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1. 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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2. 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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3. Unified Semantic Typing with Meaningful Label Inference

   https://doi.org/10.18653/v1/2022.naacl-main.190  

   Huang, James Y.; Li, Bangzheng; Xu, Jiashu; Chen, Muhao (January 2022, Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies)

   Semantic typing aims at classifying tokens or spans of interest in a textual context into semantic categories such as relations, entity types, and event types. The inferred labels of semantic categories meaningfully interpret how machines understand components of text. In this paper, we present UniST, a unified framework for semantic typing that captures label semantics by projecting both inputs and labels into a joint semantic embedding space. To formulate different lexical and relational semantic typing tasks as a unified task, we incorporate task descriptions to be jointly encoded with the input, allowing UniST to be adapted to different tasks without introducing task-specific model components. UniST optimizes a margin ranking loss such that the semantic relatedness of the input and labels is reflected from their embedding similarity. Our experiments demonstrate that UniST achieves strong performance across three semantic typing tasks: entity typing, relation classification and event typing. Meanwhile, UniST effectively transfers semantic knowledge of labels and substantially improves generalizability on inferring rarely seen and unseen types. In addition, multiple semantic typing tasks can be jointly trained within the unified framework, leading to a single compact multi-tasking model that performs comparably to dedicated single-task models, while offering even better transferability. 

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4. Finding Interior Optimum of Black-box Constrained Objective with Bayesian Optimization

   Zhang, F; Chen, Y (July 2025, The 41st Conference on Uncertainty in Artificial Intelligence)

   Optimizing objectives under constraints, where both the objectives and constraints are black box functions, is a common scenario in real-world applications such as the design of medical therapies, industrial process optimization, and hyperparameter optimization. One popular approach to handle these complex scenarios is Bayesian Optimization (BO). However, when it comes to the theoretical understanding of constrained Bayesian optimization (CBO), the existing framework often relies on heuristics, approximations, or relaxation of objectives and, therefore, lacks the same level of theoretical guarantees as in canonical BO. In this paper, we exclude the boundary candidates that could be compromised by noise perturbation and aim to find the interior optimum of the black-box-constrained objective. We rely on the insight that optimizing the objective and learning the constraints can both help identify the high-confidence regions of interest (ROI) that potentially contain the interior optimum. We propose an efficient CBO framework that intersects the ROIs identified from each aspect on a discretized search space to determine the general ROI. Then, on the ROI, we optimize the acquisition functions, balancing the learning of the constraints and the optimization of the objective. We showcase the efficiency and robustness of our proposed CBO framework through the high probability regret bounds for the algorithm and extensive empirical evidence. 

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5. 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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