TractCloud: Registration-free tractography parcellation with a novel local-global streamline point cloud representation

Diffusion MRI tractography parcellation classifies streamlines into anatomical fiber tracts to enable quantification and visualization for clinical and scientific applications. Current tractography parcellation methods rely heavily on registration, but registration inaccuracies can affect parcellation and the computational cost of registration is high for large-scale datasets. Recently, deep-learning-based methods have been proposed for tractography parcellation using various types of representations for streamlines. However, these methods only focus on the information from a single streamline, ignoring geometric relationships between the streamlines in the brain. We propose TractCloud, a registration-free framework that performs whole-brain tractography parcellation directly in individual subject space. We propose a novel, learnable, local-global streamline representation that leverages information from neighboring and whole-brain streamlines to describe the local anatomy and global pose of the brain. We train our framework on a large-scale labeled tractography dataset, which we augment by applying synthetic transforms including rotation, scaling, and translations. We test our framework on five independently acquired datasets across populations and health conditions. TractCloud significantly outperforms several state-of-the-art methods on all testing datasets. TractCloud achieves efficient and consistent whole-brain white matter parcellation across the lifespan (from neonates to elderly subjects, including brain tumor patients) without the need for registration. The robustness and high inference speed of TractCloud make it suitable for large-scale tractography data analysis. Our project page is available at https://tractcloud.github.io/.

Data-Driven Optimal Control of Tethered Space Robot Deployment with Learning Based Koopman Operator

To avoid complex constraints of the traditional nonlinear method for tethered space robot (TSR) deployment, this paper proposes a data-driven optimal control framework with an improved deep learning based Koopman operator that could be applied to complex environments. In consideration of TSR's nonlinearity, its finite dimensional lifted representation is derived with the state-dependent only embedding functions in the Koopman framework. A deep learning approach is adopted to approximate the global linear representation of TSR. Deep neural networks (DNN) are developed to parameterize Koopman operator and its embedding functions. An auxiliary neural network is developed to encode the nonlinear control term of finite dimensional lifted system. In addition, the state matrix A and control matrix B of lifted linear system in the embedding space are also estimated during training DNN. Then three loss functions that related to reconstruction and prediction ability of network and controllability of lifted linear system are designed for training the entire network. With the global linear system produced from DNN, Linear Quadratic Regulator (LQR) is applied to derive the optimal control policy for the TSR deployment. Finally, simulation results verify the effectiveness of proposed framework and show that it could deploy tethered space robot more quickly with less swing of in-plane angle.

Generative Pretraining in Multimodality

We present Emu, a Transformer-based multimodal foundation model, which can seamlessly generate images and texts in multimodal context. This omnivore model can take in any single-modality or multimodal data input indiscriminately (e.g., interleaved image, text and video) through a one-model-for-all autoregressive training process. First, visual signals are encoded into embeddings, and together with text tokens form an interleaved input sequence. Emu is then end-to-end trained with a unified objective of classifying the next text token or regressing the next visual embedding in the multimodal sequence. This versatile multimodality empowers the exploration of diverse pretraining data sources at scale, such as videos with interleaved frames and text, webpages with interleaved images and text, as well as web-scale image-text pairs and video-text pairs. Emu can serve as a generalist multimodal interface for both image-to-text and text-to-image tasks, and supports in-context image and text generation. Across a broad range of zero-shot/few-shot tasks including image captioning, visual question answering, video question answering and text-to-image generation, Emu demonstrates superb performance compared to state-of-the-art large multimodal models. Extended capabilities such as multimodal assistants via instruction tuning are also demonstrated with impressive performance.

ATWM: Defense against adversarial malware based on adversarial training

Deep learning technology has made great achievements in the field of image. In order to defend against malware attacks, researchers have proposed many Windows malware detection models based on deep learning. However, deep learning models are vulnerable to adversarial example attacks. Malware can generate adversarial malware with the same malicious function to attack the malware detection model and evade detection of the model. Currently, many adversarial defense studies have been proposed, but existing adversarial defense studies are based on image sample and cannot be directly applied to malware sample. Therefore, this paper proposes an adversarial malware defense method based on adversarial training. This method uses preprocessing to defend simple adversarial examples to reduce the difficulty of adversarial training. Moreover, this method improves the adversarial defense capability of the model through adversarial training. We experimented with three attack methods in two sets of datasets, and the results show that the method in this paper can improve the adversarial defense capability of the model without reducing the accuracy of the model.

TractGeoNet: A geometric deep learning framework for pointwise analysis of tract microstructure to predict language assessment performance

We propose a geometric deep-learning-based framework, TractGeoNet, for performing regression using diffusion magnetic resonance imaging (dMRI) tractography and associated pointwise tissue microstructure measurements. By employing a point cloud representation, TractGeoNet can directly utilize pointwise tissue microstructure and positional information from all points within a fiber tract. To improve regression performance, we propose a novel loss function, the Paired-Siamese Regression loss, which encourages the model to focus on accurately predicting the relative differences between regression label scores rather than just their absolute values. In addition, we propose a Critical Region Localization algorithm to identify highly predictive anatomical regions within the white matter fiber tracts for the regression task. We evaluate the effectiveness of the proposed method by predicting individual performance on two neuropsychological assessments of language using a dataset of 20 association white matter fiber tracts from 806 subjects from the Human Connectome Project. The results demonstrate superior prediction performance of TractGeoNet compared to several popular regression models. Of the twenty tracts studied, we find that the left arcuate fasciculus tract is the most highly predictive of the two studied language performance assessments. The localized critical regions are widespread and distributed across both hemispheres and all cerebral lobes, including areas of the brain considered important for language function such as superior and anterior temporal regions, pars opercularis, and precentral gyrus. Overall, TractGeoNet demonstrates the potential of geometric deep learning to enhance the study of the brain's white matter fiber tracts and to relate their structure to human traits such as language performance.

Identification of Causal Relationship between Amyloid-beta Accumulation and Alzheimer's Disease Progression via Counterfactual Inference

Alzheimer's disease (AD) is a neurodegenerative disorder that is beginning with amyloidosis, followed by neuronal loss and deterioration in structure, function, and cognition. The accumulation of amyloid-beta in the brain, measured through 18F-florbetapir (AV45) positron emission tomography (PET) imaging, has been widely used for early diagnosis of AD. However, the relationship between amyloid-beta accumulation and AD pathophysiology remains unclear, and causal inference approaches are needed to uncover how amyloid-beta levels can impact AD development. In this paper, we propose a graph varying coefficient neural network (GVCNet) for estimating the individual treatment effect with continuous treatment levels using a graph convolutional neural network. We highlight the potential of causal inference approaches, including GVCNet, for measuring the regional causal connections between amyloid-beta accumulation and AD pathophysiology, which may serve as a robust tool for early diagnosis and tailored care.

OpenClinicalAI: An Open and Dynamic Model for Alzheimer's Disease Diagnosis

Although Alzheimer's disease (AD) cannot be reversed or cured, timely diagnosis can significantly reduce the burden of treatment and care. Current research on AD diagnosis models usually regards the diagnosis task as a typical classification task with two primary assumptions: 1) All target categories are known a priori; 2) The diagnostic strategy for each patient is consistent, that is, the number and type of model input data for each patient are the same. However, real-world clinical settings are open, with complexity and uncertainty in terms of both subjects and the resources of the medical institutions. This means that diagnostic models may encounter unseen disease categories and need to dynamically develop diagnostic strategies based on the subject's specific circumstances and available medical resources. Thus, the AD diagnosis task is tangled and coupled with the diagnosis strategy formulation. To promote the application of diagnostic systems in real-world clinical settings, we propose OpenClinicalAI for direct AD diagnosis in complex and uncertain clinical settings. This is the first powerful end-to-end model to dynamically formulate diagnostic strategies and provide diagnostic results based on the subject's conditions and available medical resources. OpenClinicalAI combines reciprocally coupled deep multiaction reinforcement learning (DMARL) for diagnostic strategy formulation and multicenter meta-learning (MCML) for open-set recognition. The experimental results show that OpenClinicalAI achieves better performance and fewer clinical examinations than the state-of-the-art model. Our method provides an opportunity to embed the AD diagnostic system into the current health care system to cooperate with clinicians to improve current health care.

SkillNet-X: A Multilingual Multitask Model with Sparsely Activated Skills

Traditional multitask learning methods basically can only exploit common knowledge in task- or language-wise, which lose either cross-language or cross-task knowledge. This paper proposes a general multilingual multitask model, named SkillNet-X, which enables a single model to tackle many different tasks from different languages. To this end, we define several language-specific skills and task-specific skills, each of which corresponds to a skill module. SkillNet-X sparsely activates parts of the skill modules which are relevant either to the target task or the target language. Acting as knowledge transit hubs, skill modules are capable of absorbing task-related knowledge and language-related knowledge consecutively. Based on Transformer, we modify the multi-head attention layer and the feed forward network layer to accommodate skill modules. We evaluate SkillNet-X on eleven natural language understanding datasets in four languages. Results show that SkillNet-X performs better than task-specific baselines and two multitask learning baselines (i.e., dense joint model and Mixture-of-Experts model). Furthermore, skill pre-training further improves the performance of SkillNet-X on almost all datasets. To investigate the generalization of our model, we conduct experiments on two new tasks and find that SkillNet-X significantly outperforms baselines.

HiNeRV: Video Compression with Hierarchical Encoding based Neural Representation

Learning-based video compression is currently one of the most popular research topics, offering the potential to compete with conventional standard video codecs. In this context, Implicit Neural Representations (INRs) have previously been used to represent and compress image and video content, demonstrating relatively high decoding speed compared to other methods. However, existing INR-based methods have failed to deliver rate quality performance comparable with the state of the art in video compression. This is mainly due to the simplicity of the employed network architectures, which limit their representation capability. In this paper, we propose HiNeRV, an INR that combines bilinear interpolation with novel hierarchical positional encoding. This structure employs depth-wise convolutional and MLP layers to build a deep and wide network architecture with much higher capacity. We further build a video codec based on HiNeRV and a refined pipeline for training, pruning and quantization that can better preserve HiNeRV's performance during lossy model compression. The proposed method has been evaluated on both UVG and MCL-JCV datasets for video compression, demonstrating significant improvement over all existing INRs baselines and competitive performance when compared to learning-based codecs (72.3% overall bit rate saving over HNeRV and 43.4% over DCVC on the UVG dataset, measured in PSNR).

Reconstructing the somatotopic organization of the corticospinal tract remains a challenge for modern tractography methods

The corticospinal tract (CST) is a critically important white matter fiber tract in the human brain that enables control of voluntary movements of the body. Diffusion MRI tractography is the only method that enables the study of the anatomy and variability of the CST pathway in human health. In this work, we explored the performance of six widely used tractography methods for reconstructing the CST and its somatotopic organization. We perform experiments using diffusion MRI data from the Human Connectome Project. Four quantitative measurements including reconstruction rate, the WM-GM interface coverage, anatomical distribution of streamlines, and correlation with cortical volumes to assess the advantages and limitations of each method. Overall, we conclude that while current tractography methods have made progress toward the well-known challenge of improving the reconstruction of the lateral projections of the CST, the overall problem of performing a comprehensive CST reconstruction, including clinically important projections in the lateral (hand and face area) and medial portions (leg area), remains an important challenge for diffusion MRI tractography.