Nonnegative matrix factorization: When data is not nonnegative

Wu, Siyuan; Wang, Jim

doi:10.1109/bmei.2014.7002775

Cited by 3 publications

(2 citation statements)

References 53 publications

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“…One alternative to PCA is non-negative matrix factorization, but classically this requires the data to also be non-negative, an assumption obviously unmet by neural field time series. However, formulations of nonnegative matrix factorization have been proposed which relax this constraint (Wu & Wang, 2014), and are a promising approach for future studies.…”

Section: Discussionmentioning

confidence: 99%

Diverse beta burst waveform motifs characterize movement-related cortical dynamics

Szul

Papadopoulos

Alavizadeh

et al. 2022

Preprint

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Classical analyses of induced, frequency-specific neural activity typically average band-limited power over trials. More recently, it has become widely appreciated that in individual trials, beta band activity occurs as transient bursts rather than amplitude-modulated oscillations. Most studies of beta bursts treat them as unitary, and having a stereotyped waveform. However, we show there is a wide diversity of burst shapes. Using a biophysical model of burst generation, we demonstrate that waveform variability is predicted by variability in the synaptic drives that generate beta bursts. We then use a novel, adaptive burst detection algorithm to identify bursts from human MEG sensor data recorded during a joystick-based reaching task, and apply principal component analysis to burst waveforms to define a set of dimensions, or motifs, that best explain waveform variance. Finally, we show that bursts with a particular range of waveform motifs, ones not fully accounted for by the biophysical model, differentially contribute to movement-related beta dynamics. Sensorimotor beta bursts are therefore not homogeneous events and likely reflect distinct computational processes.

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Section: Discussionmentioning

confidence: 99%

Diverse beta burst waveform motifs characterize movement-related cortical dynamics

Szul

Papadopoulos

Alavizadeh

et al. 2022

Preprint

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“…We optimize this overall objective function based on the multiplicative update algorithm (Zhang et al 2008;Wu and Wang 2014) to guarantee non-negativity. The algorithm requires the specifications of the penalty parameters, , , , and .…”

Section: Automated Single Cell Proteomics Data Annotation Modelmentioning

confidence: 99%

ProtAnno, an Automated Cell Type Annotation Tool for Single Cell Proteomics Data that integrates information from Multiple Reference Sources

Deng

Zhu

Park

et al. 2021

Preprint

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Compared with sequencing-based global genomic profiling, cytometry labels targeted surface markers on millions of cells in parallel either by conjugated rare earth metal particles or Unique Molecular Identifier (UMI) barcodes. Correct annotation of these cells to specific cell types is a key step in the analysis of these data. However, there is no computational tool that automatically annotates single cell proteomics data for cell type inference. In this manuscript, we propose an automated single cell proteomics data annotation approach called ProtAnno to facilitate cell type assignments without laborious manual gating. ProtAnno is designed to incorporate information from annotated single cell RNA-seq (scRNA-seq), CITE-seq, and prior data knowledge (which can be imprecise) on biomarkers for different cell types. We have performed extensive simulations to demonstrate the accuracy and robustness of ProtAnno. For several single cell proteomics datasets that have been manually labeled, ProtAnno was able to correctly label most single cells. In summary, ProtAnno offers an accurate and robust tool to automate cell type annotations for large single cell proteomics datasets, and the analysis of such annotated cell types can offer valuable biological insights.

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Diverse beta burst waveform motifs characterize movement-related cortical dynamics

Szul

Papadopoulos

Alavizadeh

et al. 2023

Progress in Neurobiology

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Nonnegative matrix factorization: When data is not nonnegative

Cited by 3 publications

References 53 publications

Diverse beta burst waveform motifs characterize movement-related cortical dynamics

Diverse beta burst waveform motifs characterize movement-related cortical dynamics

ProtAnno, an Automated Cell Type Annotation Tool for Single Cell Proteomics Data that integrates information from Multiple Reference Sources

Diverse beta burst waveform motifs characterize movement-related cortical dynamics

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