Background: Clear cell renal cell carcinoma (ccRCC) is the most common renal-related tumor with high heterogeneity. There is still an urgent need for novel diagnostic and prognostic biomarkers for ccRCC. Methods: We proposed a weakly-supervised deep learning strategy using conventional histology of 1752 whole slide images from multiple centers. Our study was demonstrated through internal cross-validation and external validations for the deep learning-based models. Results: Automatic diagnosis for ccRCC through intelligent subtyping of renal cell carcinoma was proved in this study. Our graderisk achieved aera the curve (AUC) of 0.840 (95% confidence interval: 0.805-0.871) in the TCGA cohort, 0.840 (0.805-0.871) in the General cohort, and 0.840 (0.805-0.871) in the CPTAC cohort for the recognition of high-grade tumor. The OSrisk for the prediction of 5-year survival status achieved AUC of 0.784 (0.746-0.819) in the TCGA cohort, which was further verified in the independent General cohort and the CPTAC cohort, with AUC of 0.774 (0.723-0.820) and 0.702 (0.632-0.765), respectively. Cox regression analysis indicated that graderisk, OSrisk, tumor grade, and tumor stage were found to be independent prognostic factors, which were further incorporated into the competing-risk nomogram (CRN). Kaplan-Meier survival analyses further illustrated that our CRN could significantly distinguish patients with high survival risk, with hazard ratio of 5.664 (3.893-8.239, p < 0.0001) in the TCGA cohort, 35.740 (5.889-216.900, p < 0.0001) in the General cohort and 6.107 (1.815 to 20.540, p < 0.0001) in the CPTAC cohort. Comparison analyses conformed that our CRN outperformed current prognosis indicators in the prediction of survival status, with higher concordance index for clinical prognosis.
The joint hyperspectral image (HSI) and LiDAR data classification aims to interpret ground objects at more detailed and precise level. Although deep learning methods have shown remarkable success in the multisource data classification task, self-supervised learning has rarely been explored. It is commonly nontrivial to build a robust self-supervised learning model for multisource data classification, due to the fact that the semantic similarities of neighborhood regions are not exploited in existing contrastive learning framework. Furthermore, the heterogeneous gap induced by the inconsistent distribution of multisource data impedes the classification performance. To overcome these disadvantages, we propose a Nearest Neighbor-based Contrastive Learning Network (NNCNet), which takes full advantage of large amounts of unlabeled data to learn discriminative feature representations. Specifically, we propose a nearest neighbor-based data augmentation scheme to use enhanced semantic relationships among nearby regions. The intermodal semantic alignments can be captured more accurately. In addition, we design a bilinear attention module to exploit the second-order and even high-order feature interactions between the HSI and LiDAR data. Extensive experiments on four public datasets demonstrate the superiority of our NNCNet over state-of-the-art methods. The source codes are available at \url{https://github.com/summitgao/NNCNet}.
A key goal for the advancement of AI is to develop technologies that serve the needs not just of one group but of all communities regardless of their geographical region. In fact, a significant proportion of knowledge is locally shared by people from certain regions but may not apply equally in other regions because of cultural differences. If a model is unaware of regional characteristics, it may lead to performance disparity across regions and result in bias against underrepresented groups. We propose GIVL, a Geographically Inclusive Vision-and-Language Pre-trained model. There are two attributes of geo-diverse visual concepts which can help to learn geo-diverse knowledge: 1) concepts under similar categories have unique knowledge and visual characteristics, 2) concepts with similar visual features may fall in completely different categories. Motivated by the attributes, we design new pre-training objectives Image Knowledge Matching (IKM) and Image Edit Checking (IEC) to pre-train GIVL. Compared with similar-size models pre-trained with similar scale of data, GIVL achieves state-of-the-art (SOTA) and more balanced performance on geo-diverse V&L tasks.
Drug-Drug Interactions (DDIs) prediction is an essential issue in the molecular field. Traditional methods of observing DDIs in medical experiments require plenty of resources and labor. In this paper, we present a computational model dubbed MedKGQA based on Graph Neural Networks to automatically predict the DDIs after reading multiple medical documents in the form of multi-hop machine reading comprehension. We introduced a knowledge fusion system to obtain the complete nature of drugs and proteins and exploited a graph reasoning system to infer the drugs and proteins contained in the documents. Our model significantly improves the performance compared to previous state-of-the-art models on the QANGAROO MedHop dataset, which obtained a 4.5% improvement in terms of DDIs prediction accuracy.
Recent breakthroughs in Vision-Language (V&L) joint research have achieved remarkable results in various text-driven tasks. High-quality Text-to-video (T2V), a task that has been long considered mission-impossible, was proven feasible with reasonably good results in latest works. However, the resulting videos often have undesired artifacts largely because the system is purely data-driven and agnostic to the physical laws. To tackle this issue and further push T2V towards high-level physical realism, we present an autonomous data generation technique and a dataset, which intend to narrow the gap with a large number of multi-modal, 3D Text-to-Video/Simulation (T2V/S) data. In the dataset, we provide high-resolution 3D physical simulations for both solids and fluids, along with textual descriptions of the physical phenomena. We take advantage of state-of-the-art physical simulation methods (i) Incremental Potential Contact (IPC) and (ii) Material Point Method (MPM) to simulate diverse scenarios, including elastic deformations, material fractures, collisions, turbulence, etc. Additionally, high-quality, multi-view rendering videos are supplied for the benefit of T2V, Neural Radiance Fields (NeRF), and other communities. This work is the first step towards fully automated Text-to-Video/Simulation (T2V/S). Live examples and subsequent work are at https://sites.google.com/view/tpa-net.
As a burgeoning medical imaging method based on hybrid fusion of light and ultrasound, photoacoustic imaging (PAI) has demonstrated high potential in various biomedical applications recently, especially in revealing the functional and molecular information to improve diagnostic accuracy. However, stemming from weak amplitude and unavoidable random noise, caused by limited laser power and severe attenuation in deep tissue imaging, PA signals are usually of low signal-to-noise ratio (SNR), and reconstructed PA images are of low quality. Despite that conventional Kalman Filter (KF) can remove Gaussian noise in time domain, it lacks adaptability in real-time estimating condition due to its fixed model. Moreover, KF-based de-noising algorithm has not been applied in PAI before. In this paper, we propose an adaptive Modified Kalman Filter (MKF) targeted at PAI de-noising by tuning system noise matrix Q and measurement noise matrix R in the conventional KF model. Additionally, in order to compensate the signal skewing caused by KF, we cascade the backward part of Rauch-Tung-Striebel smoother (BRTS), which also utilizes the newly determined Q. Finally, as a supplement, we add a commonly used differential filter to remove in-band reflection artifacts. Experimental results using phantom and ex vivo colorectal tissue are provided to prove the validity of the algorithm.
The domain of joint vision-language understanding, especially in the context of reasoning in Visual Question Answering (VQA) models, has garnered significant attention in the recent past. While most of the existing VQA models focus on improving the accuracy of VQA, the way models arrive at an answer is oftentimes a black box. As a step towards making the VQA task more explainable and interpretable, our method is built upon the SOTA VQA framework by augmenting it with an end-to-end explanation generation module. In this paper, we investigate two network architectures, including Long Short-Term Memory (LSTM) and Transformer decoder, as the explanation generator. Our method generates human-readable textual explanations while maintaining SOTA VQA accuracy on the GQA-REX (77.49%) and VQA-E (71.48%) datasets. Approximately 65.16% of the generated explanations are approved by humans as valid. Roughly 60.5% of the generated explanations are valid and lead to the correct answers.
Task-Oriented Dialogue (TOD) systems are drawing more and more attention in recent studies. Current methods focus on constructing pre-trained models or fine-tuning strategies while the evaluation of TOD is limited by a policy mismatch problem. That is, during evaluation, the user utterances are from the annotated dataset while these utterances should interact with previous responses which can have many alternatives besides annotated texts. Therefore, in this work, we propose an interactive evaluation framework for TOD. We first build a goal-oriented user simulator based on pre-trained models and then use the user simulator to interact with the dialogue system to generate dialogues. Besides, we introduce a sentence-level and a session-level score to measure the sentence fluency and session coherence in the interactive evaluation. Experimental results show that RL-based TOD systems trained by our proposed user simulator can achieve nearly 98% inform and success rates in the interactive evaluation of MultiWOZ dataset and the proposed scores measure the response quality besides the inform and success rates. We are hoping that our work will encourage simulator-based interactive evaluations in the TOD task.
In this work we introduce CUTS (Contrastive and Unsupervised Training for Segmentation) the first fully unsupervised deep learning framework for medical image segmentation, facilitating the use of the vast majority of imaging data that is not labeled or annotated. Segmenting medical images into regions of interest is a critical task for facilitating both patient diagnoses and quantitative research. A major limiting factor in this segmentation is the lack of labeled data, as getting expert annotations for each new set of imaging data or task can be expensive, labor intensive, and inconsistent across annotators: thus, we utilize self-supervision based on pixel-centered patches from the images themselves. Our unsupervised approach is based on a training objective with both contrastive learning and autoencoding aspects. Previous contrastive learning approaches for medical image segmentation have focused on image-level contrastive training, rather than our intra-image patch-level approach or have used this as a pre-training task where the network needed further supervised training afterwards. By contrast, we build the first entirely unsupervised framework that operates at the pixel-centered-patch level. Specifically, we add novel augmentations, a patch reconstruction loss, and introduce a new pixel clustering and identification framework. Our model achieves improved results on several key medical imaging tasks, as verified by held-out expert annotations on the task of segmenting geographic atrophy (GA) regions of images of the retina.
Recently, change detection methods for synthetic aperture radar (SAR) images based on convolutional neural networks (CNN) have gained increasing research attention. However, existing CNN-based methods neglect the interactions among multilayer convolutions, and errors involved in the preclassification restrict the network optimization. To this end, we proposed a layer attention-based noise-tolerant network, termed LANTNet. In particular, we design a layer attention module that adaptively weights the feature of different convolution layers. In addition, we design a noise-tolerant loss function that effectively suppresses the impact of noisy labels. Therefore, the model is insensitive to noisy labels in the preclassification results. The experimental results on three SAR datasets show that the proposed LANTNet performs better compared to several state-of-the-art methods. The source codes are available at https://github.com/summitgao/LANTNet