Streamline tractography of the fetal brain in utero with machine learning

Diffusion-weighted magnetic resonance imaging (dMRI) is the only non-invasive tool for studying white matter tracts and structural connectivity of the brain. These assessments rely heavily on tractography techniques, which reconstruct virtual streamlines representing white matter fibers. Much effort has been devoted to improving tractography methodology for adult brains, while tractography of the fetal brain has been largely neglected. Fetal tractography faces unique difficulties due to low dMRI signal quality, immature and rapidly developing brain structures, and paucity of reference data. This work presents the first machine learning model for fetal tractography. The model input consists of five sources of information: (1) Fiber orientation, inferred from a diffusion tensor fit to the dMRI signal; (2) Directions of recent propagation steps; (3) Global spatial information, encoded as distances to keypoints in the brain cortex; (4) Tissue segmentation information; and (5) Prior information about the expected local fiber orientations supplied with an atlas. In order to mitigate the local tensor estimation error, a large spatial context around the current point in the diffusion tensor image is encoded using convolutional and attention neural network modules. Moreover, the diffusion tensor information at a hypothetical next point is included in the model input. Filtering rules based on anatomically constrained tractography are applied to prune implausible streamlines. We trained the model on manually-refined whole-brain fetal tractograms and validated the trained model on an independent set of 11 test scans with gestational ages between 23 and 36 weeks. Results show that our proposed method achieves superior performance across all evaluated tracts. The new method can significantly advance the capabilities of dMRI for studying normal and abnormal brain development in utero.

Gaussian Mixture based Evidential Learning for Stereo Matching

In this paper, we introduce a novel Gaussian mixture based evidential learning solution for robust stereo matching. Diverging from previous evidential deep learning approaches that rely on a single Gaussian distribution, our framework posits that individual image data adheres to a mixture-of-Gaussian distribution in stereo matching. This assumption yields more precise pixel-level predictions and more accurately mirrors the real-world image distribution. By further employing the inverse-Gamma distribution as an intermediary prior for each mixture component, our probabilistic model achieves improved depth estimation compared to its counterpart with the single Gaussian and effectively captures the model uncertainty, which enables a strong cross-domain generation ability. We evaluated our method for stereo matching by training the model using the Scene Flow dataset and testing it on KITTI 2015 and Middlebury 2014. The experiment results consistently show that our method brings improvements over the baseline methods in a trustworthy manner. Notably, our approach achieved new state-of-the-art results on both the in-domain validated data and the cross-domain datasets, demonstrating its effectiveness and robustness in stereo matching tasks.

Enhancing Incomplete Multi-modal Brain Tumor Segmentation with Intra-modal Asymmetry and Inter-modal Dependency

Deep learning-based brain tumor segmentation (BTS) models for multi-modal MRI images have seen significant advancements in recent years. However, a common problem in practice is the unavailability of some modalities due to varying scanning protocols and patient conditions, making segmentation from incomplete MRI modalities a challenging issue. Previous methods have attempted to address this by fusing accessible multi-modal features, leveraging attention mechanisms, and synthesizing missing modalities using generative models. However, these methods ignore the intrinsic problems of medical image segmentation, such as the limited availability of training samples, particularly for cases with tumors. Furthermore, these methods require training and deploying a specific model for each subset of missing modalities. To address these issues, we propose a novel approach that enhances the BTS model from two perspectives. Firstly, we introduce a pre-training stage that generates a diverse pre-training dataset covering a wide range of different combinations of tumor shapes and brain anatomy. Secondly, we propose a post-training stage that enables the model to reconstruct missing modalities in the prediction results when only partial modalities are available. To achieve the pre-training stage, we conceptually decouple the MRI image into two parts: `anatomy' and `tumor'. We pre-train the BTS model using synthesized data generated from the anatomy and tumor parts across different training samples. ... Extensive experiments demonstrate that our proposed method significantly improves the performance over the baseline and achieves new state-of-the-art results on three brain tumor segmentation datasets: BRATS2020, BRATS2018, and BRATS2015.

Graph Neural Networks for Protein-Protein Interactions -- A Short Survey

Protein-protein interactions (PPIs) play key roles in a broad range of biological processes. Numerous strategies have been proposed for predicting PPIs, and among them, graph-based methods have demonstrated promising outcomes owing to the inherent graph structure of PPI networks. This paper reviews various graph-based methodologies, and discusses their applications in PPI prediction. We classify these approaches into two primary groups based on their model structures. The first category employs Graph Neural Networks (GNN) or Graph Convolutional Networks (GCN), while the second category utilizes Graph Attention Networks (GAT), Graph Auto-Encoders and Graph-BERT. We highlight the distinctive methodologies of each approach in managing the graph-structured data inherent in PPI networks and anticipate future research directions in this domain.

Learning Intra-view and Cross-view Geometric Knowledge for Stereo Matching

Geometric knowledge has been shown to be beneficial for the stereo matching task. However, prior attempts to integrate geometric insights into stereo matching algorithms have largely focused on geometric knowledge from single images while crucial cross-view factors such as occlusion and matching uniqueness have been overlooked. To address this gap, we propose a novel Intra-view and Cross-view Geometric knowledge learning Network (ICGNet), specifically crafted to assimilate both intra-view and cross-view geometric knowledge. ICGNet harnesses the power of interest points to serve as a channel for intra-view geometric understanding. Simultaneously, it employs the correspondences among these points to capture cross-view geometric relationships. This dual incorporation empowers the proposed ICGNet to leverage both intra-view and cross-view geometric knowledge in its learning process, substantially improving its ability to estimate disparities. Our extensive experiments demonstrate the superiority of the ICGNet over contemporary leading models.

LCReg: Long-Tailed Image Classification with Latent Categories based Recognition

In this work, we tackle the challenging problem of long-tailed image recognition. Previous long-tailed recognition approaches mainly focus on data augmentation or re-balancing strategies for the tail classes to give them more attention during model training. However, these methods are limited by the small number of training images for the tail classes, which results in poor feature representations. To address this issue, we propose the Latent Categories based long-tail Recognition (LCReg) method. Our hypothesis is that common latent features shared by head and tail classes can be used to improve feature representation. Specifically, we learn a set of class-agnostic latent features shared by both head and tail classes, and then use semantic data augmentation on the latent features to implicitly increase the diversity of the training sample. We conduct extensive experiments on five long-tailed image recognition datasets, and the results show that our proposed method significantly improves the baselines.

ELFNet: Evidential Local-global Fusion for Stereo Matching

Although existing stereo matching models have achieved continuous improvement, they often face issues related to trustworthiness due to the absence of uncertainty estimation. Additionally, effectively leveraging multi-scale and multi-view knowledge of stereo pairs remains unexplored. In this paper, we introduce the \textbf{E}vidential \textbf{L}ocal-global \textbf{F}usion (ELF) framework for stereo matching, which endows both uncertainty estimation and confidence-aware fusion with trustworthy heads. Instead of predicting the disparity map alone, our model estimates an evidential-based disparity considering both aleatoric and epistemic uncertainties. With the normal inverse-Gamma distribution as a bridge, the proposed framework realizes intra evidential fusion of multi-level predictions and inter evidential fusion between cost-volume-based and transformer-based stereo matching. Extensive experimental results show that the proposed framework exploits multi-view information effectively and achieves state-of-the-art overall performance both on accuracy and cross-domain generalization. The codes are available at https://github.com/jimmy19991222/ELFNet.

Integrating Large Pre-trained Models into Multimodal Named Entity Recognition with Evidential Fusion

Multimodal Named Entity Recognition (MNER) is a crucial task for information extraction from social media platforms such as Twitter. Most current methods rely on attention weights to extract information from both text and images but are often unreliable and lack interpretability. To address this problem, we propose incorporating uncertainty estimation into the MNER task, producing trustworthy predictions. Our proposed algorithm models the distribution of each modality as a Normal-inverse Gamma distribution, and fuses them into a unified distribution with an evidential fusion mechanism, enabling hierarchical characterization of uncertainties and promotion of prediction accuracy and trustworthiness. Additionally, we explore the potential of pre-trained large foundation models in MNER and propose an efficient fusion approach that leverages their robust feature representations. Experiments on two datasets demonstrate that our proposed method outperforms the baselines and achieves new state-of-the-art performance.

Harmonizing Base and Novel Classes: A Class-Contrastive Approach for Generalized Few-Shot Segmentation

Current methods for few-shot segmentation (FSSeg) have mainly focused on improving the performance of novel classes while neglecting the performance of base classes. To overcome this limitation, the task of generalized few-shot semantic segmentation (GFSSeg) has been introduced, aiming to predict segmentation masks for both base and novel classes. However, the current prototype-based methods do not explicitly consider the relationship between base and novel classes when updating prototypes, leading to a limited performance in identifying true categories. To address this challenge, we propose a class contrastive loss and a class relationship loss to regulate prototype updates and encourage a large distance between prototypes from different classes, thus distinguishing the classes from each other while maintaining the performance of the base classes. Our proposed approach achieves new state-of-the-art performance for the generalized few-shot segmentation task on PASCAL VOC and MS COCO datasets.

CRCNet: Few-shot Segmentation with Cross-Reference and Region-Global Conditional Networks

Few-shot segmentation aims to learn a segmentation model that can be generalized to novel classes with only a few training images. In this paper, we propose a Cross-Reference and Local-Global Conditional Networks (CRCNet) for few-shot segmentation. Unlike previous works that only predict the query image's mask, our proposed model concurrently makes predictions for both the support image and the query image. Our network can better find the co-occurrent objects in the two images with a cross-reference mechanism, thus helping the few-shot segmentation task. To further improve feature comparison, we develop a local-global conditional module to capture both global and local relations. We also develop a mask refinement module to refine the prediction of the foreground regions recurrently. Experiments on the PASCAL VOC 2012, MS COCO, and FSS-1000 datasets show that our network achieves new state-of-the-art performance.