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The business of extracting knowledge from academic publications

markusstrasser.org

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Re: The business of extracting knowledge from academic publications

#111

Post by tsbischof »

kkylin wrote: post #39
cousin_it wrote: post #16

I can confirm that in my current area of interest (how to synthesize a cello or saxophone sound), there are hundreds of academic papers published over decades, each of them says "our method sounds more realistic than others", but code and audio samples are never available, and verbal descriptions always skip crucial details. I have no doubt that academics have a ton of expertise, but their output in paper form is bas…

I'm an academic (applied math) and want to respond to this: academic papers are the way they are for lots of reasons, many of which (not so good) have been mentioned on HN. There are a couple that I do not see very often however: (1) Many academics aren't aware non-academics read their papers at all: we work with other academics, go to conferences with other academics, and on the rare occasions we hear from readers,…

> What can help make the literature more accessible?

Publishing code and data associated with figures. A significant amount of the confusion about the literature comes from the difference between the documentation laid out in a paper and the reality of the actual implementation. Plus any peer review of the actual code used is checking the reality of the paper, rather than a description of what we think reality is.

Making this part of the publication process is vital, because there is such a high barrier to actually requesting this information later.

Re: The business of extracting knowledge from academic publications

#112

Post by jcrben »

If someone published a promising in vitro study, the mere fact that it was done and even the barest hint of a conclusion can dramatically impact one's decision to pursue that line of research. So I'm a bit skeptical that there's negligible value in biomedical research papers.

Re: The business of extracting knowledge from academic publications

#113

Post by cousin_it »

ska wrote: post #102
cousin_it wrote: post #16

I can confirm that in my current area of interest (how to synthesize a cello or saxophone sound), there are hundreds of academic papers published over decades, each of them says "our method sounds more realistic than others", but code and audio samples are never available, and verbal descriptions always skip crucial details. I have no doubt that academics have a ton of expertise, but their output in paper form is bas…

> but their output in paper form is basically unusable Others have commented as well but I will reinforce: their output is basically unusable for you for the purpose you want to put it to. Which is fair, but you should also recognize that you are not the audience of the papers and for good or for ill the system is not set up to help you with this.

I don't see how the system is very good for its intended audience either. If papers about making sound with code actually included sound and code, people in academia would be better off too. It would make it easier to search through literature, and to build on each other's work.

Re: The business of extracting knowledge from academic publications

#114

Post by jvvw »

Tomte wrote: post #53
kkylin wrote: post #39

Earlier quoted context omitted.

I'm an academic (applied math) and want to respond to this: academic papers are the way they are for lots of reasons, many of which (not so good) have been mentioned on HN. There are a couple that I do not see very often however: (1) Many academics aren't aware non-academics read their papers at all: we work with other academics, go to conferences with other academics, and on the rare occasions we hear from readers,…

> What can help make the literature more accessible? Review articles, sometimes called surveys. I've always thought that new PhDs would be excellent authors for those, having digested lots literature for their dissertation.

There's very little academic kudos survey articles or other educational articles (as another commentator mentioned, PhD theses are often the best place to go for those types of summary). I'm not sure how one changes that. I remember thinking during my PhD how helpful it would be to have more survey type articles - especially for the subfields adjacent to one's own - you want to know if there are useful connections to your work but you don't want to delve through dozens of extremely dense papers.

Re: The business of extracting knowledge from academic publications

#115

Post by Ldorigo »

JackFr wrote: post #55

It's interesting that OP did seemingy little research with respect to existing work in the field. https://www.nlm.nih.gov/medline/medline_overview.html Medline, a searchable online directory of medical research papers has existed for 50 years. The National Library of Medicine for many years was a leader in document search and retrieval before there was a web. In the 80's they were doing vector cosine document similar…

Medline is great on all levels but what does it have to do with the author's work/product/topic? It's a database of biomedical articles. It's searchable using usual text search ("concept A" AND "concept B"), and has some additional features like MESH terms and metadata.

The author is talking about extracting entity-level information from those article and building knowledge bases. Medline provides access to the raw data, but it does nothing like what the article describes (well - there's https://lhncbc.nlm.nih.gov/ii/tools/SemRep_SemMedDB_SKR.html , so not entirely true. But it's hardly a final answer to the problem or even close to being usable enough that it makes commercial solutions pointless)

Re: The business of extracting knowledge from academic publications

#116

Post by ska »

cousin_it wrote: post #113
ska wrote: post #102

Earlier quoted context omitted.

> but their output in paper form is basically unusable Others have commented as well but I will reinforce: their output is basically unusable for you for the purpose you want to put it to. Which is fair, but you should also recognize that you are not the audience of the papers and for good or for ill the system is not set up to help you with this.

I don't see how the system is very good for its intended audience either. If papers about making sound with code actually included sound and code, people in academia would be better off too. It would make it easier to search through literature, and to build on each other's work.

Papers are a conversation as much as anything else.

I agree that these days the tooling makes it much easier to distribute code & data somehow to match up, but there is also a cost/incentive mismatch. Basically to do a decent release of what you are working on and worse, potentially support it, costs time but has no real career value (yet). Which means it's mostly only done by people who are philosophically convinced of its value.

I think this will change over time, at least in some areas, but it won't be quick.

Re: The business of extracting knowledge from academic publications

#117

Post by markusstrasser »

tvhahn wrote: post #97
pezzana wrote: post #92

> My biggest mistake was that I didn't have experience as a biotech researcher or postdoc working in a lab. That is is big problem - good to recognize it as such. I can tell because the article, though lengthy, never seems to state an explicit problem to be solved. Rather, various ways to apply technology to a field are discussed. This is a recipe for failure. You need 3 things: 1. a problem to be solved 2. a custome…

Yes. I wonder if the author had first worked on the patent side (I'd be interested to hear more about this idea). Perhaps working on patents first would be a path to get experience (and product-market-fit). From there, one could branch out into other domains (e.g. bio).

Patents were the more obvious go to but we didn't want to work with obfuscated patent descriptions for the next years

Re: The business of extracting knowledge from academic publications

#119

Post by gardenfelder »

Nalta wrote: post #80

For anyone interested, my whole PhD was in biomedical hypothesis generation! I think the most "serious" attempts at building these systems have been focused around providing assistance to scientists, and not just coming up with new ideas on their own. here's an actual medical paper that my first system, Moliere, was able to help discover: https://link.springer.com/article/10.1007/s11481-019-09885-8

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8048136/

Re: The business of extracting knowledge from academic publications

#120

Post by gardenfelder »

PaulHoule wrote: post #28

This paper touches one aspect of it, which is that the source material is bad, but it doesn’t even start on the fact that the tools aren’t good enough and that many of the fashionable ideas (Word embeddings) are dead ends.

The very idea that "word embededings are dead ends" requires citations, evidence.
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