Biology subjects

Wu, H.-T.

Publications and source records attributed to Wu, H.-T..

4 recordsLinked to original sources

bioRxiv2021

Get rid of the beat in mobile EEG applications: A framework towards automated cardiogenic artifact detection and removal in single-channel EEG

Brain activity recordings outside clinical or laboratory settings using mobile EEG systems have recently gained popular interest allowing for realistic long-term monitoring and eventually leading to identification of possible biomarkers for diseases. The less obtrusive, minimized systems (e.g. single-channel EEG, no ECG reference) have the drawback of artifact contamination with varying intensity that are particularly difficult to identify and remove. We developed brMEGA, the first algorithm for automated detection and removal of cardiogenic artifacts using non-linear time-frequency analysis and machine learning to (1) detect whether and where cardiogenic artifacts exist, and (2) remove those artifacts. We compare our algorithm against visual artifact identification and a previously established approach and validate it in one real and semi-real datasets. We demonstrated that brMEGA successfully identifies and substantially removes cardiogenic artifacts in single-channel EEG recordings. Moreover, recovery of cardiogenic artifacts gives the opportunity for future extraction of heart rate features without ECG measurement.

neuroscience↗

bioRxiv2020

Scientific impact of the standard phase reconstruction method and its clinical applications

Phase is the most fundamental physical quantity when we study an oscillatory time series. There are many tools aiming to estimate phase, most of them are developed based on the analytic function model. Unfortunately, this approach might not be suitable for modern signals with intrinsic nonstartionary structure, including multiple oscillatory components, each with time-varying frequency, amplitude, and non-sinusoidal oscillation, e.g., biomedical signals. Specifically, due to the lack of consensus of model and algorithm, phases estimated from signals simultaneously recorded from different sensors for the same physiological system from the same subject might be different. This fact might challenge reproducibility, communication, and scientific interpretation and thus we need a standardized approach with theoretical support over a unified model. In this paper, after summarizing existing models for phase and discussing the main challenge caused by the above-mentioned intrinsic nonstartionary structure, we introduce the adaptive non-harmonic model (ANHM), provide a definition of phase called fundamental phase, which is a vector-valued function describing the dynamics of all oscillatory components in the signal, and suggest a time-varying bandpass filter (tvBPF) scheme based on time-frequency analysis tools to estimate the fundamental phase. The proposed approach is validated with a simulated database and a real-world database with experts labels, and it is applied to two real-world databases, each of which has biomedical signals recorded from different sensors, to show how to standardize the definition of phase in the real-world experimental environment. Specifically, we report that the phase describing a physiological system, if properly modeled and extracted, is immune to the selected sensor for that system, while other approaches might fail. In conclusion, the proposed approach resolves the above-mentioned scientific challenge. We expect its scientific impact on a broad range of applications.

physiology↗

bioRxiv2020

Robust and scalable manifold learning via landmark diffusion for long-term medical signal processing

Motivated by analyzing long-term physiological time series, we design a robust and scalable spectral embedding algorithm, coined the algorithm RObust and Scalable Embedding via LANdmark Diffusion (ROSE-LAND). The key is designing a diffusion process on the dataset, where the diffusion is forced to interchange on a small subset called the landmark set. In addition to demonstrating its application to spectral clustering and image segmentation, the algorithm is applied to study the long-term arterial blood pressure waveform dynamics during a liver transplant operation lasting for 12 hours long.

bioinformatics↗

bioRxiv2017

Identifying structural variants using linked-read sequencing data

Structural variation, including large deletions, duplications, inversions, translocations, and other rearrangements, is common in human and cancer genomes. A number of methods have been developed to identify structural variants from Illumina short-read sequencing data. However, reliable identification of structural variants remains challenging because many variants have breakpoints in repetitive regions of the genome and thus are difficult to identify with short reads. The recently developed linked-read sequencing technology from 10X Genomics combines a novel barcoding strategy with Illumina sequencing. This technology labels all reads that originate from a small number (~5-10) DNA molecules ~50Kbp in length with the same molecular barcode. These barcoded reads contain long-range sequence information that is advantageous for identification of structural variants. We present Novel Adjacency Identification with Barcoded Reads (NAIBR), an algorithm to identify structural variants in linked-read sequencing data. NAIBR predicts novel adjacencies in a individual genome resulting from structural variants using a probabilistic model that combines multiple signals in barcoded reads. We show that NAIBR outperforms several existing methods for structural variant identification - including two recent methods that also analyze linked-reads - on simulated sequencing data and 10X whole-genome sequencing data from the NA12878 human genome and the HCC1954 breast cancer cell line. Several of the novel somatic structural variants identified in HCC1954 overlap known cancer genes.

genomics↗