A novel method for tracking the tidal volume (TV) from electrocardiogram (ECG) is presented. The method is based on the amplitude of ECG-derived respiration (EDR) signals. Three different morphology-based EDR signals and three different amplitude estimation methods have been studied, leading to a total of 9 amplitude-EDR (AEDR) signals per ECG channel. The potential of these AEDR signals to track the changes in TV was analyzed. These methods do not need a calibration process. In addition, a personalized-calibration approach for TV estimation is proposed, based on a linear model that uses all AEDR signals from a device. All methods have been validated with two different ECG devices: a commercial Holter monitor, and a custom-made wearable armband. The lowest errors for the personalized-calibration methods, compared to a reference TV, were -3.48% [-17.41% / 12.93%] (median [first quartile / third quartile]) for the Holter monitor, and 0.28% [-10.90% / 17.15%] for the armband. On the other hand, medians of correlations to the reference TV were higher than 0.8 for uncalibrated methods, while they were higher than 0.9 for personal-calibrated methods. These results suggest that TV changes can be tracked from ECG using either a conventional (Holter) setup, or our custom-made wearable armband. These results also suggest that the methods are not as reliable in applications that induce small changes in TV, but they can be potentially useful for detecting large changes in TV, such as sleep apnea/hypopnea and/or exacerbations of a chronic respiratory disease.

Protein methylation is one of the most important reversible post-translational modifications (PTMs), playing a vital role in the regulation of gene expression. Protein methylation sites serve as biomarkers in cardiovascular and pulmonary diseases, influencing various aspects of normal cell biology and pathogenesis. Nonetheless, the majority of existing computational methods for predicting protein methylation sites (PMSP) have been constructed based on protein sequences, with few methods leveraging the topological information of proteins. To address this issue, we propose an innovative framework for predicting Methylation Sites using Graphs (GraphMethySite) that employs graph convolution network in conjunction with Bayesian Optimization (BO) to automatically discover the graphical structure surrounding a candidate site and improve the predictive accuracy. In order to extract the most optimal subgraphs associated with methylation sites, we extend GraphMethySite by coupling it with a hybrid Bayesian optimization (together named GraphMethySite +) to determine and visualize the topological relevance among amino-acid residues. We evaluated our framework on two extended protein methylation datasets, and empirical results demonstrate that it outperforms existing state-of-the-art methylation prediction methods.

Causality holds profound potentials to dissipate confusion and improve accuracy in cuffless continuous blood pressure (BP) estimation, an area often neglected in current research. In this study, we propose a two-stage framework, CiGNN, that seamlessly integrates causality and graph neural network (GNN) for cuffless continuous BP estimation. The first stage concentrates on the generation of a causal graph between BP and wearable features from the the perspective of causal inference, so as to identify features that are causally related to BP variations. This stage is pivotal for the identification of novel causal features from the causal graph beyond pulse transit time (PTT). We found these causal features empower better tracking in BP changes compared to PTT. For the second stage, a spatio-temporal GNN (STGNN) is utilized to learn from the causal graph obtained from the first stage. The STGNN can exploit both the spatial information within the causal graph and temporal information from beat-by-beat cardiac signals for refined cuffless continuous BP estimation. We evaluated the proposed method with three datasets that include 305 subjects (102 hypertensive patients) with age ranging from 20-90 and BP at different levels, with the continuous Finapres BP as references. The mean absolute difference (MAD) for estimated systolic blood pressure (SBP) and diastolic blood pressure (DBP) were 3.77 mmHg and 2.52 mmHg, respectively, which outperformed comparison methods. In all cases including subjects with different age groups, while doing various maneuvers that induces BP changes at different levels and with or without hypertension, the proposed CiGNN method demonstrates superior performance for cuffless continuous BP estimation. These findings suggest that the proposed CiGNN is a promising approach in elucidating the causal mechanisms of cuffless BP estimation and can substantially enhance the precision of BP measurement.

Automated segmentation of liver tumors in CT scans is pivotal for diagnosing and treating liver cancer, offering a valuable alternative to labor-intensive manual processes and ensuring the provision of accurate and reliable clinical assessment. However, the inherent variability of liver tumors, coupled with the challenges posed by blurred boundaries in imaging characteristics, presents a substantial obstacle to achieving their precise segmentation. In this paper, we propose a novel dual-branch liver tumor segmentation model, SBCNet, to address these challenges effectively. Specifically, our proposed method introduces a contextual encoding module, which enables a better identification of tumor variability using an advanced multiscale adaptive kernel. Moreover, a boundary enhancement module is designed for the counterpart branch to enhance the perception of boundaries by incorporating contour learning with the Sobel operator. Finally, we propose a hybrid multi-task loss function, concurrently concerning tumors' scale and boundary features, to foster interaction across different tasks of dual branches, further improving tumor segmentation. Experimental validation on the publicly available LiTS dataset demonstrates the practical efficacy of each module, with SBCNet yielding competitive results compared to other state-of-the-art methods for liver tumor segmentation. The code can be available at https://github.com/gardnerzhou/SBCNet.

Cataract surgery remains the only definitive treatment for visually significant cataracts, which are a major cause of preventable blindness worldwide. Successful performance of cataract surgery relies on stable dilation of the pupil. Automated pupil segmentation from surgical videos can assist surgeons in detecting risk factors for pupillary instability prior to the development of surgical complications. However, surgical illumination variations, surgical instrument obstruction, and lens material hydration during cataract surgery can limit pupil segmentation accuracy. To address these problems, we propose a novel method named adaptive wavelet tensor feature extraction (AWTFE). AWTFE is designed to enhance the accuracy of deep learning-powered pupil recognition systems. First, we represent the correlations among spatial information, color channels, and wavelet subbands by constructing a third-order tensor. We then utilize higher-order singular value decomposition to eliminate redundant information adaptively and estimate pupil feature information. We evaluated the proposed method by conducting experiments with state-of-the-art deep learning segmentation models on our BigCat dataset consisting of 5,700 annotated intraoperative images from 190 cataract surgeries and a public CaDIS dataset. The experimental results reveal that the AWTFE method effectively identifies features relevant to the pupil region and improved the overall performance of segmentation models by up to 2.26% (BigCat) and 3.31% (CaDIS). Incorporation of the AWTFE method led to statistically significant improvements in segmentation performance (P < 1.29  ×  10-10 for each model) and yielded the highest-performing model overall (Dice coefficients of 94.74% and 96.71% for the BigCat and CaDIS datasets, respectively). In performance comparisons, the AWTFE consistently outperformed other feature extraction methods in enhancing model performance. In addition, the proposed AWTFE method significantly improved pupil recognition performance by up to 2.87% in particularly challenging phases of cataract surgery.

With a growing body of evidence establishing circular RNAs (circRNAs) are widely exploited in eukaryotic cells and have a significant contribution in the occurrence and development of many complex human diseases. Disease-associated circRNAs can serve as clinical diagnostic biomarkers and therapeutic targets, providing novel ideas for biopharmaceutical research. However, available computation methods for predicting circRNA-disease associations (CDAs) do not sufficiently consider the contextual information of biological network nodes, making their performance limited. In this work, we propose a multi-hop attention graph neural network-based approach MAGCDA to infer potential CDAs. Specifically, we first construct a multi-source attribute heterogeneous network of circRNAs and diseases, then use a multi-hop strategy of graph nodes to deeply aggregate node context information through attention diffusion, thus enhancing topological structure information and mining data hidden features, and finally use random forest to accurately infer potential CDAs. In the four gold standard data sets, MAGCDA achieved prediction accuracy of 92.58%, 91.42%, 83.46% and 91.12%, respectively. MAGCDA has also presented prominent achievements in ablation experiments and in comparisons with other models. Additionally, 18 and 17 potential circRNAs in top 20 predicted scores for MAGCDA prediction scores were confirmed in case studies of the complex diseases breast cancer and Almozheimer's disease, respectively. These results suggest that MAGCDA can be a practical tool to explore potential disease-associated circRNAs and provide a theoretical basis for disease diagnosis and treatment.

The prediction of molecular properties remains a challenging task in the field of drug design and development. Recently, there has been a growing interest in the analysis of biological images. Molecular images, as a novel representation, have proven to be competitive, yet they lack explicit information and detailed semantic richness. Conversely, semantic information in SMILES sequences is explicit but lacks spatial structural details. Therefore, in this study, we focus on and explore the relationship between these two types of representations, proposing a novel multimodal architecture named ISMol. ISMol relies on a cross-attention mechanism to extract information representations of molecules from both images and SMILES strings, thereby predicting molecular properties. Evaluation results on 14 small molecule ADMET datasets indicate that ISMol outperforms machine learning (ML) and deep learning (DL) models based on single-modal representations. In addition, we analyze our method through a large number of experiments to test the superiority, interpretability and generalizability of the method. In summary, ISMol offers a powerful deep learning toolbox for drug discovery in a variety of molecular properties.