scholarly journals Bayesian Topology Learning and noise removal from network data

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Mahmoud Ramezani Mayiami ◽  
Mohammad Hajimirsadeghi ◽  
Karl Skretting ◽  
Xiaowen Dong ◽  
Rick S. Blum ◽  
...  

AbstractLearning the topology of a graph from available data is of great interest in many emerging applications. Some examples are social networks, internet of things networks (intelligent IoT and industrial IoT), biological connection networks, sensor networks and traffic network patterns. In this paper, a graph topology inference approach is proposed to learn the underlying graph structure from a given set of noisy multi-variate observations, which are modeled as graph signals generated from a Gaussian Markov Random Field (GMRF) process. A factor analysis model is applied to represent the graph signals in a latent space where the basis is related to the underlying graph structure. An optimal graph filter is also developed to recover the graph signals from noisy observations. In the final step, an optimization problem is proposed to learn the underlying graph topology from the recovered signals. Moreover, a fast algorithm employing the proximal point method has been proposed to solve the problem efficiently. Experimental results employing both synthetic and real data show the effectiveness of the proposed method in recovering the signals and inferring the underlying graph.

Methodology ◽  
2018 ◽  
Vol 14 (4) ◽  
pp. 188-196 ◽  
Author(s):  
Esther T. Beierl ◽  
Markus Bühner ◽  
Moritz Heene

Abstract. Factorial validity is often assessed using confirmatory factor analysis. Model fit is commonly evaluated using the cutoff values for the fit indices proposed by Hu and Bentler (1999) . There is a body of research showing that those cutoff values cannot be generalized. Model fit does not only depend on the severity of misspecification, but also on nuisance parameters, which are independent of the misspecification. Using a simulation study, we demonstrate their influence on measures of model fit. We specified a severe misspecification, omitting a second factor, which signifies factorial invalidity. Measures of model fit showed only small misfit because nuisance parameters, magnitude of factor loadings and a balanced/imbalanced number of indicators per factor, also influenced the degree of misfit. Drawing from our results, we discuss challenges in the assessment of factorial validity.


2019 ◽  
Author(s):  
Ashita S. Gurnani ◽  
Shayne S.-H. Lin ◽  
Brandon E Gavett

Objective: The Colorado Cognitive Assessment (CoCA) was designed to improve upon existing screening tests in a number of ways, including enhanced psychometric properties and minimization of bias across diverse groups. This paper describes the initial validation study of the CoCA, which seeks to describe the test; demonstrate its construct validity; measurement invariance to age, education, sex, and mood symptoms; and compare it to the Montreal Cognitive Assessment (MoCA). Method: Participants included 151 older adults (MAge = 71.21, SD = 8.05) who were administered the CoCA, MoCA, Judgment test from the Neuropsychological Assessment Battery (NAB), 15-item version of the Geriatric Depression Scale (GDS-15), and 10-item version of the Geriatric Anxiety Scale (GAS-10). Results: A single factor confirmatory factor analysis model of the CoCA fit the data well, CFI = 0.955; RMSEA = 0.033. The CoCA’s internal consistency reliability was .84, compared to .74 for the MoCA. The CoCA had stronger disattenuated correlations with the MoCA (r = .79) and NAB Judgment (r = .47) and weaker correlations with the GDS-15 (r = -.36) and GAS-10 (r = -.15), supporting its construct validity. Finally, when analyzed using multiple indicators, multiple causes (MIMIC) modeling, the CoCA showed no evidence of measurement non-invariance, unlike the MoCA. Conclusions: These results provide initial evidence to suggest that the CoCA is a valid cognitive screening tool that offers numerous advantages over the MoCA, including superior psychometric properties and measurement non-invariance. Additional validation and normative studies are warranted.


1997 ◽  
Vol 24 (1) ◽  
pp. 3-18 ◽  
Author(s):  
Michael W. Browne ◽  
Krishna Tateneni

2018 ◽  
Vol 66 ◽  
pp. S11-S12 ◽  
Author(s):  
A. Coni ◽  
S. Mellone ◽  
M. Colpo ◽  
S. Bandinelli ◽  
L. Chiari

2020 ◽  
Author(s):  
Weiguang Mao ◽  
Maziyar Baran Pouyan ◽  
Dennis Kostka ◽  
Maria Chikina

AbstractMotivationSingle cell RNA sequencing (scRNA-seq) enables transcriptional profiling at the level of individual cells. With the emergence of high-throughput platforms datasets comprising tens of thousands or more cells have become routine, and the technology is having an impact across a wide range of biomedical subject areas. However, scRNA-seq data are high-dimensional and affected by noise, so that scalable and robust computational techniques are needed for meaningful analysis, visualization and interpretation. Specifically, a range of matrix factorization techniques have been employed to aid scRNA-seq data analysis. In this context we note that sources contributing to biological variability between cells can be discrete (or multi-modal, for instance cell-types), or continuous (e.g. pathway activity). However, no current matrix factorization approach is set up to jointly infer such mixed sources of variability.ResultsTo address this shortcoming, we present a new probabilistic single-cell factor analysis model, Non-negative Independent Factor Analysis (NIFA), that combines features of complementary approaches like Independent Component Analysis (ICA), Principal Component Analysis (PCA), and Non-negative Matrix Factorization (NMF). NIFA simultaneously models uni- and multi-modal latent factors and can so isolate discrete cell-type identity and continuous pathway-level variations into separate components. Similar to NMF, NIFA constrains factor loadings to be non-negative in order to increase biological interpretability. We apply our approach to a range of data sets where cell-type identity is known, and we show that NIFA-derived factors outperform results from ICA, PCA and NMF in terms of cell-type identification and biological interpretability. Studying an immunotherapy dataset in detail, we show that NIFA identifies biomedically meaningful sources of variation, derive an improved expression signature for regulatory T-cells, and identify a novel myeloid cell subtype associated with treatment response. Overall, NIFA is a general approach advancing scRNA-seq analysis capabilities and it allows researchers to better take advantage of their data. NIFA is available at https://github.com/wgmao/[email protected]


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