arXiv subjects

Siqi Li

Publications and source records attributed to Siqi Li.

At least 109 records · Page 6Linked to original sources

arXiv2023

Federated and distributed learning applications for electronic health records and structured medical data: A scoping review

Federated learning (FL) has gained popularity in clinical research in recent years to facilitate privacy-preserving collaboration. Structured data, one of the most prevalent forms of clinical data, has experienced significant growth in volume concurrently, notably with the widespread adoption of electronic health records in clinical practice. This review examines FL applications on structured medical data, identifies contemporary limitations and discusses potential innovations. We searched five databases, SCOPUS, MEDLINE, Web of Science, Embase, and CINAHL, to identify articles that applied FL to structured medical data and reported results following the PRISMA guidelines. Each selected publication was evaluated from three primary perspectives, including data quality, modeling strategies, and FL frameworks. Out of the 1160 papers screened, 34 met the inclusion criteria, with each article consisting of one or more studies that used FL to handle structured clinical/medical data. Of these, 24 utilized data acquired from electronic health records, with clinical predictions and association studies being the most common clinical research tasks that FL was applied to. Only one article exclusively explored the vertical FL setting, while the remaining 33 explored the horizontal FL setting, with only 14 discussing comparisons between single-site (local) and FL (global) analysis. The existing FL applications on structured medical data lack sufficient evaluations of clinically meaningful benefits, particularly when compared to single-site analyses. Therefore, it is crucial for future FL applications to prioritize clinical motivations and develop designs and methodologies that can effectively support and aid clinical practice and research.

cs.LG↗

arXiv2023

UFO2: A unified pre-training framework for online and offline speech recognition

In this paper, we propose a Unified pre-training Framework for Online and Offline (UFO2) Automatic Speech Recognition (ASR), which 1) simplifies the two separate training workflows for online and offline modes into one process, and 2) improves the Word Error Rate (WER) performance with limited utterance annotating. Specifically, we extend the conventional offline-mode Self-Supervised Learning (SSL)-based ASR approach to a unified manner, where the model training is conditioned on both the full-context and dynamic-chunked inputs. To enhance the pre-trained representation model, stop-gradient operation is applied to decouple the online-mode objectives to the quantizer. Moreover, in both the pre-training and the downstream fine-tuning stages, joint losses are proposed to train the unified model with full-weight sharing for the two modes. Experimental results on the LibriSpeech dataset show that UFO2 outperforms the SSL-based baseline method by 29.7% and 18.2% relative WER reduction in offline and online modes, respectively.

eess.AS↗

arXiv2023

Photon Energy-Resolved Velocity Map Imaging from Spectral Domain Ghost Imaging

We present an approach that combines photon spectrum correlation analysis with the reconstruction of three-dimensional momentum distribution from velocity map images in an efficient, single-step procedure. We demonstrate its efficacy with the results from the photoionization of the $2p$-shell of argon using the FLASH free-electron laser~(FEL). Distinct spectral features due to the spin-orbit splitting of Ar$^+(2p^{-1})$ are resolved, despite the large average bandwidth of the ionizing pulses from the FEL. This demonstrates a clear advantage over the conventional analysis method, and it will be broadly beneficial for velocity map imaging experiments with FEL sources. The retrieved linewidth of the binding energy spectrum approaches the resolution limitation prescribed by the spectrometers used to collect the data. Our approach presents a path to extend spectral-domain ghost imaging to the case where the photoproduct observable is high-dimensional.

physics.atom-ph↗

arXiv2023

FedScore: A privacy-preserving framework for federated scoring system development

We propose FedScore, a privacy-preserving federated learning framework for scoring system generation across multiple sites to facilitate cross-institutional collaborations. The FedScore framework includes five modules: federated variable ranking, federated variable transformation, federated score derivation, federated model selection and federated model evaluation. To illustrate usage and assess FedScore's performance, we built a hypothetical global scoring system for mortality prediction within 30 days after a visit to an emergency department using 10 simulated sites divided from a tertiary hospital in Singapore. We employed a pre-existing score generator to construct 10 local scoring systems independently at each site and we also developed a scoring system using centralized data for comparison. We compared the acquired FedScore model's performance with that of other scoring models using the receiver operating characteristic (ROC) analysis. The FedScore model achieved an average area under the curve (AUC) value of 0.763 across all sites, with a standard deviation (SD) of 0.020. We also calculated the average AUC values and SDs for each local model, and the FedScore model showed promising accuracy and stability with a high average AUC value which was closest to the one of the pooled model and SD which was lower than that of most local models. This study demonstrates that FedScore is a privacy-preserving scoring system generator with potentially good generalizability.

cs.LG↗

arXiv2023

The variance-gamma ratio distribution

Let $X$ and $Y$ be independent variance-gamma random variables with zero location parameter; then the exact probability density function of the ratio $X/Y$ is derived. Some basic distributional properties are also derived, including identification of parameter regimes under which the density is bounded, asymptotic approximations of tail probabilities, and fractional moments; in particular, we see that the mean is undefined. In the case that $X$ and $Y$ are independent symmetric variance-gamma random variables, an exact formula is also given for the cumulative distribution function of the ratio $X/Y$.

math.PR↗

arXiv2022

Bounding Kolmogorov distances through Wasserstein and related integral probability metrics

We establish general upper bounds on the Kolmogorov distance between two probability distributions in terms of the distance between these distributions as measured with respect to the Wasserstein or smooth Wasserstein metrics. These bounds generalise existing results from the literature. To illustrate the broad applicability of our general bounds, we apply them to extract Kolmogorov distance bounds from multivariate normal, beta and variance-gamma approximations that have been established in the Stein's method literature.

math.PR↗

arXiv2022

Parotid Gland MRI Segmentation Based on Swin-Unet and Multimodal Images

Background and objective: Parotid gland tumors account for approximately 2% to 10% of head and neck tumors. Preoperative tumor localization, differential diagnosis, and subsequent selection of appropriate treatment for parotid gland tumors are critical. However, the relative rarity of these tumors and the highly dispersed tissue types have left an unmet need for a subtle differential diagnosis of such neoplastic lesions based on preoperative radiomics. Recently, deep learning methods have developed rapidly, especially Transformer beats the traditional convolutional neural network in computer vision. Many new Transformer-based networks have been proposed for computer vision tasks. Methods: In this study, multicenter multimodal parotid gland MR images were collected. The Swin-Unet which was based on Transformer was used. MR images of short time inversion recovery, T1-weighted and T2-weighted modalities were combined into three-channel data to train the network. We achieved segmentation of the region of interest for parotid gland and tumor. Results: The Dice-Similarity Coefficient of the model on the test set was 88.63%, Mean Pixel Accuracy was 99.31%, Mean Intersection over Union was 83.99%, and Hausdorff Distance was 3.04. Then a series of comparison experiments were designed in this paper to further validate the segmentation performance of the algorithm. Conclusions: Experimental results showed that our method has good results for parotid gland and tumor segmentation. The Transformer-based network outperforms the traditional convolutional neural network in the field of medical images.

eess.IV↗

arXiv2022

Neural KEM: A Kernel Method with Deep Coefficient Prior for PET Image Reconstruction

Image reconstruction of low-count positron emission tomography (PET) data is challenging. Kernel methods address the challenge by incorporating image prior information in the forward model of iterative PET image reconstruction. The kernelized expectation-maximization (KEM) algorithm has been developed and demonstrated to be effective and easy to implement. A common approach for a further improvement of the kernel method would be adding an explicit regularization, which however leads to a complex optimization problem. In this paper, we propose an implicit regularization for the kernel method by using a deep coefficient prior, which represents the kernel coefficient image in the PET forward model using a convolutional neural-network. To solve the maximum-likelihood neural network-based reconstruction problem, we apply the principle of optimization transfer to derive a neural KEM algorithm. Each iteration of the algorithm consists of two separate steps: a KEM step for image update from the projection data and a deep-learning step in the image domain for updating the kernel coefficient image using the neural network. This optimization algorithm is guaranteed to monotonically increase the data likelihood. The results from computer simulations and real patient data have demonstrated that the neural KEM can outperform existing KEM and deep image prior methods.

eess.IV↗

arXiv2022

Investigating End-user Acceptance of Last-mile Delivery by Autonomous Vehicles in the United States

This paper investigates the end-user acceptance of last-mile delivery carried out by autonomous vehicles within the United States. A total of 296 participants were presented with information on this technology and then asked to complete a questionnaire on their perceptions to gauge their behavioral intention concerning acceptance. Structural equation modeling of the partial least squares flavor (PLS-SEM) was employed to analyze the collected data. The results indicated that the perceived usefulness of the technology played the greatest role in end-user acceptance decisions, followed by the influence of others, and then the enjoyment received by interacting with the technology. Furthermore, the perception of risk associated with using autonomous delivery vehicles for last-mile delivery led to a decrease in acceptance. However, most participants did not perceive the use of this technology to be risky. The paper concludes by summarizing the implications our findings have on the respective stakeholders and proposing the next steps in this area of research.

cs.CY↗

arXiv2022

Handling missing values in healthcare data: A systematic review of deep learning-based imputation techniques

Objective: The proper handling of missing values is critical to delivering reliable estimates and decisions, especially in high-stakes fields such as clinical research. The increasing diversity and complexity of data have led many researchers to develop deep learning (DL)-based imputation techniques. We conducted a systematic review to evaluate the use of these techniques, with a particular focus on data types, aiming to assist healthcare researchers from various disciplines in dealing with missing values. Methods: We searched five databases (MEDLINE, Web of Science, Embase, CINAHL, and Scopus) for articles published prior to August 2021 that applied DL-based models to imputation. We assessed selected publications from four perspectives: health data types, model backbone (i.e., main architecture), imputation strategies, and comparison with non-DL-based methods. Based on data types, we created an evidence map to illustrate the adoption of DL models. Results: We included 64 articles, of which tabular static (26.6%, 17/64) and temporal data (37.5%, 24/64) were the most frequently investigated. We found that model backbone(s) differed among data types as well as the imputation strategy. The "integrated" strategy, that is, the imputation task being solved concurrently with downstream tasks, was popular for tabular temporal (50%, 12/24) and multi-modal data (71.4%, 5/7), but limited for other data types. Moreover, DL-based imputation methods yielded better imputation accuracy in most studies, compared with non-DL-based methods. Conclusion: DL-based imputation models can be customized based on data type, addressing the corresponding missing patterns, and its associated "integrated" strategy can enhance the efficacy of imputation, especially in scenarios where data is complex. Future research may focus on the portability and fairness of DL-based models for healthcare data imputation.

cs.LG↗

arXiv2022

Deep Kernel Representation for Image Reconstruction in PET

Image reconstruction for positron emission tomography (PET) is challenging because of the ill-conditioned tomographic problem and low counting statistics. Kernel methods address this challenge by using kernel representation to incorporate image prior information in the forward model of iterative PET image reconstruction. Existing kernel methods construct the kernels commonly using an empirical process, which may lead to unsatisfactory performance. In this paper, we describe the equivalence between the kernel representation and a trainable neural network model. A deep kernel method is then proposed by exploiting a deep neural network to enable automated learning of an improved kernel model and is directly applicable to single subjects in dynamic PET. The training process utilizes available image prior data to form a set of robust kernels in an optimized way rather than empirically. The results from computer simulations and a real patient dataset demonstrate that the proposed deep kernel method can outperform the existing kernel method and neural network method for dynamic PET image reconstruction.

eess.IV↗

arXiv2022

Benchmarking emergency department triage prediction models with machine learning and large public electronic health records

The demand for emergency department (ED) services is increasing across the globe, particularly during the current COVID-19 pandemic. Clinical triage and risk assessment have become increasingly challenging due to the shortage of medical resources and the strain on hospital infrastructure caused by the pandemic. As a result of the widespread use of electronic health records (EHRs), we now have access to a vast amount of clinical data, which allows us to develop predictive models and decision support systems to address these challenges. To date, however, there are no widely accepted benchmark ED triage prediction models based on large-scale public EHR data. An open-source benchmarking platform would streamline research workflows by eliminating cumbersome data preprocessing, and facilitate comparisons among different studies and methodologies. In this paper, based on the Medical Information Mart for Intensive Care IV Emergency Department (MIMIC-IV-ED) database, we developed a publicly available benchmark suite for ED triage predictive models and created a benchmark dataset that contains over 400,000 ED visits from 2011 to 2019. We introduced three ED-based outcomes (hospitalization, critical outcomes, and 72-hour ED reattendance) and implemented a variety of popular methodologies, ranging from machine learning methods to clinical scoring systems. We evaluated and compared the performance of these methods against benchmark tasks. Our codes are open-source, allowing anyone with MIMIC-IV-ED data access to perform the same steps in data processing, benchmark model building, and experiments. This study provides future researchers with insights, suggestions, and protocols for managing raw data and developing risk triaging tools for emergency care.

cs.LG↗

arXiv2022

A novel interpretable machine learning system to generate clinical risk scores: An application for predicting early mortality or unplanned readmission in a retrospective cohort study

Risk scores are widely used for clinical decision making and commonly generated from logistic regression models. Machine-learning-based methods may work well for identifying important predictors, but such 'black box' variable selection limits interpretability, and variable importance evaluated from a single model can be biased. We propose a robust and interpretable variable selection approach using the recently developed Shapley variable importance cloud (ShapleyVIC) that accounts for variability across models. Our approach evaluates and visualizes overall variable contributions for in-depth inference and transparent variable selection, and filters out non-significant contributors to simplify model building steps. We derive an ensemble variable ranking from variable contributions, which is easily integrated with an automated and modularized risk score generator, AutoScore, for convenient implementation. In a study of early death or unplanned readmission, ShapleyVIC selected 6 of 41 candidate variables to create a well-performing model, which had similar performance to a 16-variable model from machine-learning-based ranking.

cs.LG↗

arXiv2021

Attosecond Coherent Electron Motion in Auger-Meitner Decay

In quantum systems, coherent superpositions of electronic states evolve on ultrafast timescales (few femtosecond to attosecond, 1 as = 0.001 fs = 10^{-18} s), leading to a time dependent charge density. Here we exploit the first attosecond soft x-ray pulses produced by an x-ray free-electron laser to induce a coherent core-hole excitation in nitric oxide. Using an additional circularly polarized infrared laser pulse we create a clock to time-resolve the electron dynamics, and demonstrate control of the coherent electron motion by tuning the photon energy of the x-ray pulse. Core-excited states offer a fundamental test bed for studying coherent electron dynamics in highly excited and strongly correlated matter.

physics.chem-ph↗

arXiv2021

View-Guided Point Cloud Completion

This paper presents a view-guided solution for the task of point cloud completion. Unlike most existing methods directly inferring the missing points using shape priors, we address this task by introducing ViPC (view-guided point cloud completion) that takes the missing crucial global structure information from an extra single-view image. By leveraging a framework that sequentially performs effective cross-modality and cross-level fusions, our method achieves significantly superior results over typical existing solutions on a new large-scale dataset we collect for the view-guided point cloud completion task.

cs.CV↗

arXiv2021

Modified Kernel MLAA Using Autoencoder for PET-enabled Dual-Energy CT

Combined use of PET and dual-energy CT provides complementary information for multi-parametric imaging. PETenabled dual-energy CT combines a low-energy x-ray CT image with a high-energy &γ&-ray CT (GCT) image reconstructed from time-of-flight PET emission data to enable dual-energy CT material decomposition on a PET/CT scanner. The maximumlikelihood attenuation and activity (MLAA) algorithm has been used for GCT reconstruction but suffers from noise. Kernel MLAA exploits an x-ray CT image prior through the kernel framework to guide GCT reconstruction and has demonstrated substantial improvements in noise suppression. However, similar to other kernel methods for image reconstruction, the existing kernel MLAA uses image intensity-based features to construct the kernel representation, which is not always robust and may lead to suboptimal reconstruction with artifacts. In this paper, we propose a modified kernel method by using an autoencoder convolutional neural network (CNN) to extract an intrinsic feature set from the x-ray CT image prior. A computer simulation study was conducted to compare the autoencoder CNN-derived feature representation with raw image patches for evaluation of kernel MLAA for GCT image reconstruction and dual-energy multimaterial decomposition. The results show that the autoencoder kernel MLAA method can achieve a significant image quality improvement for GCT and material decomposition as compared to the existing kernel MLAA algorithm. A weakness of the proposed method is its potential over-smoothness in a bone region, indicating the importance of further optimization in future work. The codes is available on https://github.com/SiqiLi1020/Autoencoder- Kernel-MLAA.

physics.med-ph↗

arXiv2020

Low-Dose CT Image Denoising Using Parallel-Clone Networks

Deep neural networks have a great potential to improve image denoising in low-dose computed tomography (LDCT). Popular ways to increase the network capacity include adding more layers or repeating a modularized clone model in a sequence. In such sequential architectures, the noisy input image and end output image are commonly used only once in the training model, which however limits the overall learning performance. In this paper, we propose a parallel-clone neural network method that utilizes a modularized network model and exploits the benefit of parallel input, parallel-output loss, and clone-toclone feature transfer. The proposed model keeps a similar or less number of unknown network weights as compared to conventional models but can accelerate the learning process significantly. The method was evaluated using the Mayo LDCT dataset and compared with existing deep learning models. The results show that the use of parallel input, parallel-output loss, and clone-to-clone feature transfer all can contribute to an accelerated convergence of deep learning and lead to improved image quality in testing. The parallel-clone network has been demonstrated promising for LDCT image denoising.

eess.IV↗

arXiv2020

Attention-based Multi-modal Fusion Network for Semantic Scene Completion

This paper presents an end-to-end 3D convolutional network named attention-based multi-modal fusion network (AMFNet) for the semantic scene completion (SSC) task of inferring the occupancy and semantic labels of a volumetric 3D scene from single-view RGB-D images. Compared with previous methods which use only the semantic features extracted from RGB-D images, the proposed AMFNet learns to perform effective 3D scene completion and semantic segmentation simultaneously via leveraging the experience of inferring 2D semantic segmentation from RGB-D images as well as the reliable depth cues in spatial dimension. It is achieved by employing a multi-modal fusion architecture boosted from 2D semantic segmentation and a 3D semantic completion network empowered by residual attention blocks. We validate our method on both the synthetic SUNCG-RGBD dataset and the real NYUv2 dataset and the results show that our method respectively achieves the gains of 2.5% and 2.6% on the synthetic SUNCG-RGBD dataset and the real NYUv2 dataset against the state-of-the-art method.

cs.CV↗