The Pain of Recording Patient Risk Factors as Illuminated by Apixio (Part 2 of 2)

The previous section of this article introduced Apixio’s analytics for payers in the Medicare Advantage program. Now we’ll step through how Apixio extracts relevant diagnostic data.

The technology of PDF scraping
Providers usually submit SOAP notes to the Apixio web site in the form of PDFs. This comes to me as a surprise, after hearing about the extravagant efforts that have gone into new CCDs and other formats such as the Blue Button project launched by the VA. Normally provided in an XML format, these documents claim to adhere to standards and offer a relatively gentle face to a computer program. In contrast, a PDF is one of the most challenging formats to parse: words and other characters are reduced to graphical symbols, while layout bears little relation to the human meaning of the data.

Structured documents such as CCDs contain only about 20% of what CMS requires, and often are formatted in idiosyncratic ways so that even the best CCDs would be no more informative than a Word document or PDF. But the main barrier to getting information, according to Schneider, is that Medicare Advantage works through the payers, and providers can be reluctant to give payers direct access to their EHR data. This reluctance springs from a variety of reasons, including worries about security, the feeling of being deluged by requests from payers, and a belief that the providers’ IT infrastructure cannot handle the burden of data extraction. Their stance has nothing to do with protecting patient privacy, because HIPAA explicitly allows providers to share patient data for treatment, payment, and operations, and that is what they are doing giving sensitive data to Apixio in PDF form. Thus, Apixio had to master OCR and text processing to serve that market.

Processing a PDF requires several steps, integrated within Apixio’s platform:

  1. Optical character recognition to re-create the text from a photo of the PDF.

  2. Further structuring to recognize, for instance, when the PDF contains a table that needs to be broken up horizontally into columns, or constructs such the field name “Diagnosis” followed by the desired data.

  3. Natural language processing to find the grammatical patterns in the text. This processing naturally must understand medical terminology, common abbreviations such as CHF, and codings.

  4. Analytics that pull out the data relevant to risk and presents it in a usable format to a human coder.

Apixio can accept dozens of notes covering the patient’s history. It often turns up diagnoses that “fell through the cracks,” as Schneider puts it. The diagnostic information Apixio returns can be used by medical professionals to generate reports for Medicare, but it has other uses as well. Apixio tells providers when they are treating a patient for an illness that does not appear in their master database. Providers can use that information to deduce when patients are left out of key care programs that can help them. In this way, the information can improve patient care. One coder they followed could triple her rate of reviewing patient charts with Apixio’s service.

Caught between past and future
If the Apixio approach to culling risk factors appears round-about and overwrought, like bringing in a bulldozer to plant a rosebush, think back to the role of historical factors in health care. Given the ways doctors have been taught to record medical conditions, and available tools, Apixio does a small part in promoting the progressive role of accountable care.

Hopefully, changes to the health care field will permit more direct ways to deliver accountable care in the future. Medical schools will convey the requirements of accountable care to their students and teach them how to record data that satisfies these requirements. Technologies will make it easier to record risk factors the first time around. Quality measures and the data needed by policy-makers will be clarified. And most of all, the advantages of collaboration will lead providers and payers to form business agreements or even merge, at which point the EHR data will be opened to the payer. The contortions providers currently need to go through, in trying to achieve 21st-century quality, reminds us of where the field needs to go.

About the author

Andy Oram

Andy Oram

Andy Oram writes and edits documents about many aspects of computing, ranging in size from blog postings to full-length books. Topics cover a wide range of computer technologies: data science and machine learning, programming languages, Web performance, Internet of Things, databases, free and open source software, and more. My editorial output at O'Reilly Media included the first books ever published commercially in the United States on Linux, the 2001 title Peer-to-Peer (frequently cited in connection with those technologies), and the 2007 title Beautiful Code. He is a regular correspondent on health IT and health policy for He also contributes to other publications about policy issues related to the Internet and about trends affecting technical innovation and its effects on society. Print publications where his work has appeared include The Economist, Communications of the ACM, Copyright World, the Journal of Information Technology & Politics, Vanguardia Dossier, and Internet Law and Business.


  • Andy, I think you are completely missing the point. Risk data belongs to the PATIENT. It does not belong to either the provider or the payer because both are conflicted and significantly incentivized to game the system.

    Patients are the center of risk because risk is combined across all of the various providers that contribute to their health records. Patients also bear the consequences of risk. Our federal regulators are still a long way from effectively preventing information blocking by establishing a strong patient right to direct the entirety of their health records, in real time, to any destination they choose. This destination could then include independent and privacy preserving risk assessment services.

  • Good observation, Adrian. The article is in line with your view, but I explicitly say that Apixio is dealing with the health care regime we have now, not the one we might like to have. The whole service is a work-around in a broken payment model. My last paragraph suggests some factors pushing us toward reform. Patient ownership of data would be a great addition. But few patients care about payments. That will remain the concern of the doctors and insurers–and probably their first concern.

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