Constructing and Exploring Intermediate Domains in Mixed Domain Semi-supervised Medical Image Segmentation

Both limited annotation and domain shift are prevalent challenges in medical image segmentation. Traditional semi-supervised segmentation and unsupervised domain adaptation methods address one of these issues separately. However, the coexistence of limited annotation and domain shift is quite common, which motivates us to introduce a novel and challenging scenario: Mixed Domain Semi-supervised medical image Segmentation (MiDSS). In this scenario, we handle data from multiple medical centers, with limited annotations available for a single domain and a large amount of unlabeled data from multiple domains. We found that the key to solving the problem lies in how to generate reliable pseudo labels for the unlabeled data in the presence of domain shift with labeled data. To tackle this issue, we employ Unified Copy-Paste (UCP) between images to construct intermediate domains, facilitating the knowledge transfer from the domain of labeled data to the domains of unlabeled data. To fully utilize the information within the intermediate domain, we propose a symmetric Guidance training strategy (SymGD), which additionally offers direct guidance to unlabeled data by merging pseudo labels from intermediate samples. Subsequently, we introduce a Training Process aware Random Amplitude MixUp (TP-RAM) to progressively incorporate style-transition components into intermediate samples. Compared with existing state-of-the-art approaches, our method achieves a notable 13.57% improvement in Dice score on Prostate dataset, as demonstrated on three public datasets. Our code is available at https://github.com/MQinghe/MiDSS .

SETA: Semantic-Aware Token Augmentation for Domain Generalization

Domain generalization (DG) aims to enhance the model robustness against domain shifts without accessing target domains. A prevalent category of methods for DG is data augmentation, which focuses on generating virtual samples to simulate domain shifts. However, existing augmentation techniques in DG are mainly tailored for convolutional neural networks (CNNs), with limited exploration in token-based architectures, i.e., vision transformer (ViT) and multi-layer perceptrons (MLP) models. In this paper, we study the impact of prior CNN-based augmentation methods on token-based models, revealing their performance is suboptimal due to the lack of incentivizing the model to learn holistic shape information. To tackle the issue, we propose the SEmantic-aware Token Augmentation (SETA) method. SETA transforms token features by perturbing local edge cues while preserving global shape features, thereby enhancing the model learning of shape information. To further enhance the generalization ability of the model, we introduce two stylized variants of our method combined with two state-of-the-art style augmentation methods in DG. We provide a theoretical insight into our method, demonstrating its effectiveness in reducing the generalization risk bound. Comprehensive experiments on five benchmarks prove that our method achieves SOTA performances across various ViT and MLP architectures. Our code is available at https://github.com/lingeringlight/SETA.

Concatenate, Fine-tuning, Re-training: A SAM-enabled Framework for Semi-supervised 3D Medical Image Segmentation

Segment Anything Model (SAM) fine-tuning has shown remarkable performance in medical image segmentation in a fully supervised manner, but requires precise annotations. To reduce the annotation cost and maintain satisfactory performance, in this work, we leverage the capabilities of SAM for establishing semi-supervised medical image segmentation models. Rethinking the requirements of effectiveness, efficiency, and compatibility, we propose a three-stage framework, i.e., Concatenate, Fine-tuning, and Re-training (CFR). The current fine-tuning approaches mostly involve 2D slice-wise fine-tuning that disregards the contextual information between adjacent slices. Our concatenation strategy mitigates the mismatch between natural and 3D medical images. The concatenated images are then used for fine-tuning SAM, providing robust initialization pseudo-labels. Afterwards, we train a 3D semi-supervised segmentation model while maintaining the same parameter size as the conventional segmenter such as V-Net. Our CFR framework is plug-and-play, and easily compatible with various popular semi-supervised methods. Extensive experiments validate that our CFR achieves significant improvements in both moderate annotation and scarce annotation across four datasets. In particular, CFR framework improves the Dice score of Mean Teacher from 29.68% to 74.40% with only one labeled data of LA dataset.

Learning Generalizable Models via Disentangling Spurious and Enhancing Potential Correlations

Domain generalization (DG) intends to train a model on multiple source domains to ensure that it can generalize well to an arbitrary unseen target domain. The acquisition of domain-invariant representations is pivotal for DG as they possess the ability to capture the inherent semantic information of the data, mitigate the influence of domain shift, and enhance the generalization capability of the model. Adopting multiple perspectives, such as the sample and the feature, proves to be effective. The sample perspective facilitates data augmentation through data manipulation techniques, whereas the feature perspective enables the extraction of meaningful generalization features. In this paper, we focus on improving the generalization ability of the model by compelling it to acquire domain-invariant representations from both the sample and feature perspectives by disentangling spurious correlations and enhancing potential correlations. 1) From the sample perspective, we develop a frequency restriction module, guiding the model to focus on the relevant correlations between object features and labels, thereby disentangling spurious correlations. 2) From the feature perspective, the simple Tail Interaction module implicitly enhances potential correlations among all samples from all source domains, facilitating the acquisition of domain-invariant representations across multiple domains for the model. The experimental results show that Convolutional Neural Networks (CNNs) or Multi-Layer Perceptrons (MLPs) with a strong baseline embedded with these two modules can achieve superior results, e.g., an average accuracy of 92.30% on Digits-DG.

PG-LBO: Enhancing High-Dimensional Bayesian Optimization with Pseudo-Label and Gaussian Process Guidance

Variational Autoencoder based Bayesian Optimization (VAE-BO) has demonstrated its excellent performance in addressing high-dimensional structured optimization problems. However, current mainstream methods overlook the potential of utilizing a pool of unlabeled data to construct the latent space, while only concentrating on designing sophisticated models to leverage the labeled data. Despite their effective usage of labeled data, these methods often require extra network structures, additional procedure, resulting in computational inefficiency. To address this issue, we propose a novel method to effectively utilize unlabeled data with the guidance of labeled data. Specifically, we tailor the pseudo-labeling technique from semi-supervised learning to explicitly reveal the relative magnitudes of optimization objective values hidden within the unlabeled data. Based on this technique, we assign appropriate training weights to unlabeled data to enhance the construction of a discriminative latent space. Furthermore, we treat the VAE encoder and the Gaussian Process (GP) in Bayesian optimization as a unified deep kernel learning process, allowing the direct utilization of labeled data, which we term as Gaussian Process guidance. This directly and effectively integrates the goal of improving GP accuracy into the VAE training, thereby guiding the construction of the latent space. The extensive experiments demonstrate that our proposed method outperforms existing VAE-BO algorithms in various optimization scenarios. Our code will be published at https://github.com/TaicaiChen/PG-LBO.

Roll With the Punches: Expansion and Shrinkage of Soft Label Selection for Semi-supervised Fine-Grained Learning

While semi-supervised learning (SSL) has yielded promising results, the more realistic SSL scenario remains to be explored, in which the unlabeled data exhibits extremely high recognition difficulty, e.g., fine-grained visual classification in the context of SSL (SS-FGVC). The increased recognition difficulty on fine-grained unlabeled data spells disaster for pseudo-labeling accuracy, resulting in poor performance of the SSL model. To tackle this challenge, we propose Soft Label Selection with Confidence-Aware Clustering based on Class Transition Tracking (SoC) by reconstructing the pseudo-label selection process by jointly optimizing Expansion Objective and Shrinkage Objective, which is based on a soft label manner. Respectively, the former objective encourages soft labels to absorb more candidate classes to ensure the attendance of ground-truth class, while the latter encourages soft labels to reject more noisy classes, which is theoretically proved to be equivalent to entropy minimization. In comparisons with various state-of-the-art methods, our approach demonstrates its superior performance in SS-FGVC. Checkpoints and source code are available at https://github.com/NJUyued/SoC4SS-FGVC.

FreeMask: Synthetic Images with Dense Annotations Make Stronger Segmentation Models

Semantic segmentation has witnessed tremendous progress due to the proposal of various advanced network architectures. However, they are extremely hungry for delicate annotations to train, and the acquisition is laborious and unaffordable. Therefore, we present FreeMask in this work, which resorts to synthetic images from generative models to ease the burden of both data collection and annotation procedures. Concretely, we first synthesize abundant training images conditioned on the semantic masks provided by realistic datasets. This yields extra well-aligned image-mask training pairs for semantic segmentation models. We surprisingly observe that, solely trained with synthetic images, we already achieve comparable performance with real ones (e.g., 48.3 vs. 48.5 mIoU on ADE20K, and 49.3 vs. 50.5 on COCO-Stuff). Then, we investigate the role of synthetic images by joint training with real images, or pre-training for real images. Meantime, we design a robust filtering principle to suppress incorrectly synthesized regions. In addition, we propose to inequally treat different semantic masks to prioritize those harder ones and sample more corresponding synthetic images for them. As a result, either jointly trained or pre-trained with our filtered and re-sampled synthesized images, segmentation models can be greatly enhanced, e.g., from 48.7 to 52.0 on ADE20K. Code is available at https://github.com/LiheYoung/FreeMask.

Exploring Flat Minima for Domain Generalization with Large Learning Rates

Domain Generalization (DG) aims to generalize to arbitrary unseen domains. A promising approach to improve model generalization in DG is the identification of flat minima. One typical method for this task is SWAD, which involves averaging weights along the training trajectory. However, the success of weight averaging depends on the diversity of weights, which is limited when training with a small learning rate. Instead, we observe that leveraging a large learning rate can simultaneously promote weight diversity and facilitate the identification of flat regions in the loss landscape. However, employing a large learning rate suffers from the convergence problem, which cannot be resolved by simply averaging the training weights. To address this issue, we introduce a training strategy called Lookahead which involves the weight interpolation, instead of average, between fast and slow weights. The fast weight explores the weight space with a large learning rate, which is not converged while the slow weight interpolates with it to ensure the convergence. Besides, weight interpolation also helps identify flat minima by implicitly optimizing the local entropy loss that measures flatness. To further prevent overfitting during training, we propose two variants to regularize the training weight with weighted averaged weight or with accumulated history weight. Taking advantage of this new perspective, our methods achieve state-of-the-art performance on both classification and semantic segmentation domain generalization benchmarks. The code is available at https://github.com/koncle/DG-with-Large-LR.

Enhancing Sample Utilization through Sample Adaptive Augmentation in Semi-Supervised Learning

In semi-supervised learning, unlabeled samples can be utilized through augmentation and consistency regularization. However, we observed certain samples, even undergoing strong augmentation, are still correctly classified with high confidence, resulting in a loss close to zero. It indicates that these samples have been already learned well and do not provide any additional optimization benefits to the model. We refer to these samples as ``naive samples". Unfortunately, existing SSL models overlook the characteristics of naive samples, and they just apply the same learning strategy to all samples. To further optimize the SSL model, we emphasize the importance of giving attention to naive samples and augmenting them in a more diverse manner. Sample adaptive augmentation (SAA) is proposed for this stated purpose and consists of two modules: 1) sample selection module; 2) sample augmentation module. Specifically, the sample selection module picks out {naive samples} based on historical training information at each epoch, then the naive samples will be augmented in a more diverse manner in the sample augmentation module. Thanks to the extreme ease of implementation of the above modules, SAA is advantageous for being simple and lightweight. We add SAA on top of FixMatch and FlexMatch respectively, and experiments demonstrate SAA can significantly improve the models. For example, SAA helped improve the accuracy of FixMatch from 92.50% to 94.76% and that of FlexMatch from 95.01% to 95.31% on CIFAR-10 with 40 labels.

Theoretical Explanation of Activation Sparsity through Flat Minima and Adversarial Robustness

A recent empirical observation of activation sparsity in MLP layers offers an opportunity to drastically reduce computation costs for free. Despite several works attributing it to training dynamics, the theoretical explanation of activation sparsity's emergence is restricted to shallow networks, small training steps well as modified training, even though the sparsity has been found in deep models trained by vanilla protocols for large steps. To fill the three gaps, we propose the notion of gradient sparsity as the source of activation sparsity and a theoretical explanation based on it that explains gradient sparsity and then activation sparsity as necessary steps to adversarial robustness w.r.t. hidden features and parameters, which is approximately the flatness of minima for well-learned models. The theory applies to standardly trained LayerNorm-ed pure MLPs, and further to Transformers or other architectures if noises are added to weights during training. To eliminate other sources of flatness when arguing sparsities' necessity, we discover the phenomenon of spectral concentration, i.e., the ratio between the largest and the smallest non-zero singular values of weight matrices is small. We utilize random matrix theory (RMT) as a powerful theoretical tool to analyze stochastic gradient noises and discuss the emergence of spectral concentration. With these insights, we propose two plug-and-play modules for both training from scratch and sparsity finetuning, as well as one radical modification that only applies to from-scratch training. Another under-testing module for both sparsity and flatness is also immediate from our theories. Validational experiments are conducted to verify our explanation. Experiments for productivity demonstrate modifications' improvement in sparsity, indicating further theoretical cost reduction in both training and inference.