Clinical Domain Knowledge-Derived Template Improves Post Hoc AI Explanations in Pneumothorax Classification

Background: Pneumothorax is an acute thoracic disease caused by abnormal air collection between the lungs and chest wall. To address the opaqueness often associated with deep learning (DL) models, explainable artificial intelligence (XAI) methods have been introduced to outline regions related to pneumothorax diagnoses made by DL models. However, these explanations sometimes diverge from actual lesion areas, highlighting the need for further improvement. Method: We propose a template-guided approach to incorporate the clinical knowledge of pneumothorax into model explanations generated by XAI methods, thereby enhancing the quality of these explanations. Utilizing one lesion delineation created by radiologists, our approach first generates a template that represents potential areas of pneumothorax occurrence. This template is then superimposed on model explanations to filter out extraneous explanations that fall outside the template's boundaries. To validate its efficacy, we carried out a comparative analysis of three XAI methods with and without our template guidance when explaining two DL models in two real-world datasets. Results: The proposed approach consistently improved baseline XAI methods across twelve benchmark scenarios built on three XAI methods, two DL models, and two datasets. The average incremental percentages, calculated by the performance improvements over the baseline performance, were 97.8% in Intersection over Union (IoU) and 94.1% in Dice Similarity Coefficient (DSC) when comparing model explanations and ground-truth lesion areas. Conclusions: In the context of pneumothorax diagnoses, we proposed a template-guided approach for improving AI explanations. We anticipate that our template guidance will forge a fresh approach to elucidating AI models by integrating clinical domain expertise.

Efficient scene text image super-resolution with semantic guidance

Scene text image super-resolution has significantly improved the accuracy of scene text recognition. However, many existing methods emphasize performance over efficiency and ignore the practical need for lightweight solutions in deployment scenarios. Faced with the issues, our work proposes an efficient framework called SGENet to facilitate deployment on resource-limited platforms. SGENet contains two branches: super-resolution branch and semantic guidance branch. We apply a lightweight pre-trained recognizer as a semantic extractor to enhance the understanding of text information. Meanwhile, we design the visual-semantic alignment module to achieve bidirectional alignment between image features and semantics, resulting in the generation of highquality prior guidance. We conduct extensive experiments on benchmark dataset, and the proposed SGENet achieves excellent performance with fewer computational costs. Code is available at https://github.com/SijieLiu518/SGENet

Foundation Model Makes Clustering a Better Initialization for Active Learning

Active learning selects the most informative samples from the unlabeled dataset to annotate in the context of a limited annotation budget. While numerous methods have been proposed for subsequent sample selection based on an initialized model, scant attention has been paid to the indispensable phase of active learning: selecting samples for model initialization. Most of the previous studies resort to random sampling or naive clustering. However, random sampling is prone to fluctuation, and naive clustering suffers from convergence speed, particularly when dealing with high-dimensional data such as imaging data. In this work, we propose to integrate foundation models with clustering methods to select samples for active learning initialization. Foundation models refer to those trained on massive datasets by the self-supervised paradigm and capable of generating informative and compacted embeddings for various downstream tasks. Leveraging these embeddings to replace raw features such as pixel values, clustering quickly converges and identifies better initial samples. For a comprehensive comparison, we included a classic ImageNet-supervised model to acquire embeddings. Experiments on two clinical tasks of image classification and segmentation demonstrated that foundation model-based clustering efficiently pinpointed informative initial samples, leading to models showcasing enhanced performance than the baseline methods. We envisage that this study provides an effective paradigm for future active learning.

Leveraging Anatomical Constraints with Uncertainty for Pneumothorax Segmentation

Pneumothorax is a medical emergency caused by abnormal accumulation of air in the pleural space - the potential space between the lungs and chest wall. On 2D chest radiographs, pneumothorax occurs within the thoracic cavity and outside of the mediastinum and we refer to this area as "lung+ space". While deep learning (DL) has increasingly been utilized to segment pneumothorax lesions in chest radiographs, many existing DL models employ an end-to-end approach. These models directly map chest radiographs to clinician-annotated lesion areas, often neglecting the vital domain knowledge that pneumothorax is inherently location-sensitive. We propose a novel approach that incorporates the lung+ space as a constraint during DL model training for pneumothorax segmentation on 2D chest radiographs. To circumvent the need for additional annotations and to prevent potential label leakage on the target task, our method utilizes external datasets and an auxiliary task of lung segmentation. This approach generates a specific constraint of lung+ space for each chest radiograph. Furthermore, we have incorporated a discriminator to eliminate unreliable constraints caused by the domain shift between the auxiliary and target datasets. Our results demonstrated significant improvements, with average performance gains of 4.6%, 3.6%, and 3.3% regarding Intersection over Union (IoU), Dice Similarity Coefficient (DSC), and Hausdorff Distance (HD). Our research underscores the significance of incorporating medical domain knowledge about the location-specific nature of pneumothorax to enhance DL-based lesion segmentation.

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.

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.

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.

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.

Deep learning for temporal data representation in electronic health records: A systematic review of challenges and methodologies

Objective: Temporal electronic health records (EHRs) can be a wealth of information for secondary uses, such as clinical events prediction or chronic disease management. However, challenges exist for temporal data representation. We therefore sought to identify these challenges and evaluate novel methodologies for addressing them through a systematic examination of deep learning solutions. Methods: We searched five databases (PubMed, EMBASE, the Institute of Electrical and Electronics Engineers [IEEE] Xplore Digital Library, the Association for Computing Machinery [ACM] digital library, and Web of Science) complemented with hand-searching in several prestigious computer science conference proceedings. We sought articles that reported deep learning methodologies on temporal data representation in structured EHR data from January 1, 2010, to August 30, 2020. We summarized and analyzed the selected articles from three perspectives: nature of time series, methodology, and model implementation. Results: We included 98 articles related to temporal data representation using deep learning. Four major challenges were identified, including data irregularity, data heterogeneity, data sparsity, and model opacity. We then studied how deep learning techniques were applied to address these challenges. Finally, we discuss some open challenges arising from deep learning. Conclusion: Temporal EHR data present several major challenges for clinical prediction modeling and data utilization. To some extent, current deep learning solutions can address these challenges. Future studies can consider designing comprehensive and integrated solutions. Moreover, researchers should incorporate additional clinical domain knowledge into study designs and enhance the interpretability of the model to facilitate its implementation in clinical practice.

AutoScore-Imbalance: An interpretable machine learning tool for development of clinical scores with rare events data

Background: Medical decision-making impacts both individual and public health. Clinical scores are commonly used among a wide variety of decision-making models for determining the degree of disease deterioration at the bedside. AutoScore was proposed as a useful clinical score generator based on machine learning and a generalized linear model. Its current framework, however, still leaves room for improvement when addressing unbalanced data of rare events. Methods: Using machine intelligence approaches, we developed AutoScore-Imbalance, which comprises three components: training dataset optimization, sample weight optimization, and adjusted AutoScore. All scoring models were evaluated on the basis of their area under the curve (AUC) in the receiver operating characteristic analysis and balanced accuracy (i.e., mean value of sensitivity and specificity). By utilizing a publicly accessible dataset from Beth Israel Deaconess Medical Center, we assessed the proposed model and baseline approaches in the prediction of inpatient mortality. Results: AutoScore-Imbalance outperformed baselines in terms of AUC and balanced accuracy. The nine-variable AutoScore-Imbalance sub-model achieved the highest AUC of 0.786 (0.732-0.839) while the eleven-variable original AutoScore obtained an AUC of 0.723 (0.663-0.783), and the logistic regression with 21 variables obtained an AUC of 0.743 (0.685-0.800). The AutoScore-Imbalance sub-model (using down-sampling algorithm) yielded an AUC of 0. 0.771 (0.718-0.823) with only five variables, demonstrating a good balance between performance and variable sparsity. Conclusions: The AutoScore-Imbalance tool has the potential to be applied to highly unbalanced datasets to gain further insight into rare medical events and to facilitate real-world clinical decision-making.