancing Multivariate Time Series Classification via a Time-aware Multiple Instance Learning

Deep neural networks, including transformers and convolutional neural networks, have significantly improved multivariate time series classification (MTSC). However, these methods often rely on supervised learning, which does not fully account for the sparsity and locality of patterns in time series data (e.g., diseases-related anomalous points in ECG). To address this challenge, we formally reformulate MTSC as a weakly supervised problem, introducing a novel multiple-instance learning (MIL) framework for better localization of patterns of interest and modeling time dependencies within time series. Our novel approach, TimeMIL, formulates the temporal correlation and ordering within a time-aware MIL pooling, leveraging a tokenized transformer with a specialized learnable wavelet positional token. The proposed method surpassed 26 recent state-of-the-art methods, underscoring the effectiveness of the weakly supervised TimeMIL in MTSC.

Imaging Signal Recovery Using Neural Network Priors Under Uncertain Forward Model Parameters

Inverse imaging problems (IIPs) arise in various applications, with the main objective of reconstructing an image from its compressed measurements. This problem is often ill-posed for being under-determined with multiple interchangeably consistent solutions. The best solution inherently depends on prior knowledge or assumptions, such as the sparsity of the image. Furthermore, the reconstruction process for most IIPs relies significantly on the imaging (i.e. forward model) parameters, which might not be fully known, or the measurement device may undergo calibration drifts. These uncertainties in the forward model create substantial challenges, where inaccurate reconstructions usually happen when the postulated parameters of the forward model do not fully match the actual ones. In this work, we devoted to tackling accurate reconstruction under the context of a set of possible forward model parameters that exist. Here, we propose a novel Moment-Aggregation (MA) framework that is compatible with the popular IIP solution by using a neural network prior. Specifically, our method can reconstruct the signal by considering all candidate parameters of the forward model simultaneously during the update of the neural network. We theoretically demonstrate the convergence of the MA framework, which has a similar complexity with reconstruction under the known forward model parameters. Proof-of-concept experiments demonstrate that the proposed MA achieves performance comparable to the forward model with the known precise parameter in reconstruction across both compressive sensing and phase retrieval applications, with a PSNR gap of 0.17 to 1.94 over various datasets, including MNIST, X-ray, Glas, and MoNuseg. This highlights our method's significant potential in reconstruction under an uncertain forward model.

AgileFormer: Spatially Agile Transformer UNet for Medical Image Segmentation

In the past decades, deep neural networks, particularly convolutional neural networks, have achieved state-of-the-art performance in a variety of medical image segmentation tasks. Recently, the introduction of the vision transformer (ViT) has significantly altered the landscape of deep segmentation models. There has been a growing focus on ViTs, driven by their excellent performance and scalability. However, we argue that the current design of the vision transformer-based UNet (ViT-UNet) segmentation models may not effectively handle the heterogeneous appearance (e.g., varying shapes and sizes) of objects of interest in medical image segmentation tasks. To tackle this challenge, we present a structured approach to introduce spatially dynamic components to the ViT-UNet. This adaptation enables the model to effectively capture features of target objects with diverse appearances. This is achieved by three main components: \textbf{(i)} deformable patch embedding; \textbf{(ii)} spatially dynamic multi-head attention; \textbf{(iii)} deformable positional encoding. These components were integrated into a novel architecture, termed AgileFormer. AgileFormer is a spatially agile ViT-UNet designed for medical image segmentation. Experiments in three segmentation tasks using publicly available datasets demonstrated the effectiveness of the proposed method. The code is available at \href{https://github.com/sotiraslab/AgileFormer}{https://github.com/sotiraslab/AgileFormer}.

D-Net: Dynamic Large Kernel with Dynamic Feature Fusion for Volumetric Medical Image Segmentation

Hierarchical transformers have achieved significant success in medical image segmentation due to their large receptive field and capabilities of effectively leveraging global long-range contextual information. Convolutional neural networks (CNNs) can also deliver a large receptive field by using large kernels, enabling them to achieve competitive performance with fewer model parameters. However, CNNs incorporated with large convolutional kernels remain constrained in adaptively capturing multi-scale features from organs with large variations in shape and size due to the employment of fixed-sized kernels. Additionally, they are unable to utilize global contextual information efficiently. To address these limitations, we propose Dynamic Large Kernel (DLK) and Dynamic Feature Fusion (DFF) modules. The DLK module employs multiple large kernels with varying kernel sizes and dilation rates to capture multi-scale features. Subsequently, a dynamic selection mechanism is utilized to adaptively highlight the most important spatial features based on global information. Additionally, the DFF module is proposed to adaptively fuse multi-scale local feature maps based on their global information. We integrate DLK and DFF in a hierarchical transformer architecture to develop a novel architecture, termed D-Net. D-Net is able to effectively utilize a multi-scale large receptive field and adaptively harness global contextual information. Extensive experimental results demonstrate that D-Net outperforms other state-of-the-art models in the two volumetric segmentation tasks, including abdominal multi-organ segmentation and multi-modality brain tumor segmentation. Our code is available at https://github.com/sotiraslab/DLK.

SC-MIL: Sparsely Coded Multiple Instance Learning for Whole Slide Image Classification

Multiple Instance Learning (MIL) has been widely used in weakly supervised whole slide image (WSI) classification. Typical MIL methods include a feature embedding part that embeds the instances into features via a pre-trained feature extractor and the MIL aggregator that combines instance embeddings into predictions. The current focus has been directed toward improving these parts by refining the feature embeddings through self-supervised pre-training and modeling the correlations between instances separately. In this paper, we proposed a sparsely coded MIL (SC-MIL) that addresses those two aspects at the same time by leveraging sparse dictionary learning. The sparse dictionary learning captures the similarities of instances by expressing them as a sparse linear combination of atoms in an over-complete dictionary. In addition, imposing sparsity help enhance the instance feature embeddings by suppressing irrelevant instances while retaining the most relevant ones. To make the conventional sparse coding algorithm compatible with deep learning, we unrolled it into an SC module by leveraging deep unrolling. The proposed SC module can be incorporated into any existing MIL framework in a plug-and-play manner with an acceptable computation cost. The experimental results on multiple datasets demonstrated that the proposed SC module could substantially boost the performance of state-of-the-art MIL methods. The codes are available at \href{https://github.com/sotiraslab/SCMIL.git}{https://github.com/sotiraslab/SCMIL.git}.

NSOTree: Neural Survival Oblique Tree

Survival analysis is a statistical method employed to scrutinize the duration until a specific event of interest transpires, known as time-to-event information characterized by censorship. Recently, deep learning-based methods have dominated this field due to their representational capacity and state-of-the-art performance. However, the black-box nature of the deep neural network hinders its interpretability, which is desired in real-world survival applications but has been largely neglected by previous works. In contrast, conventional tree-based methods are advantageous with respect to interpretability, while consistently grappling with an inability to approximate the global optima due to greedy expansion. In this paper, we leverage the strengths of both neural networks and tree-based methods, capitalizing on their ability to approximate intricate functions while maintaining interpretability. To this end, we propose a Neural Survival Oblique Tree (NSOTree) for survival analysis. Specifically, the NSOTree was derived from the ReLU network and can be easily incorporated into existing survival models in a plug-and-play fashion. Evaluations on both simulated and real survival datasets demonstrated the effectiveness of the proposed method in terms of performance and interpretability.