7 ms·

Algorithm Finds Thousands of Unknown Drug Interaction Side Effects

103 points by voodoochilo 15y ago

scotch_drinker 15y ago
This should come as no surprise as our effort at better living through chemistry is barely in its infancy. Millions of people take drugs prescribed to them by their physicians with the implicit understanding that they are safe because the USDA says they are when in fact we have precious little idea if they really are. The potential revenue from new pharmaceuticals is huge and the pressure to get new drugs out into the market is immense. It's initially comforting to see that people are working on this problem of drug interactions since as the article mentions, we couldn't do it in the clinical trials. Still, the cynic in me thinks this is just another step in getting everyone taking more and more prescription medicines. If the pharmaceutical industry can show that two drugs have no interactive side effects, it's much easier to convince a patient to begin taking a new drug. Western medicine is already heavily dependent on fixing the symptoms instead of the cause. It's clear that in many cases we have almost no clue why a particular drug works. It's thrilling to see risks removed from the system by finding drug interactions previously unknown. However, it's frightening how much more likely it is that physicians will rely on prescribing a pill because it's easier than convincing the patient to change.
- weavejester 15y ago
  "Western medicine"? As opposed to what?
  - scotch_drinker 15y ago
    As opposed to a more holistic approach beyond "You have high cholesterol, take this pill for the rest of your life". Some of this is our natural inclination to do things that are easy (taking a pill is easy, fixing your diet is not) but as we become more and more reliant on prescription medicines to treat symptoms and disease, we will naturally become less and less inclined in the medical profession to advocate strongly for a different patient lifestyle before putting them on the meds.
    - onemoreact 15y ago
      All Doctors treating the average american say to eat better, exercise more, and get more sleep. The only difference is when people don't do these things they still get better with "Western medicine" vs. blaming the patent.
      - scotch_drinker 15y ago
        That's not true on several fronts. One, doctors spend little time explaining options to patients oftentimes because they don't actually know the options. Drugs are almost always the first line of defense. Obviously, this is partially because drugs are easy. It's also because doctors don't have to worry about it since the USDA says it's fine whereas if they tell a patient to alter their diet and take supplemental iodine to treat hypothyroidism, they have no support for that treatment plan. Secondly, many times patients do not get better. Statins are prescribed in astronomically large numbers in this country to lower cholesterol when the science behind the benefits of lower cholesterol is highly mixed. In many of the supposedly supporting studies, overall mortality is unchanged in groups taking statins. This has nothing to do with blaming the patient. It has everything to do with the fact we have little comprehensive understanding of the long term ramifications of our increasing reliance on chemicals to help us live more healthy lives. Hopefully finding ways to identify drug interactions is a first step towards current complications but it doesn't change the fact that this will only make it easier to prescribe medications for symptoms without treating the underlying cause.
        carbocation 15y ago
        Teach the controversy! In the meantime, the data supporting statins are among the best ever compiled. The advances contributed by groups calling themselves "holistic" are entirely absent. And the willingness of modern medicine to introspect and change in the face of data is slow but meaningful. I asked this same question the other day and still have yet to get a meaningful response: what is the "holistic" treatment for HIV?
        15y ago
  - usaar333 15y ago
    I cringe whenever I hear the term "Western medicine" being used to describe modern evidence-based medicine. There's little Western cultural bias to this approach; a drug, lifestyle, whatever either has significant effects on health or it doesn't. Just as the unproven components of traditional Western medicine (leaches anyone?) are mostly bunk, so are such aspects of traditional Eastern Medicine/alternative medicine/whatever.
- threejay 15y ago
  You mean the FDA? No offense, but just because you are well versed in one subject does not mean you really understand the idiosyncracies of another. Every time I see a drug / medicine related thread on HN I cringe. Much in the same way you would if you read a technology related post on a forum geared towards doctors and pharmacists.
  - andrewwc 15y ago
    As a pharmacist, I approve this comment!
  - morestuff 15y ago
    All that cringing and you only call out a misnamed variable?
utopkara 15y ago
Obviously this algorithm has lots of false positives.
- politician 15y ago
  Why is that obvious?
  - pwhelan 15y ago
    A false positive costs much lower than a false negative in this instance so it should follow that FP should be more common. However, without the data it is still speculation.
    - carbocation 15y ago
      Whether false positives or false negatives are more harmful is a difficult question. A false positive might stop millions from taking a life-saving drug. A false negative might cause millions to take a life-threatening drug.
      - pwhelan 15y ago
        By nature a false positive interaction could be re-tested more easily than a false negative though, correct? Also, that fits in with medical "first, do no harm" framework more readily.
        carbocation 15y ago
        Regarding your second point, I agree. But it must be balanced against the other tenets of medical ethics. At any rate, this seems to be an important study. I look forward to seeing the same study carried out across different EMR databases and then meta-analyzed. That will be extremely powerful.
  - rsheridan6 15y ago
    Typically scientists try to reject the null hypothesis (in this case, that a particular pair of drugs do not interact) by showing that it's unlikely (less than a 5% chance) that an apparent interaction is caused by random chance. But if you go looking at millions of possible interactions, you're going to find a lot that seem to meet that criteria by chance. 5% of a million is 50,000. 0.1% of a million is 1,000. That's why drug companies have to prespecify the outcomes they're looking for before starting the study. If you look through your data after the fact, you're going to find something that makes your drug look good just by chance.
brador 15y ago
Anyone know if that dataset is publicly available?
- DevX101 15y ago
  Yes, its public. I think the below link should have some of the data. http://www.fda.gov/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/ucm082193 http://www.fda.gov/Drugs/GuidanceComplianceRegulatoryInforma...
phalanx 15y ago
Mike McCandless, a search expert who does a lot of work with Lucene wrote about what he found in this mit paper about extracting side effect info from online health forums: http://people.csail.mit.edu/seneff/IMMM.pdf http://people.csail.mit.edu/seneff/IMMM.pdf Here is the less lengthy, less academic blog post from him, he may be talking about the same thing that nature is talking about, or at least it's something very similar: http://architects.dzone.com/articles/crawling-crowd-data-spots-side?mz=33057-solr_lucene http://architects.dzone.com/articles/crawling-crowd-data-spo...
carbocation 15y ago
Just to be fair, the original title of the research article is "Data-Driven Prediction of Drug Effects and Interactions" ( http://stm.sciencemag.org/content/4/125/125ra31 http://stm.sciencemag.org/content/4/125/125ra31 ). Emphasis on 'Prediction' mine. 47 are then supported by retrospective analysis of an EMR database.

103 points by voodoochilo 15y ago

This should come as no surprise as our effort at better living through chemistry is barely in its infancy. Millions of people take drugs prescribed to them by their physicians with the implicit understanding that they are safe because the USDA says they are when in fact we have precious little idea if they really are. The potential revenue from new pharmaceuticals is huge and the pressure to get new drugs out into the market is immense. It's initially comforting to see that people are working on this problem of drug interactions since as the article mentions, we couldn't do it in the clinical trials. Still, the cynic in me thinks this is just another step in getting everyone taking more and more prescription medicines. If the pharmaceutical industry can show that two drugs have no interactive side effects, it's much easier to convince a patient to begin taking a new drug. Western medicine is already heavily dependent on fixing the symptoms instead of the cause. It's clear that in many cases we have almost no clue why a particular drug works. It's thrilling to see risks removed from the system by finding drug interactions previously unknown. However, it's frightening how much more likely it is that physicians will rely on prescribing a pill because it's easier than convincing the patient to change.

weavejester 15y ago
"Western medicine"? As opposed to what?
- scotch_drinker 15y ago
  As opposed to a more holistic approach beyond "You have high cholesterol, take this pill for the rest of your life". Some of this is our natural inclination to do things that are easy (taking a pill is easy, fixing your diet is not) but as we become more and more reliant on prescription medicines to treat symptoms and disease, we will naturally become less and less inclined in the medical profession to advocate strongly for a different patient lifestyle before putting them on the meds.
  - onemoreact 15y ago
    All Doctors treating the average american say to eat better, exercise more, and get more sleep. The only difference is when people don't do these things they still get better with "Western medicine" vs. blaming the patent.
    - scotch_drinker 15y ago
      That's not true on several fronts. One, doctors spend little time explaining options to patients oftentimes because they don't actually know the options. Drugs are almost always the first line of defense. Obviously, this is partially because drugs are easy. It's also because doctors don't have to worry about it since the USDA says it's fine whereas if they tell a patient to alter their diet and take supplemental iodine to treat hypothyroidism, they have no support for that treatment plan. Secondly, many times patients do not get better. Statins are prescribed in astronomically large numbers in this country to lower cholesterol when the science behind the benefits of lower cholesterol is highly mixed. In many of the supposedly supporting studies, overall mortality is unchanged in groups taking statins. This has nothing to do with blaming the patient. It has everything to do with the fact we have little comprehensive understanding of the long term ramifications of our increasing reliance on chemicals to help us live more healthy lives. Hopefully finding ways to identify drug interactions is a first step towards current complications but it doesn't change the fact that this will only make it easier to prescribe medications for symptoms without treating the underlying cause.
      - carbocation 15y ago
        Teach the controversy! In the meantime, the data supporting statins are among the best ever compiled. The advances contributed by groups calling themselves "holistic" are entirely absent. And the willingness of modern medicine to introspect and change in the face of data is slow but meaningful. I asked this same question the other day and still have yet to get a meaningful response: what is the "holistic" treatment for HIV?
        15y ago
- usaar333 15y ago
  I cringe whenever I hear the term "Western medicine" being used to describe modern evidence-based medicine. There's little Western cultural bias to this approach; a drug, lifestyle, whatever either has significant effects on health or it doesn't. Just as the unproven components of traditional Western medicine (leaches anyone?) are mostly bunk, so are such aspects of traditional Eastern Medicine/alternative medicine/whatever.
threejay 15y ago
You mean the FDA? No offense, but just because you are well versed in one subject does not mean you really understand the idiosyncracies of another. Every time I see a drug / medicine related thread on HN I cringe. Much in the same way you would if you read a technology related post on a forum geared towards doctors and pharmacists.
- andrewwc 15y ago
  As a pharmacist, I approve this comment!
- morestuff 15y ago
  All that cringing and you only call out a misnamed variable?

utopkara 15y ago

Obviously this algorithm has lots of false positives.

politician 15y ago
Why is that obvious?
- pwhelan 15y ago
  A false positive costs much lower than a false negative in this instance so it should follow that FP should be more common. However, without the data it is still speculation.
  - carbocation 15y ago
    Whether false positives or false negatives are more harmful is a difficult question. A false positive might stop millions from taking a life-saving drug. A false negative might cause millions to take a life-threatening drug.
    - pwhelan 15y ago
      By nature a false positive interaction could be re-tested more easily than a false negative though, correct? Also, that fits in with medical "first, do no harm" framework more readily.
      - carbocation 15y ago
        Regarding your second point, I agree. But it must be balanced against the other tenets of medical ethics. At any rate, this seems to be an important study. I look forward to seeing the same study carried out across different EMR databases and then meta-analyzed. That will be extremely powerful.
- rsheridan6 15y ago
  Typically scientists try to reject the null hypothesis (in this case, that a particular pair of drugs do not interact) by showing that it's unlikely (less than a 5% chance) that an apparent interaction is caused by random chance. But if you go looking at millions of possible interactions, you're going to find a lot that seem to meet that criteria by chance. 5% of a million is 50,000. 0.1% of a million is 1,000. That's why drug companies have to prespecify the outcomes they're looking for before starting the study. If you look through your data after the fact, you're going to find something that makes your drug look good just by chance.

brador 15y ago

Anyone know if that dataset is publicly available?

DevX101 15y ago
Yes, its public. I think the below link should have some of the data. http://www.fda.gov/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/ucm082193 http://www.fda.gov/Drugs/GuidanceComplianceRegulatoryInforma...

phalanx 15y ago

Mike McCandless, a search expert who does a lot of work with Lucene wrote about what he found in this mit paper about extracting side effect info from online health forums: http://people.csail.mit.edu/seneff/IMMM.pdf http://people.csail.mit.edu/seneff/IMMM.pdf Here is the less lengthy, less academic blog post from him, he may be talking about the same thing that nature is talking about, or at least it's something very similar: http://architects.dzone.com/articles/crawling-crowd-data-spots-side?mz=33057-solr_lucene http://architects.dzone.com/articles/crawling-crowd-data-spo...

carbocation 15y ago

Just to be fair, the original title of the research article is "Data-Driven Prediction of Drug Effects and Interactions" ( http://stm.sciencemag.org/content/4/125/125ra31 http://stm.sciencemag.org/content/4/125/125ra31 ). Emphasis on 'Prediction' mine. 47 are then supported by retrospective analysis of an EMR database.