some thoughts on concurrency in the Intellectual Ventures HIV model

Yesterday two of the HIV modelling folks from Intellectual Ventures presented their model in the CSSS seminar and met with the Network Modelling group.  I was really impressed with their work, as was Martina.  Much of what we talked about was the partnership formation model.  Basically, they have a queueing process and individuals join the queue at some rate lambda.  There are three separate types of relationships: transitory, informal, and marriage.  These differ in their prevalence over the life span, age mixing patterns, duration, sexual frequency, condom use and perhaps other factors.  So, let's say a 39 year old man triggers to join the queue.  He is assigned a relationship type, say informal, consults the appropriate age mixing matrix and is probabilistically assigned a partner, most likely a 30-35 year old woman. If there is already such a woman seeking a 35-40 yo man for an informal relationship, then he is paired with such a woman.  They keep the system at equilbirum by adjusting the lambdas based on the current contents of the queue.

We spent a while talking about different models for this process that distinguish preference and availability. In other words, as a demographic group becomes more or less prevalent due to baby booms or differential mortality or other factors, how should that affect the number of relationships that involve that group.  There are a variety of answers. One is that the number of partnerships stays the same because the contact rate (number of partners per individual in the group) goes up or down. Fewer young black men means they have more partners because the number of  women who want young black male partners hasn't changed, so they have to start sharing.  Another possibility is that the contact rate stays the same but the number of partnerships goes down.  Fewer young black males means fewer partnerships that involve young black males, and a greater number of young black women with no partners.  There are a range of possibilities in between but we didn't talk much about the details of them. I think these are the sorts of log-linear models which give a mixing parameter based on the odds ratio between the observed number of partnerships and the number expected under random mixing with any given distribution of the population.

The most curious thing about the Intellectual Ventures model is the way it handled concurrency.  There were three yes/no characteristics that each person in the model has a probability to have, one for each relationship type, that indicated whether you would still join the queue for a new relationship if you were already in a relationship of that type.  In other words, some people will pursue a new relationship if they are in a transitory relationship, but not if they are in an informal or marriage relationship.  Others might pursue a relationship if they are in a marriage or transitory, but not in an informal.  There was also a limit on the max number of concurrent relationships (I don't remember what it was but it was fairly high, at least 5 I think).  I never got clarification on this, but if I understand it correctly, it does lead to potentially strange situations if one tries to interpret these characteristics and their proportions rather than just regarding them as parameters in the model. For example, it is not true that someone who is transitory-concurrent but not informal-concurrent or marriage-concurrent is just someone willing to play the field for a while before settling down - they can be in a transitory relationship and start a marriage while that transitory is still on-going! Now, because transitories are short, this state of affairs probably doesn't last long and then being married they can't start new transitory relationships.  (This example actually is probably a pretty common occurrence in the real world if we consider that "marriage" here doesn't mean a legal marriage, just one that has the duration, sex frequency, exclusion, etc of a marriage and furthermore that any relationship that eventually becomes a marriage is classified as such from the beginning - though this does point out a potential problem.  Just because you eventually get married to someone and don't use condoms doesn't mean that condom use is low at the beginning of that relationship.)

During the presentation, Martina commented that these factors were created "at birth" like some kind of genetic defect. (I may take her to task on this.)  But in the networks meeting, I pointed out that this isn't really any different than our practice of "backdating" marriages as described above - determining immediately on formation whether a relationship is classified as a marriage or non-marriage rather than modelling a process whereby non-marriage relationships transform into marriage relationships.  And as the only distinction our models made for this distinction was in relationship duration, this completely doesn't matter.  I think it may be also be true for their concurrency variables, as well.  I also pointed out the similarity to the long-term partnership model Steve has sometimes used where for each person  10% of the population is randomly pre-specified as soulmates and whenever you form a relationship with a soulmate, it is a long-term relationship (more properly, a less-likely-to-dissolve-each-day relationship) and whenever you form a relationship with a person who isn't a soulmate, that's a short term relationship.  Steve and I joke about how ridiculous this model is and yet it seems to be the way that so many people actually believe the world works.  I'm not sure whether soulmate-ness is necessarily reciprocal in these models or if a relationship is LTR if either one is a soulmate for the other.  I'd guess it is reciprocal and just formed with a static ERGM before running the real model.

Martina suggested that it was problematic to assume these concurrency-possible traits were stable over the life span and showed an interesting plot that I haven't previously seen.  The figure had a row for each race and age categories along the x axis.  Each age-race combination had a dot-and-whisker plot of the rate of concurrency in that subgroup.  The interesting thing is that in whites, there is very high concurrency in young adulthood, but that drops quickly and then there is very, very little after that.  In blacks, the rate dropped much more slowly and remained noticeable throughout the life span.  There was another group (unsure if it was Hispanic or Asian) that seemed like a mix of the white and black patterns - started moderately high dropped slowly but eventually reached near zero.

I pointed out that this is consistent with the IV model so long as the concurrency types have race-specific probabilities. It could be that whites have high rates of transitory-concurrents, and because transitory relationships are rare beyond a certain age, so is concurrency in whites.  Blacks on the other hand are more likely to be marriage-concurrent, thus preserving measurable concurrency rates later in life.  It's an interesting model and I'll have to think more on it.

thoughts on funerals

I went  to the third funeral of my life today. It was for the baby of two friends. Emma was c-sectioned in her 23rd week because she and her twin sister had something called Twin-to-Twin-Transfusion Syndrome. Basically, most of mom's blood and associated resources were going to Ella who was getting too much, while Emma was getting too little and not developing. So out they came.  Emma was in the NICU for her entire life. She was also born with a ventricular septal defect - a whole in her heart. A few weeks ago, she stopped gaining weight and was still a bit under the weight they were trying to get her to before having open heart surgery to repair the defect. So she went under the knife too small. She survived the surgery, but developed sepsis. She fought off the sepsis initially, but relapsed and died a week later.  

The high point of the event for me were some comments by Jordan.  This is from memory, but here is basically what he said:

     Have you ever noticed yourself doing something that you just know came from someone else? We pick up mannerisms from those 
     around us all the time.  I think that what we are is a collection of habits, behaviors, choices and so on. When we interact with others, it
     changes them and their lives.  People say that someone has "rubbed off on them".  I don't think that's just a phrase. I think it's true, that a 
     little part of them has attached itself to you.  Emma has rubbed off on the 1,000 people who have been following her struggle, and we all  
     carry a part of her with us now.

I am a big fan of stuff like this that takes whacky spiritual ideas and says think about it. It really is actually true.  I'm also a fan of this particular idea. I've written a few things about it myself and made a similar point when I spoke at my mom's funeral, remarking how much better I got to know mom and how much closer to her I got after she died.  But I really like bringing the rubbing off on you phrase into it.  And I felt like he just did a great job expressing it in a way that clear and compelling and fresh, when something like this can easily veer into trite, cliche and hackneyed.

I was talking with Khayah before it about how ti was kind of a weird funeral - really and I was wondering what it would be like.  I was reminded of my feeling before mom's funeral that the only memorial I'd been to before was very abnormal (it was held by an academic dept in a conference room after one of the dept staff killed himself shortly after losing his job). I remember feeling like I had no idea what went on at a funeral - just what I'd seen in movies.  Now I felt like even having been to a third, I still hadn't ever been to a "normal" funeral, but began to think maybe there isn't really such a thing. Maybe they're more like people - there is no such thing as a typical person, we're diverse and different and varied. Our lives are and our deaths are; a celebration of someone's life should naturally reflect that.

extra ticket to see The Wet Spots tonight

 I have an extra ticket to see The Wet Spots at Comedy Underground tonight at 8:30. Give me a call if you're interested: 999 6866.
At this late date, I just want to see the seat get filled -  it's on me.

Here's how they describe themselves:

The Wet Spots (Cass King and John Woods) are a musical sex comedy duo who write sophisticated lyrics paired with sweet, catchy melodies. Their musical repertoire is inspired by the risque satirical songs of Monty Python, South Park, Tenacious D and musical comedy legend Rusty Warren. They are known for their lively shows, which include sing-alongs, spankings, and bawdy sex-ed.

Here's a link to one of their generally Not Safe For Work videos:

(no subject)

My funding at work is running out over the course of this month and it has kind of snuck up on me.  I know I was aware of it in like October or November, but somehow the word "May" got into my head instead of "March" and so I didn't realize it was going to be quite so soon or quite so all at once.  I've called in some IOUs and so I'm okay until about late May, by which time the radiology folks will need more work, so I'll be fine for a good long while.  That said, the definition of "okay" here is 50% time, because that's the cutoff to get health insurance. I can live acceptably on half my salary, it'll make paying off the credit cards take longer, but that can be managed.

This has however lead to me looking into switching jobs.  Which I have very mixed feelings about.  I applied for a job at the Child Health Institute last weekend and I've had a few folks point out things I might do at the usual round of techie suspects around here.  There are some advantages to switching even if I stay within the university.  It's a chance to renegotiate a much better salary if nothing else. It's also occurred to me just how many times I've counselled someone about the exponential growth of savings and why if you are going to sell out it is best to do it now and then go follow your bliss later rather than the reverse. It could be time to follow my own advice. On the other hand, it is also making me realize how much I love working at CFAR.  Even the job at CHI, which would still have been an academic biostat job, still had me wondering how I'd feel about evaluating multimedia interventions to get diabetics to manage their insulin better rather than multimedia interventions about using condoms correctly.   (Of course, the funny thing is that it's not like I actually even watch these interventions.  Coding up a GEE model is pretty similar in either case)  And even less interest in comparing the effectiveness of two sets of code for inclusion in the latest version of some web app.

(no subject)

 I did something unpleasant to my hamstring last night at soccer. I'm really mostly fine, but prudence dictated that I not go slide down mountains for the next four days.  So I'm surprised to find myself in town with no plans.  Anything fun and nonstrenuous that I should do?

scooped by Sewall Wright

So it turns out that this solution to a problem that I've been working on is essentially identical to Wright's Fst. I guess if you're going to spend time replicating someone else's work, you could do worse than the guy who invented the field. It is a little embarrassing to have not done a decent enough literature search to find it though. It's an interesting mix of emotions - feeling vindicated but also negligent, smart but dumb.

the love - hate relationship with work

Funny story from today:

We had an early soccer game this evening and so a few of us went out for beers afterwards. We were discussing the work involved in managing the team and someone was talking about a webpage that the manager of his other team uses which alleviates some of the work by essentially automatically collating and tabulating players' reports on whether they will be at the upcoming game. And so we join our heroes...

Mark: Yeah, I have something similar almost set up, but it's not quite working yet.
Dell: I was going to say. Aren't you some kind of computer person?
Mark: That's exactly the problem. [Explains his job.] After 9-10 hours at my computer writing
code, the last thing I want to do when I get home is sit at my computer and write more
Dell: I can see that. I'm certainly not going to come home and remodel the bathroom.
Mark: Whereas that sounds great to me.
Dell: I'm just the opposite, about all I'm good for is sitting at the computer doing nothing:
check my email, watch a little porn.
David: I dated this porn star for a while. And y'know, everyone always fantasizes about that,
but as it turns out...
Miles: What? Sorry, honey, I've been fucking all day.
David: Exactly. All she was interested in was having dinner and then doing some math before
we went to sleep.

Amusingly enough, when we left the bar shortly afterwards, I found that I had a text message asking me a stats question.

* * *

No, I haven't actually dated a porn star. I just couldn't resist. However, I did recently come across a recommendation of this
interview with porn star Sasha Grey.
(Warning: much of the visual is her doing a semi-nude photo shoot with the interview voiceover). I've only watched part 1 so far, but it was pretty interesting. I mention it here because she makes a few comments about how being a porn star inhibits her sex life ("can't come to work with bruises").

* * *

I'm also reminded of a conversation I had a few weeks ago about having hobbies which generate income - even if it is less than required to pay for itself - and the sort of weird cognitive space occupied by such an ...uh... occupation. It's not something you do for the money, you'd do it anyway, the money is simply a pleasant side effect. This leads to the question of whether you can view your job that way, too. One of the things that I realized during my stint between grad schools doing clerical temp work was that contrary to the "I'd like to be able to leave my work at the office." line, that I feel that anything I'm going to spend 40 hours a week doing should be something that I enjoy well enough that I *want* to think about it in off hours. That's not a far cry from "something I'd do even if they weren't paying me". Which eventually lead to the line: "Hey, I'm not here for the money. Being a grocery clerk is my hobby."

It's interesting though. I do love my job quite a bit. And I'd like to say that I'd do it even if they weren't paying me. To a certain extent, I clearly would. I do have volunteer projects. I've been known to do nontrivial things just in yammering on my mailing lists. But it is funny how sometimes I nevertheless don't seem to get very much work done. And I haven't been for the past couple weeks, although I'm starting to pick up again. It's been easy to feel overwhelmed, especially with all the house stuff as well, and I've spent too much time in the "Oh my god, I have so much shit to do. How will I manage it?" Not by spinning wheels contemplating with terrible awe the sheer magnitude of the task list, that's for sure.

(no subject)

In the past week I:

sent off 3 grant proposals and a late breaker abstract

designed an analysis for the multiple cervical biopsy study that's been vexing me for ages. now i just have to implement it

had a new housemate move in

realized that my recent solution to "the hard problem" is less novel than I thought

went to an annex play and helped with strike

had a 4 stop Friday evening - toward the end, corrie was talking about liberty and says something about "i'm sure dave's been there" response: "i've been there twice today."

falsified another theory about why the subaru doesnt start sometimes - or at least how to fix it (mild percussive maintenance doesn't work)

went to a party where i knew only the host. met a neat person who is 1 degree away from me. got into a minor argument with a long time west seattlite about the (okay, my) "it's hard to feel too sorry for someone who has so much money they can't afford it all" view of property tax

tried red wine vinegar instead of lemon juice in risi y bisi with great success - and learned that vinegar substitutes for lemon juice at about half the amount

filed 3 years of taxes

learned the difference between settling stones and developing them.

learned about the physiology of taste and how it varies from person to person - and what a supertaster really is.


wrote a journal entry.

(no subject)

I had a lot of trouble getting to sleep last night - went to sleep shortly after 1:30. When I gave up on getting to sleep and got up, it was 4:00. I spent about 2 hours on the computer, mostly catching up on responding to email, before crashing. Surprisingly, I woke up about 10:30, feeling not very well rested, but not feeling like I could go back to sleep either. I got up and after a half hour of feeling groggy, recalled that Ryan - who was here chatting until 1:30 - was getting up at some insane hour to go meditate. I'd said last night - as I have every couple of weeks lately - that I want to start meditating again and probably would soon. I was never much of a morning meditator, it was really more of a midday recharge sort of thing for me. But remembering some comments Ryan made that implied it was part of his morning routine - coupled with the thought that when I do it, I find it a useful way for me to combat fatigue and drowsiness, so I decided there's no time like the present. I decided 10 minutes was a nice goal for being so out of practice (I've probably done it about 3 or 4 times in as many years), grabbed my phone and punched it into the calendar with an alarm to go off in 10 minutes and started concentrating on my breath. It started out going pretty well for a while, but then I started to have trouble concentrating, got fidgety, my hips/upper thighs got tired and achy, and I began having a lot of thoughts like "Wow is 10 minutes a long time." and "Maybe I should check that alarm." At one point I unthinkingly opened my eyes and looked down at the phone, but rather than bring up a screen and check, decided to continue and closed my eyes and went back to my breath. Eventually I began to get really unfocused and gave up. Turns out it was 25 minutes later, I'd put it into the calendar as 11:10 - 11:20, but that meant the alarm wanted to go off at 11:10, which was when I'd started. Yay team. Go me.

Now after a couple hours of half useful frittering, I'm yawny again. Might be time to take a nap.

my housing history

I wrote this up in comment to Terri Kim saying that she'd been moving a lot. Figured I might as well record it here:

You keep moving? How's this:

dawn of my memory - 5/79: a house in South Bend, IN. Moved because Dad finished residency and was recruited by a clinic in Quincy, IL

5/79 - 6/86: Cheshire Ct Quincy, IL. Parents divorced in 84, mom subesequently sells house and moves to cheaper house

7/86 - 6/87: 10th&Ohio Quincy IL. House was horrid. Found a nicer house for similar rent and moved.

6/87 - 8/87: Lindell St Quincy IL. Mom is talking about moving out of town, so I arrange to get myself shipped off to boarding school on the state's dime.

8/87 - 11/87: Dorm 8A IMSA Aurora, IL. Contractor hasn't finished 2 new dorms, so I'm living in a temporary dorm: 3 adjacent classrooms- one has 20 beds, one has 20 wardrobes, one has 20 desks. There's a bathroom 50 feet down the hall, but showers are at the gym on the other side of the school.

11/87 - 5/88:Dorm 1504 Aurora, IL. Move into swanky 2 person dorm room with Steve.

6/88 - 7/88: School's out for summer (But not forever. Sorry Alice.) Back to Lindell St. Just in time to move to Bloomington, IN.

7/88 - 8/88: Morningside Dr townhome, Bloomington, IN. Mom is saving money by getting a 2BR place - she and my sister have rooms, I sleep on the livng room hide-a-bed when I'm visiting.

9/88- 6/89: Dorm 1504 Aurora, IL. With Steve again, identical but different room. School year ends, he graduates. I decide to spend most of the summer at my dad's.

6/89 - 8/89: 17th & Ohio Quincy, IL. Live with Dad, Step-mom, step-sister and step-brother. As a 17 year old who had been living semi-unsupervised for most of past 2 years, there's uh, some conflict between me and dad

9/89 - 6/90: Dorm 1505. Same cookei cutter swanky dorm room, new roommate Rich. Graduate, back to Dad's for a summer.

6/90 - 8/90: 17th& Ohio again. Next off to college.

8/90 - 6/91: Bromley Hall (privately owned dorm at UIUC). Roomed with Mez. We get an apartment starting in the fall along with Gabe and Dana, I sublet in Champaign for the summer.

6/91 - 8/91: The Hovel. Tiny 2 BR apartment with Brad (and essentially Melissa, his gf. If you asked where she lived, she said "out of my car." she sometimes stayed with her parents 20 miles away, but mostly lived with Brad/us.)

8/91 - 7/92: Daniel St apt C-U, IL. With Mez, Dana, Gabe. Apt was pricey, found a big, cheap old house for next year.

8/92 - 7/93: White st house C-U, IL. With Mez, Dana, Gabe, CJ. CJ graduated, house was sold from cool landlord to annoying landlord, upstairs bedrooms were freezing.

8/93 - 7/94: Fifth Ave apt C-U, IL With MGD. M+D graduated, G+me move to new apt with new Jim + Pacia

8/94 - 7/95: John st apt C-U. With Gabe, Jim, Pacia. I graduate and move to Pittsburgh for grad school.

8/95 - 7/96: Wilkins St apt, Pgh, PA. With Schwern. Tiny, emergency I-need-to-find-a-place-fast apt, foudn cooler house as I got to know the city a bit.

8/96 - 7/97: Point Breeze house, Pgh, PA. With Carl, Glenn, Tammy. I drop out of grad school to move to Seattle

8/97 - 10/97: Seventh Maze living room in Cap Hill. WIth Madelynn, Mez, Ethan, Sev. Mad and I took a while to find a place, and were fortunate to have generous friends willing to put us up for a longish time.

11/97 - 8/98: Russell Ave in Ballard. With Mad. She moved back to Pgh in 5/98 and paid out the rest of her lease, but I couldn't afford it myself and it was a 1 BR.

8/98 - 7/99: Franklin ave in Eastlake. With Matt and Nathan (in 11/98 or so Nathan moved out and Sarah moved in). Matt was the bldg manager, he moved out and the landlord elected to hire a married couple for it rather than me in hopes of reducing turnover.

8/99 - 4/02: Question House in Wallingford. With Eric and Heather, later adding Leah. Note this is the first time in 15 years that I live at the same place for more than 12 months. Heather and I buy a house.

5/02 - 6/04: Ivory Tower in Cap Hill. With Heather,later adding Ryan. I bought a house. FInally, I'll put down some roots. Or maybe Heather and I will break up, and I'll move elsewhere.

6/04 - present: Hellmouth in the CD/Madrona. With Jen and Scotto, til they bought a house. Now looking for a housemate (or couple).

All told that's 25 moves among 23 residences with 32 other people (51 if you count the 19 in the temp dorms) in 28 years (23 in 21 if you start with leaving the Cheshire Ct house). And that doesn't count the 4-5 houses/moves before I was 5 years old because I don't have actual memories of them. But, it has actually slowed down - only 3 moves in the 5 years since I turned 30.

And if you know anyone who's looking for a room in a 2BR house for ~$800 incl utilities, internet, housekeeper, put them in touch with me.