Weighted Concordance Index Loss-based Multimodal Survival Modeling for Radiation Encephalopathy Assessment in Nasopharyngeal Carcinoma Radiotherapy

Radiation encephalopathy (REP) is the most common complication for nasopharyngeal carcinoma (NPC) radiotherapy. It is highly desirable to assist clinicians in optimizing the NPC radiotherapy regimen to reduce radiotherapy-induced temporal lobe injury (RTLI) according to the probability of REP onset. To the best of our knowledge, it is the first exploration of predicting radiotherapy-induced REP by jointly exploiting image and non-image data in NPC radiotherapy regimen. We cast REP prediction as a survival analysis task and evaluate the predictive accuracy in terms of the concordance index (CI). We design a deep multimodal survival network (MSN) with two feature extractors to learn discriminative features from multimodal data. One feature extractor imposes feature selection on non-image data, and the other learns visual features from images. Because the priorly balanced CI (BCI) loss function directly maximizing the CI is sensitive to uneven sampling per batch. Hence, we propose a novel weighted CI (WCI) loss function to leverage all REP samples effectively by assigning their different weights with a dual average operation. We further introduce a temperature hyper-parameter for our WCI to sharpen the risk difference of sample pairs to help model convergence. We extensively evaluate our WCI on a private dataset to demonstrate its favourability against its counterparts. The experimental results also show multimodal data of NPC radiotherapy can bring more gains for REP risk prediction.

Structure-consistent Restoration Network for Cataract Fundus Image Enhancement

Fundus photography is a routine examination in clinics to diagnose and monitor ocular diseases. However, for cataract patients, the fundus image always suffers quality degradation caused by the clouding lens. The degradation prevents reliable diagnosis by ophthalmologists or computer-aided systems. To improve the certainty in clinical diagnosis, restoration algorithms have been proposed to enhance the quality of fundus images. Unfortunately, challenges remain in the deployment of these algorithms, such as collecting sufficient training data and preserving retinal structures. In this paper, to circumvent the strict deployment requirement, a structure-consistent restoration network (SCR-Net) for cataract fundus images is developed from synthesized data that shares an identical structure. A cataract simulation model is firstly designed to collect synthesized cataract sets (SCS) formed by cataract fundus images sharing identical structures. Then high-frequency components (HFCs) are extracted from the SCS to constrain structure consistency such that the structure preservation in SCR-Net is enforced. The experiments demonstrate the effectiveness of SCR-Net in the comparison with state-of-the-art methods and the follow-up clinical applications. The code is available at https://github.com/liamheng/ArcNet-Medical-Image-Enhancement.

Siamese Encoder-based Spatial-Temporal Mixer for Growth Trend Prediction of Lung Nodules on CT Scans

In the management of lung nodules, we are desirable to predict nodule evolution in terms of its diameter variation on Computed Tomography (CT) scans and then provide a follow-up recommendation according to the predicted result of the growing trend of the nodule. In order to improve the performance of growth trend prediction for lung nodules, it is vital to compare the changes of the same nodule in consecutive CT scans. Motivated by this, we screened out 4,666 subjects with more than two consecutive CT scans from the National Lung Screening Trial (NLST) dataset to organize a temporal dataset called NLSTt. In specific, we first detect and pair regions of interest (ROIs) covering the same nodule based on registered CT scans. After that, we predict the texture category and diameter size of the nodules through models. Last, we annotate the evolution class of each nodule according to its changes in diameter. Based on the built NLSTt dataset, we propose a siamese encoder to simultaneously exploit the discriminative features of 3D ROIs detected from consecutive CT scans. Then we novelly design a spatial-temporal mixer (STM) to leverage the interval changes of the same nodule in sequential 3D ROIs and capture spatial dependencies of nodule regions and the current 3D ROI. According to the clinical diagnosis routine, we employ hierarchical loss to pay more attention to growing nodules. The extensive experiments on our organized dataset demonstrate the advantage of our proposed method. We also conduct experiments on an in-house dataset to evaluate the clinical utility of our method by comparing it against skilled clinicians.

Structure Unbiased Adversarial Model for Medical Image Segmentation

Generative models have been widely proposed in image recognition to generate more images where the distribution is similar to that of the real images. It often introduces a discriminator network to discriminate original real data and generated data. However, such discriminator often considers the distribution of the data and did not pay enough attention to the intrinsic gap due to structure. In this paper, we reformulate a new image to image translation problem to reduce structural gap, in addition to the typical intensity distribution gap. We further propose a simple yet important Structure Unbiased Adversarial Model for Medical Image Segmentation (SUAM) with learnable inverse structural deformation for medical image segmentation. It consists of a structure extractor, an attention diffeomorphic registration and a structure \& intensity distribution rendering module. The structure extractor aims to extract the dominant structure of the input image. The attention diffeomorphic registration is proposed to reduce the structure gap with an inverse deformation field to warp the prediction masks back to their original form. The structure rendering module is to render the deformed structure to an image with targeted intensity distribution. We apply the proposed SUAM on both optical coherence tomography (OCT), magnetic resonance imaging (MRI) and computerized tomography (CT) data. Experimental results show that the proposed method has the capability to transfer both intensity and structure distributions.

One Model to Synthesize Them All: Multi-contrast Multi-scale Transformer for Missing Data Imputation

Multi-contrast magnetic resonance imaging (MRI) is widely used in clinical practice as each contrast provides complementary information. However, the availability of each contrast may vary amongst patients in reality. This poses challenges to both radiologists and automated image analysis algorithms. A general approach for tackling this problem is missing data imputation, which aims to synthesize the missing contrasts from existing ones. While several convolutional neural network (CNN) based algorithms have been proposed, they suffer from the fundamental limitations of CNN models, such as requirement for fixed numbers of input and output channels, inability to capture long-range dependencies, and lack of interpretability. In this paper, we formulate missing data imputation as a sequence-to-sequence learning problem and propose a multi-contrast multi-scale Transformer (MMT), which can take any subset of input contrasts and synthesize those that are missing. MMT consists of a multi-scale Transformer encoder that builds hierarchical representations of inputs combined with a multi-scale Transformer decoder that generates the outputs in a coarse-to-fine fashion. Thanks to the proposed multi-contrast Swin Transformer blocks, it can efficiently capture intra- and inter-contrast dependencies for accurate image synthesis. Moreover, MMT is inherently interpretable. It allows us to understand the importance of each input contrast in different regions by analyzing the in-built attention maps of Transformer blocks in the decoder. Extensive experiments on two large-scale multi-contrast MRI datasets demonstrate that MMT outperforms the state-of-the-art methods quantitatively and qualitatively.

An Annotation-free Restoration Network for Cataractous Fundus Images

Cataracts are the leading cause of vision loss worldwide. Restoration algorithms are developed to improve the readability of cataract fundus images in order to increase the certainty in diagnosis and treatment for cataract patients. Unfortunately, the requirement of annotation limits the application of these algorithms in clinics. This paper proposes a network to annotation-freely restore cataractous fundus images (ArcNet) so as to boost the clinical practicability of restoration. Annotations are unnecessary in ArcNet, where the high-frequency component is extracted from fundus images to replace segmentation in the preservation of retinal structures. The restoration model is learned from the synthesized images and adapted to real cataract images. Extensive experiments are implemented to verify the performance and effectiveness of ArcNet. Favorable performance is achieved using ArcNet against state-of-the-art algorithms, and the diagnosis of ocular fundus diseases in cataract patients is promoted by ArcNet. The capability of properly restoring cataractous images in the absence of annotated data promises the proposed algorithm outstanding clinical practicability.

Deep Learning for Computational Cytology: A Survey

Computational cytology is a critical, rapid-developing, yet challenging topic in the field of medical image computing which analyzes the digitized cytology image by computer-aided technologies for cancer screening. Recently, an increasing number of deep learning (DL) algorithms have made significant progress in medical image analysis, leading to the boosting publications of cytological studies. To investigate the advanced methods and comprehensive applications, we survey more than 120 publications of DL-based cytology image analysis in this article. We first introduce various deep learning methods, including fully supervised, weakly supervised, unsupervised, and transfer learning. Then, we systematically summarize the public datasets, evaluation metrics, versatile cytology image analysis applications including classification, detection, segmentation, and other related tasks. Finally, we discuss current challenges and potential research directions of computational cytology.

Unified Named Entity Recognition as Word-Word Relation Classification

So far, named entity recognition (NER) has been involved with three major types, including flat, overlapped (aka. nested), and discontinuous NER, which have mostly been studied individually. Recently, a growing interest has been built for unified NER, tackling the above three jobs concurrently with one single model. Current best-performing methods mainly include span-based and sequence-to-sequence models, where unfortunately the former merely focus on boundary identification and the latter may suffer from exposure bias. In this work, we present a novel alternative by modeling the unified NER as word-word relation classification, namely W^2NER. The architecture resolves the kernel bottleneck of unified NER by effectively modeling the neighboring relations between entity words with Next-Neighboring-Word (NNW) and Tail-Head-Word-* (THW-*) relations. Based on the W^2NER scheme we develop a neural framework, in which the unified NER is modeled as a 2D grid of word pairs. We then propose multi-granularity 2D convolutions for better refining the grid representations. Finally, a co-predictor is used to sufficiently reason the word-word relations. We perform extensive experiments on 14 widely-used benchmark datasets for flat, overlapped, and discontinuous NER (8 English and 6 Chinese datasets), where our model beats all the current top-performing baselines, pushing the state-of-the-art performances of unified NER.

Interpolated Joint Space Adversarial Training for Robust and Generalizable Defenses

Adversarial training (AT) is considered to be one of the most reliable defenses against adversarial attacks. However, models trained with AT sacrifice standard accuracy and do not generalize well to novel attacks. Recent works show generalization improvement with adversarial samples under novel threat models such as on-manifold threat model or neural perceptual threat model. However, the former requires exact manifold information while the latter requires algorithm relaxation. Motivated by these considerations, we exploit the underlying manifold information with Normalizing Flow, ensuring that exact manifold assumption holds. Moreover, we propose a novel threat model called Joint Space Threat Model (JSTM), which can serve as a special case of the neural perceptual threat model that does not require additional relaxation to craft the corresponding adversarial attacks. Under JSTM, we develop novel adversarial attacks and defenses. The mixup strategy improves the standard accuracy of neural networks but sacrifices robustness when combined with AT. To tackle this issue, we propose the Robust Mixup strategy in which we maximize the adversity of the interpolated images and gain robustness and prevent overfitting. Our experiments show that Interpolated Joint Space Adversarial Training (IJSAT) achieves good performance in standard accuracy, robustness, and generalization in CIFAR-10/100, OM-ImageNet, and CIFAR-10-C datasets. IJSAT is also flexible and can be used as a data augmentation method to improve standard accuracy and combine with many existing AT approaches to improve robustness.