Thursday, August 1, 2019

glm versus lm



I'm not satisfied with the answers here so I'll chime in: the model fit by lm is a special case of the model fit by glm.
lm fits models of the form: Y = XB + e where e~Normal( 0, s2 ).
glm fits models of the form g(Y) = XB + e, where the function g() and the sampling distribution of e need to be specified. The function 'g' is called the "link function". The default link function for glm is the "identity function" such that g(Y) = Y, and the default error distribution is Normal. As you can see, with these defaults glm is fitting the same model fit by lm.
The latter model above is a "generalized" linear model (hence "glm") in that the relationship between the regressors and the target is not strictly linear, but under a transformation (the link function) they are.
The most common glm's are poisson regression and logistic regression. Technically "normal" regression is the most common glm, but we generally don't refer to this as a "generalized" linear model, since it's the primary case upon which the general model is based.
TL;DR: The fact that you're getting the same answer is a good thing. It would be concerning if you weren't.

Thursday, July 25, 2019

etherpad

Discussion Board (Etherpad)
https://etherpad.wikimedia.org/p/UTC-R-bootcamp2019

Tuesday, July 16, 2019

convolution versus max pooling




my understanding is that convolution kernel is a sliding window method, but max-pooling is a deserted down-samples method.  




diagram to explain disordered proteins


diagram to explain disordered proteins, Figure 2

https://www.tandfonline.com/doi/full/10.1080/21690707.2015.1135015

Wednesday, July 10, 2019

RLS ration and n_D


JK showed a results of 800 data points of n_D and RLS ratio. There was no obvious linear correlation, but there seems to be three clusters of data points.


Friday, July 5, 2019

HERITABILITY OF LONGEVITY

Reposted from Gavrilov's Facebook post

HERITABILITY OF LONGEVITY
Got an interesting question from Andrew Steele about our studies quantifying heritability of longevity.
Here are some our publications on related topic:
1. Gavrilov L.A., Gavrilova N.S., Krut'ko, V.N. New evidence that protective effects of familial longevity expire at older ages. Innovation in Aging, 2017, Vol. 1, No. S1, p.896.
http://longevity-science.org/pdf/Gavrilov-Inn-Aging-2017.pdf
2. Gavrilova N.S., Gavrilov L.A. Genetic Influences in Later Life. In: D. Carr (Editor), Encyclopedia of the Life Course and Human Development, Detroit: Macmillan Reference USA, 2009, vol.3, pp.165-170.
http://longevity-science.org/pdf/Genetic-Influences.pdf
3. Gavrilov L.A., Gavrilova N.S., Olshansky S.J., Carnes B.A. Genealogical data and biodemography of human longevity. Social Biology, 2002, 49(3-4): 160-173.
http://longevity-science.org/Social-Biology-02.pdf
4. Gavrilov, L.A., Gavrilova, N.S. Biodemographic study of familial determinants of human longevity. Population: An English Selection, 2001, 13(1): 197-222.
http://longevity-science.org/Biodemography-2001.pdf
5. Gavrilova, N.S., Gavrilov, L.A. When does human longevity start?: Demarcation of the boundaries for human longevity. Journal of Anti-Aging Medicine, 2001, 4(2): 115-124.
http://longevity-science.org/JAAM-Boundaries-for-Human-Long…
6. Gavrilova, N.S., Gavrilov, L.A., Evdokushkina G.N., Semyonova, V.G., Gavrilova, A.L., Evdokushkina, N.N., Kushnareva, Yu.E., Kroutko, V.N., Andreyev, A.Yu. Evolution, mutations and human longevity. Human Biology, 1998, 70(4): 799-804.
http://longevity-science.org/HumanBiology.pdf

Monday, June 24, 2019

MBI rule of lie


Karl Niklas, I keep thinking genome is a library, and plasmids keep knocking on it.
Plants are extremely responsive to external cues.
Plants are bags of water filled with chemicals.
Stopped writing grants 20 years ago.
Life responds, always change to survive.
Simple multi-cellular is often unsuccesful than compelx cellularity in competition in environments?

Cell fate specification? Genome plasticity. The beginning of stem cells.

Q: is symmetry a null model? So, polarity is an alternative model in life?

Biofilm is a  model for transient multi-cellular organism.




Thursday, June 13, 2019

finding your inner model

Finding your inner model, UAB,


Daniel Szymanski, Joe Turner, epidermal morphogenesis with integrated experimental verification
Finite element method modeling of cell wall for plant morphology.
Start with simple model, and add complexity as needed.
Empirical rule for model training (fitting), 3-5% error?



UTC EMCS Shipping address



UTC CECS
EMCS 319
735 VINE ST
CHATTANOOGA, TN 37403

Hong Qin
College of Engineering & Computer Science
University of Tennessee at Chattanooga
EMCS 319
735 VINE ST
CHATTANOOGA, TN 37403