scholarly journals Empirical Bayes conditional independence graphs for regulatory network recovery

2012 ◽  
Vol 28 (15) ◽  
pp. 2029-2036 ◽  
Author(s):  
R. Mahdi ◽  
A. S. Madduri ◽  
G. Wang ◽  
Y. Strulovici-Barel ◽  
J. Salit ◽  
...  
2017 ◽  
Vol 59 (5) ◽  
pp. 932-947 ◽  
Author(s):  
Gino B. Kpogbezan ◽  
Aad W. van der Vaart ◽  
Wessel N. van Wieringen ◽  
Gwenaël G. R. Leday ◽  
Mark A. van de Wiel

Author(s):  
Xiaoyi Yang ◽  
Nynke M. D. Niezink ◽  
Rebecca Nugent

AbstractAccurately describing the lives of historical figures can be challenging, but unraveling their social structures perhaps is even more so. Historical social network analysis methods can help in this regard and may even illuminate individuals who have been overlooked by historians, but turn out to be influential social connection points. Text data, such as biographies, are a useful source of information for learning historical social networks but the identifcation of links based on text data can be challenging. The Local Poisson Graphical Lasso model models social networks by conditional independence structures, and leverages the number of name co-mentions in the text to infer relationships. However, this method does not take into account the abundance of covariate information that is often available in text data. Conditional independence structure like Poisson Graphical Model, which makes use name mention counts in the text can be useful tools to avoid false positive links due to the co-mentions but given historical tendency of frequently used or common names, without additional distinguishing information, we may introduce incorrect connections. In this work, we therefore extend the Local Poisson Graphical Lasso model with a (multiple) penalty structure that incorporates covariates, opening up the opportunity for similar individuals to have a higher probability of being connected. We propose both greedy and Bayesian approaches to estimate the penalty parameters. We present results on data simulated with characteristics of historical networks and show that this type of penalty structure can improve network recovery as measured by precision and recall. We also illustrate the approach on biographical data of individuals who lived in early modern Britain between 1500 and 1575. We will show how these covariates affect the statistical model’s performance using simulations, discuss how it helps to better identify links for the people with common names and those who are traditionally underrepresented in the biography text data.


2021 ◽  
Author(s):  
Kateřina Podolská ◽  
Petra Koucká Knížová ◽  
Jaroslav Chum

<p>We investigated seasonal variations of relationships between main ionospheric characteristics and solar and geomagnetic indices in longitudinal perspective. We consider statistically significant differences in connections of ionospheric response to the F10.7cm, R, and Kp indices on seasonal time-scales during years 1975 – 2010 covering 21<sup>st</sup> – 23<sup>rd</sup> Solar Cycles. The periods of 21 days before and after Winter/Summer Solstices and Vernal/Autumnal Equinoces are considered as season. The foF2 time series in our analysis represent measurements of daily observational data which were obtained using mid-latitude (41.4°N – 54°N) ionosondes (Chilton, Slough RL052/SL051, Juliusruh/Rugen JR055, Boulder BC840). We used local time noon 5-hour foF2 averages. For the investigation, we used seasonal differences method of conditional independence graphs (CIG) models. Significant seasonal variations are visible during ascending and descending phases of Solar cycles.</p>


2012 ◽  
pp. 1699-1720
Author(s):  
Frank Wimberly ◽  
David Danks ◽  
Clark Glymour ◽  
Tianjiao Chu

Machine learning methods to find graphical models of genetic regulatory networks from cDNA microarray data have become increasingly popular in recent years. We provide three reasons to question the reliability of such methods: (1) a major theoretical challenge to any method using conditional independence relations; (2) a simulation study using realistic data that confirms the importance of the theoretical challenge; and (3) an analysis of the computational complexity of algorithms that avoid this theoretical challenge. We have no proof that one cannot possibly learn the structure of a genetic regulatory network from microarray data alone, nor do we think that such a proof is likely. However, the combination of (i) fundamental challenges from theory, (ii) practical evidence that those challenges arise in realistic data, and (iii) the difficulty of avoiding those challenges leads us to conclude that it is unlikely that current microarray technology will ever be successfully applied to this structure learning problem.


2015 ◽  
Vol 11 (11) ◽  
pp. e1004534 ◽  
Author(s):  
Max Hinne ◽  
Ronald J. Janssen ◽  
Tom Heskes ◽  
Marcel A.J. van Gerven

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