Parkinson's disease (PD) shows heterogeneous, evolving brain-morphometry patterns. Modeling these longitudinal trajectories enables mechanistic insight, treatment development, and individualized ‘digital-twin’ forecasting. However, existing methods usually adopt recurrent neural networks and transformer architectures, which rely on discrete, regularly sampled data while struggling to handle irregular and sparse magnetic resonance imaging (MRI) in PD cohorts. Moreover, these methods have difficulty capturing individual heterogeneity including variations in disease onset, progression rate, and symptom severity, which is a hallmark of PD. To address these challenges, we propose CNODE (Conditional Neural ODE), a novel framework for continuous, individualized PD progression forecasting. The core of CNODE is to model morphological brain changes as continuous temporal processes using a neural ODE model. In addition, we jointly learn patient-specific initial time and progress speed to align individual trajectories into a shared progression trajectory. We validate CNODE on the Parkinson's Progression Markers Initiative (PPMI) dataset. Experimental results show that our method outperforms state-of-the-art baselines in forecasting longitudinal PD progression.

The Evidential Regression Network (ERN) represents a novel approach that integrates deep learning with Dempster-Shafer's theory to predict a target and quantify the associated uncertainty. Guided by the underlying theory, specific activation functions must be employed to enforce non-negative values, which is a constraint that compromises model performance by limiting its ability to learn from all samples. This paper provides a theoretical analysis of this limitation and introduces an improvement to overcome it. Initially, we define the region where the models can't effectively learn from the samples. Following this, we thoroughly analyze the ERN and investigate this constraint. Leveraging the insights from our analysis, we address the limitation by introducing a novel regularization term that empowers the ERN to learn from the whole training set. Our extensive experiments substantiate our theoretical findings and demonstrate the effectiveness of the proposed solution.

Independent and identically distributed (i.i.d.) data is essential to many data analysis and modeling techniques. In the medical domain, collecting data from multiple sites or institutions is a common strategy that guarantees sufficient clinical diversity, determined by the decentralized nature of medical data. However, data from various sites are easily biased by the local environment or facilities, thereby violating the i.i.d. rule. A common strategy is to harmonize the site bias while retaining important biological information. The ComBat is among the most popular harmonization approaches and has recently been extended to handle distributed sites. However, when faced with situations involving newly joined sites in training or evaluating data from unknown/unseen sites, ComBat lacks compatibility and requires retraining with data from all the sites. The retraining leads to significant computational and logistic overhead that is usually prohibitive. In this work, we develop a novel Cluster ComBat harmonization algorithm, which leverages cluster patterns of the data in different sites and greatly advances the usability of ComBat harmonization. We use extensive simulation and real medical imaging data from ADNI to demonstrate the superiority of the proposed approach. Our codes are provided in https://github.com/illidanlab/distributed-cluster-harmonization.

Recently, brain networks have been widely adopted to study brain dynamics, brain development, and brain diseases. Graph representation learning techniques on brain functional networks can facilitate the discovery of novel biomarkers for clinical phenotypes and neurodegenerative diseases. However, current graph learning techniques have several issues on brain network mining. First, most current graph learning models are designed for unsigned graph, which hinders the analysis of many signed network data (e.g., brain functional networks). Meanwhile, the insufficiency of brain network data limits the model performance on clinical phenotypes' predictions. Moreover, few of the current graph learning models are interpretable, which may not be capable of providing biological insights for model outcomes. Here, we propose an interpretable hierarchical signed graph representation learning (HSGPL) model to extract graph-level representations from brain functional networks, which can be used for different prediction tasks. To further improve the model performance, we also propose a new strategy to augment functional brain network data for contrastive learning. We evaluate this framework on different classification and regression tasks using data from human connectome project (HCP) and open access series of imaging studies (OASIS). Our results from extensive experiments demonstrate the superiority of the proposed model compared with several state-of-the-art techniques. In addition, we use graph saliency maps, derived from these prediction tasks, to demonstrate detection and interpretation of phenotypic biomarkers.

Mapping the connectome of the human brain using structural or functional connectivity has become one of the most pervasive paradigms for neuroimaging analysis. Recently, Graph Neural Networks (GNNs) motivated from geometric deep learning have attracted broad interest due to their established power for modeling complex networked data. Despite their superior performance in many fields, there has not yet been a systematic study of how to design effective GNNs for brain network analysis. To bridge this gap, we present BrainGB, a benchmark for brain network analysis with GNNs. BrainGB standardizes the process by (1) summarizing brain network construction pipelines for both functional and structural neuroimaging modalities and (2) modularizing the implementation of GNN designs. We conduct extensive experiments on datasets across cohorts and modalities and recommend a set of general recipes for effective GNN designs on brain networks. To support open and reproducible research on GNN-based brain network analysis, we host the BrainGB website at https://braingb.us with models, tutorials, examples, as well as an out-of-box Python package. We hope that this work will provide useful empirical evidence and offer insights for future research in this novel and promising direction.

Mapping the connectome of the human brain using structural or functional connectivity has become one of the most pervasive paradigms for neuroimaging analysis. Recently, Graph Neural Networks (GNNs) motivated from geometric deep learning have attracted broad interest due to their established power for modeling complex networked data. Despite their superior performance in many fields, there has not yet been a systematic study of how to design effective GNNs for brain network analysis. To bridge this gap, we present BrainGB, a benchmark for brain network analysis with GNNs. BrainGB standardizes the process by (1) summarizing brain network construction pipelines for both functional and structural neuroimaging modalities and (2) modularizing the implementation of GNN designs. We conduct extensive experiments on datasets across cohorts and modalities and recommend a set of general recipes for effective GNN designs on brain networks. To support open and reproducible research on GNN-based brain network analysis, we host the BrainGBwebsite at https://braingb.us with models, tutorials, examples, as well as an out-of-box Python package. We hope that this work will provide useful empirical evidence and offer insights for future research in this novel and promising direction.

State sharing can help network functions (NFs) provide support for clustered deployment and minimize the jitter caused by elastic scaling, one of the central futures of NFV. But the network overhead of remote access and the dynamically changing workload restrict the performance of the state sharing framework. The state-of-the-art state sharing frameworks mainly use the affinity strategy to migrate the target state from another node to itself. This strategy is unsuitable for asymmetric routing scenario because multiple nodes will access the same state. This paper presents RedKV, a fast and flexible Remote Direct Memory Access (RDMA) Enhanced Distributed Key-Value store that supports low-latency state sharing both in symmetric and asymmetric routing scenarios. RedKV has two unconventional designs: First, it scatters states over cluster nodes without affinity strategy and uses a unified addressing (UA) space to hide the complexity of state access. Second, it accelerates the operation with RDMA and optimizes the process according to the characteristics of RDMA and NF to mitigate the cost of remote access. Our evaluation shows that RedKV can help network functions share states with an added latency overhead of 2.26µs, outperforming state-of-art solutions by 4.6 times. The pause time caused by the scaling event has also been reduced by 81.5%.

The vulnerability of deep neural networks has gained a great upsurge of research attention, which engages well-designed examples through adding little perturbations to fool a well-performed network. Meanwhile, a progress has been made in leveraging adversarial examples to boost the robustness of deep cross-modal networks. However, for cross-modal learning, both the causes of adversarial examples and their latent advantages in learning cross-modal correlations are under-explored. In this paper, we propose novel Disentangled Adversarial examples for Cross-Modal learning, dubbed DACM. Specifically, we first divide cross-modal data into two aspects, namely modality-related component and modality-unrelated counterpart, and then learn to improve the reliability of network using the modality-related component. To achieve this goal, we apply the generation of adversarial perturbations to strengthen cross-modal correlations, wherein the modality-related component is acquired through gradually detaching the modality-unrelated component. Finally, the proposed DACM is employed to create modality-related examples towards the application of cross-modal hashing retrieval. Extensive experiments carried out on two cross-modal benchmarks show that the adversarial examples learned by DACM are efficient at fooling a target deep cross-modal hashing network. On the other hand, training this target model by merely leveraging our created modality-related examples in turn significantly promotes the robustness of this model itself.

Multimodal learning aims at utilizing information from a variety of data modalities to improve the generalization performance. One common approach is to seek the common information that is shared among different modalities for learning, whereas we can also fuse the supplementary information to leverage modality-specific information. Though the supplementary information is often desired, most existing multimodal approaches can only learn from samples with complete modalities, which wastes a considerable amount of data collected. Otherwise, model-based imputation needs to be used to complete the missing values and yet may introduce undesired noise, especially when the sample size is limited. In this paper, we proposed a framework based on knowledge distillation, utilizing the supplementary information from all modalities, and avoiding imputation and noise associated with it. Specifically, we first train models on each modality independently using all the available data. Then the trained models are used as teachers to teach the student model, which is trained with the samples having complete modalities. We demonstrate the effectiveness of the proposed method in extensive empirical studies on both synthetic datasets and real-world datasets.

Over the past decade a wide spectrum of machine learning models have been developed to model the neurodegenerative diseases, associating biomarkers, especially non-intrusive neuroimaging markers, with key clinical scores measuring the cognitive status of patients. Multi-task learning (MTL) has been commonly utilized by these studies to address high dimensionality and small cohort size challenges. However, most existing MTL approaches are based on linear models and suffer from two major limitations: 1) they cannot explicitly consider upper/lower bounds in these clinical scores; 2) they lack the capability to capture complicated non-linear interactions among the variables. In this paper, we propose Subspace Network, an efficient deep modeling approach for non-linear multi-task censored regression. Each layer of the subspace network performs a multi-task censored regression to improve upon the predictions from the last layer via sketching a low-dimensional subspace to perform knowledge transfer among learning tasks. Under mild assumptions, for each layer the parametric subspace can be recovered using only one pass of training data. Empirical results demonstrate that the proposed subspace network quickly picks up the correct parameter subspaces, and outperforms state-of-the-arts in predicting neurodegenerative clinical scores using information in brain imaging.

Alzheimer's disease (AD), one of the most common causes of dementia, is a severe irreversible neurodegenerative disease that results in loss of mental functions. The transitional stage between the expected cognitive decline of normal aging and AD, mild cognitive impairment (MCI), has been widely regarded as a suitable time for possible therapeutic intervention. The challenging task of MCI detection is therefore of great clinical importance, where the key is to effectively fuse predictive information from multiple heterogeneous data sources collected from the patients. In this paper, we propose a framework to fuse multiple data modalities for predictive modeling using deep matrix factorization, which explores the non-linear interactions among the modalities and exploits such interactions to transfer knowledge and enable high performance prediction. Specifically, the proposed collective deep matrix factorization decomposes all modalities simultaneously to capture non-linear structures of the modalities in a supervised manner, and learns a modality specific component for each modality and a modality invariant component across all modalities. The modality invariant component serves as a compact feature representation of patients that has high predictive power. The modality specific components provide an effective means to explore imaging genetics, yielding insights into how imaging and genotype interact with each other non-linearly in the AD pathology. Extensive empirical studies using various data modalities provided by Alzheimer's Disease Neuroimaging Initiative (ADNI) demonstrate the effectiveness of the proposed method for fusing heterogeneous modalities.