Month: October 2013

Trust, but verify

October 26, 2013 Links No comments

“Doveryai, no proveryai” (translated as “trust, but verify”) is a Russian proverb, which became a signature phrase of Ronald Reagan during his nuclear-disarmament negotiations with Mikhail Gorbachev.

Last week, this phrase was used by *The Economist * to describe the troublesome state of modern scientific research. The editorial article How science goes wrong states

“A SIMPLE idea underpins science: “trust, but verify”. Results should always be subject to challenge from experiment. That simple but powerful idea has generated a vast body of knowledge. Since its birth in the 17th century, modern science has changed the world beyond recognition, and overwhelmingly for the better. But success can breed complacency. Modern scientists are doing too much trusting and not enough verifying—to the detriment of the whole of science, and of humanity.”

The article goes on to describe the problems of non-reproducible unverifiable science

“Too many of the findings that fill the academic ether are the result of shoddy experiments or poor analysis. A rule of thumb among biotechnology venture-capitalists is that half of published research cannot be replicated. Even that may be optimistic…”

and eventually suggests a possible cure

“Ideally, research protocols should be registered in advance and monitored in virtual notebooks. This would curb the temptation to fiddle with the experiment’s design midstream so as to make the results look more substantial than they are. Where possible, trial data also should be open for other researchers to inspect and test.”

This sounds like another powerful message in support of reproducible research and a call for changes in the culture of scientific publications. In application to computational science, “virtual notebooks” are reproducible scripts that, in words of Jon Claerbout, “along with required data should be linked with the document itself”. The article ends with a call to science to fix itself

“Science still commands enormous—if sometimes bemused—respect. But its privileged status is founded on the capacity to be right most of the time and to correct its mistakes when it gets things wrong. And it is not as if the universe is short of genuine mysteries to keep generations of scientists hard at work. The false trails laid down by shoddy research are an unforgivable barrier to understanding.”

DSR eikonal tomography

October 16, 2013 Documentation No comments

A new paper is added to the collection of reproducible documents:
First-break traveltime tomography with the double-square-root eikonal equation

First-break traveltime tomography is based on the eikonal equation. Since the eikonal equation is solved at fixed shot positions and only receiver positions can move along the ray-path, the adjoint-state tomography relies on inversion to resolve possible contradicting information between independent shots. The double-square-root eikonal equation allows not only the receivers but also the shots to change position, and thus describes the prestack survey as a whole. Consequently, its linearized tomographic operator naturally handles all shots together, in contrast with the shot-wise approach in the traditional eikonal-based framework. The double-square-root eikonal equation is singular for the horizontal waves, which require special handling. Although it is possible to recover all branches of the solution through post-processing, our current forward modeling and tomography focus on the diving wave branch only. We consider two upwind discretizations of the double-square-root eikonal equation and show that the explicit scheme is only conditionally convergent and relies on non-physical stability conditions. We then prove that an implicit upwind discretization is unconditionally convergent and monotonically causal. The latter property makes it possible to introduce a modified fast marching method thus obtaining first-break traveltimes both efficiently and accurately. To compare the new double-square-root eikonal-based tomography and traditional eikonal-based tomography, we perform linearizations and apply the same adjoint-state formulation and upwind finite-differences implementation to both approaches. Synthetic model examples justify that the proposed approach converges faster and is more robust than the traditional one.

Seismic data decomposition into spectral components

October 9, 2013 Documentation No comments

A new paper is added to the collection of reproducible documents:
Seismic data decomposition into spectral components using regularized nonstationary autoregression

Seismic data can be decomposed into nonstationary spectral components with smoothly variable frequencies and smoothly variable amplitudes. To estimate local frequencies, I use a nonstationary version of Prony’s spectral analysis method defined with the help of regularized nonstationary autoregression (RNAR). To estimate local amplitudes of different components, I fit their sum to the data using regularized nonstationary regression (RNR). Shaping regularization ensures stability of the estimation process and provides controls on smoothness of the estimated parameters. Potential applications of the proposed technique include noise attenuation, seismic data compression, and seismic data regularization.

Ray tracing on GPU

October 9, 2013 Documentation No comments

A new paper is added to the collection of reproducible documents:
Shortest path ray tracing on parallel GPU devices

A new parallel algorithm for shortest path ray tracing on graphics processing units was implemented. This algorithm avoids the enforcing of mutual exclusion during path calculation that is found in other parallel graph algorithms and that degrades their performance. Tests with velocity models composed of millions of vertices with a high conectivity degree show that this parallel algorithm outperforms the sequential implementation.

This is a contribution from Jorge Monsegny, UP Consultorias, and William Agudelo, ICP-Ecopetrol.

Program of the month: sfunif2

October 3, 2013 Programs No comments

sfunif2 creates a layered model from specified interfaces. It is inspired by an analogous program in Seismic Unix.

The following example from rsf/su/rsfmodel shows a simple model generated with sfunif2 and reproduced from an example in the book Seismic Data Processing with Seismic Un*x by David Forel, Thomas Benz, and Wayne Pennington.

The input to sfunif2 is a file containing sampled interfaces. The velocities in the layers can be specified as linear distributions
$$v(z,x) = v_0 + v_z\,(z-z_0)+v_x\,(x-x_0)$$
with parameters given by v00=, dvdz=, dvdx=, z0=, and x0=. These parameters should be lists, with the number of elements greater by one than the number of interfaces. The desired sampling of the depth axis is specified by n1=, o1=, and d1= parameters.

The 3-D version is sfunif3. See the following example from rsf/rsf/unif3

In addition to specifying layer velocities as linear (constant gradient) distributions, sfunif3 allows these properties to be specified in an optional file.

10 previous programs of the month