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Nuclei detection and segmentation in hematoxylin and eosin-stained (H&E) tissue images are important clinical tasks and crucial for a wide range of applications. However, it is a challenging task due to nuclei variances in staining and size, overlapping boundaries, and nuclei clustering. While convolutional neural networks have been extensively used for this task, we explore the potential of Transformer-based networks in this domain. Therefore, we introduce a new method for automated instance segmentation of cell nuclei in digitized tissue samples using a deep learning architecture based on Vision Transformer called CellViT. CellViT is trained and evaluated on the PanNuke dataset, which is one of the most challenging nuclei instance segmentation datasets, consisting of nearly 200,000 annotated Nuclei into 5 clinically important classes in 19 tissue types. We demonstrate the superiority of large-scale in-domain and out-of-domain pre-trained Vision Transformers by leveraging the recently published Segment Anything Model and a ViT-encoder pre-trained on 104 million histological image patches - achieving state-of-the-art nuclei detection and instance segmentation performance on the PanNuke dataset with a mean panoptic quality of 0.51 and an F1-detection score of 0.83. The code is publicly available at //github.com/TIO-IKIM/CellViT

Federated Learning (FL) has been widely concerned for it enables decentralized learning while ensuring data privacy. However, most existing methods unrealistically assume that the classes encountered by local clients are fixed over time. After learning new classes, this assumption will make the model's catastrophic forgetting of old classes significantly severe. Moreover, due to the limitation of communication cost, it is challenging to use large-scale models in FL, which will affect the prediction accuracy. To address these challenges, we propose a novel framework, Federated Enhanced Transformer (FedET), which simultaneously achieves high accuracy and low communication cost. Specifically, FedET uses Enhancer, a tiny module, to absorb and communicate new knowledge, and applies pre-trained Transformers combined with different Enhancers to ensure high precision on various tasks. To address local forgetting caused by new classes of new tasks and global forgetting brought by non-i.i.d (non-independent and identically distributed) class imbalance across different local clients, we proposed an Enhancer distillation method to modify the imbalance between old and new knowledge and repair the non-i.i.d. problem. Experimental results demonstrate that FedET's average accuracy on representative benchmark datasets is 14.1% higher than the state-of-the-art method, while FedET saves 90% of the communication cost compared to the previous method.

Despite the tremendous success in text-to-image generative models, localized text-to-image generation (that is, generating objects or features at specific locations in an image while maintaining a consistent overall generation) still requires either explicit training or substantial additional inference time. In this work, we show that localized generation can be achieved by simply controlling cross attention maps during inference. With no additional training, model architecture modification or inference time, our proposed cross attention control (CAC) provides new open-vocabulary localization abilities to standard text-to-image models. CAC also enhances models that are already trained for localized generation when deployed at inference time. Furthermore, to assess localized text-to-image generation performance automatically, we develop a standardized suite of evaluations using large pretrained recognition models. Our experiments show that CAC improves localized generation performance with various types of location information ranging from bounding boxes to semantic segmentation maps, and enhances the compositional capability of state-of-the-art text-to-image generative models.

Feature-Imitating-Networks (FINs) are neural networks with weights that are initialized to approximate closed-form statistical features. In this work, we perform the first-ever evaluation of FINs for biomedical image processing tasks. We begin by training a set of FINs to imitate six common radiomics features, and then compare the performance of networks with and without the FINs for three experimental tasks: COVID-19 detection from CT scans, brain tumor classification from MRI scans, and brain-tumor segmentation from MRI scans; we find that FINs provide best-in-class performance for all three tasks, while converging faster and more consistently when compared to networks with similar or greater representational power. The results of our experiments provide evidence that FINs may provide state-of-the-art performance for a variety of other biomedical image processing tasks.

Deep learning-based super-resolution models have the potential to revolutionize biomedical imaging and diagnoses by effectively tackling various challenges associated with early detection, personalized medicine, and clinical automation. However, the requirement of an extensive collection of high-resolution images presents limitations for widespread adoption in clinical practice. In our experiment, we proposed an approach to effectively train the deep learning-based super-resolution models using only one real image by leveraging self-generated high-resolution images. We employed a mixed metric of image screening to automatically select images with a distribution similar to ground truth, creating an incrementally curated training data set that encourages the model to generate improved images over time. After five training iterations, the proposed deep learning-based super-resolution model experienced a 7.5\% and 5.49\% improvement in structural similarity and peak-signal-to-noise ratio, respectively. Significantly, the model consistently produces visually enhanced results for training, improving its performance while preserving the characteristics of original biomedical images. These findings indicate a potential way to train a deep neural network in a self-revolution manner independent of real-world human data.

Transformer-based language models have achieved impressive success in various natural language processing tasks due to their ability to capture complex dependencies and contextual information using self-attention mechanisms. However, they are not without limitations. These limitations include hallucinations, where they produce incorrect outputs with high confidence, and alignment issues, where they generate unhelpful and unsafe outputs for human users. These limitations stem from the absence of implicit and missing context in the data alone. To address this, researchers have explored augmenting these models with external knowledge from knowledge graphs to provide the necessary additional context. However, the ad-hoc nature of existing methods makes it difficult to properly analyze the effects of knowledge infusion on the many moving parts or components of a transformer. This paper introduces a systematic method for infusing knowledge into different components of a transformer-based model. A modular framework is proposed to identify specific components within the transformer architecture, such as the self-attention mechanism, encoder layers, or the input embedding layer, where knowledge infusion can be applied. Additionally, extensive experiments are conducted on the General Language Understanding Evaluation (GLUE) benchmark tasks, and the findings are reported. This systematic approach aims to facilitate more principled approaches to incorporating knowledge into language model architectures.

The real-world data tends to be heavily imbalanced and severely skew the data-driven deep neural networks, which makes Long-Tailed Recognition (LTR) a massive challenging task. Existing LTR methods seldom train Vision Transformers (ViTs) with Long-Tailed (LT) data, while the off-the-shelf pretrain weight of ViTs always leads to unfair comparisons. In this paper, we systematically investigate the ViTs' performance in LTR and propose LiVT to train ViTs from scratch only with LT data. With the observation that ViTs suffer more severe LTR problems, we conduct Masked Generative Pretraining (MGP) to learn generalized features. With ample and solid evidence, we show that MGP is more robust than supervised manners. In addition, Binary Cross Entropy (BCE) loss, which shows conspicuous performance with ViTs, encounters predicaments in LTR. We further propose the balanced BCE to ameliorate it with strong theoretical groundings. Specially, we derive the unbiased extension of Sigmoid and compensate extra logit margins to deploy it. Our Bal-BCE contributes to the quick convergence of ViTs in just a few epochs. Extensive experiments demonstrate that with MGP and Bal-BCE, LiVT successfully trains ViTs well without any additional data and outperforms comparable state-of-the-art methods significantly, e.g., our ViT-B achieves 81.0% Top-1 accuracy in iNaturalist 2018 without bells and whistles. Code is available at //github.com/XuZhengzhuo/LiVT.

Multiple instance learning (MIL) is a powerful tool to solve the weakly supervised classification in whole slide image (WSI) based pathology diagnosis. However, the current MIL methods are usually based on independent and identical distribution hypothesis, thus neglect the correlation among different instances. To address this problem, we proposed a new framework, called correlated MIL, and provided a proof for convergence. Based on this framework, we devised a Transformer based MIL (TransMIL), which explored both morphological and spatial information. The proposed TransMIL can effectively deal with unbalanced/balanced and binary/multiple classification with great visualization and interpretability. We conducted various experiments for three different computational pathology problems and achieved better performance and faster convergence compared with state-of-the-art methods. The test AUC for the binary tumor classification can be up to 93.09% over CAMELYON16 dataset. And the AUC over the cancer subtypes classification can be up to 96.03% and 98.82% over TCGA-NSCLC dataset and TCGA-RCC dataset, respectively.

We present ResMLP, an architecture built entirely upon multi-layer perceptrons for image classification. It is a simple residual network that alternates (i) a linear layer in which image patches interact, independently and identically across channels, and (ii) a two-layer feed-forward network in which channels interact independently per patch. When trained with a modern training strategy using heavy data-augmentation and optionally distillation, it attains surprisingly good accuracy/complexity trade-offs on ImageNet. We will share our code based on the Timm library and pre-trained models.

Few-shot image classification aims to classify unseen classes with limited labeled samples. Recent works benefit from the meta-learning process with episodic tasks and can fast adapt to class from training to testing. Due to the limited number of samples for each task, the initial embedding network for meta learning becomes an essential component and can largely affects the performance in practice. To this end, many pre-trained methods have been proposed, and most of them are trained in supervised way with limited transfer ability for unseen classes. In this paper, we proposed to train a more generalized embedding network with self-supervised learning (SSL) which can provide slow and robust representation for downstream tasks by learning from the data itself. We evaluate our work by extensive comparisons with previous baseline methods on two few-shot classification datasets ({\em i.e.,} MiniImageNet and CUB). Based on the evaluation results, the proposed method achieves significantly better performance, i.e., improve 1-shot and 5-shot tasks by nearly \textbf{3\%} and \textbf{4\%} on MiniImageNet, by nearly \textbf{9\%} and \textbf{3\%} on CUB. Moreover, the proposed method can gain the improvement of (\textbf{15\%}, \textbf{13\%}) on MiniImageNet and (\textbf{15\%}, \textbf{8\%}) on CUB by pretraining using more unlabeled data. Our code will be available at \hyperref[//github.com/phecy/SSL-FEW-SHOT.]{//github.com/phecy/ssl-few-shot.}