This paper extends SHORAH to better infer global haplotypes.
The work is a collaboration between Niko Beerenwinkel's group and Volker Roth's group. Roth is at the the U Basel computer science department. Other authors are Melanie Rey, Osvaldo Zagordi, Huldrych Günthard, and Karin Metzner.
the paper really isn't clear on how they move from local to global reconstruction.
They introduce the following soft constraint. If two reads are assigned to different local haplotypes (i.e. differ in their local window) then they must be assinged to different haplotypes at the global level. Such do-not-link constraints are incorporated into the prior distribution of the subequent class assignments
Wednesday, August 31, 2011
Sugihara: Nonlinear forecasting as a way of distinguishing chaos from measurement error in time series
Heard about this paper from a short bio of the author, Sugihara
He, along with Robert May, coauthored several papers on chaos theory and financial markets. This lead to him being given a huge pile of money by Deutsche Bank.
Robert May ended up as Baron of Oxford, among other honors.
This paper presents an approach for making short-term predictions about the trajectories of chaotic dynamical systems. The method is applied to data on measles, chickenpox, and marine phytoplankton populations, to show how apparent noise associated with deterministic chaos can be distinguished from sampling error and other sources of externally induced environmental noise.
He, along with Robert May, coauthored several papers on chaos theory and financial markets. This lead to him being given a huge pile of money by Deutsche Bank.
Robert May ended up as Baron of Oxford, among other honors.
This paper presents an approach for making short-term predictions about the trajectories of chaotic dynamical systems. The method is applied to data on measles, chickenpox, and marine phytoplankton populations, to show how apparent noise associated with deterministic chaos can be distinguished from sampling error and other sources of externally induced environmental noise.
Samantha Power on a complicated hero (2008)
Samantha Power's talk.
Starts out discussing the birth in the 21st century of the "save the people" movement, like early environmentalism but dedicated to ending genocide. This movement is mostly US-based, and largely on college campuses. She then segues into a hero of hers,
Sergio Vieira de Mello.
Sergio worked tirelessly to confront evildoeers.
Samantha Power started (?) as a journalist covering the Yugoslav Wars. She then attended Harvard Law School, where a paper she wrote on genocide turned into the book The Problem from Hell, is a survey of genocide. This got her named by Time Magazine as a top thinker. She then took a position working with Senator Obama on foreign policy. She continues to be active in his administration as the Senior Director for Multilateral Affairs, as well as holding a professorship.
Starts out discussing the birth in the 21st century of the "save the people" movement, like early environmentalism but dedicated to ending genocide. This movement is mostly US-based, and largely on college campuses. She then segues into a hero of hers,
Sergio Vieira de Mello.
Sergio worked tirelessly to confront evildoeers.
Samantha Power started (?) as a journalist covering the Yugoslav Wars. She then attended Harvard Law School, where a paper she wrote on genocide turned into the book The Problem from Hell, is a survey of genocide. This got her named by Time Magazine as a top thinker. She then took a position working with Senator Obama on foreign policy. She continues to be active in his administration as the Senior Director for Multilateral Affairs, as well as holding a professorship.
Tuesday, August 30, 2011
cuevana
http://www.cuevana.tv/peliculas/mejorpuntuadas/
For movies. Requires a special plug-in. Not sure if I trust the plug-in
For movies. Requires a special plug-in. Not sure if I trust the plug-in
Immorality of debt
More inspiration for the paper I wish I had time to write on this!!
David Graeber interview
First comes gift-giving (which creates reciprical obligation). This becomes encoded in debt, which leads to money. Barter only comes later.
The old myth is that barter came first, then money. Rebuttal: "Think about what they’re saying here – basically: that a bunch of Neolithic farmers in a village somewhere will be engaging in transactions only through the spot trade."
David Graeber interview
First comes gift-giving (which creates reciprical obligation). This becomes encoded in debt, which leads to money. Barter only comes later.
The old myth is that barter came first, then money. Rebuttal: "Think about what they’re saying here – basically: that a bunch of Neolithic farmers in a village somewhere will be engaging in transactions only through the spot trade."
Sean Gourley on the mathematics of war
Sean Gourley
Dr. Gourley's team wrote a Nature paper defining how to measure an insurgency.
“Common Ecology Quantifies Human Insurgency“
The size distributions of casualties both in whole wars from 1816 to 1980 and terrorist attacks have separately been shown to follow approximate power-law distributions6, 7, 9, 10. However, the possibility of universal patterns ranging across wars in the size distribution or timing of within-conflict events has barely been explored. Here we show that the sizes and timing of violent events within different insurgent conflicts exhibit remarkable similarities. We propose a unified model of human insurgency that reproduces these commonalities, and explains conflict-specific variations quantitatively in terms of underlying rules of engagement. Our model treats each insurgent population as an ecology of dynamically evolving, self-organized groups following common decision-making processes
See also http://mathematicsofwar.com/
I want to link his evolution of insurgency models to my own viral evolution work. He specifically discusses that when an insurgent group breaks up, the parts don't dissapear, they re-associate with remaining groups-- showing preferential attachment. Also, strongest groups grow fastest.
Dr. Gourley's team wrote a Nature paper defining how to measure an insurgency.
“Common Ecology Quantifies Human Insurgency“
The size distributions of casualties both in whole wars from 1816 to 1980 and terrorist attacks have separately been shown to follow approximate power-law distributions6, 7, 9, 10. However, the possibility of universal patterns ranging across wars in the size distribution or timing of within-conflict events has barely been explored. Here we show that the sizes and timing of violent events within different insurgent conflicts exhibit remarkable similarities. We propose a unified model of human insurgency that reproduces these commonalities, and explains conflict-specific variations quantitatively in terms of underlying rules of engagement. Our model treats each insurgent population as an ecology of dynamically evolving, self-organized groups following common decision-making processes
See also http://mathematicsofwar.com/
I want to link his evolution of insurgency models to my own viral evolution work. He specifically discusses that when an insurgent group breaks up, the parts don't dissapear, they re-associate with remaining groups-- showing preferential attachment. Also, strongest groups grow fastest.
Bruce Bueno de Mesquita predicts Iran's future
Bruce Bueno
Dr. de Mequita uses game theory to model all the parties in a negotiation and finds equilibrium points. He can thus predict, with high accuracy, what the eventual settlement will be based on known data at the start.
http://politics.as.nyu.edu/object/brucebuenodemesquita.html
Dr. de Mequita uses game theory to model all the parties in a negotiation and finds equilibrium points. He can thus predict, with high accuracy, what the eventual settlement will be based on known data at the start.
http://politics.as.nyu.edu/object/brucebuenodemesquita.html
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