
IBM Watson fires its own cancer-fighting ‘moonshot’ - prateekj
http://venturebeat.com/2013/10/18/ibm-watson-fires-its-own-cancer-fighting-moonshot/
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dnautics
Instead of Jeopardy, I always wanted Watson to go on "are you smarter than a
fifth grader" and throw questions like "think of the second color of the
rainbow. What large bird starts with the same first letter?"

Or: "If I call A 5, B 4, and C 3, then what do I call D?"

As a scientist (working on cancer, no less), more than just churning through
terabytes of data, it strikes me that THESE sorts of questions are the ones
you'll need to be able to answer. There's also a lot of "reading between the
lines" you'll need to do, and a lot of "small pattern extrapolation". For
example, the drug candidate I'm working on is one of a family of about let's
say, 16 known compounds. All of them kill cancer cells, fourteen are
cardiotoxic. The two that are not, lack a single oxygen atom. Maybe that
oxygen atom lets the molecule block the mitochondrion (sort of important for
heart cells)? Why? Because the molecule family looks sort of like Coenzyme Q10
- if you use your imagination and remember some of your chemical reactivity
rules from Grad-level Ochem - and supplementation of Q10 alleviated the
cardiotoxicity in one study on rats for one of the molecules.

Ultimately, my previous boss was bold enough to latch onto that and give it a
shot - can we take this molecule that is the most potent of the group (but
unfortunately cardiotoxic), delete the homologous oxygen atom and make
something that still works and is less cardiotoxic?

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jknightco
I'm legitimately stumped. Which large bird starts with 'O'? Or is it second
from the top.. so an Ibis?

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ramchip
Ostrich?

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jknightco
I'm going to go sit in the corner and cry now.

Thanks!

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JunkDNA
As far as I'm aware there have been zero peer reviewed publications showing
Watson actually doing something in medicine. When a doctor thinks he or she
has a better approach than what is being done, they use the scientific method
to find out of their hypothesis holds up. So far I've seen lots of IBM
conference presentations and press conferences. But where is the data? Where
are the increased survival rates? Where are the reduced medical errors
compared to controls? _That_ is science. Everything else is snake oil unless
you have that.

~~~
dbcooper
Indeed. It's a little annoying to keep seeing these IBM PR releases about
fictional medical suppositions, when one is working on drug screening,
diagnostics, and such from within a reality constrained lab!

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bglazer
This is truly incredible stuff. Hats off to IBM for pushing the field of
machine learning forward.

This statement really struck me: "“In the Jeopardy days [in 2011], Watson was
running off 90 servers and could store 15 terabytes of memory,” said Gold.
That’s not your typical household integration. “Now it’s far more affordable
and runs 240 times faster, so we can do far more with less.” Moreover, the
size of IBM’s server is now smaller than a pizza box and can fit in any data
center."

How is this possible?

~~~
ancarda
I'm assuming they mean 1 server is a pizza box (ie. it's a 1U rack server), so
you'd still need ~90U of space.

Either that or IBM has made some breakthroughs in the last 2 years.

~~~
drblast
You can almost hear the article author completely misunderstanding what he was
told.

I'm betting it was something like, "For Jeopardy, Watson was using 15
Terabytes of data stored on 90 servers. And those servers were large back
then, now they're your standard pizza box 1U's. And because of advances in
storage technology we can store a lot more in the same space."

Isn't there some sort of basic tech literacy class for people who write these
articles? It's like reading the sports section and seeing "The Seattle
Seahawks are a group of big men and they ran at another group of big men, and
they've been doing that a lot, and faster lately. Some of the men in the
Seahawks group are smaller and faster, so they are harder to catch by the
other group of big men. The Seahawks grouping of men is like a successful
business, because they've been winning competitions against other groups."

~~~
cstross
There is some more prize gibberish in that article:

 _Saxena said IBM is ready to make a big a bet on Watson, as it did in the
1970s when it invested in the emergence of the mainframe._

Leaving aside the grammatical error (it's probably just an editing artefact),
_what_ bed did IBM make in the 1970s on the emergence of the mainframe? Is
that a typo for 1950s? Or just unvarnished ignorance of computing history?

It's stuff like this that makes me mistrust a news source: if they get it
blazingly wrong about something I know enough about to have a working bullshit
detector for, what are the chances that they're not also getting it wrong
about everything else?

~~~
nl
To be fair, the System/360 (which was the first to run the classic OS/360
operating system) was released in '64[1], and was replaced in the '70s by the
S/370.

Certainly mainframes were in use prior to the '70s, but the S/360 was the
first "classic" mainframe in that it was designed for both business &
scientific use[2], and it wasn't until the 70's that they began to become more
popular in areas outside their traditional use.

[1]
[http://en.wikipedia.org/wiki/IBM_System/360](http://en.wikipedia.org/wiki/IBM_System/360)

[2]

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whiddershins
Even if all some AI system did was take a list of symptoms, anonymize them,
suggest a diagnosis, and then take the MD's actual diagnosis, track outcomes,
and compare results over time, it would be a huge advancement.

Right now, unless I misunderstand something structural about our medical
system, most of the data gathered by MDs are wasted, because there is no
digital record of much of it and patient privacy legalities prevent wholesale
entering of symptoms and case outcomes in to any sort of freely available
(inter)national database.

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PaulHoule
Why is it always cancer?

I'd be impressed if somebody was trying to cure ALS or Tourette's syndrome.

~~~
teraflop
Maybe because cancer is ridiculously more common than both of those disorders
combined?

~~~
thaumasiotes
Sure, but obviously curing cancer is a waste of research effort... what they
should be trying to cure is disease.

~~~
foobarbazqux
Why is it a waste of research effort? We've made dramatic non-palliative
strides in the area of cancer treatment, and most importantly have been able
to induce complete remission in a significant number of cases.

~~~
thaumasiotes
see my sibling comment.

~~~
foobarbazqux
Sorry, I don't understand. If you meant PaulHoule's comment I'm not sure how
that answers my question, and I didn't find any other comments by you. Do you
mean because cancer isn't a simple, isolated thing like polio or TB?

~~~
thaumasiotes
Yes, I meant PaulHoule's comment. If the reason for studying "cancer" is that
"cancer" is more widespread than better-defined illnesses, then the reasoning
is misplaced; it's surely better to focus on something more widespread, like
"illness".

I have seen it expressed, though not in these terms, that asking for a "cure
for cancer" is equivalent to asking for bug-free software. Cancer isn't
something that afflicts you from without; it's just a failure mode for cells.
They can fail for all kinds of reasons (indeed, note that one of our best
methods of causing cancer, radiation, works on the principle of "make random
changes to the cell's genetic code, and it will eventually become cancerous").

~~~
foobarbazqux
So I think the general claim is that focusing on cancer is a middle ground
between seeking treatments for obscure well-defined illnesses and searching
for a panacea for illness or disease in general. Cancer has a precise
operational definition: unregulated cell growth. It isn't nearly as vague as
illness or disease. We understand a lot about all the different pathways
inside cells that can lead to it. A "cure for cancer" is an attempt to address
the issue upstream, such that it will affect all different types of cancer in
the body. Unlike seeking a panacea for all illness, this is not obviously a
waste of research effort. There are highly similar mechanisms at work in every
cancer. Even if a cure-all cannot be found (I would be surprised, personally),
just trying to understand the mechanisms still has value.

~~~
thaumasiotes
Actually, a cyst meets your definition of unregulated cell growth. It's just
slower / less greedy. The distinction between a benign tumor and a malignant
one is generally ascertained by the process of "let's watch it and see what it
does", so I'm not convinced that "cancer" is defined more usefully than
"illness".

In my opinion, and my medically-educated mother's opinion (really, I get it
from her), people don't look for "a cure for cancer" because they think they
can make progress from that viewpoint. They do it because they're looking for
funding.

edit:

You might compare "died of cancer" to "died of old age". Old age used to be an
accepted cause of death. When autopsies started happening, it was quickly
noticed that people who had died of "old age" always had some other, more
immediate cause of death. But it turns out that if you take an old person and
do your utmost to prevent / cure / treat all of those more proximate causes,
eventually one will get past you and they will die.

~~~
foobarbazqux
Okay, but that's not actually how cysts work if you look it up. They are sacs
that can have cancerous tissue inside them, but they can also have fluid or
air. The operational definition of benign and malignant tumors that doctors
use boils down to rudimentary observation, yes, but in the lab we've really
identified many of the key mutations in the transition from benign to
malignant. So I guess you could say we have a reasonably good idea of what
cancer is and how it works, but it hasn't fully made its way onto the front
lines yet, either in terms of assessment or treatment.

I understand your cynical point of view about funding, but I guess I would say
two things. First, cynicism is a cancer unto itself (ha), and all academics
are faced with the corrupting influence of money. Second, if you go and talk
to the cancer researchers in the nearest university you'll probably find a
great deal of them really do care about the work; they just might care about a
very tiny corner of it rather than a cure-all solution.

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nnq
Where can one learn more about how Watson actually works?

...starting from the IBM website and Wikipedia one mostly gets to whitepapers
and high level descriptions. I hope at least bits of it are open source or at
least have the math and logic underlying them well documented.

