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As an important task in remote sensing image analysis, remote sensing change detection (RSCD) aims to identify changes of interest in a region from spatially co-registered multi-temporal remote sensing images, so as to monitor the local development. Existing RSCD methods usually formulate RSCD as a binary classification task, representing changes of interest by merely feature concatenation or feature subtraction and recovering the spatial details via densely connected change representations, whose performances need further improvement. In this paper, we propose STNet, a RSCD network based on spatial and temporal feature fusions. Specifically, we design a temporal feature fusion (TFF) module to combine bi-temporal features using a cross-temporal gating mechanism for emphasizing changes of interest; a spatial feature fusion module is deployed to capture fine-grained information using a cross-scale attention mechanism for recovering the spatial details of change representations. Experimental results on three benchmark datasets for RSCD demonstrate that the proposed method achieves the state-of-the-art performance. Code is available at https://github.com/xwmaxwma/rschange., Accepted by ICME 2023

3D reconstruction of medical images from 2D images has increasingly become a challenging research topic with the advanced development of deep learning methods. Previous work in 3D reconstruction from limited (generally one or two) X-ray images mainly relies on learning from paired 2D and 3D images. In 3D oral reconstruction from panoramic imaging, the model also relies on some prior individual information, such as the dental arch curve or voxel-wise annotations, to restore the curved shape of the mandible during reconstruction. These limitations have hindered the use of single X-ray tomography in clinical applications. To address these challenges, we propose a new model that relies solely on projection data, including imaging direction and projection image, during panoramic scans to reconstruct the 3D oral structure. Our model builds on the neural radiance field by introducing multi-head prediction, dynamic sampling, and adaptive rendering, which accommodates the projection process of panoramic X-ray in dental imaging. Compared to end-to-end learning methods, our method achieves state-of-the-art performance without requiring additional supervision or prior knowledge.

Novel view synthesis with sparse inputs is a challenging problem for neural radiance fields (NeRF). Recent efforts alleviate this challenge by introducing external supervision, such as pre-trained models and extra depth signals, and by non-trivial patch-based rendering. In this paper, we present Frequency regularized NeRF (FreeNeRF), a surprisingly simple baseline that outperforms previous methods with minimal modifications to the plain NeRF. We analyze the key challenges in few-shot neural rendering and find that frequency plays an important role in NeRF's training. Based on the analysis, we propose two regularization terms. One is to regularize the frequency range of NeRF's inputs, while the other is to penalize the near-camera density fields. Both techniques are ``free lunches'' at no additional computational cost. We demonstrate that even with one line of code change, the original NeRF can achieve similar performance as other complicated methods in the few-shot setting. FreeNeRF achieves state-of-the-art performance across diverse datasets, including Blender, DTU, and LLFF. We hope this simple baseline will motivate a rethinking of the fundamental role of frequency in NeRF's training under the low-data regime and beyond., Project page: https://jiawei-yang.github.io/FreeNeRF/, Code at: https://github.com/Jiawei-Yang/FreeNeRF

We hypothesize that similar objects should have similar outlier scores. To our knowledge, all existing outlier detectors calculate the outlier score for each object independently regardless of the outlier scores of the other objects. Therefore, they do not guarantee that similar objects have similar outlier scores. To verify our proposed hypothesis, we propose an outlier score post-processing technique for outlier detectors, called neighborhood averaging(NA), which pays attention to objects and their neighbors and guarantees them to have more similar outlier scores than their original scores. Given an object and its outlier score from any outlier detector, NA modifies its outlier score by combining it with its k nearest neighbors' scores. We demonstrate the effectivity of NA by using the well-known k-nearest neighbors (k-NN). Experimental results show that NA improves all 10 tested baseline detectors by 13% (from 0.70 to 0.79 AUC) on average evaluated on nine real-world datasets. Moreover, even outlier detectors that are already based on k-NN are also improved. The experiments also show that in some applications, the choice of detector is no more significant when detectors are jointly used with NA, which may pose a challenge to the generally considered idea that the data model is the most important factor. We open our code on www.outlierNet.com for reproducibility.

Accurate brain tumor segmentation from Magnetic Resonance Imaging (MRI) is desirable to joint learning of multimodal images. However, in clinical practice, it is not always possible to acquire a complete set of MRIs, and the problem of missing modalities causes severe performance degradation in existing multimodal segmentation methods. In this work, we present the first attempt to exploit the Transformer for multimodal brain tumor segmentation that is robust to any combinatorial subset of available modalities. Concretely, we propose a novel multimodal Medical Transformer (mmFormer) for incomplete multimodal learning with three main components: the hybrid modality-specific encoders that bridge a convolutional encoder and an intra-modal Transformer for both local and global context modeling within each modality; an inter-modal Transformer to build and align the long-range correlations across modalities for modality-invariant features with global semantics corresponding to tumor region; a decoder that performs a progressive up-sampling and fusion with the modality-invariant features to generate robust segmentation. Besides, auxiliary regularizers are introduced in both encoder and decoder to further enhance the model's robustness to incomplete modalities. We conduct extensive experiments on the public BraTS $2018$ dataset for brain tumor segmentation. The results demonstrate that the proposed mmFormer outperforms the state-of-the-art methods for incomplete multimodal brain tumor segmentation on almost all subsets of incomplete modalities, especially by an average 19.07% improvement of Dice on tumor segmentation with only one available modality. The code is available at https://github.com/YaoZhang93/mmFormer., Accepted to MICCAI 2022

Few-shot learning is an established topic in natural images for years, but few work is attended to histology images, which is of high clinical value since well-labeled datasets and rare abnormal samples are expensive to collect. Here, we facilitate the study of few-shot learning in histology images by setting up three cross-domain tasks that simulate real clinics problems. To enable label-efficient learning and better generalizability, we propose to incorporate contrastive learning (CL) with latent augmentation (LA) to build a few-shot system. CL learns useful representations without manual labels, while LA transfers semantic variations of the base dataset in an unsupervised way. These two components fully exploit unlabeled training data and can scale gracefully to other label-hungry problems. In experiments, we find i) models learned by CL generalize better than supervised learning for histology images in unseen classes, and ii) LA brings consistent gains over baselines. Prior studies of self-supervised learning mainly focus on ImageNet-like images, which only present a dominant object in their centers. Recent attention has been paid to images with multi-objects and multi-textures. Histology images are a natural choice for such a study. We show the superiority of CL over supervised learning in terms of generalization for such data and provide our empirical understanding for this observation. The findings in this work could contribute to understanding how the model generalizes in the context of both representation learning and histological image analysis. Code is available.

Whole slide image (WSI) classification often relies on deep weakly supervised multiple instance learning (MIL) methods to handle gigapixel resolution images and slide-level labels. Yet the decent performance of deep learning comes from harnessing massive datasets and diverse samples, urging the need for efficient training pipelines for scaling to large datasets and data augmentation techniques for diversifying samples. However, current MIL-based WSI classification pipelines are memory-expensive and computation-inefficient since they usually assemble tens of thousands of patches as bags for computation. On the other hand, despite their popularity in other tasks, data augmentations are unexplored for WSI MIL frameworks. To address them, we propose ReMix, a general and efficient framework for MIL based WSI classification. It comprises two steps: reduce and mix. First, it reduces the number of instances in WSI bags by substituting instances with instance prototypes, i.e., patch cluster centroids. Then, we propose a ``Mix-the-bag'' augmentation that contains four online, stochastic and flexible latent space augmentations. It brings diverse and reliable class-identity-preserving semantic changes in the latent space while enforcing semantic-perturbation invariance. We evaluate ReMix on two public datasets with two state-of-the-art MIL methods. In our experiments, consistent improvements in precision, accuracy, and recall have been achieved but with orders of magnitude reduced training time and memory consumption, demonstrating ReMix's effectiveness and efficiency. Code is available., Comment: Published in MICCAI 2022. Code: https://github.com/Jiawei-Yang/ReMix or https://github.com/TencentAILabHealthcare/ReMix

Recently, deep neural networks have greatly advanced histopathology image segmentation but usually require abundant annotated data. However, due to the gigapixel scale of whole slide images and pathologists' heavy daily workload, obtaining pixel-level labels for supervised learning in clinical practice is often infeasible. Alternatively, weakly-supervised segmentation methods have been explored with less laborious image-level labels, but their performance is unsatisfactory due to the lack of dense supervision. Inspired by the recent success of self-supervised learning methods, we present a label-efficient tissue prototype dictionary building pipeline and propose to use the obtained prototypes to guide histopathology image segmentation. Particularly, taking advantage of self-supervised contrastive learning, an encoder is trained to project the unlabeled histopathology image patches into a discriminative embedding space where these patches are clustered to identify the tissue prototypes by efficient pathologists' visual examination. Then, the encoder is used to map the images into the embedding space and generate pixel-level pseudo tissue masks by querying the tissue prototype dictionary. Finally, the pseudo masks are used to train a segmentation network with dense supervision for better performance. Experiments on two public datasets demonstrate that our human-machine interactive tissue prototype learning method can achieve comparable segmentation performance as the fully-supervised baselines with less annotation burden and outperform other weakly-supervised methods. Codes will be available upon publication., Comment: IPMI2023 camera ready

Detectingandsegmentingobjectswithinwholeslideimagesis essential in computational pathology workflow. Self-supervised learning (SSL) is appealing to such annotation-heavy tasks. Despite the extensive benchmarks in natural images for dense tasks, such studies are, unfortunately, absent in current works for pathology. Our paper intends to narrow this gap. We first benchmark representative SSL methods for dense prediction tasks in pathology images. Then, we propose concept contrastive learning (ConCL), an SSL framework for dense pre-training. We explore how ConCL performs with concepts provided by different sources and end up with proposing a simple dependency-free concept generating method that does not rely on external segmentation algorithms or saliency detection models. Extensive experiments demonstrate the superiority of ConCL over previous state-of-the-art SSL methods across different settings. Along our exploration, we distll several important and intriguing components contributing to the success of dense pre-training for pathology images. We hope this work could provide useful data points and encourage the community to conduct ConCL pre-training for problems of interest. Code is available., Comment: Accepted as an ECCV 2022 paper. Code is available at https://github.com/Jiawei-Yang/ConCL or https://github.com/TencentAILabHealthcare/ConCL

Liver cancer is one of the most common cancers worldwide. Due to inconspicuous texture changes of liver tumor, contrast-enhanced computed tomography (CT) imaging is effective for the diagnosis of liver cancer. In this paper, we focus on improving automated liver tumor segmentation by integrating multi-modal CT images. To this end, we propose a novel mutual learning (ML) strategy for effective and robust multi-modal liver tumor segmentation. Different from existing multi-modal methods that fuse information from different modalities by a single model, with ML, an ensemble of modality-specific models learn collaboratively and teach each other to distill both the characteristics and the commonality between high-level representations of different modalities. The proposed ML not only enables the superiority for multi-modal learning but can also handle missing modalities by transferring knowledge from existing modalities to missing ones. Additionally, we present a modality-aware (MA) module, where the modality-specific models are interconnected and calibrated with attention weights for adaptive information exchange. The proposed modality-aware mutual learning (MAML) method achieves promising results for liver tumor segmentation on a large-scale clinical dataset. Moreover, we show the efficacy and robustness of MAML for handling missing modalities on both the liver tumor and public brain tumor (BRATS 2018) datasets. Our code is available at https://github.com/YaoZhang93/MAML.

Convolutional networks (ConvNets) have achieved promising accuracy for various anatomical segmentation tasks. Despite the success, these methods can be sensitive to data appearance variations. Considering the large variability of scans caused by artifacts, pathologies, and scanning setups, robust ConvNets are vital for clinical applications, while have not been fully explored. In this paper, we propose to mitigate the challenge by enabling ConvNets' awareness of the underlying anatomical invariances among imaging scans. Specifically, we introduce a fully convolutional Constraint Adoption Module (CAM) that incorporates probabilistic atlas priors as explicit constraints for predictions over a locally connected Conditional Random Field (CFR), which effectively reinforces the anatomical consistency of the labeling outputs. We design the CAM to be flexible for boosting various ConvNet, and compact for co-optimizing with ConvNets for fusion parameters that leads to the optimal performance. We show the advantage of such atlas priors fusion is two-fold with two brain parcellation tasks. First, our models achieve state-of-the-art accuracy among ConvNet-based methods on both datasets, by significantly reducing structural abnormalities of predictions. Second, we can largely boost the robustness of existing ConvNets, proved by: (i) testing on scans with synthetic pathologies, and (ii) training and evaluation on scans of different scanning setups across datasets. Our method is proposing to be easily adopted to existing ConvNets by fine-tuning with CAM plugged in for accuracy and robustness boosts.

3D teeth reconstruction from X-ray is important for dental diagnosis and many clinical operations. However, no existing work has explored the reconstruction of teeth for a whole cavity from a single panoramic radiograph. Different from single object reconstruction from photos, this task has the unique challenge of constructing multiple objects at high resolutions. To conquer this task, we develop a novel ConvNet X2Teeth that decomposes the task into teeth localization and single-shape estimation. We also introduce a patch-based training strategy, such that X2Teeth can be end-to-end trained for optimal performance. Extensive experiments show that our method can successfully estimate the 3D structure of the cavity and reflect the details for each tooth. Moreover, X2Teeth achieves a reconstruction IoU of 0.681, which significantly outperforms the encoder-decoder method by $1.71X and the retrieval-based method by $1.52X. Our method can also be promising for other multi-anatomy 3D reconstruction tasks.

Deep learning models are notoriously data-hungry. Thus, there is an urging need for data-efficient techniques in medical image analysis, where well-annotated data are costly and time consuming to collect. Motivated by the recently revived "Copy-Paste" augmentation, we propose TumorCP, a simple but effective object-level data augmentation method tailored for tumor segmentation. TumorCP is online and stochastic, providing unlimited augmentation possibilities for tumors' subjects, locations, appearances, as well as morphologies. Experiments on kidney tumor segmentation task demonstrate that TumorCP surpasses the strong baseline by a remarkable margin of 7.12% on tumor Dice. Moreover, together with image-level data augmentation, it beats the current state-of-the-art by 2.32% on tumor Dice. Comprehensive ablation studies are performed to validate the effectiveness of TumorCP. Meanwhile, we show that TumorCP can lead to striking improvements in extremely low-data regimes. Evaluated with only 10% labeled data, TumorCP significantly boosts tumor Dice by 21.87%. To the best of our knowledge, this is the very first work exploring and extending the "Copy-Paste" design in medical imaging domain. Code is available at: https://github.com/YaoZhang93/TumorCP.

Over the decades, traditional outlier detectors have ignored the group-level factor when calculating outlier scores for objects in data by evaluating only the object-level factor, failing to capture the collective outliers. To mitigate this issue, we present a method called neighborhood representative (NR), which empowers all the existing outlier detectors to efficiently detect outliers, including collective outliers, while maintaining their computational integrity. It achieves this by selecting representative objects, scoring these objects, then applies the score of the representative objects to its collective objects. Without altering existing detectors, NR is compatible with existing detectors, while improving performance on real world datasets with +8% (0.72 to 0.78 AUC) relative to state-of-the-art outlier detectors.

Panoramic X-ray (PX) provides a 2D picture of the patient's mouth in a panoramic view to help dentists observe the invisible disease inside the gum. However, it provides limited 2D information compared with cone-beam computed tomography (CBCT), another dental imaging method that generates a 3D picture of the oral cavity but with more radiation dose and a higher price. Consequently, it is of great interest to reconstruct the 3D structure from a 2D X-ray image, which can greatly explore the application of X-ray imaging in dental surgeries. In this paper, we propose a framework, named Oral-3D, to reconstruct the 3D oral cavity from a single PX image and prior information of the dental arch. Specifically, we first train a generative model to learn the cross-dimension transformation from 2D to 3D. Then we restore the shape of the oral cavity with a deformation module with the dental arch curve, which can be obtained simply by taking a photo of the patient's mouth. To be noted, Oral-3D can restore both the density of bony tissues and the curved mandible surface. Experimental results show that Oral-3D can efficiently and effectively reconstruct the 3D oral structure and show critical information in clinical applications, e.g., tooth pulling and dental implants. To the best of our knowledge, we are the first to explore this domain transformation problem between these two imaging methods.

Accurate segmentation of cardiac structures can assist doctors to diagnose diseases, and to improve treatment planning, which is highly demanded in the clinical practice. However, the shortage of annotation and the variance of the data among different vendors and medical centers restrict the performance of advanced deep learning methods. In this work, we present a fully automatic method to segment cardiac structures including the left (LV) and right ventricle (RV) blood pools, as well as for the left ventricular myocardium (MYO) in MRI volumes. Specifically, we design a semi-supervised learning method to leverage unlabelled MRI sequence timeframes by label propagation. Then we exploit style transfer to reduce the variance among different centers and vendors for more robust cardiac image segmentation. We evaluate our method in the M&Ms challenge 7 , ranking 2nd place among 14 competitive teams., The method that won 2nd place in MICCAI 2020 MnM's Challenge

Seizure prediction has attracted a growing attention as one of the most challenging predictive data analysis efforts in order to improve the life of patients living with drug-resistant epilepsy and tonic seizures. Many outstanding works have been reporting great results in providing a sensible indirect (warning systems) or direct (interactive neural-stimulation) control over refractory seizures, some of which achieved high performance. However, many works put heavily handcraft feature extraction and/or carefully tailored feature engineering to each patient to achieve very high sensitivity and low false prediction rate for a particular dataset. This limits the benefit of their approaches if a different dataset is used. In this paper we apply Convolutional Neural Networks (CNNs) on different intracranial and scalp electroencephalogram (EEG) datasets and proposed a generalized retrospective and patient-specific seizure prediction method. We use Short-Time Fourier Transform (STFT) on 30-second EEG windows with 50% overlapping to extract information in both frequency and time domains. A standardization step is then applied on STFT components across the whole frequency range to prevent high frequencies features being influenced by those at lower frequencies. A convolutional neural network model is used for both feature extraction and classification to separate preictal segments from interictal ones. The proposed approach achieves sensitivity of 81.4%, 81.2%, 82.3% and false prediction rate (FPR) of 0.06/h, 0.16/h, 0.22/h on Freiburg Hospital intracranial EEG (iEEG) dataset, Children's Hospital of Boston-MIT scalp EEG (sEEG) dataset, and Kaggle American Epilepsy Society Seizure Prediction Challenge's dataset, respectively. Our prediction method is also statistically better than an unspecific random predictor for most of patients in all three datasets.

Detecting seizure using brain neuroactivations recorded by intracranial electroencephalogram (iEEG) has been widely used for monitoring, diagnosing, and closed-loop therapy of epileptic patients, however, computational efficiency gains are needed if state-of-the-art methods are to be implemented in implanted devices. We present a novel method for automatic seizure detection based on iEEG data that outperforms current state-of-the-art seizure detection methods in terms of computational efficiency while maintaining the accuracy. The proposed algorithm incorporates an automatic channel selection (ACS) engine as a pre-processing stage to the seizure detection procedure. The ACS engine consists of supervised classifiers which aim to find iEEGchannelswhich contribute the most to a seizure. Seizure detection stage involves feature extraction and classification. Feature extraction is performed in both frequency and time domains where spectral power and correlation between channel pairs are calculated. Random Forest is used in classification of interictal, ictal and early ictal periods of iEEG signals. Seizure detection in this paper is retrospective and patient-specific. iEEG data is accessed via Kaggle, provided by International Epilepsy Electro-physiology Portal. The dataset includes a training set of 6.5 hours of interictal data and 41 minin ictal data and a test set of 9.14 hours. Compared to the state-of-the-art on the same dataset, we achieve 49.4% increase in computational efficiency and 400 mins better in average for detection delay. The proposed model is able to detect a seizure onset at 91.95% sensitivity and 94.05% specificity with a mean detection delay of 2.77 s. The area under the curve (AUC) is 96.44%, that is comparable to the current state-of-the-art with AUC of 96.29%.