keskiviikko 16. marraskuuta 2016

Guinney et al. The Lancet Oncology: Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data

Guinney et al. 

The Lancet Oncology: Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data 

I am a shared first author, and this is the result of DREAM 9.5 mCRPC challenge. Hoping to have this as the crown jewel of my dissertation.

http://www.thelancet.com/journals/lancet/article/PIIS1470-2045(16)30560-5/fulltext

sunnuntai 13. marraskuuta 2016

The Mensa-Dilemma

The Mensa-Dilemma


So I happened to bump into a friend's forum post with claimed high IQ from a Mensa test today and it reminded me of what I've dubbed 'the Mensa-Dilemma', first time like a year ago. I've been sometimes intrigued of taking a Mensa test, and being what I am, I've evaluated that I'd pass the test. By how much, that I wouldn't know. I could be delusional and might very well fail it as well, so that option has to be open. If I am delusional I'd estimate that I'd still be approximately at the borderline, by mirroring my academic/career/skill achievements in comparison to the common populace (if I remember right Mensa was supposed to be top 5%, 2.5% or 1%, forgot the exact quantile). IQs seem to be kind-of pitch in freebies in certain forums, with nothing to back it up with (i.e. proof), and even if there was, it is used in irrelevant contexts (a high IQ person may very well be incapable of functioning in a specific narrow field).

But what leads to the dilemma is that I loathe the term IQ. Reducing human intelligence (or artificial intelligence or what-ever sentient being in question) to a single numeric value is fundamentally absurd. I've always admired people like ancient Greek philosopher-mathematicians or people like Da Vinci, who were geniuses on multiple fields: inventor, painter, mathematician. Quite the genius, nobody can deny that. However, when projected to a single dimensional numeric value, which bases emphasis on logical thinking, they might've ended up being "mediocre geniuses". So a 170er could go to a 150er and boast in the smaller quantile digits of how they're in the 170er-club. Human mind is nearly incapable of compherehending extremely small or high numbers or probabilities, as well as distribution quantiles, thus in practice this 150er probably is just as smart as the 170er.

The mixture of loathing IQ and the intiguing curiousity of a Mensa-test result form the basis of what I called the Mensa-Dilemma, here as a 2x2 table:

.........Did I take a Mensa test?
................................._____Yes_(A)__________No_(B)_____
Did I pass?..............Yes_(1).|......A1......|.......B1.......|
.........................No__(2).|......A2......|.......B2.......|
.................................---------------------------------


The problem rises when I consider all the 4 possibilities, as I can only lose in this game:

- A1: I took a test and I passed test. I feel guilty for trying to prove myself, while already in the beginning I had already estimated that I'd quite easily pass the test. The margin by which I'd pass might affect my opinion. But most likely I'd just cancel my membership right away after feeding my curiousity, but in order to not go for a holier than thou -attitude, I'd probably only tell my wife about the whole thing. I'd regret taking the test because I was right right in the start, and I "lowered" myself in my own standards due low self-esteem or some strange need to prove myself. But it's only a test. People who throw around Mensa-stuff are generally doing it randomly and it only makes the conversations awkward or malicious.

- A2: So I took a test and I failed. This would of course be a big bump on my self esteem. So am I just a random stranger in the street? Why am I even considering philosophical, artistical, or natural scientific achievements, when I have been shown by a metric to be possibly only a mediocre citizen? That'd be hard to swallow. I might go into researching IQ tests more in detail and come up with a false explanation as to why this whole thing's a fiasco, but I don't think I'd fall that low.

- B1: So I never took the test, but if I did, I would pass. I will never find out that I would've passed the test (or by how much), and every time Mensa pops up, I will probably presume I would belong to B1-category - but I got nothing to back it up with. "Sure I could take a Mensa test and top it easily" sounds as vain as it can be.

- B2: So I never took the test, but if I did, I wouldn't even pass. I live in happy ignorance of my own mediocrity, but still I presumably consider myself to be á priori B1-class. It will probably affect my conclusions, behaviour, human interactions, et cetra. But there is always the scare in the back of my head, that what if I'm a B2'er? I must know, I couldn't be a B1'er... could I? Without the test, I would find myself somewhat restless.


So whatever I got, A1, A2, B1, or B2, I'd be discontent. I'd always find a way to be displeased of the outcome anyhow (and let's neglect the aspect of how high the result was, just the Mensa-eligible threshold). So that causes me a dilemma. There is no way I can 'win'.

In some applications, 'the only way to win is to not play at all'. I was thinking that'd probably be the solution in this problem. I'm not an expert in game theory, but however unfortunately here 'not playing' would fall into a choice for the category B, leading again to a B1 or B2, thus a loss.

In reality, amusingly, the only way for me to win is to add a category C, which stands for 'forgot the whole damn thing'. It has now happened to me twice. Approximately year ago I remembered Mensa and checked their local test times - and noticed that the coming Saturday had a single test coming up in my town. However, the week after I remember that particular test, and that I forgot to go to it - well, I won! My dilemma is still unsolved, so I don't have to pick anywhere in A1 - B2! Yay, C-category is the way to go. However now that I was reminded of this, I did check the test schedules again - and luckily there were no upcoming tests within a reasonable interval in our city. Victory, C-category again!

.........Did I take a Mensa test? ................................._____Yes_(A)__________No_(B)_____I forgot the thing (C)_ Did I pass?..............Yes_(1).|......A1......|.......B1.......|..........C1..........| .........................No__(2).|......A2......|.......B2.......|..........C2..........| .................................--------------------------------------------------------

This has so far guaranteed that I can sleep my nights in peace, to exaggerate:

- C1: Too bad, I would've been a Mensa member, but I forgot the whole thing and I'll continue my life like before. I don't think I'd lose anything.

- C2: Whew, I never got to know I wouldn't be eligible. Ignorance is bliss!

It's only a matter of time though when I consciously can't avoid C-category any more. I both wait and fear that day (again exaggeration, it's not really that big of a deal). For the time being I haven't ever taken a Mensa test. Here I completely omitted the factor of how much one would pass the test by (i.e. the exact value of IQ, not just the threshold). I hope I won't have to think about that any day soon.

I've heard rumors that people that attend to Mensa meetings are just like anybody. They play board games, talk about mundane things or sometimes more philosophical, but nothing out of the scope of e.g. a club for students of topic X in University. Maybe I'm shooting a fly with a cannon just because I want to shoot a cannon. Still, 'The Mensa-Dilemma' sounds pretty good, eh?

maanantai 7. marraskuuta 2016

Longitudinal modeling of ultrasensitive and traditional prostate-specific antigen and prediction of biochemical recurrence after radical prostatectomy

Our paper on modeling PSA (Prostate-Specific Antigen) and exploring differences in more accurate panels (so-called ultrasensitive-PSA, u-PSA) and the traditional higher concentration ranges ("traditional-PSA") is out:

http://www.nature.com/articles/srep36161

Overall, ultrasensitive-PSA seems robust and has potential for early prediction of biochemical relapse. I acknowledge that there are a lot of criticism pointed towards ultrasensitive-PSA, e.g. that even low levels of PSA can be detected in women, but with feasible mathematical modeling one can predict PSA curvature quite early after radical prostatectomy. Hopefully this will lead towards more interest in exploring clinical potential in u-PSA.

Early detection of relapse may make the difference between life and death.

-TDL

torstai 3. marraskuuta 2016

Saksisatu

Saksisatu

(A Fairytale of Scissors)


Olipa kerran yksinäiset sakset. Ne olisivat kovin tahtoneet leikata kaikkea, mutta ne eivät tienneet mitä ja missä ne voisivat leikata. Siksipä sakset lähtivät etsimään mitä kaikkea kivaa voisi leikata.

Niinpä ne päättivät mennä olohuoneen sohvalle. Sieltä löytyi saksien iloiseksi onneksi äidin paita joka oli sohvanreunuksella! Sakset olivat juuri napsaisemassa äidin paidasta palasen, kun äiti parahti "Voi ei sakset! Älä vain leikkaa minun kaunista paitaani, sain sen juuri ja pidän siitä kovasti!". Sakset pelästyi ja sanoi "Voi, anteeksi! En minä tarkoittanut, tahdon vain kovasti löytää jotain saksittavaa."

Sitten sakset päättivät mennä isin työhuoneeseen. Siellä oli paljon jännittäviä työpapereita ja julisteita, ja sakset olivat juuri napsaisemassa isin julisteista ison palasen kun isi parahti "voi ei sakset! Minun tärkeät julisteeni, en niin tahtoisi että niitä saksittaisi! Minun pitää huomenna esittää niitä työkavereilleni ja en voi esittää niitä jos ne ovat riekaleina". Siihen sakset taas sanoivat "Voi anteeksi! En tiennyt niiden olevan tärkeitä, ne vain näyttivät niin kiinnostavilta."

Sitten sakset menivät makuuhuoneeseen, missä pikkusisko Vilja oli nukkumassa. Sakset näkivät Viljan kauniin peiton ja mietti mielessään, miten kauniita tilkkuja siitä saisi. Sakset olivat juuri napsaisemassa Viljan nukkumaviltistä aimo vonkaleen, kun Vilja heräsi ja rupesi itkemään: "Voi, minun peittoni - nyt on talvi ja minulle tulee niin kovin kylmä, jos minun peittoni leikataan!" Niinpä sakset taas pahoittelivat "Voi ei, en tietenkään tahdo että sinulle tulisi kylmä ja että heräisit - siitä olisi vain saanut niin kivoja pieniä tilkkuja. Kauniita unia Vilja!"

Vaan sittenpä Elea löysi sakset. "Hei sakset! Minä kovin tahtoisin leikata ja liimata ja askarrella, ja olen kuullut että sitä kovin haluaisit löytää leikattavaa. Tulisitko minun ystäväkseni askartelemaan pahvista ja paperista kaikkea kaunista?" Siitähän sakset vasta innostuivat "Vau! Voi onnen päivää, tätä minä juuri olen odottanut!" Niinpä Elea ja sakset viettivät joka päivä aikaa leikaten eri värisiä papereita ja pahveja ja tekivät niistä kauniita askartelulahjoja niin äidille, isille kuin Viljallekin, ja Eleasta ja saksista tuli todella hyvät ystävät.

Ja niin ne tekevät vielä tänäkin päivänä - loppu!

perjantai 23. syyskuuta 2016

Sextennial (Self-)portraits

I was up for making some art yesterday. I've felt the need to open my insides and have been working on this (right-most) piece for quite some while. I didn't feel like I got it completely right on spot, but I'm still happy. It is influenced by Orwell and Huxley, and the dystopian feeling of "being a mechanical part of the machine". It's interesting to see a development in periods of 6 years (first one is me, though it "artistically" portraits only the view of whoever took the school shots back then). Others are solely made by me.

Sextennial (Self-)portraits, TDL 2016



Zoom in for a proper view.

In 1998, I spent most of my time in the internet, isolated to some degree.
In 2004, I felt I was destined to fail in finding my place within the reality.
In 2010, I was having memory problems and perplexing anxiety, fearing I was losing my mind.
In 2016, I am struggling with existential nihilism.

-TDL, Sep 2016

tiistai 9. elokuuta 2016

Optimized design and analysis of preclinical intervention studies in vivo



Optimized design and analysis of preclinical intervention studies in vivo



We published our work on improving experiment design in preclinical in vivo experiments in Scientific Reports just now:

http://www.nature.com/articles/srep30723


I sure hope many experimenters will pick up at least the concept of how important sufficient sample sizes, good blinding, masking and randomization, as well as feasible post-intervention testing are. There's so many references out there telling how appalling the attrition rates in these experiments are at the moment, and I have personally also experienced this - preclinical experimenters should at least consult a biostatistician/-informatician on good design. Anyway, there's an R-package I maintain with this publication called 'hamlet' that's available on CRAN (comes additional machine learning trinkets):

https://cran.r-project.org/package=hamlet

-TDL, August 2016

For Vilja

I recited this poem at my second daughter's, Vilja's (2mo), baby dedication on last Sunday.

For Vilja


So my lips speak in a foreign tongue out of courtesy
With the intention inscribed in a fatherly tendency
The words are for all those in presence of your dedication
But the message is a seed for nurturing a human foundation

My heart an unfinished puzzle with now your piece found
Gladly I stand here again at pillars of mankind profound
While pieces are yet to come and some will still be lost
Knowing with these blessings I am luckier than the most

In sadness we will count and collect your tears
When the dark days come we'll wipe away the fears
Together with your mother whose signet you carry
Please be young for long as many forget to tarry

In happiness and success participating in the joy
Your life renews also mine and that journey I enjoy
In challenges there to help you stand on your feet
And should we depart let our paths once again meet

I will that you be siblings of hand-in-hand union
Have each support the other as a beloved companion
Let neither tower be covered by the shadow of another
Thicker the blood bond tightly knit you two together

Let your choices be guided by a more capable hand
Your life composing a chant of a glorifying stand
And where my power and wisdom end on this earth
The destiny you forge yet be enchanted by mirth

With this I pour my strength unto you to guide thee
A father equipping his daughters for an unknown sea
As we do not know what tomorrow brings in its wake
Today we gladly company you in this dear daybreak

So I pray - - be happy and care-free
My silvery - - beautiful, willow tree

(TDL, August 2016)

tiistai 19. heinäkuuta 2016

Kuuden Jalan Unilaulu

Kuuden Jalan Unilaulu


Verestävä tiimalasi sikiön ääriviivaan piirrettiin
Kudottiin kohdussa ajat tulevat syntyneen sinettiin

Tyhjän taulun vahassa tummia jälkiä eripuria
Menneistä ajoista vuollettu sisimpään jo uria

Vanhana syntyi varjoon kasken maan pohjolan
Tuhkaa silloin varpahilla asti hällä kuuden jalan

Elon kujilla vaunun rattaat eteenpäin kävi ain
Sivukujilla sortui joku ennen aikaansa vainahain 

Ajallaan sulkeutuu kerran maa peitoksi jokaisen
Kuminaa soi turvekaton päällä askeleet tantereen

Kapaloonsa hyiseen ulkokuoren sen kietoo äitimaa
Huopanaan multaa kerros ohut läheisten lapioimaa

Kehdosta tästä huokailevat nukkuneet sukupolvet
Ihmisestä vie koivu iäiseen majaan tuoreet juuret

Mahlaa ja puusokeria uuttaa eesmennyt laps tää
Toviksi armosta viel siis hetkeks keskuutemme jää


(TDL, July 2016; Updated in August and September 2016)


torstai 14. heinäkuuta 2016

Esikoiselle

Kirjoitin oheisen runon tulevalle esikoisellemme odotuksen aikana marraskuussa 2013, ja odotus täyttyi kun Elea syntyi maailmaan 14.5.2014.

Esikoiselle


Voi kunpa et perisi isäsi raskasta mieltä,
vaan liitäisit lintuna taivaan valkeasta sieltä

Sukupuolesta en tiedä, vaikka itse mies oon,
katsoo elämä silmästä silmään itse olentoon

Poika jos oot, toivon et enempi syvän sininen,
ois miete pyyteetön ja aatteet jalomielisen

Tytär jos oot, tulisit upeaan äitiis hentoinen,
tulena puhtaana mut vahvana oisit loimuten

Sisarparvea lisää jos suotais vanhemmilles,
soisin et oisit paimen karitsoille nuoremmilles

Kohtelisit hyvin toinen toista vailla taka-aietta,
ei löytyis tarkoitusperissäs velkojan ahneutta

Ja vaikeaan hetkeen, lähenevään pimeän ääreen,
soisin et muistaisit valon väreen ja lempeän äänen

Jos en sua koskaan tuntemaan oppia saa,
tiedä että hartaasti rakas olit jo ajatuksissaan

Olet sä virran alku jonka urat hakee polkuaan,
joilla jätät sä kerran jalanjälkes tähän maailmaan

Henkäys hyvä ylettäis tänne katkeran maan varjoon,
puhkeis siitä syntymäsi kevät täyteläiseen kukintoon



(TDL; Marraskuu 2013)

torstai 7. heinäkuuta 2016

A Coma-inducing Injection of Life

A Coma-inducing Injection of Life


"Discount ticket for one", I recall offering the fee  
At a film threater, wide screen, easily seats for dozens 
but the cashier winked and said "this one's for free"
Companied by an audience in shackles, restraints, frozen

Maybe a small box office hit, director's shooting star
In the the opening night I shivered, felt so real back then
Genre of drama, maybe mystery, rumored a cheap CGI spar
This movie measured, weighted, and found an ok 6.5 out of 10

Some applaud out of the kind habit and vanish to the mist
Once it's over, familiar faces shake hands yet flee to stroll 
The memories turned to ash and I dwelled in-within my cyst
I leave last as I turn off the lights and halt the film roll

A lifetime later I wander searching for a decent copy 
So I discover myself as a VCR at some flimsy flea market
But at least the cover art's decent, can't pass it by
Remember no refunds, just mind the case is like a casket

My mind is as bland as the plastic memoir, made in China
The tape melts and slithers between my fingers as dust
The anxiety sets in, and I start to produce more saliva
I grab, gather and devour it to satisfy my curious lust

The dirt is bitter and sweet, like my life turned migraine 
Desperately I decide to snort and shoot it deeper within
The flesh howls in pain, but I inject the signal yet again
My veins cry for mercy, yet seeking for meaning there-in

Then I snap; I was sitting in the theater alone, alone all the years
I imagined all the people there, I imagined the whole bloody flick
There never was a theater, I was just bound in a mind behind my eyes
Did I ever even exist? Is this a sick joke, I mean, what the fuck?

A brain in a jar
Life behind bars