"We Can Predict Your Face" and Put It on a Billboard

An article entitled Craig Venter’s Latest Production (Arlene Weintraub, MIT Technology Review, Sept.-Oct. 2016, at 94) reports that

At Human Longevity Inc. (HLI) in La Jolla, California, more than two dozen machines work around the clock, sequencing one human genome every 15 minutes at a cost of under $2,000 per genome. The whole operation fits comfortably in three rooms. Back in 2000, when its founder, J. Craig Venter, first sequenced a human genome, it cost $100 million and took a building-size, $50 million computer nine months to complete. [¶] Venter’s goal is to sequence at least one million genomes, something that seems likely to take the better part of a decade ...

Seated behind his desk in his office two floors above the sequencing lab, his red poodle Darwin sleeping quietly at his feet, Venter has pulled up images on his computer that show how in one early experiment HLI scientists were able to sequence 1,000 people’s genomes and then reconstruct their faces solely on the basis of the genetic data. “We can predict your face, your height, your body mass index, your eye color, you hair color and texture,” he says, marveling at how closely one of the reconstructed faces matches the photo of the actual study participant.

It would be nice to have a decently designed study of how well all the 1,000 (adult?) faces match the photos. As Richard Feynman once told his students,

The first principle is that you must not fool yourself — and you are the easiest person to fool.

But why wait for whole genome sequencing to "predict" faces? Scores of police agencies already use a different company's product. Parabon Snapshot provides pictures as part of a "scientifically objective description" so "you can conduct your investigation more efficiently and close cases more quickly." Ellen Greytak, director of bioinformatics for Parabon, says that "So far, we've done more than sixty different cases, and we've also done evaluations at the local, state, federal and international levels." In fact, "we've had one conviction and a few other arrests." Michael Roberts, Could DNA Imaging Used in Bennett Family Murder Break JonBenet Case?, Westword, Sept. 16, 2016. Although "none of the police agencies in question has gone public with the technology's role in the cases thus far, she teases that an announcement about a success is pending." Id.

"The composite isn't intended to be like a driver's license photo, but it will bear a resemblance. And if you have a list of 1,000 people who were nearby that day, you can put the ones that match the most at the top, and the ones that match the least at the bottom." Id. (quoting Greytak). Parabon's website explains that this achievement comes from "using deep data mining and advanced machine learning algorithms in a specialized bioinformatics pipeline."

Maybe I missed it, but I saw no references to cross-validation studies of whatever oozed out of the pipeline. Nevertheless, "Snapshot trait predictions are presented with a corresponding measure of confidence, which reflects the degree to which such factors influence each particular trait. Traits, such as eye color, that are highly heritable (i.e., are not greatly affected by environmental factors) are predicted with higher accuracy and confidence than those that have lower heritability; these differences are shown in the confidence metrics that accompany each Snapshot trait prediction."

A "confidence metric" seems to be missing from an unusual advertising campaign called "The Face of Litter" in Hong Kong:

Using the “Snapshot” DNA phenotyping services of a company called Parabon Nanolabs, Ogilvy [a marketing firm] collected litter from the streets and using DNA obtained from the litter, created profiles of the offenders ... . These profiles are now posted on outdoor ads at bus stops, subway and train stations, and even on highway billboards.

Nanalyze, Parabon Nanolabs and DNA Phenotyping, Apr. 30, 2015. Parabon calls this a "social experiment," calling to mind the dismissive remark, "That's not an experiment, it's an experience."

(Last updated 11/29/16)