arXiv subjects

Chengyu Liu

Publications and source records attributed to Chengyu Liu.

30 records · Page 2Linked to original sources

arXiv2023

ECG-CL: A Comprehensive Electrocardiogram Interpretation Method Based on Continual Learning

Electrocardiogram (ECG) monitoring is one of the most powerful technique of cardiovascular disease (CVD) early identification, and the introduction of intelligent wearable ECG devices has enabled daily monitoring. However, due to the need for professional expertise in the ECGs interpretation, general public access has once again been restricted, prompting the need for the development of advanced diagnostic algorithms. Classic rule-based algorithms are now completely outperformed by deep learning based methods. But the advancement of smart diagnostic algorithms is hampered by issues like small dataset, inconsistent data labeling, inefficient use of local and global ECG information, memory and inference time consuming deployment of multiple models, and lack of information transfer between tasks. We propose a multi-resolution model that can sustain high-resolution low-level semantic information throughout, with the help of the development of low-resolution high-level semantic information, by capitalizing on both local morphological information and global rhythm information. From the perspective of effective data leverage and inter-task knowledge transfer, we develop a parameter isolation based ECG continual learning (ECG-CL) approach. We evaluated our model's performance on four open-access datasets by designing segmentation-to-classification for cross-domain incremental learning, minority-to-majority class for category incremental learning, and small-to-large sample for task incremental learning. Our approach is shown to successfully extract informative morphological and rhythmic features from ECG segmentation, leading to higher quality classification results. From the perspective of intelligent wearable applications, the possibility of a comprehensive ECG interpretation algorithm based on single-lead ECGs is also confirmed.

eess.SP↗

arXiv2023

An orthogonalization-free implementation of the LOBPCG method in solving Kohn-Sham equation

In the classic implementation of the LOBPCG method, orthogonalization and the R-R (Rayleigh-Ritz) procedure cost nonignorable CPU time. Especially this consumption could be very expensive to deal with situations with large block sizes. In this paper, we propose an orthogonalization-free framework of implementing the LOBPCG method for SCF (self-consistent field) iterations in solving the Kohn-Sham equation. In this framework, orthogonalization is avoided in calculations, which can decrease the computational complexity. And the R-R procedure is implemented parallelly through OpenMP, which can further reduce computational time. During numerical experiments, an effective preconditioning strategy is designed, which can accelerate the LOBPCG method remarkably. Consequently, the efficiency of the LOBPCG method can be significantly improved. Based on this, the SCF iteration can solve the Kohn-Sham equation efficiently. A series of numerical experiments are inducted to demonstrate the effectiveness of our implementation, in which significant improvements in computational time can be observed.

math.NA↗

arXiv2023

An MP-DWR method for $h$-adaptive finite element methods

In a dual weighted residual method based on the finite element framework, the Galerkin orthogonality is an issue that prevents solving the dual equation in the same space as the one for the primal equation. In the literature, there have been two popular approaches to constructing a new space for the dual problem, i.e., refining mesh grids ($h$-approach) and raising the order of approximate polynomials ($p$-approach). In this paper, a novel approach is proposed for the purpose based on the multiple-precision technique, i.e., the construction of the new finite element space is based on the same configuration as the one for the primal equation, except for the precision in calculations. The feasibility of such a new approach is discussed in detail in the paper. In numerical experiments, the proposed approach can be realized conveniently with C++ \textit{template}. Moreover, the new approach shows remarkable improvements in both efficiency and storage compared with the $h$-approach and the $p$-approach. It is worth mentioning that the performance of our approach is comparable with the one through a higher order interpolation ($i$-approach) in the literature. The combination of these two approaches is believed to further enhance the efficiency of the dual weighted residual method.

math.NA↗

arXiv2022

A Causal Intervention Scheme for Semantic Segmentation of Quasi-periodic Cardiovascular Signals

Precise segmentation is a vital first step to analyze semantic information of cardiac cycle and capture anomaly with cardiovascular signals. However, in the field of deep semantic segmentation, inference is often unilaterally confounded by the individual attribute of data. Towards cardiovascular signals, quasi-periodicity is the essential characteristic to be learned, regarded as the synthesize of the attributes of morphology (Am) and rhythm (Ar). Our key insight is to suppress the over-dependence on Am or Ar while the generation process of deep representations. To address this issue, we establish a structural causal model as the foundation to customize the intervention approaches on Am and Ar, respectively. In this paper, we propose contrastive causal intervention (CCI) to form a novel training paradigm under a frame-level contrastive framework. The intervention can eliminate the implicit statistical bias brought by the single attribute and lead to more objective representations. We conduct comprehensive experiments with the controlled condition for QRS location and heart sound segmentation. The final results indicate that our approach can evidently improve the performance by up to 0.41% for QRS location and 2.73% for heart sound segmentation. The efficiency of the proposed method is generalized to multiple databases and noisy signals.

eess.SP↗

arXiv2022

Neural network facilitated ab initio derivation of linear formula: A case study on formulating the relationship between DNA motifs and gene expression

Developing models with high interpretability and even deriving formulas to quantify relationships between biological data is an emerging need. We propose here a framework for ab initio derivation of sequence motifs and linear formula using a new approach based on the interpretable neural network model called contextual regression model. We showed that this linear model could predict gene expression levels using promoter sequences with a performance comparable to deep neural network models. We uncovered a list of 300 motifs with important regulatory roles on gene expression and showed that they also had significant contributions to cell-type specific gene expression in 154 diverse cell types. This work illustrates the possibility of deriving formulas to represent biology laws that may not be easily elucidated. (https://github.com/Wang-lab-UCSD/Motif_Finding_Contextual_Regression)

q-bio.QM↗

arXiv2021

HRnV-Calc: A software package for heart rate n-variability and heart rate variability analysis

Objective: Heart rate variability (HRV) has been proven to be an important indicator of physiological status for numerous applications. Despite the progress and active developments made in HRV metric research over the last few decades, the representation of the heartbeat sequence upon which HRV is based has received relatively little attention. The recently introduced heart rate n-variability (HRnV) offers an alternative to R-to-R peak interval representations which complements conventional HRV analysis by considering HRV behavior on varying scales. Although HRnV has been shown to improve triage in pilot studies, there is currently no open and standard software to support future research of HRnV and its broader clinical applications. We aimed to develop an open, reliable, and easy to use software package implementing HRnV for further research and improvements of HRnV. This package has been designed to facilitate collaborative investigations between clinicians and researchers to study HRnV in various contexts and applications. Approach: We developed an open-source software, HRnV-Calc, based on the PhysioNet Cardiovascular Signal Toolbox (PCST), which features comprehensive graphical user interfaces (GUIs) for HRnV and HRV analysis. Main results: While preserving the core functionalities and performance of PCST, HRnV-Calc enables step-by-step manual inspection and configuration of HRV and HRnV analysis, so that results can be debugged, easily interpreted, and integrated to downstream applications. Significance: The open-source HRnV-Calc software, an accessible and standardized HRV and HRnV analysis platform, enhances the scope of HRV assessment and is designed to assist in future improvements and applications of HRnV and related research.

cs.CE↗

arXiv2021

Subject Envelope based Multitype Reconstruction Algorithm of Speech Samples of Parkinson's Disease

The risk of Parkinson's disease (PD) is extremely serious, and PD speech recognition is an effective method of diagnosis nowadays. However, due to the influence of the disease stage, corpus, and other factors on data collection, the ability of every samples within one subject to reflect the status of PD vary. No samples are useless totally, and not samples are 100% perfect. This characteristic means that it is not suitable just to remove some samples or keep some samples. It is necessary to consider the sample transformation for obtaining high quality new samples. Unfortunately, existing PD speech recognition methods focus mainly on feature learning and classifier design rather than sample learning, and few methods consider the sample transformation. To solve the problem above, a PD speech sample transformation algorithm based on multitype reconstruction operators is proposed in this paper. The algorithm is divided into four major steps. Three types of reconstruction operators are designed in the algorithm: types A, B and C. Concerning the type A operator, the original dataset is directly reconstructed by designing a linear transformation to obtain the first dataset. The type B operator is designed for clustering and linear transformation of the dataset to obtain the second new dataset. The third operator, namely, the type C operator, reconstructs the dataset by clustering and convolution to obtain the third dataset. Finally, the base classifier is trained based on the three new datasets, and then the classification results are fused by decision weighting. In the experimental section, two representative PD speech datasets are used for verification. The results show that the proposed algorithm is effective. Compared with other algorithms, the proposed algorithm achieves apparent improvements in terms of classification accuracy.

cs.SD↗

arXiv2020

Remote health monitoring and diagnosis in the time of COVID-19

Coronavirus disease (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that is rapidly spreading across the globe. The clinical spectrum of SARS-CoV-2 pneumonia ranges from mild to critically ill cases and requires early detection and monitoring, within a clinical environment for critical cases and remotely for mild cases. The fear of contamination in clinical environments has led to a dramatic reduction in on-site referrals for routine care. There has also been a perceived need to continuously monitor non-severe COVID- 19 patients, either from their quarantine site at home, or dedicated quarantine locations (e.g., hotels). Thus, the pandemic has driven incentives to innovate and enhance or create new routes for providing healthcare services at distance. In particular, this has created a dramatic impetus to find innovative ways to remotely and effectively monitor patient health status. In this paper we present a short review of remote health monitoring initiatives taken in 19 states during the time of the pandemic. We emphasize in the discussion particular aspects that are common ground for the reviewed states, in particular the future impact of the pandemic on remote health monitoring and consideration on data privacy.

cs.CY↗

arXiv2020

Temporal-Framing Adaptive Network for Heart Sound Segmentation without Prior Knowledge of State Duration

Objective: This paper presents a novel heart sound segmentation algorithm based on Temporal-Framing Adaptive Network (TFAN), including state transition loss and dynamic inference for decoding the most likely state sequence. Methods: In contrast to previous state-of-the-art approaches, the TFAN-based method does not require any knowledge of the state duration of heart sounds and is therefore likely to generalize to non sinus rhythm. The TFAN-based method was trained on 50 recordings randomly chosen from Training set A of the 2016 PhysioNet/Computer in Cardiology Challenge and tested on the other 12 independent training and test databases (2099 recordings and 52180 beats). The databases for segmentation were separated into three levels of increasing difficulty (LEVEL-I, -II and -III) for performance reporting. Results: The TFAN-based method achieved a superior F1 score for all 12 databases except for `Test-B', with an average of 96.7%, compared to 94.6% for the state-of-the-art method. Moreover, the TFAN-based method achieved an overall F1 score of 99.2%, 94.4%, 91.4% on LEVEL-I, -II and -III data respectively, compared to 98.4%, 88.54% and 79.80% for the current state-of-the-art method. Conclusion: The TFAN-based method therefore provides a substantial improvement, particularly for more difficult cases, and on data sets not represented in the public training data. Significance: The proposed method is highly flexible and likely to apply to other non-stationary time series. Further work is required to understand to what extent this approach will provide improved diagnostic performance, although it is logical to assume superior segmentation will lead to improved diagnostics.

eess.SP↗

arXiv2019

Active Stacking for Heart Rate Estimation

Heart rate estimation from electrocardiogram signals is very important for the early detection of cardiovascular diseases. However, due to large individual differences and varying electrocardiogram signal quality, there does not exist a single reliable estimation algorithm that works well on all subjects. Every algorithm may break down on certain subjects, resulting in a significant estimation error. Ensemble regression, which aggregates the outputs of multiple base estimators for more reliable and stable estimates, can be used to remedy this problem. Moreover, active learning can be used to optimally select a few trials from a new subject to label, based on which a stacking ensemble regression model can be trained to aggregate the base estimators. This paper proposes four active stacking approaches, and demonstrates that they all significantly outperform three common unsupervised ensemble regression approaches, and a supervised stacking approach which randomly selects some trials to label. Remarkably, our active stacking approaches only need three or four labeled trials from each subject to achieve an average root mean squared estimation error below three beats per minute, making them very convenient for real-world applications. To our knowledge, this is the first research on active stacking, and its application to heart rate estimation.

cs.LG↗

arXiv2017

Contextual Regression: An Accurate and Conveniently Interpretable Nonlinear Model for Mining Discovery from Scientific Data

Machine learning algorithms such as linear regression, SVM and neural network have played an increasingly important role in the process of scientific discovery. However, none of them is both interpretable and accurate on nonlinear datasets. Here we present contextual regression, a method that joins these two desirable properties together using a hybrid architecture of neural network embedding and dot product layer. We demonstrate its high prediction accuracy and sensitivity through the task of predictive feature selection on a simulated dataset and the application of predicting open chromatin sites in the human genome. On the simulated data, our method achieved high fidelity recovery of feature contributions under random noise levels up to 200%. On the open chromatin dataset, the application of our method not only outperformed the state of the art method in terms of accuracy, but also unveiled two previously unfound open chromatin related histone marks. Our method can fill the blank of accurate and interpretable nonlinear modeling in scientific data mining tasks.

q-bio.QM↗

arXiv2016

An Algebraic Approach to Non-Orthogonal General Joint Block Diagonalization

The exact/approximate non-orthogonal general joint block diagonalization ({\sc nogjbd}) problem of a given real matrix set $\mathcal{A}=\{A_i\}_{i=1}^m$ is to find a nonsingular matrix $W\in\mathbb{R}^{n\times n}$ (diagonalizer) such that $W^T A_i W$ for $i=1,2,\dots, m$ are all exactly/approximately block diagonal matrices with the same diagonal block structure and with as many diagonal blocks as possible. In this paper, we show that a solution to the exact/approximate {\sc nogjbd} problem can be obtained by finding the exact/approximate solutions to the system of linear equations $A_iZ=Z^TA_i$ for $i=1,\dots, m$, followed by a block diagonalization of $Z$ via similarity transformation. A necessary and sufficient condition for the equivalence of the solutions to the exact {\sc nogjbd} problem is established. Two numerical methods are proposed to solve the {\sc nogjbd} problem, and numerical examples are presented to show the merits of the proposed methods.

math.NA↗