arXiv subjects

Mingxuan Liu

Publications and source records attributed to Mingxuan Liu.

65 records · Page 4Linked to original sources

arXiv2024

Survival modeling using deep learning, machine learning and statistical methods: A comparative analysis for predicting mortality after hospital admission

Survival analysis is essential for studying time-to-event outcomes and providing a dynamic understanding of the probability of an event occurring over time. Various survival analysis techniques, from traditional statistical models to state-of-the-art machine learning algorithms, support healthcare intervention and policy decisions. However, there remains ongoing discussion about their comparative performance. We conducted a comparative study of several survival analysis methods, including Cox proportional hazards (CoxPH), stepwise CoxPH, elastic net penalized Cox model, Random Survival Forests (RSF), Gradient Boosting machine (GBM) learning, AutoScore-Survival, DeepSurv, time-dependent Cox model based on neural network (CoxTime), and DeepHit survival neural network. We applied the concordance index (C-index) for model goodness-of-fit, and integral Brier scores (IBS) for calibration, and considered the model interpretability. As a case study, we performed a retrospective analysis of patients admitted through the emergency department of a tertiary hospital from 2017 to 2019, predicting 90-day all-cause mortality based on patient demographics, clinicopathological features, and historical data. The results of the C-index indicate that deep learning achieved comparable performance, with DeepSurv producing the best discrimination (DeepSurv: 0.893; CoxTime: 0.892; DeepHit: 0.891). The calibration of DeepSurv (IBS: 0.041) performed the best, followed by RSF (IBS: 0.042) and GBM (IBS: 0.0421), all using the full variables. Moreover, AutoScore-Survival, using a minimal variable subset, is easy to interpret, and can achieve good discrimination and calibration (C-index: 0.867; IBS: 0.044). While all models were satisfactory, DeepSurv exhibited the best discrimination and calibration. In addition, AutoScore-Survival offers a more parsimonious model and excellent interpretability.

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arXiv2024

Generative Artificial Intelligence in Healthcare: Ethical Considerations and Assessment Checklist

The widespread use of ChatGPT and other emerging technology powered by generative artificial intelligence (GenAI) has drawn much attention to potential ethical issues, especially in high-stakes applications such as healthcare, but ethical discussions are yet to translate into operationalisable solutions. Furthermore, ongoing ethical discussions often neglect other types of GenAI that have been used to synthesise data (e.g., images) for research and practical purposes, which resolved some ethical issues and exposed others. We conduct a scoping review of ethical discussions on GenAI in healthcare to comprehensively analyse gaps in the current research, and further propose to reduce the gaps by developing a checklist for comprehensive assessment and transparent documentation of ethical discussions in GenAI research. The checklist can be readily integrated into the current peer review and publication system to enhance GenAI research, and may be used for ethics-related disclosures for GenAI-powered products, healthcare applications of such products and beyond.

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arXiv2023

SAM-Deblur: Let Segment Anything Boost Image Deblurring

Image deblurring is a critical task in the field of image restoration, aiming to eliminate blurring artifacts. However, the challenge of addressing non-uniform blurring leads to an ill-posed problem, which limits the generalization performance of existing deblurring models. To solve the problem, we propose a framework SAM-Deblur, integrating prior knowledge from the Segment Anything Model (SAM) into the deblurring task for the first time. In particular, SAM-Deblur is divided into three stages. First, we preprocess the blurred images, obtain segment masks via SAM, and propose a mask dropout method for training to enhance model robustness. Then, to fully leverage the structural priors generated by SAM, we propose a Mask Average Pooling (MAP) unit specifically designed to average SAM-generated segmented areas, serving as a plug-and-play component which can be seamlessly integrated into existing deblurring networks. Finally, we feed the fused features generated by the MAP Unit into the deblurring model to obtain a sharp image. Experimental results on the RealBlurJ, ReloBlur, and REDS datasets reveal that incorporating our methods improves GoPro-trained NAFNet's PSNR by 0.05, 0.96, and 7.03, respectively. Project page is available at GitHub \href{https://hplqaq.github.io/projects/sam-deblur}{HPLQAQ/SAM-Deblur}.

cs.CV↗

arXiv2023

Spiking-Diffusion: Vector Quantized Discrete Diffusion Model with Spiking Neural Networks

Spiking neural networks (SNNs) have tremendous potential for energy-efficient neuromorphic chips due to their binary and event-driven architecture. SNNs have been primarily used in classification tasks, but limited exploration on image generation tasks. To fill the gap, we propose a Spiking-Diffusion model, which is based on the vector quantized discrete diffusion model. First, we develop a vector quantized variational autoencoder with SNNs (VQ-SVAE) to learn a discrete latent space for images. In VQ-SVAE, image features are encoded using both the spike firing rate and postsynaptic potential, and an adaptive spike generator is designed to restore embedding features in the form of spike trains. Next, we perform absorbing state diffusion in the discrete latent space and construct a spiking diffusion image decoder (SDID) with SNNs to denoise the image. Our work is the first to build the diffusion model entirely from SNN layers. Experimental results on MNIST, FMNIST, KMNIST, Letters, and Cifar10 demonstrate that Spiking-Diffusion outperforms the existing SNN-based generation model. We achieve FIDs of 37.50, 91.98, 59.23, 67.41, and 120.5 on the above datasets respectively, with reductions of 58.60\%, 18.75\%, 64.51\%, 29.75\%, and 44.88\% in FIDs compared with the state-of-art work. Our code will be available at \url{https://github.com/Arktis2022/Spiking-Diffusion}.

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arXiv2023

Towards clinical AI fairness: A translational perspective

Artificial intelligence (AI) has demonstrated the ability to extract insights from data, but the issue of fairness remains a concern in high-stakes fields such as healthcare. Despite extensive discussion and efforts in algorithm development, AI fairness and clinical concerns have not been adequately addressed. In this paper, we discuss the misalignment between technical and clinical perspectives of AI fairness, highlight the barriers to AI fairness' translation to healthcare, advocate multidisciplinary collaboration to bridge the knowledge gap, and provide possible solutions to address the clinical concerns pertaining to AI fairness.

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arXiv2023

An empirical study of the effect of background data size on the stability of SHapley Additive exPlanations (SHAP) for deep learning models

Nowadays, the interpretation of why a machine learning (ML) model makes certain inferences is as crucial as the accuracy of such inferences. Some ML models like the decision tree possess inherent interpretability that can be directly comprehended by humans. Others like artificial neural networks (ANN), however, rely on external methods to uncover the deduction mechanism. SHapley Additive exPlanations (SHAP) is one of such external methods, which requires a background dataset when interpreting ANNs. Generally, a background dataset consists of instances randomly sampled from the training dataset. However, the sampling size and its effect on SHAP remain to be unexplored. In our empirical study on the MIMIC-III dataset, we show that the two core explanations - SHAP values and variable rankings fluctuate when using different background datasets acquired from random sampling, indicating that users cannot unquestioningly trust the one-shot interpretation from SHAP. Luckily, such fluctuation decreases with the increase of the background dataset size. Also, we notice an U-shape in the stability assessment of SHAP variable rankings, demonstrating that SHAP is more reliable in ranking the most and least important variables compared to moderately important ones. Overall, our results suggest that users should take into account how background data affects SHAP results, with improved SHAP stability as the background sample size increases.

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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.

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arXiv2022

Shapley variable importance cloud for machine learning models

Current practice in interpretable machine learning often focuses on explaining the final model trained from data, e.g., by using the Shapley additive explanations (SHAP) method. The recently developed Shapley variable importance cloud (ShapleyVIC) extends the current practice to a group of "nearly optimal models" to provide comprehensive and robust variable importance assessments, with estimated uncertainty intervals for a more complete understanding of variable contributions to predictions. ShapleyVIC was initially developed for applications with traditional regression models, and the benefits of ShapleyVIC inference have been demonstrated in real-life prediction tasks using the logistic regression model. However, as a model-agnostic approach, ShapleyVIC application is not limited to such scenarios. In this work, we extend ShapleyVIC implementation for machine learning models to enable wider applications, and propose it as a useful complement to the current SHAP analysis to enable more trustworthy applications of these black-box models.

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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.

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arXiv2022

Class-incremental Novel Class Discovery

We study the new task of class-incremental Novel Class Discovery (class-iNCD), which refers to the problem of discovering novel categories in an unlabelled data set by leveraging a pre-trained model that has been trained on a labelled data set containing disjoint yet related categories. Apart from discovering novel classes, we also aim at preserving the ability of the model to recognize previously seen base categories. Inspired by rehearsal-based incremental learning methods, in this paper we propose a novel approach for class-iNCD which prevents forgetting of past information about the base classes by jointly exploiting base class feature prototypes and feature-level knowledge distillation. We also propose a self-training clustering strategy that simultaneously clusters novel categories and trains a joint classifier for both the base and novel classes. This makes our method able to operate in a class-incremental setting. Our experiments, conducted on three common benchmarks, demonstrate that our method significantly outperforms state-of-the-art approaches. Code is available at https://github.com/OatmealLiu/class-iNCD

cs.CV↗

arXiv2022

Balanced background and explanation data are needed in explaining deep learning models with SHAP: An empirical study on clinical decision making

Objective: Shapley additive explanations (SHAP) is a popular post-hoc technique for explaining black box models. While the impact of data imbalance on predictive models has been extensively studied, it remains largely unknown with respect to SHAP-based model explanations. This study sought to investigate the effects of data imbalance on SHAP explanations for deep learning models, and to propose a strategy to mitigate these effects. Materials and Methods: We propose to adjust class distributions in the background and explanation data in SHAP when explaining black box models. Our data balancing strategy is to compose background data and explanation data with an equal distribution of classes. To evaluate the effects of data adjustment on model explanation, we propose to use the beeswarm plot as a qualitative tool to identify "abnormal" explanation artifacts, and quantitatively test the consistency between variable importance and prediction power. We demonstrated our proposed approach in an empirical study that predicted inpatient mortality using the Medical Information Mart for Intensive Care (MIMIC-III) data and a multilayer perceptron. Results: Using the data balancing strategy would allow us to reduce the number of the artifacts in the beeswarm plot, thus mitigating the negative effects of data imbalance. Additionally, with the balancing strategy, the top-ranked variables from the corresponding importance ranking demonstrated improved discrimination power. Discussion and Conclusion: Our findings suggest that balanced background and explanation data could help reduce the noise in explanation results induced by skewed data distribution and improve the reliability of variable importance ranking. Furthermore, these balancing procedures improve the potential of SHAP in identifying patients with abnormal characteristics in clinical applications.

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