Tag Archives: personalized medicine

Making Change

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And now for something completely different! Short fiction in honor of the recent unveiling of the Apple iWatch and Healthkit.

“I wouldn’t eat that if I were you.”

Sylvia paused, bacon cheeseburger halfway to her mouth, and peered at the neon green band wrapped around her wrist. The wraparound touchscreen was currently showing a cat emoji. It had a frowny face, expression halfway between puzzlement and alarm.

“What did you say?”

“I’m just saying,” said her Best Buddy wristband, “that when we met a few weeks ago, you mentioned wanting to keep your weight in a specific range.” The emoji shrugged. “Little friendly reminder. You know?”

Sylvia carefully put the burger back down and resisted the urge to lick grease off her fingers. She fumbled for her napkin, her fingers leaving translucent streaks on the thin, white paper.

“I–well, yeah. But, I mean, you’ve never said anything like this before like when–” She broke off, remembering the milkshake, the onion rings, the King-size Choconut bar…

“Well it’s not the first thing you do, is it? When you meet someone and you’re just getting to know them?” The cat had morphed into a light pink, animated mouse, standing on its hind legs, bashfully kicking one leg. “But now, we’re friends!” Continue reading →

Baseball, Bayes, Fisher and the problem of the well-trained mind

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One of the neat things about the people in the baseball research community is how willing many of them are to continually question the status quo. Maybe it’s because sabermetrics is itself a relatively new field, and so there’s a humility there. Assumptions always, always need to be questioned.

Case in point: a great post by Ken Arneson entitled “10 things I believe about baseball without evidence.” He uses the latest failure of the Oakland A’s in the recent MLB playoffs to highlight areas of baseball we still don’t understand, and for which we may not even be asking the right questions. Why, for example, haven’t the A’s advanced to the World Series for decades despite fielding good and often great teams? Yes there’s luck and randomness, but at some point the weight of the evidence encourages you to take a second look. Otherwise, you become as dogmatic as those who still point to RBIs as the measure of the quality of a baseball batter. Which they are not.

One of the thought-provoking things Arneson brings up is the question of whether the tools we use shape the way we study phenomena–really, the way we think–and therefore unconsciously limit the kinds of questions we choose to ask. His example is the use of SQL in creating queries and the inherent assumptions of that datatype that objects within a SQL database are individual events with no precedence or dependence upon others. And yet, as he points out, the act of hitting a baseball is an ongoing dialog between pitcher and batter. Prior events, we believe, have a strong influence on the outcome. Arneson draws an analogy to linguistic relativity, the hypothesis that the language a person speaks influences aspects of her cognition.

So let me examine this concept in the context of another area of inquiry–biological research–and ask whether something similar might be affecting (and limiting) the kinds of experiments we do and the questions we ask.

Continue reading →

Baseball analytics, arthritis, and the search for better health forecasts

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All opinions are my own and do not necessarily reflect those of Novo Nordisk.

It’s Fourth of July weekend in Seattle as I write this. Which means it’s overcast. This was predictable, just as it’s predictable that for the two months after July 4th the Pacific Northwest will be beautiful, sunny and warm. Mostly.

Too bad forecasting so many other things–baseball, earthquakes, health outcomes–isn’t nearly as easy. But that doesn’t mean people have given up. There’s a lot to be gained from better forecasting, even if the improvement is just by a little bit.

And so I was eager to see the results from a recent research competition in health forecasting. The challenge, which was organized as a crowdsourcing competition, was to find a classifier for whether and how rheumatoid arthritis (RA) patients will respond to a specific drug treatment. The winning methods are able to predict drug response to a degree significantly better than chance, which is a nice advance over previous research.

And imagine my surprise when I saw that the winning entries also have an algorithmic relationship to tools that have been used for forecasting baseball performance for years.

The best predictor was a first cousin of PECOTA. Continue reading →