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Data Mining Competition To Improve Drug Safety

ScuttleMonkey posted more than 4 years ago | from the db-mavericks-unite dept.

Math 36

An anonymous reader writes "The OMOP Cup is a competition to find new methods for detecting drug side effects. There have been several cases over the last few years where drugs have had issues that haven't been detected for years after they were released. The proliferation of electronic medical records and pharmacy claims provides a large and potentially powerful new data source for faster detection. The problem is that the techniques for doing this on a large scale are immature. The OMOP Cup is trying to help fix that. They've already given out $5,000 for top methods, and there's $15,000 still up for grabs."

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36 comments

Drug Side Effects (0)

Anonymous Coward | more than 4 years ago | (#30864230)

The side effects of drugs is that a bunch of prudes who want an excuse to run your life for you want to make all of the good ones illegal. For your protection, of course.

Re:Drug Side Effects (0)

Anonymous Coward | more than 4 years ago | (#30864626)

one time this guy showed me his 'drug free' tattoo so one day me and my
buddies pinned this guy down and injected him with heroin. he was kicking
and screaming and we all laughed and the next day we found out he killed
himself LOL

Re:Drug Side Effects (0)

Anonymous Coward | more than 4 years ago | (#30864658)

yo what drugs u into? im all about the opiumnitrous / dxm / ketamine / acid / weed / hydrocodone / ultram / oxy / demerol / morphine / codeine / dihydrocodeine / heroin / mdma / salvia / 5-meo-dipt / 5-meo-amt / amt / rohypnol / ghb / mda / hash / kavakava / adderall / dexedrine / ritalin / ephedrine / caffeine / alcohol / cocaine / shrooms / tobacco / xanax / klonopin / valium / ambien / soma / flexeril / zanaflex / zoloft / paxil / ether / spraypaint / phenobarbital / ativan / air duster

captcha: unionize

Crap derived from crap? (2, Interesting)

PSandusky (740962) | more than 4 years ago | (#30864314)

I'm curious as to what proportion of medical records were incorrect and what proportion of pharmacy claims were inaccurate. Just how useful could a database like this be, if its source data is prone to some really wacky error? Side effect misdiagnoses alone could make for a considerable slog through noise just to pick up an effect.

Re:Crap derived from crap? (0)

Anonymous Coward | more than 4 years ago | (#30864478)

I imagine that is part of the challenge of these types of analyses. Removal of noise to unearth underlying trends.

Hello, privacy? (-1, Troll)

Anonymous Coward | more than 4 years ago | (#30864498)

This is CVS pharmacy calling....KEANU REEVES...this is a RED, CIRCULAR pill with "84" on the top. TAKE WITH FOOD. I fucked your mom at a Marie Callender's 24 hour family restaurant. This recording will repeat...

Data Mining Sing Along (4, Funny)

jbezorg (1263978) | more than 4 years ago | (#30864540)

You parse 16 gigs, and what do you get?...

Re:Data Mining Sing Along (4, Funny)

dgatwood (11270) | more than 4 years ago | (#30864666)

A drug-induced tumor and deeper in debt.

Re:Data Mining Sing Along (0)

Anonymous Coward | more than 4 years ago | (#30865648)

You parse 16 gigs, and what do you get?...

A 48 gig parse tree?

Justice Dept reco: hold detainees forever (0)

Anonymous Coward | more than 4 years ago | (#30864588)

Justice task force recommends about 50 Guantanamo detainees be held indefinitely [washingtonpost.com]

A Justice Department-led task force has concluded that nearly 50 of the 196 detainees at the U.S. military prison at Guantanamo Bay, Cuba, should be held indefinitely without trial under the laws of war...

God DAMN that EVIL George W. Booosh!!!!

Only $20K? (1)

gyrogeerloose (849181) | more than 4 years ago | (#30864590)

Not very much money when you consider the amount of money that gets paid out to plaintiffs in lawsuits filed over drug side effects, such as the ones concerning Vioxx. This whole thing sounds a lot like the pharmaceutical companies are looking for a cheap fix, an alternative to the extensive drug trials they ought to be doing.

Re:Only $20K? (1)

oldhack (1037484) | more than 4 years ago | (#30864654)

Yep. I'd hold my nose and hock it to class-action specialists just to piss off the pharma bastards. Spending gobloads on TV ads, but a measly 20k for this? Scumbags.

Re:Only $20K? (1, Insightful)

Anonymous Coward | more than 4 years ago | (#30864708)

And then you *do* extensive drug trials, and people start complaining about how you torture animals, or how the price of the medicine is too high when it's finally on the market, or why they can't get the medicine while it's still in trial even though they don't fit the trial profile *at all* but it would save their kids life etc etc.

Re:Only $20K? (1)

phantomcircuit (938963) | more than 4 years ago | (#30864886)

people start complaining about how you torture animals

Who cares.

how the price of the medicine is too high when it's finally on the market

Tough shit, save medicine is expensive, surprise!

why they can't get the medicine while it's still in trial even though they don't fit the trial profile *at all* but it would save their kids life etc etc.

I still dont understand why the FDA does not allow drugs that have not been certified to be administered to terminal patients. There is no additional risk from doing it.

Re:Only $20K? (1)

causality (777677) | more than 4 years ago | (#30864932)

I still dont understand why the FDA does not allow drugs that have not been certified to be administered to terminal patients. There is no additional risk from doing it.

If the government respected a citizen's right to determine what will and won't be put into their own body, we would have never had a War on Drugs. What you mention there is just a logical extension of the idea that none of us can be trusted with the slightest degree of self-determination, not even when it cannot impact the lives of others.

Re:Only $20K? (2, Insightful)

matt4077 (581118) | more than 4 years ago | (#30865190)

"I still dont understand why the FDA does not allow drugs that have not been certified to be administered to terminal patients. There is no additional risk from doing it." Because then there's no reason for companies to do trials, and you'll only have "we don't know if they work, but we sell them anyway" drugs. You'll also have all kinds of snake oil salesmen, which you don't want in a life-or-death situation. Rationality tends to break down in extreme situations.

Say goodbye to "quality of life" drugs. (2, Insightful)

russotto (537200) | more than 4 years ago | (#30864736)

Dig through a huge dataset like this looking for problems and you will find them. For everything. And with the FDA and court's approach, that means that even tiny effects will end up getting drugs knocked off the market. The COX-2 inhibitors are a perfect example. Sure, for a tiny number of people taking them they increased the risk of heart attack. But for untold numbers of people taking them, they relieved pain either where nothing else would, or with far fewer side effects than other pain medications like opoids. But in today's society, we're not allowed to trade a tiny risk of death versus an enormous chance of pain relief. So even the very tiny risks one can find this way will end up getting whole classes of non-lifesaving drugs off the market. No more analgesics, no more antihistamines, no more decongestants (oh, wait, they already virtually banned those for the War on Drugs), no more cough medicines, etc.

ignorance != bliss (3, Insightful)

Anonymous Coward | more than 4 years ago | (#30865082)

Datamining by Kaiser Permanente helped find a previously unknown risk of heart attack for certain users of VIOXX [wikipedia.org] , and it was probably right that the drug was withdrawn. It may also be a good idea to re-approve it for those who would benefit with minimal risk. But without the post-approval datamining we would never know what the risk/benefit truly was.

That also points to some limitations of our drug approval process. Trial patients are followed only for so long. In fact, some of the trial patients who were taking it long term had heart attacks, but that data was not included because they occurred past the end of the required study period.

If you believe in the science that brings you modern medicine to begin with, then more knowledge is always better.

Re:ignorance != bliss (1)

russotto (537200) | more than 4 years ago | (#30869418)

If you believe in the science that brings you modern medicine to begin with, then more knowledge is always better.

It's not the science I object to; it's the politics. The Vioxx study, subsequent FDA action, and subsequent lawsuits resulted in nearly every COX-2 inhibitor being taken off and kept off the market, despite the tiny magnitude of the risks. Given that, I think it's better to not seek out knowledge of such small risks rather than risk that kind of overreaction.

in soviet russia (1)

larry bagina (561269) | more than 4 years ago | (#30864842)

competition to experiment with drugs on facebook and twitter mines you!

HIPAA anyone? (1)

drrobin_ (131741) | more than 4 years ago | (#30864846)

This strikes me as a huuuuuge breach of medical record confidentiality. Where exactly do they plan to legally get enough medical records to mine in the first place?

Re:HIPAA anyone? (2, Informative)

TheWingThing (686802) | more than 4 years ago | (#30866000)

This strikes me as a huuuuuge breach of medical record confidentiality. Where exactly do they plan to legally get enough medical records to mine in the first place?

As long as eighteen HIPAA identifiers are removed, the data is considered deidentified by HIPAA. Deidentified data does not need patients' consent. De-identified data-only studies only need the hospital IRB (Institutional Review Board) approval. Believe me, it's not an easy task to get the IRB approval.

Here's the list of the 18 HIPAA identifiers [uvm.edu] .

Re:HIPAA anyone? (1)

michaelhood (667393) | more than 4 years ago | (#30867572)

As long as eighteen HIPAA identifiers are removed, the data is considered deidentified by HIPAA. Deidentified data does not need patients' consent. De-identified data-only studies only need the hospital IRB (Institutional Review Board) approval. Believe me, it's not an easy task to get the IRB approval.

Here's the list of the 18 HIPAA identifiers [uvm.edu] .

Even though it's a bit of a different situation, I'm reminded of the Netflix debacle [wired.com] ..

Re:HIPAA anyone? (1)

v1x (528604) | more than 4 years ago | (#30866036)

If the data-set has been completely de-identified (with the actual dates of all events truncated/obfuscated), or otherwise meets the criteria defined under the HIPAA Safe Harbor de-identification [utah.edu] method, then it is not considered to be a HIPAA violation.

Re:HIPAA anyone? (0)

Anonymous Coward | more than 4 years ago | (#30867132)

Actually, the dataset is completely fake. A previous competition was to algorithmically generate a realistic set of data. The winner of that competition had their program used to create the data input for this competition. The bottom line is this competition is more about understanding how the dataset was generated than actually finding "hidden" adverse drug reactions.

Just quote from rules: (0)

Anonymous Coward | more than 4 years ago | (#30864954)

By submitting an Entry, Participant grants Sponsor and their respective agents and contractors an irrevocable, unlimited, worldwide, perpetual, unconditional, royalty free, fully paid up, non-exclusive license under the Participants’ copyrights, patents, or other intellectual property rights necessary to use, review, assess, test, and otherwise analyze the Entry and all its content (including the method, mathematical formulas and references, and source code) in connection with this Contest.

As a condition to receiving a Grand or Progress Prize, the winning Participant agrees to grant Sponsor and their respective agents and contractors an irrevocable, unlimited, worldwide, perpetual, unconditional, royalty free, fully paid up, non-exclusive license under the Participants’ copyrights, patents, or other intellectual property rights relating to the Entry, including the right to use, reproduce, prepare derivative works of, publicly display, publicly perform, distribute, and sublicense under an Apache license or other open source license the Entry and all its content (including the method, mathematical formulas and references, and source code) (the “License”).

All your code are belong to us !

pharmacovigilance (0)

Anonymous Coward | more than 4 years ago | (#30864978)

This is already being done, the pharmacovigilance field is growing rapidly, Oracle just began a life sciences company that focuses on this field.

How much for improving movie ratings? (2, Insightful)

CoffeeDregs (539143) | more than 4 years ago | (#30865338)

I could focus on reducing mortality due to prescription drug side-effects and maybe get $5k? That's awesome, I can totally help out my fellow ... what's that? I get $1M if I rock NetFlix's movie rating DB? Movie ratings here I come!

Re:How much for improving movie ratings? (1)

caffeinemessiah (918089) | more than 4 years ago | (#30877064)

That's awesome, I can totally help out my fellow ... what's that? I get $1M if I rock NetFlix's movie rating DB? Movie ratings here I come!

You're a little late...the Netflix contest ended quite a few months ago, with the $1M being awarded to a joint AT&T Research/Yahoo Labs team.

Come again? (1)

Angst Badger (8636) | more than 4 years ago | (#30865468)

They've already given out $5,000 for top methods, and there's $15,000 still up for grabs.

Whoa there, big spender! I'm all for serving the public good, but if I was to work all those extra hours and discovered a useful new technique for using this data, and I have to choose between maybe getting somewhat less than what I still owe on my car, or trying to sell the code to the deep pockets of Big Pharma, I know which one I'm going to go with.

Re:Come again? (1)

michaelhood (667393) | more than 4 years ago | (#30867578)

They've already given out $5,000 for top methods, and there's $15,000 still up for grabs.

Whoa there, big spender! I'm all for serving the public good, but if I was to work all those extra hours and discovered a useful new technique for using this data, and I have to choose between maybe getting somewhat less than what I still owe on my car, or trying to sell the code to the deep pockets of Big Pharma, I know which one I'm going to go with.

Can't disagree there, but I wanted to point out you probably want to sell this to class action attorneys for the real money. Pharmaceutical companies will bury this quicker than you can sign over the rights to it.

Wrong base assumptions. (1)

Hurricane78 (562437) | more than 4 years ago | (#30866404)

The base assumption of this seems to be, that the point of a pharma company is to heal people with safe drugs.

It’s not. In fact, if they don’t lose money from it, it is completely irrelevant if you die a slow and horrible death.
Proven by many, many products that are out there right now. Like Prozac. It does help nobody. In fact it does the exact opposite, because it drives people even further into repression. And therefore dependency on the stuff.

The point of pharma companies, is to make money.
As long as that is not 100% and without any loopholes, tied to what we want from them,
we will have no guarantee at all to get it.

Re:Wrong base assumptions. (1)

michaelhood (667393) | more than 4 years ago | (#30867582)

The base assumption of this seems to be, that the point of a pharma company is to heal people with safe drugs.

It’s not. In fact, if they don’t lose money from it, it is completely irrelevant if you die a slow and horrible death.
Proven by many, many products that are out there right now. Like Prozac. It does help nobody. In fact it does the exact opposite, because it drives people even further into repression. And therefore dependency on the stuff.

The point of pharma companies, is to make money.
As long as that is not 100% and without any loopholes, tied to what we want from them,
we will have no guarantee at all to get it.

You might want to consider some Prozac, you sound anxious.

I will lose money on this (1)

Kim0 (106623) | more than 4 years ago | (#30868146)

...even if I win, since the prizes are so small. Kim0

Top Methods @ Top Bargain (1)

foobsr (693224) | more than 4 years ago | (#30868676)

TFS: "They've already given out $5,000 for top methods, and there's $15,000 still up for grabs."

Imagine, $20.000 that will help the poor Pharma-Industry to avoid being sued.
Alternatively:
Imagine, $20.000 that will save the health of numerous people.

Now, that is a big deal indeed.

CC.

Drug companies are evil (1)

NSN A392-99-964-5927 (1559367) | more than 3 years ago | (#30903530)

If the government collaborate with drug companies and you are legally drugged, there is hardly any hope for mankind. I do understand from a friend in the USA that some kids are legally drugged with psychiatric drugs namely Ritalin and it has gone one step further that unless you receive shots, kids are not allowed to attend school. We have so far resisted part of this in the UK, but the drug companies and government is trying to weasel they're way around it. I also have something to say about Gulf War Syndrome from OP Desert Storm and Telic which I served in. We were almost forced to take 5 injections as immunisation against chemical weapons, VX nerve agent etc. Everyone I know that took those drugs suffer from Gulf War Syndrome and there is no admission still to this day by the gov and drug companies. As S/SGT (staff sergeant) I ordered those under my command NOT to take the drugs as I had drilled my squaddies over and over to get in NBC (Nuclear Biological Chemical) suits within 45 seconds. none in my batallion were affected, apart from the depleted uranium shells. I have my moments of being hyper as hell as do the rest of my troop, but we are alive to tell the tale. Never trust governments and drug companies. Maybe if they took their own drugs they would feel better. Being compensated for your health and sanity is not worth any amount of money. Love NSN
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