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Medical Breakthrough in Spinal Cord Injuries Was Made by a Computer Program

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Re: Medical Breakthrough in Spinal Cord Injuries Was Made by a Computer Program

#51

Post by akiselev »

nitrogen wrote: post #45
akiselev wrote: post #22

Earlier quoted context omitted.

That's simply not true. One of the most, if not the most, common ways to fail an experiment is through contamination and there are at least a dozen different types of bacteria in the average lab that are brutally efficient at outcompeting whatever is in your sample and probably thousands more that are problematic at best. Once your sample is contaminated it is useless because the number of variables out of your contr…

That failure should still be documented somewhere.

They are, in millions of lab notebooks around the world that will never see the light of day, and for good reason. There are so many more experiments that end with the unqualified final note "samples contaminated" than successful ones that if biologists spent time tracking down the source or even the type of the contamination, we probably still wouldn't have modern medicine.

Re: Medical Breakthrough in Spinal Cord Injuries Was Made by a Computer Program

#52

Post by nitrogen »

akiselev wrote: post #51
nitrogen wrote: post #45

Earlier quoted context omitted.

That failure should still be documented somewhere.

They are, in millions of lab notebooks around the world that will never see the light of day, and for good reason. There are so many more experiments that end with the unqualified final note "samples contaminated" than successful ones that if biologists spent time tracking down the source or even the type of the contamination, we probably still wouldn't have modern medicine.

Is there any kind of survey of all failed experiments and the causes? What are the numbers? What percentage of experiments fails? How can we be sure the successful trials weren't random if the failures aren't reported in any way?

Re: Medical Breakthrough in Spinal Cord Injuries Was Made by a Computer Program

#53

Post by akiselev »

nitrogen wrote: post #52
akiselev wrote: post #51

Earlier quoted context omitted.

They are, in millions of lab notebooks around the world that will never see the light of day, and for good reason. There are so many more experiments that end with the unqualified final note "samples contaminated" than successful ones that if biologists spent time tracking down the source or even the type of the contamination, we probably still wouldn't have modern medicine.

Is there any kind of survey of all failed experiments and the causes? What are the numbers? What percentage of experiments fails? How can we be sure the successful trials weren't random if the failures aren't reported in any way?

You seem to be conflating all possible modes of failure under the simplistic designation "failed experiment" and setting up impossible standards for record keeping. The clinical trial equivalent of sample contamination is a patient getting hit by a bus minutes after they receive the first treatment of a trial. Sure if its a psychoactive drug you would investigate if it contributed and you can include this tiny little blip of data in the thousands of other pages you give to the FDA but what's the point? The trial was ruined by an unpredictable act of nature and your resources can be much better spent focusing on the other patients than investigating if the driver was intoxicated or if the hospital needs more stop signs, which are entirely irrelevant to whether or not your drug works.

I am by no means advocating that well thought out and executed experiments that fail to provide evidence for the experimenter's hypothesis should be locked in a dusty file cabinet forever closed to study, but those are few compared to the total number of experiments that ended due to clumsiness, sleep deprivation, or too many undergrads in the lab. Science is all just human error, through and through.

Re: Medical Breakthrough in Spinal Cord Injuries Was Made by a Computer Program

#55

Post by Yomammas_Lemma »

Dn_Ab wrote: post #49
skywhopper wrote: post #24

The substance of the article is quite interesting, but the headline and premise--that it was a computer program and not humans who found the result--is ridiculous. The computer program did not collate and index the raw data and notes. The computer program did not choose the relevant inputs from the sum of all knowledge. And most importantly, the computer program did not write itself. Software is a tool that humans cr…

I agree that this wasn't done by the computer (did computers uncover the Higgs Boson?) but I also do not believe humans can take most of the credit: this was the result of a Man Machine System team up—trying to disentangle credit assignment is not a worthwhile activity. Roughly and from a quick reading of a paper thickly frosted with jargon I am unfamiliar with, the method works by creating networks—which highlight k…

>I agree that this wasn't done by the computer (did computers uncover the Higgs Boson?) but I also do not believe humans can take most of the credit: this was the result of a Man Machine System team up

You realize that they're using software made by a team of mathematicians and software developers, right? If you want to give credit to the software, give credit to the people who wrote the code and discovered the mathematics. This isn't any different than how physicists would use Mathematica.

Re: Medical Breakthrough in Spinal Cord Injuries Was Made by a Computer Program

#57

Post by pvnick »

topologix wrote: post #38

Hey HN folks - I am the co-founder and CEO of Ayasdi. If you have questions about the math/CS aspects of this, happy to answer.

I'd love to read a couple of journal articles that you recommend to learn about TDA. I do large scale data analysis on health care data at my university and am always on the look-out for interesting techniques.

Re: Medical Breakthrough in Spinal Cord Injuries Was Made by a Computer Program

#58

Post by steamer25 »

topologix wrote: post #38

Hey HN folks - I am the co-founder and CEO of Ayasdi. If you have questions about the math/CS aspects of this, happy to answer.

Do you recommend any good primers on topology? I thought this (https://colah.github.io/posts/2014-03-NN-Manifolds-Topology/) was an interesting article and I see what looks like some great papers and videos available at http://www.ayasdi.com/approach/data-scientist/, but I don't know the difference between homotopy and homology (yet) :) .

What kinds of infrastructure/tech do you think will have the most utility for topological data analysis in the near future? E.g., GPUs, Apache Spark, FPGAs, etc.

Any thoughts on an Ayasdi public offering? I'd like to consider investing but I don't have millions of dollars (yet) :) .

Thanks for your time.

Re: Medical Breakthrough in Spinal Cord Injuries Was Made by a Computer Program

#59

Post by xbmcuser »

Things like this why I feel something like google deepmind can be a game changer for the sciences if the research data of all human research data was available to them. They might never reach the point of true AI but they would still beat all humans and finding relationships between data humans cant even remember.

Re: Medical Breakthrough in Spinal Cord Injuries Was Made by a Computer Program

#60

Post by topologix »

steamer25 wrote: post #58
topologix wrote: post #38

Hey HN folks - I am the co-founder and CEO of Ayasdi. If you have questions about the math/CS aspects of this, happy to answer.

Do you recommend any good primers on topology? I thought this ( https://colah.github.io/posts/2014-03-NN-Manifolds-Topology/ ) was an interesting article and I see what looks like some great papers and videos available at http://www.ayasdi.com/approach/data-scientist/ , but I don't know the difference between homotopy and homology (yet) :) . What kinds of infrastructure/tech do you think will have the most utility fo…

Hey,

Some reading material: A very general blog about philosophy : http://radar.oreilly.com/2015/07/data-has-a-shape.html

		A slightly more in-depth blog : https://shapeofdata.wordpress.com/2013/08/27/mapper-and-the-choice-of-scale/

		A very accessible book about topology (especially from an algorithms perspective) : http://www.amazon.com/Computing-Cambridge-Monographs-Computational-Mathematics/dp/0521136091/ref=sr_1_1?ie=UTF8&qid=1444971634&sr=8-1&keywords=topology+for+computing

		Blog exposing persistent homology : https://normaldeviate.wordpress.com/2012/07/01/topological-data-analysis/

		Videos exposing persistent homology : 
			https://www.youtube.com/watch?v=CKfUzmznd9g
			https://www.youtube.com/watch?v=CKfUzmznd9g

	Some free software:
		Python Mapper by Daniel Müllner : http://danifold.net/mapper/index.html

		JPlex library by Harlan Sexton : http://www.math.colostate.edu/~adams/jplex/index.html

		Dionysus by Dimitriy Morozov : http://www.mrzv.org/software/dionysus/

		Topological Data Analysis in R : https://cran.r-project.org/web/packages/TDA/vignettes/article.pdf

	Infrastructure
		Our tech stack is:
			Backend
				HDFS for storage
				Our ML and Math code is hand-rolled C++ and Assembly(7% LOC)
				All coordination/distributed systems code is in Java
				ZMQ for communication
				Protocol Buffers for protocol
			Frontend
				D3
				Backbone
				Hand-rolled webGL graph visualization (we open sourced it at https://github.com/ayasdi/grapher)

		We currently don't use GPUs or any other fancy hardware primarily because today, our customers use commodity hardware and getting F1000 companies to buy cutting-edge hardware is just plain horrible.

		We have an awesome GPU rig at our offices that we test algorithms on and it can really make our algorithms scream, but again, none of our customers have/are willing to invest in GPUs.

		Apache Spark - it is interesting that in our experience, making it work for ML algorithms is really too much work unless you invest the time to understand the framework and its fundamentals. It performs very well for ETL type tasks, which is what we use it for.

	On a public offering: no comment :)

	If you have more questions - I am easy to find :)
Gurjeet
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