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Redesigning the Scientific Paper

theatlantic.com

101–110 of 110 posts

Re: Redesigning the Scientific Paper

#101
post #99
post #80

Earlier quoted context omitted.

You linked to the original dropout paper. What’s “inverse dropout”?

It is just the description of an idea I came up with without any implementation. I was leaving it purposefully vague, just do the "inverse" of what it says in that paper.

That's not a description of an idea, just like a paper doesn't only consist of the title. This kind of argument is insincere and not helpful at all.

Re: Redesigning the Scientific Paper

#102
post #85

Earlier quoted context omitted.

I'm in opto/bio/eng. I think you misunderstand the 'real' reason for research papers as they currently stand: Money. It's a bit of a path, but I'll try and explain. In the US at least, research costs a LOT of cash. Many departments are chronically underfunded. In my state, the university only gets ~10% of it's funding from the state-house. The rest is grants. The only real writers of grants are the professor corps. S…

This is spot on. I was surprised the first time I worked at a major university just how toxic the environment was and how little mindshare was spent towards actually contemplating compelling hypotheses / experiments. It was much less of the ideal "life of the mind" I thought it would be and much more like show business / social climbing, minus the widespread name recognition and glamor. I was already on the way out o…

To be fair, it's been ~50 years since the 70s. The Professor Corps should pretty much be entirely different people.

Re: Redesigning the Scientific Paper

#103
post #21
post #9

> These programs tend to be both so sloppily written and so central to the results that it’s contributed to a replication crisis, or put another way, a failure of the paper to perform its most basic task: to report what you’ve actually discovered, clearly enough that someone else can discover it for themselves. This is the crux of the of the problem IMHO - at least for the fields I study (AI/ML). Replicating the resu…

I've had a paper peer reviewed. It was ultimately rejected but I can't help but suspect that by making all my code publicly available, I hurt my chances of publication. The reviewers comments were about my coding style, my choice of build tool (I didn't use make, but something else which is just as easy to use), the choice of C vs C++... It's like best practices for computer security -- always strive to minimize the…

I recently reviewed a computational materials science paper and was quite impressed by the fact that they included some data and a Jupyter notebook. Long term, ecosystem will be an issue, but in the short term, it's invaluable. It does make it easier to check for obvious errors. I think more incentives should be given by funding agencies to encourage this.

I'm really sorry to hear about your experience.

Re: Redesigning the Scientific Paper

#104

Earlier quoted context omitted.

Seems like this could pair well with the journal crisis and suggestions to implement a blockchain journal: Your paper cannot be accepted by the journal unless it includes executable code; the results of which are then injected into the "paper" view...? So, basically - a paper consists of what it takes to replicate the paper, and the blockchain journal's first step is running the replication. This would be problematic…

So where, exactly, is a block chain required here? Everything you listed could just as easily be a requirement set by the journal, after all. I mean, every journal has at least some requirements already (at the very least, nearly all require publishing in a specific language). So aside from jumping on the blockchain bandwagon just because that's the new exciting thing, what value is added here? Good God, I'm getting…

https://news.ycombinator.com/item?id=16737642

It actually seems like journals could benefit from the application of this technology.

So yes, you don't need a block chain to set these requirements, and if you're using a blockchain you don't need these requirements, _but_, a blockchain journal and these requirements would likely pair very well together, as they cover respective weak-points (centralized journals might only ensure the journal's publisher can replicate; decentralized journals have to have some kind of automated validation).

Buzzwords become buzzwords because there's something to them, after all.

Re: Redesigning the Scientific Paper

#105
post #53

Earlier quoted context omitted.

Then do we even need peer review? In my experience it is always superficial, people just feel that they have to say something, so they say something about writing style, or similar trivia. The way it should work is you put your stuff with code and all data on github. People interested in the field or working for journals read it, and rate it, journals collect links to paper repositories that are highly rated by scien…

I've been peer reviewed once (and waiting for the second) and it was very in depth, giving me a couple of pointers to improve my paper. Field was mathematics, though.

sure it depends on field, on journal and on reviewer, and but with a github like interface, and public reviews it will only get better.

Re: Redesigning the Scientific Paper

#106
post #42
post #40

Earlier quoted context omitted.

> there is a disproportionate focus on paper quality over "project quality" One problem is bitrot. Stuff that runs now is not guaranteed to work in 1 or 2 years, let alone 10 years. Even more so when it runs on fancy hardware, like GPUs.

This is one of the main reasons to require source release. Open source software is much more likely to run in 10 years. It’s actually useful to package everything together into a container or VM so all the packages are there too. I work with some genome guys and they have this problem as their sequencers basically turn over in a year or two the advances are so fast. So they have to maintain the specimen as well as al…

The work should reproducible from not just artifacts, but also from a container. Sourcing compilers, libraries, etc is almost impossible. The NSF should really be running an archive and cluster for housing reproducible research that remains executable far into the future.

Re: Redesigning the Scientific Paper

#107
post #21
post #9

> These programs tend to be both so sloppily written and so central to the results that it’s contributed to a replication crisis, or put another way, a failure of the paper to perform its most basic task: to report what you’ve actually discovered, clearly enough that someone else can discover it for themselves. This is the crux of the of the problem IMHO - at least for the fields I study (AI/ML). Replicating the resu…

I've had a paper peer reviewed. It was ultimately rejected but I can't help but suspect that by making all my code publicly available, I hurt my chances of publication. The reviewers comments were about my coding style, my choice of build tool (I didn't use make, but something else which is just as easy to use), the choice of C vs C++... It's like best practices for computer security -- always strive to minimize the…

Aaah, brought me memories from the 7 years I was in academia. All the publish and perish and the peer reviewing process is completely broken. Academia is completely broken, I would hate having to go back to academia now that I have been 7 years in industry and earning 6 figures.

Re: Redesigning the Scientific Paper

#108

I used to work as a software developer for a research institute. I wanted to open source our research code and tools, and the department head was in favour of it because it would raise the profile of the research unit. There were two forces working against us. First many of the grants came from governments, and a stipulation was that we would devote some resources to helping startups commercialise the output of the r…

Interesting.

Maybe embargo works, to be progressively published over time, with grace period being extended by reaching goals/milestones.

In other words: use it or lose it.

Re: Redesigning the Scientific Paper

#109
post #105

Earlier quoted context omitted.

I've been peer reviewed once (and waiting for the second) and it was very in depth, giving me a couple of pointers to improve my paper. Field was mathematics, though.

sure it depends on field, on journal and on reviewer, and but with a github like interface, and public reviews it will only get better.

Problem is, if the review is public then it means the article is also in the public and some (most) publishers are not OK with that. At least yet, hopefully it will get better.

Re: Redesigning the Scientific Paper

#110
post #21

Earlier quoted context omitted.

I've had a paper peer reviewed. It was ultimately rejected but I can't help but suspect that by making all my code publicly available, I hurt my chances of publication. The reviewers comments were about my coding style, my choice of build tool (I didn't use make, but something else which is just as easy to use), the choice of C vs C++... It's like best practices for computer security -- always strive to minimize the…

In machine learning / computer vision people often release their code after the paper is already accepted. Time before the submission deadline is usually used to do more experiments and write text, not to polish the code. And after the deadline there is no hurry. What people (who want to share code) consider important is to release it till a bit before the actual conference (but this doesn't transfer to journal-based…

The paper should be accepted in rough form, but publication should be held up pending approval of the data and code.

Or a paper should be published in a probationary form, and not certified (by the journal) until an independent lab replicates the result. A paper that isn't making adequate progress toward replication should be retracted by the publishing journal.

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