Heather Kaplan of the Cincinnati Children’s Hospital, with a little help from the rest of us, published a highlight of the state of our work on the Personalized Learning System via HBS’s online blog. The article emphasizes the patient-physician collaboration model we’ve been working on and that I teased at MedicineX last week.
My Dissertation Defense Announcement
Title
Crowdsourcing Health Discoveries: from Anecdotes to Aggregated Self-Experiments
Time & Location
July 26th, 1:00 PM, E14-244
Thesis Supervisor
Frank Moss, Professor of the Practice of Media Arts and Sciences, MIT
Committee
Henry Lieberman, Principle Research Scientist, MIT
Peter Szolovits, Professor of Computer Science and Engineering, MIT
Abstract
Nearly one quarter of US adults read patient-generated health information found on blogs, forums and social media; many say they use this information to influence everyday health decisions. Topics of discussion in online forums are often poorly-addressed by existing, clinical research, so patient’s reported experiences are the only evidence. No rigorous methods exist to help patients leverage anecdotal evidence to make better decisions.
This dissertation reports on multiple prototype systems that help patients augment anecdote with data to improve individual decision making, optimize healthcare delivery, and accelerate research. The web-based systems were developed through a multi-year collaboration with individuals, advocacy organizations, healthcare providers, and biomedical researchers. The result of this work is a new scientific model for crowdsourcing health insights: Aggregated Self-Experiments.
The self-experiment, a type of single-subject (n-of-1) trial, validates the effectiveness of an intervention on a single person. Aggregating the outcomes of multiple trials can improve the efficiency of future trials and enable users to prioritize the sequencing of trials for a given condition. Successful outcomes from many patients will yield evidence to motivate future clinical research. Aggregated Personal Experiments enables user communities to replace anecdotes with repeatable trials that can be run in the context of their daily life. The properties and viability of the model were evaluated through user studies, secondary data analyses, and experience with real-world deployments.
You can check it out at http://www.personalexperiments.org
What can a concerned citizen do in the face of injustice?
The juxtaposition of verdicts in the Zimmerman and Alexander cases, and the unapologetic, non-reflective response of most of our political leadership leaves me wondering what I, as a concerned citizen I can do in the face of a pervasive national moral cowardice. As a citizen of a republic, I could choose to move to Florida or Mississippi and cast my vote against the representatives of injustice, misogyny, ignorance and racism who seem to frequent the media. But would that really have an impact proportionate to the personal sacrifice involved? Unlikely.
Continue reading “What can a concerned citizen do in the face of injustice?”
Using the crowd to help diagnose rare diseases
Earlier this week I joined NEA entrepreneur Jared Hyman of crowdmed.com and “the current” host Anna Maria Tremonti of the Canadian Broadcasting Corporation in a discussion of crowd sourcing in Healthcare. A brief summary and audiocast of the show is available.
Advanced inspector middleware for Clojure nREPL
Last night I promoted a new nREPL middleware project, ‘nrepl-inspect’, derived from the javert library.
This repository contains:
- an Emacs client file that extends nrepl.el, and
- a rich generic middleware inspector that runs under nREPL.
Key features include:
- ‘C-c C-i’ inspects the var at point, or any value returned by eval of an arbitrary expression in the current buffer’s active namespace,
- a simple model for recursing into sub-objects based on a value index map maintained in the middleware during serialization of the value, and
- a rendering method extensible for custom types.
My goal is to be able to stack navigate a Datomic database given an Entity, the example in the repository should support that with just a little more work.
Please note, while I use this in my day to day development, but it’s not yet well packaged and has been minimally tested. It currently does not truncate maps or sequences, so please don’t inspect ‘(repeat 1)’!
Personal Experiments
Last week, my collaborators from Lybba and I posted a blog entry describing my Personal Experiments project. Please enjoy this little introductory demo. Also, I’ll be announcing a new study on the platform next week; participants will receive a free Jawbone UP!
Clojure Debugging ’13: Emacs, nREPL, and Ritz
[NOTE: The release of cider deprecates much of the content here. I will post an update on Clojure Debugging ’14 early in the near year]
I’m ramping up for a new set of development projects in 2013 and 2014. My 2010 era setup with slime and swank-clojure is unlikely to remain a viable approach throughout the project. I’ve decided it is time to join the nREPL community as well as take advantage of some of architecture innovations there which may make it easier to debug the distributed systems I’m going to be working on.
Features I’m accustomed to from common lisp slime/swank:
- Code navigation via Meta-. and Meta-,
- Fuzzy completion in editor windows and the repl
- Documentation help in mini-buffer
- Object inspector. Ability to walk any value in the system
- Walkable backtraces with one-key navigation to offending source
- Evaluate an expression in a specific frame, inspect result
- Easy tracing of functions to the repl or a trace buffer (in emacs)
- Trigger a continuable backtrace via watchpoint or breakpoint
Only the first three of these features is available in the stock nrepl. The rest of this post will discuss how to setup a reasonable approximation to this feature set in Emacs using nREPL middleware providers as of May 2013.
Continue reading “Clojure Debugging ’13: Emacs, nREPL, and Ritz”
Agile Software Metrics
The rise of dynamic software development methodologies such as Extreme Programming or Agile Programming, reflect the inherent dynamism of modern software design. The malleability of software, the rapid evolution of consumer and technology driven requirements, the difficulty of writing accurate specifications given all the unknowns, and the sheer complexity of the software ecosystem itself makes the ancient development waterfall from specification through execution and QA to release a hazardous and mostly futile affair.
Most software developments fail. While the situation has improved over the last decade, this remains mostly true today. Less than a third of all software projects meet their objectives in approximately the time expected. Over 10% of all projects fail without deliver anything, and most of the rest under-deliver, are terribly late, or way over budget.
This blog post is a thinking-out-loud exploration of how modern Agile methods address these problems and how my thinking is evolving with regards to how success is defined and the probability of success maximized.
Guided by the Evidence?
I was reading an article about the controversial Dr. Oz this morning when a quote from a doctor struck a nerve. In reaction to Dr Oz’s embrace of alternative medicine, he stated: “I’m guided by the evidence.” That’s a wonderful and comforting sentiment to any logical person. We have a methodology called science which helps us move towards the truth through a repeated, disciplined process of experimentation. This process allows us to build confidence in our opinions and actions when we have accumulated sufficient evidence or can appeal to previous authority. The problem is that evidence in medicine is rarely imbued with absolute authority, yet the dogma of medicine is that peer-reviewed journal results are the primary guide to treatment. Clinical trials should be viewed as the starting point in the practice of medicine, not the destination.
Big Data, Healthcare, and the Human Lens
I’ve been following a great discussion on Susannah Fox’s blog today. The Lohr article that sparked her post and subsequent comments have taken up the position that Evidence Based Medicine tends to dismiss the role of intuition. I think that is true and reflects a cultural phenomenon that seeks a deus ex machina. Fads emerge and advocate for the latest savior (or rainmaker), eschewing the difficulties and hard work involved in engaging with truly complex, multi-factorial systems.
I’m reminded of a music professor who told my composition class that, “you can’t break the rules unless you first understand the rules.” I’ve thought about this for a long time, why is it you can’t be creative in ignorance of the rules? Ignorance of impossibility, after all, is often the fuel for innovation. Yet it seems to hold true that the best musicians don’t run away from convention, they master and move beyond it. Does a powerful command of the grammatical rules and literary traditions of English limit your creativity in writing? No, it hones and unleashes it!
In it’s ideal form, EBM is a foundation of evidence and rules that should empower and propel individual physician and patient creativity. In the quality improvement context the standard of care is there to help us avoid repeating other’s mistakes, not to tell us what to do under all circumstances. The prosaic landscape of diagnostics and therapeutics are governed by probability distributions over endpoint outcomes, but beyond this there remains endless room for innovative thinking and intuition because any time we come into connection with real people and real bodies, we exceed the ability of our formalisms to compute. We can only meet the challenge of other’s humanity through the lens of our own.
Frumious Abstractions 