Polygenic Risk Scores (PRS) developed from genome-wide association studies (GWAS) are of increasing interest for various clinical and research applications. Bayesian methods have been particularly popular for building PRS in genome-wide scale because of their natural ability to regularize model and borrow information in high-dimension. In this article, we present new theoretical results, methods, and extensive numerical studies to advance Bayesian methods for PRS applications. We conduct theoretical studies to identify causes of convergence issues of some Bayesian methods when required input GWAS summary-statistics and linkage disequilibrium (LD) (genetic correlation) data are derived from distinct samples. We propose a remedy to the problem by the projection of the summary-statistics data into the column space of the genetic correlation matrix. We further implement a PRS development algorithm under the Bayesian Bridge prior which can allow more flexible specification of effect-size distribution than those allowed under popular alternative methods. Finally, we conduct careful benchmarking studies of alternative Bayesian methods using both simulation studies and real datasets, where we carefully investigate both the effect of prior specification and estimation strategies for LD parameters. These studies show that the proposed algorithm, equipped with the projection approach, the flexible prior specification, and an efficient numerical algorithm leads to the development of the most robust PRS across a wide variety of scenarios.
Brain-related diseases are more sensitive than other diseases due to several factors, including the complexity of surgical procedures, high costs, and other challenges. Alzheimer's disease is a common brain disorder that causes memory loss and the shrinking of brain cells. Early detection is critical for providing proper treatment to patients. However, identifying Alzheimer's at an early stage using manual scanning of CT or MRI scans is challenging. Therefore, researchers have delved into the exploration of computer-aided systems, employing Machine Learning and Deep Learning methodologies, which entail the training of datasets to detect Alzheimer's disease. This study aims to present a hybrid model that combines a CNN model's feature extraction capabilities with an LSTM model's detection capabilities. This study has applied the transfer learning called VGG16 in the hybrid model to extract features from MRI images. The LSTM detects features between the convolution layer and the fully connected layer. The output layer of the fully connected layer uses the softmax function. The training of the hybrid model involved utilizing the ADNI dataset. The trial findings revealed that the model achieved a level of accuracy of 98.8%, a sensitivity rate of 100%, and a specificity rate of 76%. The proposed hybrid model outperforms its contemporary CNN counterparts, showcasing a superior performance.
Electronic health records (EHR) is an inherently multimodal register of the patient's health status characterized by static data and multivariate time series (MTS). While MTS are a valuable tool for clinical prediction, their fusion with other data modalities can possibly result in more thorough insights and more accurate results. Deep neural networks (DNNs) have emerged as fundamental tools for identifying and defining underlying patterns in the healthcare domain. However, fundamental improvements in interpretability are needed for DNN models to be widely used in the clinical setting. In this study, we present an approach built on a collection of interpretable multimodal data-driven models that may anticipate and understand the emergence of antimicrobial multidrug resistance (AMR) germs in the intensive care unit (ICU) of the University Hospital of Fuenlabrada (Madrid, Spain). The profile and initial health status of the patient are modeled using static variables, while the evolution of the patient's health status during the ICU stay is modeled using several MTS, including mechanical ventilation and antibiotics intake. The multimodal DNNs models proposed in this paper include interpretable principles in addition to being effective at predicting AMR and providing an explainable prediction support system for AMR in the ICU. Furthermore, our proposed methodology based on multimodal models and interpretability schemes can be leveraged in additional clinical problems dealing with EHR data, broadening the impact and applicability of our results.
Individualized treatment rules (ITRs) have been widely applied in many fields such as precision medicine and personalized marketing. Beyond the extensive studies on ITR for binary or multiple treatments, there is considerable interest in applying combination treatments. This paper introduces a novel ITR estimation method for combination treatments incorporating interaction effects among treatments. Specifically, we propose the generalized $\psi$-loss as a non-convex surrogate in the residual weighted learning framework, offering desirable statistical and computational properties. Statistically, the minimizer of the proposed surrogate loss is Fisher-consistent with the optimal decision rules, incorporating interaction effects at any intensity level - a significant improvement over existing methods. Computationally, the proposed method applies the difference-of-convex algorithm for efficient computation. Through simulation studies and real-world data applications, we demonstrate the superior performance of the proposed method in recommending combination treatments.
Recently, diffusion-based methods for monocular 3D human pose estimation have achieved state-of-the-art (SOTA) performance by directly regressing the 3D joint coordinates from the 2D pose sequence. Although some methods decompose the task into bone length and bone direction prediction based on the human anatomical skeleton to explicitly incorporate more human body prior constraints, the performance of these methods is significantly lower than that of the SOTA diffusion-based methods. This can be attributed to the tree structure of the human skeleton. Direct application of the disentangled method could amplify the accumulation of hierarchical errors, propagating through each hierarchy. Meanwhile, the hierarchical information has not been fully explored by the previous methods. To address these problems, a Disentangled Diffusion-based 3D Human Pose Estimation method with Hierarchical Spatial and Temporal Denoiser is proposed, termed DDHPose. In our approach: (1) We disentangle the 3D pose and diffuse the bone length and bone direction during the forward process of the diffusion model to effectively model the human pose prior. A disentanglement loss is proposed to supervise diffusion model learning. (2) For the reverse process, we propose Hierarchical Spatial and Temporal Denoiser (HSTDenoiser) to improve the hierarchical modeling of each joint. Our HSTDenoiser comprises two components: the Hierarchical-Related Spatial Transformer (HRST) and the Hierarchical-Related Temporal Transformer (HRTT). HRST exploits joint spatial information and the influence of the parent joint on each joint for spatial modeling, while HRTT utilizes information from both the joint and its hierarchical adjacent joints to explore the hierarchical temporal correlations among joints.
Recently, with increasing interest in pet healthcare, the demand for computer-aided diagnosis (CAD) systems in veterinary medicine has increased. The development of veterinary CAD has stagnated due to a lack of sufficient radiology data. To overcome the challenge, we propose a generative active learning framework based on a variational autoencoder. This approach aims to alleviate the scarcity of reliable data for CAD systems in veterinary medicine. This study utilizes datasets comprising cardiomegaly radiograph data. After removing annotations and standardizing images, we employed a framework for data augmentation, which consists of a data generation phase and a query phase for filtering the generated data. The experimental results revealed that as the data generated through this framework was added to the training data of the generative model, the frechet inception distance consistently decreased from 84.14 to 50.75 on the radiograph. Subsequently, when the generated data were incorporated into the training of the classification model, the false positive of the confusion matrix also improved from 0.16 to 0.66 on the radiograph. The proposed framework has the potential to address the challenges of data scarcity in medical CAD, contributing to its advancement.
As a kind of biometrics, the gait information of pedestrians has attracted widespread attention from both industry and academia since it can be acquired from long distances without the cooperation of targets. In recent literature, this line of research has brought exciting chances along with alarming challenges: On the positive side, gait recognition used for security applications such as suspect retrieval and safety checks is becoming more and more promising. On the negative side, the misuse of gait information may lead to privacy concerns, as lawbreakers can track subjects of interest using gait characteristics even under face-masked and clothes-changed scenarios. To handle this double-edged sword, we propose a gait attribute editing framework termed GaitEditor. It can perform various degrees of attribute edits on real gait sequences while maintaining the visual authenticity, respectively used for gait data augmentation and de-identification, thereby adaptively enhancing or degrading gait recognition performance according to users' intentions. Experimentally, we conduct a comprehensive evaluation under both gait recognition and anonymization protocols on three widely used gait benchmarks. Numerous results illustrate that the adaptable utilization of GaitEditor efficiently improves gait recognition performance and generates vivid visualizations with de-identification to protect human privacy. To the best of our knowledge, GaitEditor is the first framework capable of editing multiple gait attributes while simultaneously benefiting gait recognition and gait anonymization. The source code of GaitEditor will be available at //github.com/ShiqiYu/OpenGait.
The effectiveness of clopidogrel, a widely used antiplatelet medication, varies significantly among individuals, necessitating the development of precise predictive models to optimize patient care. In this study, we leverage federated learning strategies to address clopidogrel treatment failure detection. Our research harnesses the collaborative power of multiple healthcare institutions, allowing them to jointly train machine learning models while safeguarding sensitive patient data. Utilizing the UK Biobank dataset, which encompasses a vast and diverse population, we partitioned the data based on geographic centers and evaluated the performance of federated learning. Our results show that while centralized training achieves higher Area Under the Curve (AUC) values and faster convergence, federated learning approaches can substantially narrow this performance gap. Our findings underscore the potential of federated learning in addressing clopidogrel treatment failure detection, offering a promising avenue for enhancing patient care through personalized treatment strategies while respecting data privacy. This study contributes to the growing body of research on federated learning in healthcare and lays the groundwork for secure and privacy-preserving predictive models for various medical conditions.
Graph Neural Networks (GNNs) have received considerable attention on graph-structured data learning for a wide variety of tasks. The well-designed propagation mechanism which has been demonstrated effective is the most fundamental part of GNNs. Although most of GNNs basically follow a message passing manner, litter effort has been made to discover and analyze their essential relations. In this paper, we establish a surprising connection between different propagation mechanisms with a unified optimization problem, showing that despite the proliferation of various GNNs, in fact, their proposed propagation mechanisms are the optimal solution optimizing a feature fitting function over a wide class of graph kernels with a graph regularization term. Our proposed unified optimization framework, summarizing the commonalities between several of the most representative GNNs, not only provides a macroscopic view on surveying the relations between different GNNs, but also further opens up new opportunities for flexibly designing new GNNs. With the proposed framework, we discover that existing works usually utilize naive graph convolutional kernels for feature fitting function, and we further develop two novel objective functions considering adjustable graph kernels showing low-pass or high-pass filtering capabilities respectively. Moreover, we provide the convergence proofs and expressive power comparisons for the proposed models. Extensive experiments on benchmark datasets clearly show that the proposed GNNs not only outperform the state-of-the-art methods but also have good ability to alleviate over-smoothing, and further verify the feasibility for designing GNNs with our unified optimization framework.
Pre-trained deep neural network language models such as ELMo, GPT, BERT and XLNet have recently achieved state-of-the-art performance on a variety of language understanding tasks. However, their size makes them impractical for a number of scenarios, especially on mobile and edge devices. In particular, the input word embedding matrix accounts for a significant proportion of the model's memory footprint, due to the large input vocabulary and embedding dimensions. Knowledge distillation techniques have had success at compressing large neural network models, but they are ineffective at yielding student models with vocabularies different from the original teacher models. We introduce a novel knowledge distillation technique for training a student model with a significantly smaller vocabulary as well as lower embedding and hidden state dimensions. Specifically, we employ a dual-training mechanism that trains the teacher and student models simultaneously to obtain optimal word embeddings for the student vocabulary. We combine this approach with learning shared projection matrices that transfer layer-wise knowledge from the teacher model to the student model. Our method is able to compress the BERT_BASE model by more than 60x, with only a minor drop in downstream task metrics, resulting in a language model with a footprint of under 7MB. Experimental results also demonstrate higher compression efficiency and accuracy when compared with other state-of-the-art compression techniques.
Clinical Named Entity Recognition (CNER) aims to identify and classify clinical terms such as diseases, symptoms, treatments, exams, and body parts in electronic health records, which is a fundamental and crucial task for clinical and translational research. In recent years, deep neural networks have achieved significant success in named entity recognition and many other Natural Language Processing (NLP) tasks. Most of these algorithms are trained end to end, and can automatically learn features from large scale labeled datasets. However, these data-driven methods typically lack the capability of processing rare or unseen entities. Previous statistical methods and feature engineering practice have demonstrated that human knowledge can provide valuable information for handling rare and unseen cases. In this paper, we address the problem by incorporating dictionaries into deep neural networks for the Chinese CNER task. Two different architectures that extend the Bi-directional Long Short-Term Memory (Bi-LSTM) neural network and five different feature representation schemes are proposed to handle the task. Computational results on the CCKS-2017 Task 2 benchmark dataset show that the proposed method achieves the highly competitive performance compared with the state-of-the-art deep learning methods.