Neighborhood Averaging for Improving Outlier Detectors

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.

FreeNeRF: Improving Few-shot Neural Rendering with Free Frequency Regularization

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.

Deep-learning-based on-chip rapid spectral imaging with high spatial resolution

Spectral imaging extends the concept of traditional color cameras to capture images across multiple spectral channels and has broad application prospects. Conventional spectral cameras based on scanning methods suffer from low acquisition speed and large volume. On-chip computational spectral imaging based on metasurface filters provides a promising scheme for portable applications, but endures long computation time for point-by-point iterative spectral reconstruction and mosaic effect in the reconstructed spectral images. In this study, we demonstrated on-chip rapid spectral imaging eliminating the mosaic effect in the spectral image by deep-learning-based spectral data cube reconstruction. We experimentally achieved four orders of magnitude speed improvement than iterative spectral reconstruction and high fidelity of spectral reconstruction over 99% for a standard color board. In particular, we demonstrated video-rate spectral imaging for moving objects and outdoor driving scenes with good performance for recognizing metamerism, where the concolorous sky and white cars can be distinguished via their spectra, showing great potential for autonomous driving and other practical applications in the field of intelligent perception.

Human-machine Interactive Tissue Prototype Learning for Label-efficient Histopathology Image Segmentation

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.

ConCL: Concept Contrastive Learning for Dense Prediction Pre-training in Pathology Images

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.

ReMix: A General and Efficient Framework for Multiple Instance Learning based Whole Slide Image Classification

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.

mmFormer: Multimodal Medical Transformer for Incomplete Multimodal Learning of Brain Tumor Segmentation

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.

Decoupled Pyramid Correlation Network for Liver Tumor Segmentation from CT images

Purpose: Automated liver tumor segmentation from Computed Tomography (CT) images is a necessary prerequisite in the interventions of hepatic abnormalities and surgery planning. However, accurate liver tumor segmentation remains challenging due to the large variability of tumor sizes and inhomogeneous texture. Recent advances based on Fully Convolutional Network (FCN) for medical image segmentation drew on the success of learning discriminative pyramid features. In this paper, we propose a Decoupled Pyramid Correlation Network (DPC-Net) that exploits attention mechanisms to fully leverage both low- and high-level features embedded in FCN to segment liver tumor. Methods: We first design a powerful Pyramid Feature Encoder (PFE) to extract multi-level features from input images. Then we decouple the characteristics of features concerning spatial dimension (i.e., height, width, depth) and semantic dimension (i.e., channel). On top of that, we present two types of attention modules, Spatial Correlation (SpaCor) and Semantic Correlation (SemCor) modules, to recursively measure the correlation of multi-level features. The former selectively emphasizes global semantic information in low-level features with the guidance of high-level ones. The latter adaptively enhance spatial details in high-level features with the guidance of low-level ones. Results: We evaluate the DPC-Net on MICCAI 2017 LiTS Liver Tumor Segmentation (LiTS) challenge dataset. Dice Similarity Coefficient (DSC) and Average Symmetric Surface Distance (ASSD) are employed for evaluation. The proposed method obtains a DSC of 76.4% and an ASSD of 0.838 mm for liver tumor segmentation, outperforming the state-of-the-art methods. It also achieves a competitive results with a DSC of 96.0% and an ASSD of 1.636 mm for liver segmentation.

Towards better understanding and better generalization of few-shot classification in histology images with contrastive learning

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.

X2Teeth: 3D Teeth Reconstruction from a Single Panoramic Radiograph

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.