Training Log Archive: barb

Isak and I headed up (him running, me behind) to some mountain in Big Sur, leaving before dawn so we could check out the sunrise. The plan was for him to attempt to make it to the peak, but this trail was highly unsuitable for Peter Gagarin or Mike Waddington, and only got more unsuitable, to the point that Isak decided to go no further. We chatted on the way down.

Big Sur.
Isak went on ahead. He met some young runners on the trail and set the pace for them until they got to the Sykes hot springs, where they soaked for an hour and then headed back. I ran into them when I was about to start the last descent to the springs. I went on, but didn't soak, just went to the river, then back.
I ran several miles on the way back.

C • That's a long hike... 2

Event: Big5 O Week 2015-2016
 

Gentle hiking with Dave's mom near the ocean, Big Sur.

Around Park Forest, with Mom and Dad.
This was the last Christmas spent with them in the house where I grew up; they are moving to a senior living facility mid-2016.

A map from yesterday.

It was so great to see friends from far away! And some big surprises! Mary and Eric Smith came with Kalmia; we met one-week-old Diego for the first time (Katia & Giovanni's baby; I have a cute photo and will post), Lucas (who looks like a giant next to Diego, as Katia pointed out) with Cristina, Melissa and Cristina's mom, Linnea and family, Nancy and JJ, Sam and Daniel, Dean. Thank you so much for coming, it really meant a lot to me and it was lovely to see everyone. The XC boys showed up. We had quite a few young girls and (fewer) boys from Cambridge and nearby towns, which was great to see. A passer-by saying, wow, my grandson would love this, how do I find out more?

It was nice to see the interactions between people on teams.

I didn't have time to tabulate results yet, due to hosting a dinner party for Isabel's school friends yesterday.

Went running after getting home and unloading stuff from this morning's event at Magazine Beach.

(For tomorrow)

Tomorrow's event is currently complicated.

Isak and I, with some great mentoring from Ian Smith (who rocks) and Vlado Dancik at the Broad Institute, did well in the second round of the drug combination synergy prediction DREAM challenge (subchallenge 1A). We sent in three sets of predictions around midnight last night, and this morning the results were posted. One of our submissions scored best in the global correlation score, out of 167 submissions! Each team can send in 3 sets of predictions in each round. There are 2 or 5 scoring metrics, depending on how you count.

I guess the scores aren't visible to non-contestants, so I'll post a screenshot of the top entries, sorted by score.



When we first started working on this project, we were disappointed at what appear to be relatively low numbers for the scores, and 0.29 for a global correlation score doesn't strike me as great, even if we did WIN THIS ROUND (still celebrating...). (I woke Isak up to tell him, and even then he's going to be late for school because of how late we were up last night working on this.) The global correlation score asks how well your predictions are doing over and above how well you could do by predicting based only on cell line or drug combination, the two main variables in the dataset. So it's a much higher bar than just looking at correlation of actual with predicted values. While I understand the math behind the mean correlation score (which is taken across drug combinations), I haven't figured out the math behind the global correlation.

We used the random forest machine learning algorithm, with 100 trees, as implemented in the python scikit-learn library. As input, we provided the cell line, drug combination, and mutations and expression values for certain genes for each cell line. We selected some of the genes based on a Fisher test between synergy and mutation across the training data, but also selected genes based on number of mutations across the cell lines, only keeping genes with sufficiently different patterns of mutations. For gene expression, we took a representative sample of highly-varying genes that had different expression values.

In other news, my neighbor Elizabeth Harkavy got into MIT! Here is a picture of Elizabeth playing orienteering capture-the-flag:

C • Fantastic! 3

Isak and I are planning to offer relays on Sunday at Magazine Beach. We'd like to form teams that include an advanced orienteer (like Cristina, JJ, Ari, Alex, whoever can make it), a high school cross-country runner, a school kid, and a little kid. After hearing that a couple of you will come, we began to think about what might be possible, and came up with this. So - if you can come, let me know, and hopefully you can arrive by around 10:15. We'd like to start with a shadowing exercise and then run the relay maybe starting around 10:30 or 10:45.

C • Sounds like fun! 12

Sad news - Dave's father Chet passed away on Sunday after a year-long fight against leukemia. He lived in California, where he was a pharmacist. He loved teaching pharmacists-in-training, being a leader at his church, and following his son Mark's band. He was friendly, kind and loving. We will miss him!

C • :-( 2

work

A couple of our micro courses at Dana Park.
Another guerilla orienteering event. We were there from 10 to around 1:30; we stuck around so that the cross-country team could get there from their other event.

We offered 7 tiny little courses in the park and a 2.6k one-way street-O that Isak designed.
The tiny little courses each had 9 controls, and there were a total of 18 controls, so you had to read the map properly to do the courses. Many kids had trouble with this; I did not include the control code, in order to get them to read the map more carefully.

Thanks to Isak for getting me out the door.
I felt pain in my chest for much of the run, left side.
Feel pretty good now, after the fact.

To work. And back.
Isak's XC friends say that they had fun orienteering and want to do it again!
This strategy of embedding of European orienteers into local schools might pay off...

Alex was our guerilla dinner guest recently, and among other things sketched out a series of trainings in case I manage to pull together a more serious kids team.

Spent the morning and early afternoon doing another guerilla orienteering event at a local park. We had several families, some of whom learned about it through parent email lists (thanks Leah!). We also had Isak + 5 members of his cross-country team. One of the families was there for the 4th time! They stumbled across us at Dana Park, and have come orienteering every weekend since, including at the Blue Hills!

C • Love this 7

C • What makes it "guerilla"? 11

Isak got some of his xc teammates to come to our guerilla orienteering event today.

People are awesome.