8 ms·

Amazon Starts Selling Software to Mine Patient Health Records

114 points by dcgudeman 8y ago

markolschesky 8y ago
If you want to play with this and you're looking for a decent sample exam note, I grabbed some pieces of standard looking notes (Physical, ROS, Hand exam) and tossed them into a gist here: https://gist.github.com/molsches/32fcec2499e95b5b23bc268800e22780 https://gist.github.com/molsches/32fcec2499e95b5b23bc268800e... Mostly impressive in how it parses the data and can find conditions and tests in the unstructured data. Handles a few things strangely, but I imagine that gets better over time as it continues to be trained. I think for it to truly be useful it needs some layer of semantic data mapping to something to standards like IMO/SNOMED/LOINC/RxNorm etc but I could see that being where other companies build their "products" on top of AWS vs. AWS competing with other Healthcare ML vendors in the space.
- carbocation 8y ago
  Did you grab several pieces from several notes? This looks like a garbled mess to me, but if I understood how you had transformed it to get it into this state, it might make more sense.
  - nkrumm 8y ago
    The posted text is actually a series of "dot phrases" or "smart texts" (aka templates in EHR speak), _not_ actual notes. Mostly these are inserted into clinical notes to achieve a certain level of documentation; typically they are saved in a "all negative" format, and the relevant parts are edited to reflect the patient history and physical. These seem to have been derived from the Univ of Washington Emergency Medicine residency. These might make OK material for some initial testing but they don't reflect a real clinical note. A good source of those might be the MIMIC database [1] [1] https://mimic.physionet.org/ https://mimic.physionet.org/
    - markolschesky 8y ago
      Of course. I mostly wanted to get something out quickly. Those are all a bunch of small snippets of ROS and Physical Exams which demonstrate many of the things which the article discussed, notably finding Dx, Medications and whether or not they were negative or not. I didn't know that there was a database of notes like MIMIC! I'll have to check it out.
- moflome 8y ago
  Thanks for this sample. And for those looking for the AWS service, there is a walk-through [0] of the Amazon Comprehend NLP service online. [0] https://aws.amazon.com/blogs/aws/amazon-comprehend-medical-natural-language-processing-for-healthcare-customers/ https://aws.amazon.com/blogs/aws/amazon-comprehend-medical-n...
oatrefer 8y ago
Is there any way to access this without the WSJ paywall? Or maybe an official Amazon website on this?
dwighttk 8y ago
"It could also be an economic benefit to the Seattle-based center, Mr. Trunnell said. The center has employed about 60 people to scan and pull essential data from records on about 500,000 cancer patients. As automation does more of the work, some employees could do other tasks." or be fired
wmab 8y ago
Read it outside the WSJ paywall (normally need to Incognito it): https://www.facebook.com/flx/warn/?u=https%3A%2F%2Fwww.wsj.com%2Farticles%2Famazon-starts-selling-software-to-mine-patient-health-records-1543352136&h=AT1MqUWOSdF4oojXXfuXTOxtB0eaP4Bh8e2Z8E6QFuT6XqRlwyj05mLQHdldYS_Tn1xEfdsZlKGYU310Cr66ZB38GX2qe0MJj08PlJvXs_yMsj7Gw9_xJYrD8OoE https://www.facebook.com/flx/warn/?u=https%3A%2F%2Fwww.wsj.c...
bkuehl 8y ago
I work in the tech healthcare industry. I wonder why they only went with (or focused on?) ML/NLP text analysis to analyze data. There is a wealth of discrete data available in EMRs (pharmacy, lab, eMAR, etc.). Yes, there is plenty of diagnosis text but that is almost always associated with ICD10 codes. The only area where I believe text analysis would be useful is documentation and microbiology data, and in many cases micro is discrete as well.
- markolschesky 8y ago
  The textbook answer is typically that there is exponentially more data in unstructured data, but I agree with you. I thought about the unmodified use cases for this tooling for awhile and the major use case that I could come up with was finding unknown interactions or side-effects for medication and treatment combination regimens. That's all tracked very poorly in discrete fields today, especially with the nightmare that is cross-organization problem list management. Most drugs are approved by the FDA with the understanding that there will be post-marketing research (read this: https://undark.org/article/fda-drugs-post-marketing-research/ https://undark.org/article/fda-drugs-post-marketing-research...), which this could hypothetically streamline.
- d12345m 8y ago
  Ex-healthcare IT data person weighing in with a probably ridculous idea: The focus on NLP is because in 20-30 years, discrete data won't be entered into EMRs by providers at all. Here's the pitch: Providers hate EMRs. They begrudge the time they spend working in EMRs instead of focusing on patient care. They loathe spending their office hours working on documentation. They hate spending their time in meetings with IT staff talking about EMR workflows and form-building. They hate getting lectured by accounting staff about how their documentation affects billing. They couldn't care less about this stuff and in an ideal (or even just a slightly more efficient) world, they wouldn't have to. Every EMR that depends on webform-like inputs that map to database fields is going to be seen as a roadblock to patient care, which is what providers see as their primary concern. I think the focus on NLP makes a ton of sense if you frame the problem with EMRs that way. EMR software will continue to be the bane of providers' existence right up to the day that providers can simply talk to their EMR in whatever way they want and have the computer interpret their speech and reliably spit out the discrete data that the accountants and number-crunchers want. Obviously, I'm talking about a monumentally complicated undertaking and it's a bit on the ridiculous side. But I honestly believe we're going to go there, if only because providers won't be happy until we do.
rhacker 8y ago
This is the beginning of the final chapter in the story about the last kind of private data becoming owned by advertising companies. The final stroke of pen writing away our privacy to another institution in the name of a better future.
anfilt 8y ago
As long as none of the data goes to amazon, sure sell their software. Otherwise WTF no....
neonate 8y ago
https://outline.com/sAaAKf https://outline.com/sAaAKf
_archon_ 8y ago
Who owns a patient's medical records?
- prolikewh0a 8y ago
  Amazon will soon. HIPAA will be ignored, broken, spit on. There will be no opt out or privacy. I guarantee it.

114 points by dcgudeman 8y ago

If you want to play with this and you're looking for a decent sample exam note, I grabbed some pieces of standard looking notes (Physical, ROS, Hand exam) and tossed them into a gist here: https://gist.github.com/molsches/32fcec2499e95b5b23bc268800e22780 https://gist.github.com/molsches/32fcec2499e95b5b23bc268800e... Mostly impressive in how it parses the data and can find conditions and tests in the unstructured data. Handles a few things strangely, but I imagine that gets better over time as it continues to be trained. I think for it to truly be useful it needs some layer of semantic data mapping to something to standards like IMO/SNOMED/LOINC/RxNorm etc but I could see that being where other companies build their "products" on top of AWS vs. AWS competing with other Healthcare ML vendors in the space.

carbocation 8y ago
Did you grab several pieces from several notes? This looks like a garbled mess to me, but if I understood how you had transformed it to get it into this state, it might make more sense.
- nkrumm 8y ago
  The posted text is actually a series of "dot phrases" or "smart texts" (aka templates in EHR speak), _not_ actual notes. Mostly these are inserted into clinical notes to achieve a certain level of documentation; typically they are saved in a "all negative" format, and the relevant parts are edited to reflect the patient history and physical. These seem to have been derived from the Univ of Washington Emergency Medicine residency. These might make OK material for some initial testing but they don't reflect a real clinical note. A good source of those might be the MIMIC database [1] [1] https://mimic.physionet.org/ https://mimic.physionet.org/
  - markolschesky 8y ago
    Of course. I mostly wanted to get something out quickly. Those are all a bunch of small snippets of ROS and Physical Exams which demonstrate many of the things which the article discussed, notably finding Dx, Medications and whether or not they were negative or not. I didn't know that there was a database of notes like MIMIC! I'll have to check it out.
moflome 8y ago
Thanks for this sample. And for those looking for the AWS service, there is a walk-through [0] of the Amazon Comprehend NLP service online. [0] https://aws.amazon.com/blogs/aws/amazon-comprehend-medical-natural-language-processing-for-healthcare-customers/ https://aws.amazon.com/blogs/aws/amazon-comprehend-medical-n...

oatrefer 8y ago

Is there any way to access this without the WSJ paywall? Or maybe an official Amazon website on this?

dwighttk 8y ago

"It could also be an economic benefit to the Seattle-based center, Mr. Trunnell said. The center has employed about 60 people to scan and pull essential data from records on about 500,000 cancer patients. As automation does more of the work, some employees could do other tasks." or be fired

wmab 8y ago

Read it outside the WSJ paywall (normally need to Incognito it): https://www.facebook.com/flx/warn/?u=https%3A%2F%2Fwww.wsj.com%2Farticles%2Famazon-starts-selling-software-to-mine-patient-health-records-1543352136&h=AT1MqUWOSdF4oojXXfuXTOxtB0eaP4Bh8e2Z8E6QFuT6XqRlwyj05mLQHdldYS_Tn1xEfdsZlKGYU310Cr66ZB38GX2qe0MJj08PlJvXs_yMsj7Gw9_xJYrD8OoE https://www.facebook.com/flx/warn/?u=https%3A%2F%2Fwww.wsj.c...

bkuehl 8y ago

I work in the tech healthcare industry. I wonder why they only went with (or focused on?) ML/NLP text analysis to analyze data. There is a wealth of discrete data available in EMRs (pharmacy, lab, eMAR, etc.). Yes, there is plenty of diagnosis text but that is almost always associated with ICD10 codes. The only area where I believe text analysis would be useful is documentation and microbiology data, and in many cases micro is discrete as well.

markolschesky 8y ago
The textbook answer is typically that there is exponentially more data in unstructured data, but I agree with you. I thought about the unmodified use cases for this tooling for awhile and the major use case that I could come up with was finding unknown interactions or side-effects for medication and treatment combination regimens. That's all tracked very poorly in discrete fields today, especially with the nightmare that is cross-organization problem list management. Most drugs are approved by the FDA with the understanding that there will be post-marketing research (read this: https://undark.org/article/fda-drugs-post-marketing-research/ https://undark.org/article/fda-drugs-post-marketing-research...), which this could hypothetically streamline.
d12345m 8y ago
Ex-healthcare IT data person weighing in with a probably ridculous idea: The focus on NLP is because in 20-30 years, discrete data won't be entered into EMRs by providers at all. Here's the pitch: Providers hate EMRs. They begrudge the time they spend working in EMRs instead of focusing on patient care. They loathe spending their office hours working on documentation. They hate spending their time in meetings with IT staff talking about EMR workflows and form-building. They hate getting lectured by accounting staff about how their documentation affects billing. They couldn't care less about this stuff and in an ideal (or even just a slightly more efficient) world, they wouldn't have to. Every EMR that depends on webform-like inputs that map to database fields is going to be seen as a roadblock to patient care, which is what providers see as their primary concern. I think the focus on NLP makes a ton of sense if you frame the problem with EMRs that way. EMR software will continue to be the bane of providers' existence right up to the day that providers can simply talk to their EMR in whatever way they want and have the computer interpret their speech and reliably spit out the discrete data that the accountants and number-crunchers want. Obviously, I'm talking about a monumentally complicated undertaking and it's a bit on the ridiculous side. But I honestly believe we're going to go there, if only because providers won't be happy until we do.

rhacker 8y ago

This is the beginning of the final chapter in the story about the last kind of private data becoming owned by advertising companies. The final stroke of pen writing away our privacy to another institution in the name of a better future.

anfilt 8y ago

As long as none of the data goes to amazon, sure sell their software. Otherwise WTF no....

neonate 8y ago

https://outline.com/sAaAKf https://outline.com/sAaAKf

_archon_ 8y ago

Who owns a patient's medical records?

prolikewh0a 8y ago
Amazon will soon. HIPAA will be ignored, broken, spit on. There will be no opt out or privacy. I guarantee it.