A Continual Learning-driven Model for Accurate and Generalizable Segmentation of Clinically Comprehensive and Fine-grained Whole-body Anatomies in CT

Precision medicine in the quantitative management of chronic diseases and oncology would be greatly improved if the Computed Tomography (CT) scan of any patient could be segmented, parsed and analyzed in a precise and detailed way. However, there is no such fully annotated CT dataset with all anatomies delineated for training because of the exceptionally high manual cost, the need for specialized clinical expertise, and the time required to finish the task. To this end, we proposed a novel continual learning-driven CT model that can segment complete anatomies presented using dozens of previously partially labeled datasets, dynamically expanding its capacity to segment new ones without compromising previously learned organ knowledge. Existing multi-dataset approaches are not able to dynamically segment new anatomies without catastrophic forgetting and would encounter optimization difficulty or infeasibility when segmenting hundreds of anatomies across the whole range of body regions. Our single unified CT segmentation model, CL-Net, can highly accurately segment a clinically comprehensive set of 235 fine-grained whole-body anatomies. Composed of a universal encoder, multiple optimized and pruned decoders, CL-Net is developed using 13,952 CT scans from 20 public and 16 private high-quality partially labeled CT datasets of various vendors, different contrast phases, and pathologies. Extensive evaluation demonstrates that CL-Net consistently outperforms the upper limit of an ensemble of 36 specialist nnUNets trained per dataset with the complexity of 5% model size and significantly surpasses the segmentation accuracy of recent leading Segment Anything-style medical image foundation models by large margins. Our continual learning-driven CL-Net model would lay a solid foundation to facilitate many downstream tasks of oncology and chronic diseases using the most widely adopted CT imaging.

From Slices to Sequences: Autoregressive Tracking Transformer for Cohesive and Consistent 3D Lymph Node Detection in CT Scans

Lymph node (LN) assessment is an essential task in the routine radiology workflow, providing valuable insights for cancer staging, treatment planning and beyond. Identifying scatteredly-distributed and low-contrast LNs in 3D CT scans is highly challenging, even for experienced clinicians. Previous lesion and LN detection methods demonstrate effectiveness of 2.5D approaches (i.e, using 2D network with multi-slice inputs), leveraging pretrained 2D model weights and showing improved accuracy as compared to separate 2D or 3D detectors. However, slice-based 2.5D detectors do not explicitly model inter-slice consistency for LN as a 3D object, requiring heuristic post-merging steps to generate final 3D LN instances, which can involve tuning a set of parameters for each dataset. In this work, we formulate 3D LN detection as a tracking task and propose LN-Tracker, a novel LN tracking transformer, for joint end-to-end detection and 3D instance association. Built upon DETR-based detector, LN-Tracker decouples transformer decoder's query into the track and detection groups, where the track query autoregressively follows previously tracked LN instances along the z-axis of a CT scan. We design a new transformer decoder with masked attention module to align track query's content to the context of current slice, meanwhile preserving detection query's high accuracy in current slice. An inter-slice similarity loss is introduced to encourage cohesive LN association between slices. Extensive evaluation on four lymph node datasets shows LN-Tracker's superior performance, with at least 2.7% gain in average sensitivity when compared to other top 3D/2.5D detectors. Further validation on public lung nodule and prostate tumor detection tasks confirms the generalizability of LN-Tracker as it achieves top performance on both tasks. Datasets will be released upon acceptance.

From Histopathology Images to Cell Clouds: Learning Slide Representations with Hierarchical Cell Transformer

It is clinically crucial and potentially very beneficial to be able to analyze and model directly the spatial distributions of cells in histopathology whole slide images (WSI). However, most existing WSI datasets lack cell-level annotations, owing to the extremely high cost over giga-pixel images. Thus, it remains an open question whether deep learning models can directly and effectively analyze WSIs from the semantic aspect of cell distributions. In this work, we construct a large-scale WSI dataset with more than 5 billion cell-level annotations, termed WSI-Cell5B, and a novel hierarchical Cell Cloud Transformer (CCFormer) to tackle these challenges. WSI-Cell5B is based on 6,998 WSIs of 11 cancers from The Cancer Genome Atlas Program, and all WSIs are annotated per cell by coordinates and types. To the best of our knowledge, WSI-Cell5B is the first WSI-level large-scale dataset integrating cell-level annotations. On the other hand, CCFormer formulates the collection of cells in each WSI as a cell cloud and models cell spatial distribution. Specifically, Neighboring Information Embedding (NIE) is proposed to characterize the distribution of cells within the neighborhood of each cell, and a novel Hierarchical Spatial Perception (HSP) module is proposed to learn the spatial relationship among cells in a bottom-up manner. The clinical analysis indicates that WSI-Cell5B can be used to design clinical evaluation metrics based on counting cells that effectively assess the survival risk of patients. Extensive experiments on survival prediction and cancer staging show that learning from cell spatial distribution alone can already achieve state-of-the-art (SOTA) performance, i.e., CCFormer strongly outperforms other competing methods.

From Pixels to Gigapixels: Bridging Local Inductive Bias and Long-Range Dependencies with Pixel-Mamba

Histopathology plays a critical role in medical diagnostics, with whole slide images (WSIs) offering valuable insights that directly influence clinical decision-making. However, the large size and complexity of WSIs may pose significant challenges for deep learning models, in both computational efficiency and effective representation learning. In this work, we introduce Pixel-Mamba, a novel deep learning architecture designed to efficiently handle gigapixel WSIs. Pixel-Mamba leverages the Mamba module, a state-space model (SSM) with linear memory complexity, and incorporates local inductive biases through progressively expanding tokens, akin to convolutional neural networks. This enables Pixel-Mamba to hierarchically combine both local and global information while efficiently addressing computational challenges. Remarkably, Pixel-Mamba achieves or even surpasses the quantitative performance of state-of-the-art (SOTA) foundation models that were pretrained on millions of WSIs or WSI-text pairs, in a range of tumor staging and survival analysis tasks, {\bf even without requiring any pathology-specific pretraining}. Extensive experiments demonstrate the efficacy of Pixel-Mamba as a powerful and efficient framework for end-to-end WSI analysis.

SGTC: Semantic-Guided Triplet Co-training for Sparsely Annotated Semi-Supervised Medical Image Segmentation

Although semi-supervised learning has made significant advances in the field of medical image segmentation, fully annotating a volumetric sample slice by slice remains a costly and time-consuming task. Even worse, most of the existing approaches pay much attention to image-level information and ignore semantic features, resulting in the inability to perceive weak boundaries. To address these issues, we propose a novel Semantic-Guided Triplet Co-training (SGTC) framework, which achieves high-end medical image segmentation by only annotating three orthogonal slices of a few volumetric samples, significantly alleviating the burden of radiologists. Our method consist of two main components. Specifically, to enable semantic-aware, fine-granular segmentation and enhance the quality of pseudo-labels, a novel semantic-guided auxiliary learning mechanism is proposed based on the pretrained CLIP. In addition, focusing on a more challenging but clinically realistic scenario, a new triple-view disparity training strategy is proposed, which uses sparse annotations (i.e., only three labeled slices of a few volumes) to perform co-training between three sub-networks, significantly improving the robustness. Extensive experiments on three public medical datasets demonstrate that our method outperforms most state-of-the-art semi-supervised counterparts under sparse annotation settings. The source code is available at https://github.com/xmeimeimei/SGTC.

Decision Transformer vs. Decision Mamba: Analysing the Complexity of Sequential Decision Making in Atari Games

This work analyses the disparity in performance between Decision Transformer (DT) and Decision Mamba (DM) in sequence modelling reinforcement learning tasks for different Atari games. The study first observed that DM generally outperformed DT in the games Breakout and Qbert, while DT performed better in more complicated games, such as Hero and Kung Fu Master. To understand these differences, we expanded the number of games to 12 and performed a comprehensive analysis of game characteristics, including action space complexity, visual complexity, average trajectory length, and average steps to the first non-zero reward. In order to further analyse the key factors that impact the disparity in performance between DT and DM, we employ various approaches, including quantifying visual complexity, random forest regression, correlation analysis, and action space simplification strategies. The results indicate that the performance gap between DT and DM is affected by the complex interaction of multiple factors, with the complexity of the action space and visual complexity (particularly evaluated by compression ratio) being the primary determining factors. DM performs well in environments with simple action and visual elements, while DT shows an advantage in games with higher action and visual complexity. Our findings contribute to a deeper understanding of how the game characteristics affect the performance difference in sequential modelling reinforcement learning, potentially guiding the development of future model design and applications for diverse and complex environments.

SAFE: Slow and Fast Parameter-Efficient Tuning for Continual Learning with Pre-Trained Models

Continual learning aims to incrementally acquire new concepts in data streams while resisting forgetting previous knowledge. With the rise of powerful pre-trained models (PTMs), there is a growing interest in training incremental learning systems using these foundation models, rather than learning from scratch. Existing works often view PTMs as a strong initial point and directly apply parameter-efficient tuning (PET) in the first session for adapting to downstream tasks. In the following sessions, most methods freeze model parameters for tackling forgetting issues. However, applying PET directly to downstream data cannot fully explore the inherent knowledge in PTMs. Additionally, freezing the parameters in incremental sessions hinders models' plasticity to novel concepts not covered in the first session. To solve the above issues, we propose a Slow And Fast parameter-Efficient tuning (SAFE) framework. In particular, to inherit general knowledge from foundation models, we include a transfer loss function by measuring the correlation between the PTM and the PET-applied model. After calibrating in the first session, the slow efficient tuning parameters can capture more informative features, improving generalization to incoming classes. Moreover, to further incorporate novel concepts, we strike a balance between stability and plasticity by fixing slow efficient tuning parameters and continuously updating the fast ones. Specifically, a cross-classification loss with feature alignment is proposed to circumvent catastrophic forgetting. During inference, we introduce an entropy-based aggregation strategy to dynamically utilize the complementarity in the slow and fast learners. Extensive experiments on seven benchmark datasets verify the effectiveness of our method by significantly surpassing the state-of-the-art.

TAS: Distilling Arbitrary Teacher and Student via a Hybrid Assistant

Most knowledge distillation (KD) methodologies predominantly focus on teacher-student pairs with similar architectures, such as both being convolutional neural networks (CNNs). However, the potential and flexibility of KD can be greatly improved by expanding it to novel Cross-Architecture KD (CAKD), where the knowledge of homogeneous and heterogeneous teachers can be transferred flexibly to a given student. The primary challenge in CAKD lies in the substantial feature gaps between heterogeneous models, originating from the distinction of their inherent inductive biases and module functions. To this end, we introduce an assistant model as a bridge to facilitate smooth feature knowledge transfer between heterogeneous teachers and students. More importantly, within our proposed design principle, the assistant model combines the advantages of cross-architecture inductive biases and module functions by merging convolution and attention modules derived from both student and teacher module functions. Furthermore, we observe that heterogeneous features exhibit diverse spatial distributions in CAKD, hindering the effectiveness of conventional pixel-wise mean squared error (MSE) loss. Therefore, we leverage a spatial-agnostic InfoNCE loss to align features after spatial smoothing, thereby improving the feature alignments in CAKD. Our proposed method is evaluated across some homogeneous model pairs and arbitrary heterogeneous combinations of CNNs, ViTs, and MLPs, achieving state-of-the-art performance for distilled models with a maximum gain of 11.47% on CIFAR-100 and 3.67% on ImageNet-1K. Our code and models will be released.

End-to-end Multi-source Visual Prompt Tuning for Survival Analysis in Whole Slide Images

Survival analysis using pathology images poses a considerable challenge, as it requires the localization of relevant information from the multitude of tiles within whole slide images (WSIs). Current methods typically resort to a two-stage approach, where a pre-trained network extracts features from tiles, which are then used by survival models. This process, however, does not optimize the survival models in an end-to-end manner, and the pre-extracted features may not be ideally suited for survival prediction. To address this limitation, we present a novel end-to-end Visual Prompt Tuning framework for survival analysis, named VPTSurv. VPTSurv refines feature embeddings through an efficient encoder-decoder framework. The encoder remains fixed while the framework introduces tunable visual prompts and adaptors, thus permitting end-to-end training specifically for survival prediction by optimizing only the lightweight adaptors and the decoder. Moreover, the versatile VPTSurv framework accommodates multi-source information as prompts, thereby enriching the survival model. VPTSurv achieves substantial increases of 8.7% and 12.5% in the C-index on two immunohistochemical pathology image datasets. These significant improvements highlight the transformative potential of the end-to-end VPT framework over traditional two-stage methods.

Improved Esophageal Varices Assessment from Non-Contrast CT Scans

Esophageal varices (EV), a serious health concern resulting from portal hypertension, are traditionally diagnosed through invasive endoscopic procedures. Despite non-contrast computed tomography (NC-CT) imaging being a less expensive and non-invasive imaging modality, it has yet to gain full acceptance as a primary clinical diagnostic tool for EV evaluation. To overcome existing diagnostic challenges, we present the Multi-Organ-cOhesion-Network (MOON), a novel framework enhancing the analysis of critical organ features in NC-CT scans for effective assessment of EV. Drawing inspiration from the thorough assessment practices of radiologists, MOON establishes a cohesive multiorgan analysis model that unifies the imaging features of the related organs of EV, namely esophagus, liver, and spleen. This integration significantly increases the diagnostic accuracy for EV. We have compiled an extensive NC-CT dataset of 1,255 patients diagnosed with EV, spanning three grades of severity. Each case is corroborated by endoscopic diagnostic results. The efficacy of MOON has been substantiated through a validation process involving multi-fold cross-validation on 1,010 cases and an independent test on 245 cases, exhibiting superior diagnostic performance compared to methods focusing solely on the esophagus (for classifying severe grade: AUC of 0.864 versus 0.803, and for moderate to severe grades: AUC of 0.832 versus 0.793). To our knowledge, MOON is the first work to incorporate a synchronized multi-organ NC-CT analysis for EV assessment, providing a more acceptable and minimally invasive alternative for patients compared to traditional endoscopy.