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1. Regional imaging genetic enrichment analysis

   https://doi.org/10.1093/bioinformatics/btz948  

   Yao, Xiaohui ; Cong, Shan ; Yan, Jingwen ; Risacher, Shannon L. ; Saykin, Andrew J. ; Moore, Jason H. ; Shen, Li ; UK Brain Expression Consortium ; for the Alzheimer’s Disease Neuroimaging Initiative ; Murphy, ed., Robert ( December 2019 , Bioinformatics)

   Brain imaging genetics aims to reveal genetic effects on brain phenotypes, where most studies examine phenotypes defined on anatomical or functional regions of interest (ROIs) given their biologically meaningful interpretation and modest dimensionality compared with voxelwise approaches. Typical ROI-level measures used in these studies are summary statistics from voxelwise measures in the region, without making full use of individual voxel signals.

   In this article, we propose a flexible and powerful framework for mining regional imaging genetic associations via voxelwise enrichment analysis, which embraces the collective effect of weak voxel-level signals and integrates brain anatomical annotation information. Our proposed method achieves three goals at the same time: (i) increase the statistical power by substantially reducing the burden of multiple comparison correction; (ii) employ brain annotation information to enable biologically meaningful interpretation and (iii) make full use of fine-grained voxelwise signals. We demonstrate our method on an imaging genetic analysis using data from the Alzheimer’s Disease Neuroimaging Initiative, where we assess the collective regional genetic effects of voxelwise FDG-positron emission tomography measures between 116 ROIs and 565 373 single-nucleotide polymorphisms. Compared with traditional ROI-wise and voxelwise approaches, our method identified 2946 novel imaging genetic associations in addition to 33 ones overlapping with the two benchmark methods. In particular, two newly reported variants were further supported by transcriptome evidences from region-specific expression analysis. This demonstrates the promise of the proposed method as a flexible and powerful framework for exploring imaging genetic effects on the brain.

   The R code and sample data are freely available at https://github.com/lshen/RIGEA.

   Supplementary data are available at Bioinformatics online.

    

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2. Mining Regional Imaging Genetic Associations via Voxel-wise Enrichment Analysis

   https://doi.org/10.1109/BHI.2019.8834450  

   Yao, Xiaohui ; Cong, Shan ; Yan, Jingwen ; Risacher, Shannon L. ; Saykin, Andrew J. ; Moore, Jason H. ; Shen, Li ( May 2019 , 2019 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI))

   Brain imaging genetics aims to reveal genetic effects on brain phenotypes, where most studies examine phenotypes defined on anatomical or functional regions of interest (ROIs) given their biologically meaningful annotation and modest dimensionality compared with voxel-wise approaches. Typical ROI-level measures used in these studies are summary statistics from voxel-wise measures in the region, without making full use of individual voxel signals. In this paper, we propose a flexible and powerful framework for mining regional imaging genetic associations via voxel-wise enrichment analysis, which embraces the collective effect of weak voxel-level signals within an ROI. We demonstrate our method on an imaging genetic analysis using data from the Alzheimers Disease Neuroimaging Initiative, where we assess the collective regional genetic effects of voxel-wise FDG-PET measures between 116 ROIs and 19 AD candidate SNPs. Compared with traditional ROI-wise and voxel-wise approaches, our method identified 102 additional significant associations, some of which were further supported by evidences in brain tissue-specific expression analysis. This demonstrates the promise of the proposed method as a flexible and powerful framework for exploring imaging genetic effects on the brain. 

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3. Time-sensitive POI Recommendation by Tensor Completion with Side Information

   Hui, Bo ; Yan, Da ; Ku, Wei-Shinn ( January 2022 , Proceedings of the 38th IEEE International Conference on Data Engineering (ICDE))

   Context has been recognized as an important factor to consider in personalized recommender systems. Particularly in location-based services (LBSs), a fundamental task is to recommend to a mobile user where he/she could be interested to visit next at the right time. Additionally, location-based social networks (LBSNs) allow users to share location-embedded information with friends who often co-occur in the same or nearby points-of-interest (POIs) or share similar POI visiting histories, due to the social homophily theory and Tobler’s first law of geography. So, both the time information and LBSN friendship relations should be utilized for POI recommendation. Tensor completion has recently gained some attention in time-aware recommender systems. The problem decomposes a user-item-time tensor into low-rank embedding matrices of users, items and times using its observed entries, so that the underlying low-rank subspace structure can be tracked to fill the missing entries for time-aware recommendation. However, these tensor completion methods ignore the social-spatial context information available in LBSNs, which is important for POI recommendation since people tend to share their preferences with their friends, and near things are more related than distant things. In this paper, we utilize the side information of social networks and POI locations to enhance the tensor completion model paradigm for more effective time-aware POI recommendation. Specifically, we propose a regularization loss head based on a novel social Hausdorff distance function to optimize the reconstructed tensor. We also quantify the popularity of different POIs with location entropy to prevent very popular POIs from being over-represented hence suppressing the appearance of other more diverse POIs. To address the sensitivity of negative sampling, we train the model on the whole data by treating all unlabeled entries in the observed tensor as negative, and rewriting the loss function in a smart way to reduce the computational cost. Through extensive experiments on real datasets, we demonstrate the superiority of our model over state-of-the-art tensor completion methods. 

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4. Disentangled Sequential Graph Autoencoder for Preclinical Alzheimer’s Disease Characterizations from ADNI Study

   https://doi.org/10.1007/978-3-030-87196-3_34  

   Yang, Fan ; Meng, Rui ; Cho, Hyuna ; Guorong ; Kim, Won Hwa ( September 2021 , Medical Image Computing and Computer Assisted Intervention (MICCAI))

   Given a population longitudinal neuroimaging measurements defined on a brain network, exploiting temporal dependencies within the sequence of data and corresponding latent variables defined on the graph (i.e., network encoding relationships between regions of interest (ROI)) can highly benefit characterizing the brain. Here, it is important to distinguish time-variant (e.g., longitudinal measures) and time-invariant (e.g., gender) components to analyze them individually. For this, we propose an innovative and ground-breaking Disentangled Sequential Graph Autoencoder which leverages the Sequential Variational Autoencoder (SVAE), graph convolution and semi-supervising framework together to learn a latent space composed of time-variant and time-invariant latent variables to characterize disentangled representation of the measurements over the entire ROIs. Incorporating target information in the decoder with a supervised loss let us achieve more effective representation learning towards improved classification. We validate our proposed method on the longitudinal cortical thickness data from Alzheimer’s Disease Neuroimaging Initiative (ADNI) study. Our method outperforms baselines with traditional techniques demonstrating benefits for effective longitudinal data representation for predicting labels and longitudinal data generation. 

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5. Multi-scale representation learning for spatial feature distributions using grid cells

   Mai, Gengchen ( January 2020 , ICLR 2020)

   Unsupervised text encoding models have recently fueled substantial progress in NLP. The key idea is to use neural networks to convert words in texts to vector space representations based on word positions in a sentence and their contexts, which are suitable for end-to-end training of downstream tasks. We see a strikingly similar situation in spatial analysis, which focuses on incorporating both absolute positions and spatial contexts of geographic objects such as POIs into models. A general-purpose representation model for space is valuable for a multitude of tasks. However, no such general model exists to date beyond simply applying discretization or feed-forward nets to coordinates, and little effort has been put into jointly modeling distributions with vastly different characteristics, which commonly emerges from GIS data. Meanwhile, Nobel Prize-winning Neuroscience research shows that grid cells in mammals provide a multi-scale periodic representation that functions as a metric for location encoding and is critical for recognizing places and for path-integration. Therefore, we propose a representation learning model called Space2Vec to encode the absolute positions and spatial relationships of places. We conduct experiments on two real-world geographic data for two different tasks: 1) predicting types of POIs given their positions and context, 2) image classification leveraging their geo-locations. Results show that because of its multi-scale representations, Space2Vec outperforms well-established ML approaches such as RBF kernels, multi-layer feed-forward nets, and tile embedding approaches for location modeling and image classification tasks. Detailed analysis shows that all baselines can at most well handle distribution at one scale but show poor performances in other scales. In contrast, Space2Vec's multi-scale representation can handle distributions at different scales. 

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