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Solutions to group exercises
1. (a) Truncating the chain is equivalent to setting transition probabilities to any state in {M+1,...} to zero. Renormalizing the transition matrix to make it stochastic we get
(b) We have so
pij∗=
pij
pikk=0
M
∑pijπ i =pjiπ j
pij∗ pikk=0
M
∑ π i =pji∗ pjkk=0
M
∑ π j
and yielding detailed
balance for the truncated chain.
2. Let Zn = (X2n,X2n+1). Then Zn is a Markov chain with transition matrix
Let Tk= P(hit (0,1) before (1,0)|start at k).
First step analysis yields the equations
π i∗ =
πi pikk=0
M
∑
πl plkk=0
M
∑l=0
M
∑
P =
p02 p0q0 q0q1 q0p1
q1p0 q1q0 p1q1 p12
p02 p0q0 q0q1 q0p1
q1p0 q1q0 p1q1 p12
⎛
⎝
⎜⎜⎜⎜
⎞
⎠
⎟⎟⎟⎟
(b) If q0=p1=p we get p01,01=1/2, fair coin.3. (a)
so
whence the differential equation follows by letting .
(b) Since P1(t)=1-P0(t) we get
T00 =p02T00 +p0q0T01 +q0p1T11
T01 =q1p0T00 +q1q0 +p12T11
T11 =q1p0T00 +q1q0T01 +p12T11
P0 (t + Δt) =P0 (t)(1−αΔt+ o(Δt)) +P1(t)(βΔt+ o(Δt))P1(t+ Δt) =P1(t)(1−βΔt+ o(Δt)) +P0 (t)(αΔt+ o(Δt))
P0 (t + Δt) −P0 (t)Δt
=−αP0 (t) + βP1(t) + o(1)
Δt → 0
′P0 (t) = −(α + β)P0 (t) + β
which can either be solved directly, or one can check that the given solution satisfies the differential equation.
(c) Letting we get
This value as a starting distribution also yields a marginal distribution that is free of t, so it behaves like a stationary distribution (which we will define later).
t→ ∞ P0 (∞) =β
α +β
Announcement
MathAcrossCampus Colloquium(http://www.math.washington.edu/mac/)
Evolutionary trees, coalescents, and gene trees: can mathematicians find the woods?
JOE FELSENSTEIN Genome Sciences, UW
Thursday, November 13, 2008, 3:30 Kane Hall 210 Reception to follow
The Markov property
X(t) is a Markov process if for any n
for all j, i0,...,in in S and any t0<t1<...<tn<t.
The transition probabilities
are homogeneous if pij(s,t)=pij(0,t-s).
We will usually assume this, and write pij(t).
P(X(t) =j X(tn) =i0 , ...,X(t0 ) =in)
=P(X(t) =j X(tn) =i0 )
pij (s, t) =P(X(t) =j X(s) =i), s ≤t
Semigroup property
Let Pt be [pij(t)]. Then Pt is a substochastic semigroup, meaning that
• P0 = I
• Ps+t = PsPt
• Pt is a substochastic matrix, i.e. has nonnegative entries with row sums at most 1.
Proof
(a) ?(b)
(c)
pij (s + t) =P(X(s + t) =j X(0) =i)
= P(X(s + t) =j X(s) =k,X(0) =ik∈S∑ )
P(X(s) =k X(0) =i)= P(X(s + t) = j X(s) = k)P(X(s) = k X(0) = i)
k∈S∑
= pkj (t)pik (s)k∈S∑
pik (t) =P(X(t) ∈S X(0) =i) ≤1k∈S∑
Standard semigroup
Pt,t≥0 is a standard semigroup ifas .
Theorem:
For a standard semigroup the transition probabilities are continuous.
Proof:
By Chapman-Kolmogorov
Unless otherwise specified we will consider standard semigroups.
Pt → It ↓0
limt→ s Pt =limt→ s PsPt−s =PsI=Ps
Infinitesimal generator
By continuity of the transition probabilities, Taylor expansion suggests
We must have gij≥0, gii≤0. Let G=[gij].Then (under regularity conditions)
G is called the infinitesimal generator of Pt.
pij (h) ≈gijh, i≠j
pii (h) ≈1+giih
limh↓0
(Ph −I) / h=G
Birth process
G =
Under regularity conditions we have
so we must have
−λ0 λ0 0 L
0 −λ1 λ1 L
0 0 −λ2 λ2
L L L L
⎛
⎝
⎜⎜⎜⎜
⎞
⎠
⎟⎟⎟⎟
pij (h)j∈S∑ =1=1+h gij
j∈S∑ + o(h)
G1T =0T
Forward equations
so
and or
pij (t +h) = pik (t)pkj (h)k∈S∑
= pik (t)(gikh+ o(h))k≠j∑+pij (t)(1+gjjh+ o(h))
pij (t +h) −pij (t)h
= pik (t)gkj + o(1)k∈S∑
′pij (t) = pik (t)gkjk∈S∑ ′P (t) = P(t)G
Backward equations
Instead of looking at (t,t+h] look at (0,h]:
so
pij (t +h) = pik (h)pkj (t)k∈S∑
= pkj (t)(gikh+ o(h))k≠j∑+pjj (t)(1+gijh+ o(h))
′P (t) = GP(t)
Formal solution
In many cases we can solve both these equations by
But this can be difficult to actually calculate.
Pt =tn
n!Gn
n=0
∞
∑ ≡exp(tG)
The 0-1 case
G=−α αβ −β
⎛⎝⎜
⎞⎠⎟
det(G−λI) =(α + λ)(β + λ)−αβ=λ(α +β + λ) =0
λ =0 or − (α + β)
Gx =0 ⇒ x=11⎛⎝⎜⎞⎠⎟
(G+ (α + β)I)x=0 ⇒ x=−αβ
⎛⎝⎜
⎞⎠⎟
G=−α 1β 1
⎛⎝⎜
⎞⎠⎟
−(α +β) 00 0
⎛⎝⎜
⎞⎠⎟
−α 1β 1
⎛⎝⎜
⎞⎠⎟
−1
0-1 case, continued
Thus
Pt =tk
k!k=0
∞
∑ Gk
=I+−α 1β 1
⎛⎝⎜
⎞⎠⎟
tK
k!k=1
∞
∑ −(α +β)k 00 0
⎛
⎝⎜⎞
⎠⎟−α 1β 1
⎛⎝⎜
⎞⎠⎟
−1
=−α 1
β 1
⎛⎝⎜
⎞⎠⎟
e−(α+β)t 0
0 1
⎛
⎝⎜⎞
⎠⎟
−1
α + β
β
α + β
1
α + β
α
α + β
⎛
⎝
⎜⎜⎜⎜
⎞
⎠
⎟⎟⎟⎟
=1
α + β
αe−(α+β)t α(1− e−(α+β)t )
β(1− e−(α+β)t ) α + βe−(α+β)t
⎛
⎝⎜⎞
⎠⎟
Marginal distribution
Let . Then for a starting distribution π(0) we have π(t)=π(0)Pt.
For the 0-1 process we get
πk(t) = P(X t = k)
(π0(0 ) 1−π0
(0 ) )1
α + βαe−(α+β)t α(1−e−(α+β)t )
β(1−e−(α+β)t ) α + βe−(α+β)t
⎛
⎝⎜⎞
⎠⎟
=(β
α +β+ π0
(0 ) −β
α +β⎧⎨⎩
⎫⎬⎭e−(α+β)t 1−L )
Exponential holding times
Suppose X(t)=j. Consider
Let be the time spent in j until the next transition after time t. By the Markov property, P(stay in j in (u,u+v], given stays at least u) is precisely P(stay in j v time units). Mathematically
Let g(v)=P(>v). Then we have g(u+v)=g(u)g(v), and it follows that g(u)=exp(-λu). By the backward eqn
and P(>v)=pjj(v).
P(X(t +u) =j,0 < u≤α X(t) =j)
P( > u+ v > u) =P( > v)
′p jj (0) = gjj
Jump chain
Given that the chain jumps from i at a particular time, the probability that it jumps to j is -gij/gii.
Here is why (roughly):
Suppose t<<t+h, and there is only one jump in (t,t+h] (likely for small h). Then
P(X(t +h) =j X(t) =i, jump in (t, t+h])
==pij (h) + o(h)
1−pii (h) + o(h)→ −
gijgii
Construction
The way the continuous time Markov chains work is:
(1) Draw an initial value i0 from π(0)
(2) If , stay in i0 for a random time which is
(3) Draw a new state from the distribution where
gi0i0< 0
Exp(−gi0i0 )
Ri0 ,k R jk =−gjk / gjj
Death process
Let gi,i-1 = i = - gi,i. The forward equation is
Write . Then
This is a Lagrange equation with sln
or
′pNk (t) = −μkpNk (t) + μ(k + 1)pN,k+1(t)
G(s; t) = skpNk (t)∑∂G(s; t)
∂t= −μ kskpNk (t) +∑ μ (k + 1)skpN,k+1(t)∑
=−s∂G(s; t)
∂s+ μ
∂G(s; t)
∂s
G(s; t) =(1−(1−s)e−t )N
pNk (t) =N
k⎛⎝⎜⎞⎠⎟e−kt (1−e−t )N−k