The gist here is to model a genetic network as a dynamical system with two attractor states (in this case, it's leukemia and the states are apoptosis on-versus-off).
I'm looking for leads to papers that apply this type of approach to model genetic networks (not neural circuits) that have something a bit more to do with the brain; ideally not cancer.
(This is not my field). Huntington's? Fragile X? Anything neuron related?
@NicoleCRust Take a look at: Bagchee‐Clark, Ashis J., et al. "Pathway‐extended gene expression signatures integrate novel biomarkers that improve predictions of patient responses to kinase inhibitors." MedComm 1.3 (2020): 311-327.(https://onlinelibrary.wiley.com/doi/pdf/10.1002/mco2.46). We found likely attractors in pathway extended chemotherapy signatures.(and cite Kauffman): .
Looking for: complex systems that defy model reduction.
The behavior of a complex system is hard to predict from its parts alone because it follows from how the parts interact.
Model reduction is a way to capture the behavior of a complex system more simply (eg to capture the magnetism of 1g of Fe2O3, you don't have to model all 1022 molecules and their interactions). My sense is that model reduction works best when you have many repeated copies.
I'm looking for some good (ideally concrete) examples of complex systems that defy model reduction. I anticipate that they will be made of heterogeneous parts.
@NicoleCRust What do you think about artificial deep neural networks? There have been many attempts to try to decompose these into pieces, but, particularly deeper layers seem to have "entangled" a lot of concepts that are intuitive to humans. Maybe we just need to work harder to understand how to reduce them, so it is a bit of an unknown, e.g. this work https://transformer-circuits.pub/2021/framework/index.html
Parts are quite homogeneous in architecture, but heterogeneous in learned weights.
For highD, best way is to "visualize" such oscillators as traveling/moving on a n-torus in the phase space. (they can be quasi-periodic etc., which is its own thing including as a transition to chaos and intermittency).
With regards to the Rajan et al., paper, we can suppress chaos in high dimensional RNNs quite well even without invoking stimulus dependency (i.e., driven activity), a global "adaptation level" with competitive dynamics can avert chaos in autonomous systems.
Here's the introduction from a great paper from my PhD advisor from 1978, which I believe should be cited more:
"The following problem, in one form or another, has intrigued philosophers and scientists for hundreds of years: How do arbitrarily many individuals,
populations, or states, each obeying unique and personal laws, ever succeed in harmoniously interacting with each other to form some sort of stable society, or collective mode of behavior? Otherwise expressed, if each individual obeys complex laws, and is ignorant of other individuals except via locally received
signals, how is social chaos averted? How can local ignorance and global order,
or consensus, be reconciled? This paper considers a class of systems in which this dilemma is overcome."
That phrase is just so great. It's easy to see how it's counterpart slipped through the cracks. "Judicious model robustification" - who can claim not to aspire to that as well?
To all modelers out there, may your model be judiciously robustified!
Kiedys wznosil trofea najwiekszych turniejow na swiecie jako zawodnik #VirtusPro, dzisiaj wznosi pierwsze w historii trofeum turnieju #CS2 jako trener #FaZeClan - Filip #NEO Kubski 🇵🇱
Polska ma sie z czego cieszyc - mamy zawodnikow grajacych w topowych zespolach, mamy trenera jednej z najlepszych organizacji. Oby ta forma utrzymala sie do #IEMKatowice - to bedzie wyjatkowy turniej 🤩
Piekny turniej, piekny final, dokladnie taki na jaki kibice w Sydney i na calym swiecie zaslugiwali, a dla #Complexity uklony za walke do samego konca
"Freakin' Counter-Strike!"
Za to kocham profesjonalnego CS-a - nie tylko dlatego, ze FaZe znowu jest na szczycie, po dlugim okresie, kiedy wielu juz ich zaczynalo skreslac, ale tez dlatego, ze Complexity pokazalo niespodziewanie taka forme po tym jak byli wysmiewani jako typowe #NACS
LIVING IN THE #METACRISIS with Jonathan Rowson
"Jonathan Rowson is co-founder and Director of Perspectiva and author of the Joyous Struggle on Substack. He was previously Director of the Social Brain Centre at the RSA where he authored a range of influential research reports on behaviour change, climate change and spirituality. Jonathan is an applied philosopher with degrees from Oxford, Harvard and Bristol Universities. In a former life he was a #chess Grandmaster and British Champion and views the game as a continuing source of insight and inspiration. His book, "The Moves that Matter – A Grandmaster on the Game of Life" was published in 2019. #overshoot#ClimateChange#permaculture#infopollution Bioregion #GreatTransition#collapse#cosmolocalism#complexity#potential#consciousness https://youtu.be/IjOQB608ylQ
@mcpinson A teenage conservative is a libertarian because their brains just aren't developed enough to think through the consequences of their decisions...
A new #ComplexityThougths short essay is out: this time I write about the ongoing debate around the Nature paper on assembly theory. The essay features comments by Sara Imari Walker, Ricard Solè and Hector Zenil, and it's an attempt to provide a balanced overview of what's going on.
A straight line of closely spaced sapling maples twice as tall as me paralleling the curb at the intersection of it and the asphalt. A groundcover of seedling maples sprouts beneath their dappled shade.