Functional MRI (fMRI) and single-cell transcriptomics are pivotal in Alzheimer's disease (AD) research, each providing unique insights into neural function and molecular mechanisms. However, integrating these complementary modalities remains largely unexplored. Here, we introduce scBIT, a novel method for enhancing AD prediction by combining fMRI with single-nucleus RNA (snRNA). scBIT leverages snRNA as an auxiliary modality, significantly improving fMRI-based prediction models and providing comprehensive interpretability. It employs a sampling strategy to segment snRNA data into cell-type-specific gene networks and utilizes a self-explainable graph neural network to extract critical subgraphs. Additionally, we use demographic and genetic similarities to pair snRNA and fMRI data across individuals, enabling robust cross-modal learning. Extensive experiments validate scBIT's effectiveness in revealing intricate brain region-gene associations and enhancing diagnostic prediction accuracy. By advancing brain imaging transcriptomics to the single-cell level, scBIT sheds new light on biomarker discovery in AD research. Experimental results show that incorporating snRNA data into the scBIT model significantly boosts accuracy, improving binary classification by 3.39% and five-class classification by 26.59%. The codes were implemented in Python and have been released on GitHub (https://github.com/77YQ77/scBIT) and Zenodo (https://zenodo.org/records/11599030) with detailed instructions.

Neuroimaging analysis aims to reveal the information-processing mechanisms of the human brain in a noninvasive manner. In the past, graph neural networks (GNNs) have shown promise in capturing the non-Euclidean structure of brain networks. However, existing neuroimaging studies focused primarily on spatial functional connectivity, despite temporal dynamics in complex brain networks. To address this gap, we propose a spatio-temporal interactive graph representation framework (STIGR) for dynamic neuroimaging analysis that encompasses different aspects from classification and regression tasks to interpretation tasks. STIGR leverages a dynamic adaptive-neighbor graph convolution network to capture the interrelationships between spatial and temporal dynamics. To address the limited global scope in graph convolutions, a self-attention module based on Transformers is introduced to extract long-term dependencies. Contrastive learning is used to adaptively contrast similarities between adjacent scanning windows, modeling cross-temporal correlations in dynamic graphs. Extensive experiments on six public neuroimaging datasets demonstrate the competitive performance of STIGR across different platforms, achieving state-of-the-art results in classification and regression tasks. The proposed framework enables the detection of remarkable temporal association patterns between regions of interest based on sequential neuroimaging signals, offering medical professionals a versatile and interpretable tool for exploring task-specific neurological patterns. Our codes and models are available at https://github.com/77YQ77/STIGR/.

Expensive optimization problems (EOPs) have attracted increasing research attention over the decades due to their ubiquity in a variety of practical applications. Despite many sophisticated surrogate-assisted evolutionary algorithms (SAEAs) that have been developed for solving such problems, most of them lack the ability to transfer knowledge from previously-solved tasks and always start their search from scratch, making them troubled by the notorious cold-start issue. A few preliminary studies that integrate transfer learning into SAEAs still face some issues, such as defective similarity quantification that is prone to underestimate promising knowledge, surrogate-dependency that makes the transfer methods not coherent with the state-of-the-art in SAEAs, etc. In light of the above, a plug and play competitive knowledge transfer (CKT) method is proposed to boost various SAEAs in this article. Specifically, both the optimized solutions from the source tasks and the promising solutions acquired by the target surrogate are treated as task-solving knowledge, enabling them to compete with each other to elect the winner for expensive evaluation, thus boosting the search speed on the target task. Moreover, the lower bound of the convergence gain brought by the knowledge competition is mathematically analyzed, which is expected to strengthen the theoretical foundation of sequential transfer optimization. Experimental studies conducted on a series of benchmark problems and a practical application from the petroleum industry verify the efficacy of the proposed method. The source code of the CKT is available athttps://github.com/XmingHsueh/SAS-CKT.

Content-based medical image retrieval (CBMIR) enables physicians to make evidence-based diagnoses by retrieving similar medical images and recalling previous cases stored in databases. However, existing CBMIR models are prone to capturing superficial correlations due to confounding factors such as complex host organs and lesions, imaging discrepancies, artifacts, and inconsistent protocols. To address this issue, we propose a plug-and-play anti-confounding hashing (ACH) method, which uses debiased sample weighting and lesion counterfactual reasoning (LCR) to directly capture the natural direct effect (NDE) of lesions on query medical images without bias. The devised debiased weighting (DBW) loss adopts a backdoor adjustment to separate lesions from confounders. To effectively locate salient areas of lesions, we present a coarse-to-fine lesion positioning (C2F-LP) module by counterfactual reasoning. On two real-world radiological image datasets, ACH achieves 0.2%-9% improvement in mean average precision (mAP) over the six state-of-the-art methods, when using code lengths ranging from 8-bit to 32-bit. Its robustness to confounding factors is demonstrated through explainable visual analysis.

To relieve the growing burden of mental disorders, deep learning techniques have emerged as a promising tool to aid clinicians by detecting abnormal patterns in neuroimaging data. However, the efficacy of such models is contingent upon access to vast pools of patient data, which is impractical for individual healthcare institutions. Moreover, the privacy-preserving policy regulations governing medical images further complicate the pooling of information necessary for training robust models. Federated Learning (FL) offers a solution to this dilemma by aggregating the local model updates without compromising patient privacy. However, current studies fail to adequately account for the need to personalize models according to the diverse structures of local data. In this work, an effective heterogeneous structured FL framework using graph convolutional aggregation dubbed GAHFL is proposed to diagnose mental disorders on functional magnetic resonance imaging data. In addition, we propose to perform the global model self-evaluation to enable the training to emphasize the samples that are difficult to classify. To solve the catastrophic forgetting problem, we build a historical logit pool to awaken the global model’s recognition ability by performing a server knowledge self-distillation. Empirical evaluations demonstrate that the proposed framework achieves averaged diagnosis AUC values of 69.01% and 69.04% with different sizes of public datasets of ABIDE-I and ADHD-200 datasets, respectively. The ablation studies and robustness validation test further demonstrate the superior performance of our framework.

The globally rising prevalence of mental disorders leads to shortfalls in timely diagnosis and therapy to reduce patients' suffering. Facing such an urgent public health problem, professional efforts based on symptom criteria are seriously overstretched. Recently, the successful applications of computer-aided diagnosis approaches have provided timely opportunities to relieve the tension in healthcare services. Particularly, multimodal representation learning gains increasing attention thanks to the high temporal and spatial resolution information extracted from neuroimaging fusion. In this work, we propose an efficient multimodality fusion framework to identify multiple mental disorders based on the combination of functional and structural magnetic resonance imaging. A multioutput conditional generative adversarial network (GAN) is developed to address the scarcity of multimodal data for augmentation. Based on the augmented training data, the multiheaded gating fusion model is proposed for classification by extracting the complementary features across different modalities. The experiments demonstrate that the proposed model can achieve robust accuracies of 75.1 ± 1.5 %, 72.9 ± 1.1 %, and 87.2 ± 1.5 % for autism spectrum disorder (ASD), attention deficit/hyperactivity disorder, and schizophrenia, respectively. In addition, the interpretability of our model is expected to enable the identification of remarkable neuropathology diagnostic biomarkers, leading to well-informed therapeutic decisions.

Neuroimaging techniques have been widely adopted to detect the neurological brain structures and functions of the nervous system. As an effective noninvasive neuroimaging technique, functional magnetic resonance imaging (fMRI) has been extensively used in computer-aided diagnosis (CAD) of mental disorders, e.g., autism spectrum disorder (ASD) and attention deficit/hyperactivity disorder (ADHD). In this study, we propose a spatial-temporal co-attention learning (STCAL) model for diagnosing ASD and ADHD from fMRI data. In particular, a guided co-attention (GCA) module is developed to model the intermodal interactions of spatial and temporal signal patterns. A novel sliding cluster attention module is designed to address global feature dependency of self-attention mechanism in fMRI time series. Comprehensive experimental results demonstrate that our STCAL model can achieve competitive accuracies of 73.0 ± 4.5%, 72.0 ± 3.8%, and 72.5 ± 4.2% on the ABIDE I, ABIDE II, and ADHD-200 datasets, respectively. Moreover, the potential for feature pruning based on the co-attention scores is validated by the simulation experiment. The clinical interpretation analysis of STCAL can allow medical professionals to concentrate on the discriminative regions of interest and key time frames from fMRI data.

The high prevalence of mental disorders gradually poses a huge pressure on the public healthcare services. Deep learning-based computer-aided diagnosis (CAD) has emerged to relieve the tension in healthcare institutions by detecting abnormal neuroimaging-derived phenotypes. However, training deep learning models relies on sufficient annotated datasets, which can be costly and laborious. Semi-supervised learning (SSL) and transfer learning (TL) can mitigate this challenge by leveraging unlabeled data within the same institution and advantageous information from source domain, respectively. This work is the first attempt to propose an effective semi-supervised transfer learning (SSTL) framework dubbed S3TL for CAD of mental disorders on fMRI data. Within S3TL, a secure cross-domain feature alignment method is developed to generate target-related source model in SSL. Subsequently, we propose an enhanced dual-stage pseudo-labeling approach to assign pseudo-labels for unlabeled samples in target domain. Finally, an advantageous knowledge transfer method is conducted to improve the generalization capability of the target model. Comprehensive experimental results demonstrate that S3TL achieves competitive accuracies of 69.14%, 69.65%, and 72.62% on ABIDE-I, ABIDE-II, and ADHD-200 datasets, respectively. Furthermore, the simulation experiments also demonstrate the application potential of S3TL through model interpretation analysis and federated learning extension.

The high prevalence of mental disorders gradually poses a huge pressure on the public healthcare services. Recently, deep learning-based computer-aided diagnosis has been introduced to relieve the tension in healthcare institutions by automatically detecting abnormal neuroimaging-derived pheno-types in patients. However, the training of deep learning models relies on sufficiently large annotated datasets, which can be costly, time-consuming, and laborious. Semi-supervised learning (SSL) can mitigate this challenge by leveraging both labeled and unlabeled samples. In this work, an effective dual-stage pseudo-labeling based classification framework dubbed DSPL is proposed to diagnose mental disorders on functional magnetic resonance imaging data. A bicriteria-based pseudo-labels selection method is developed to filter out inferior pseudo-labeled samples. Subsequently, we further propose a self-mutual learning enhanced pseudo-labeling generation approach to mitigate the adverse effects bought by the noisy pseudo-labeled samples. On real-world datasets, the proposed method achieves diagnosis accuracies of 68.09%, 67.94%, and 68.13% on ABIDE-I, ABIDE-II, and ADHD-200, respectively. Ablation study suggests that each component in DSPL makes a great contribution to performance improvement.

Evolutionary sequential transfer optimization is a paradigm that leverages search experience from solved source optimization tasks to accelerate the evolutionary search of a target task. Even though many algorithms have been developed, they mainly focus on objective-homogeneous problems, where the source and target tasks possess a similar number of objectives. In this work, we explore objective-heterogeneous problems, in which knowledge transfers across single-objective optimization problems (SOPs), multiobjective optimization problems (MOPs), and many-objective optimization problems (MaOPs). Objective-heterogeneous problems challenge the existing methods due to the diverse search and objective spaces between the source and the target task. To address this issue, we present a decision variable analysis-based transfer method that can conduct knowledge transfer across problems with the different numbers of objectives. We first separate decision variables of MOPs and MaOPs into convergence-related variables (CVs) and diversity-related variables (DVs), according to their roles while treating variables of SOPs as CVs. Then, we propose a convergence transfer module to transfer knowledge of CVs to speed up the convergence. It aligns both solutions and fitness ranks for preserving fitness rank consistency between the source and target tasks, whereby accelerating search speed. Besides, a diversity transfer module is presented to refine the distribution of DVs to maintain the population diversity. The experimental results on objective-heterogeneous test problems and a real-world case study have demonstrated the effectiveness of the proposed algorithm.