Covid19:传染病模型SIR/SEIR on Network


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SIR model on Network

We here reconsider the SIR model in network where k k k is the number of neighbor and v ( t ) v(t) v(t) is the average number of infected neighbor, v v v is the average ratio of infected neighbor, w ( t ) w(t) w(t) is the average number of neighbors recovered. We have:

d s k d t = − β k v s k d i k d t = β k v s k − γ i k d r k d t = γ i k v ( t ) = ∑ k = 0 ∞ q k i k ( t ) w ( t ) = ∑ k = 0 ∞ q k r k ( t ) T a k e   t h e   d e r i v a t i v e   o f   w ( t ) = ∑ k = 0 ∞ q k r k ( t ) d w d t = ∑ k = 0 ∞ q k d r k d t = γ ∑ k = 0 ∞ q k i k = γ v ( t ) ∴ v ( t ) = 1 γ d w d t d s k d t = − β k v s k ⇔ d s k d t = − β k 1 γ d w d t s k \frac{ds_k}{dt}=-\beta kvs_k\\ \frac{di_k}{dt}=\beta kvs_k-\gamma i_k\\ \frac{dr_k}{dt}=\gamma i_k\\ v(t)=\sum_{k=0}^\infin q_k i_k(t)\\ w(t)=\sum_{k=0}^\infin q_k r_k(t)\\ Take~the~derivative~of~ w(t)=\sum_{k=0}^\infin q_k r_k(t)\\ \frac{dw}{dt}=\sum_{k=0}^\infin q_k \frac{dr_k}{dt}=\gamma \sum_{k=0}^\infin q_ki_k=\gamma v(t)\\ \therefore v(t)=\frac{1}{\gamma}\frac{dw}{dt}\\ \frac{ds_k}{dt}=-\beta kvs_k\Leftrightarrow \frac{ds_k}{dt}=-\beta k\frac{1} {\gamma}\frac{dw}{dt}s_k\\ dtdsk=βkvskdtdik=βkvskγikdtdrk=γikv(t)=k=0qkik(t)w(t)=k=0qkrk(t)Take the derivative of w(t)=k=0qkrk(t)dtdw=k=0qkdtdrk=γk=0qkik=γv(t)v(t)=γ1dtdwdtdsk=βkvskdtdsk=βkγ1dtdwsk
We could solve these equation and get:

s k = s 0 e − β γ k w = s 0 [ e − β γ w ] k = s 0 [ u ( t ) ] k   w h e r e   u ( t ) = e − β γ w   w ( t ) = − γ β l n u s_k=s_0e^{-\frac{\beta}{\gamma}kw}\\ =s_0[e^{-\frac{\beta}{\gamma}w}]^k\\ =s_0[u(t)]^k~\\ where~u(t)=e^{-\frac{\beta}{\gamma}w}\\ ~w(t)=-\frac{\gamma}{\beta}ln u\\ sk=s0eγβkw=s0[eγβw]k=s0[u(t)]k where u(t)=eγβw w(t)=βγlnu
With s + i + r = 1 s+i+r=1 s+i+r=1, we could drive:

v ( t ) = ∑ k = 0 ∞ q k i k ( t ) = ∑ k = 0 ∞ q k ( 1 − r k − s k ) = 1 − w ( t ) − s 0 ∑ k = 0 ∞ q k u k = 1 + γ β l n u − s 0 G 1 ( u ) ∵ w ( t ) = − γ β l n u d w d t = γ v ( t ) ⇔ − γ β 1 u d u d t = − γ [ 1 + γ β l n u − s 0 G 1 ( u ) ] ∴ d u d t = − β u [ 1 + γ β l n u − s 0 G 1 ( u ) ] v(t)=\sum_{k=0}^\infin q_k i_k(t)\\ =\sum_{k=0}^\infin q_k(1-r_k-s_k)\\ =1-w(t)-s_0\sum_{k=0}^\infin q_ku^k\\ =1+\frac{\gamma}{\beta}ln u-s_0G_1(u)\\ \because w(t)=-\frac{\gamma}{\beta}ln u\\ \frac{dw}{dt}=\gamma v(t)\Leftrightarrow -\frac{\gamma}{\beta}\frac{1}{u}\frac{du}{dt}=-\gamma[1+\frac{\gamma}{\beta}ln u-s_0G_1(u)]\\ \therefore \frac{du}{dt}=-\beta u[1+\frac{\gamma}{\beta}ln u-s_0G_1(u)] v(t)=k=0qkik(t)=k=0qk(1rksk)=1w(t)s0k=0qkuk=1+βγlnus0G1(u)w(t)=βγlnudtdw=γv(t)βγu1dtdu=γ[1+βγlnus0G1(u)]dtdu=βu[1+βγlnus0G1(u)]

Set u = 1 − ϵ u=1-\epsilon u=1ϵ we could get

d ϵ d t = [ β G 1 ′ ( 1 ) − γ ] ϵ a s s u m e   s 0 = 1 u ( t ) = 1 − ϵ ( t ) = 1 − e ( β G 1 ′ ( 1 ) − γ ) t s k ( t ) = u k = [ 1 − e ( β G 1 ′ ( 1 ) − γ ) t ] k ≃ 1 − e k ( β G 1 ′ ( 1 ) − γ ) t \frac{d\epsilon }{dt}=[\beta G_1'(1)-\gamma]\epsilon \\ assume~s_0=1\\ u(t)=1-\epsilon (t)=1-e^{(\beta G_1'(1)-\gamma)t}\\ s_k(t)=u^k=[1-e^{(\beta G_1'(1)-\gamma)t}]^k\simeq 1-e^{k(\beta G_1'(1)-\gamma)t}\\ dtdϵ=[βG1(1)γ]ϵassume s0=1u(t)=1ϵ(t)=1e(βG1(1)γ)tsk(t)=uk=[1e(βG1(1)γ)t]k1ek(βG1(1)γ)t

S e t   s 0 = 1 d u d t = − β u [ 1 + γ β l n u − G 1 ( u ) ] s + i + r = 1 s = u k Set~s_0=1\\ \frac{du}{dt}=-\beta u[1+\frac{\gamma}{\beta}ln u-G_1(u)]\\ s+i+r=1\\ s=u^k Set s0=1dtdu=βu[1+βγlnuG1(u)]s+i+r=1s=uk

With the above equations, we could fit the lines of the rate of susceptible, infectious and recovered people and get the parameter estimation of γ \gamma γ and β \beta β. ( γ \gamma γ in the MGF method is just parameter for τ i \tau_i τi, since p ( τ ) d τ = γ e γ τ d τ p(\tau)d\tau=\gamma e^{\gamma \tau}d\tau p(τ)dτ=γeγτdτ, β \beta β is the T i j T_{ij} Tij which is simplified for the paired transmission)

If we set s k ( t ) = 0 s_k(t)=0 sk(t)=0, we could get
β γ = 1 G 1 ′ ( 1 ) \frac{\beta}{\gamma}=\frac{1}{G_1'(1)}\\ γβ=G1(1)1
Thus, average outbreak size here is β γ \frac{\beta}{\gamma} γβ.

Here, we could rewrite the model of SIR on network:
s k ( t ) = u ( t ) k d u d t = − β u [ 1 + γ β l n u − s 0 G 1 ( u ) ] u ( t ) = 1 − e ( β G 1 ′ ( 1 ) − γ ) t d i k d t = k u ( t ) k − 1 d u d t − γ i k d r k d t = γ i k s + i + r = 1 s_k(t)=u(t)^k\\ \frac{du}{dt}=-\beta u[1+\frac{\gamma}{\beta}ln u-s_0G_1(u)]\\ u(t)=1-e^{(\beta G_1'(1)-\gamma)t}\\ \frac{di_k}{dt}=ku(t)^{k-1}\frac{du}{dt}-\gamma i_k\\ \frac{dr_k}{dt}=\gamma i_k\\ s+i+r=1\\ sk(t)=u(t)kdtdu=βu[1+βγlnus0G1(u)]u(t)=1e(βG1(1)γ)tdtdik=ku(t)k1dtduγikdtdrk=γiks+i+r=1
Also, we could drive their iteration form with S = s N , I = i N , R = r N S=sN, I=iN, R=rN S=sN,I=iN,R=rN and let c c c be the number of people one contact:
U n = U n − 1 − β U n − 1 [ 1 + γ β l n U n − 1 − s 0 G 1 ( U n − 1 ) ] S n = U n k I n = I n − 1 − k U n − 1 ( t ) k β U n − 1 [ 1 + γ β l n U n − 1 − s 0 G 1 ( U n − 1 ) ] − γ I n − 1 R n = R n − 1 + γ I n − 1 U_n=U_{n-1}-\beta U_{n-1}[1+\frac{\gamma}{\beta}ln U_{n-1}-s_0G_1(U_{n-1})]\\ S_n=U_n^k\\ I_n=I_{n-1}-kU_{n-1}(t)^k\beta U_{n-1}[1+\frac{\gamma}{\beta}ln U_{n-1}-s_0G_1(U_{n-1})]-\gamma I_{n-1}\\ R_n=R_{n-1}+\gamma I_{n-1}\\ Un=Un1βUn1[1+βγlnUn1s0G1(Un1)]Sn=UnkIn=In1kUn1(t)kβUn1[1+βγlnUn1s0G1(Un1)]γIn1Rn=Rn1+γIn1

SEIR model on Network

We here reconsider the SEIR model in network where k k k is the number of neighbor and v ( t ) v(t) v(t) is the average number of infected neighbor, v v v is the average ratio of infected neighbor, m ( t ) m(t) m(t) is the average number of exposed neighbor, w ( t ) w(t) w(t) is the average number of neighbors recovered. We have:

d s k d t = − β k v s k d e k d t = β k v s k − α e k d i k d t = α e k − γ i k d r k d t = γ i k v ( t ) = ∑ k = 0 ∞ q k i k ( t ) m ( t ) = ∑ k = 0 ∞ q k e k ( t ) w ( t ) = ∑ k = 0 ∞ q k r k ( t ) T a k e   t h e   d e r i v a t i v e   o f   w ( t ) = ∑ k = 0 ∞ q k r k ( t ) d w d t = ∑ k = 0 ∞ q k d r k d t = γ ∑ k = 0 ∞ q k i k = γ v ( t ) ∴ v ( t ) = 1 γ d w d t d s k d t = − β k v s k ⇔ d s k d t = − β k 1 γ d w d t s k T a k e   t h e   d e r i v a t i v e   o f   m ( t ) = ∑ k = 0 ∞ q k e k ( t ) d m ( t ) d t = ∑ k = 0 ∞ q k d e k d t = β k v ∑ k = 0 ∞ q k s k − ∑ k = 0 ∞ q k α e k = β k v ∑ k = 0 ∞ q k s k − α m ( t ) T a k e   t h e   d e r i v a t i v e   o f   v ( t ) = ∑ k = 0 ∞ q k i k ( t ) d v ( t ) d t = ∑ k = 0 ∞ q k d i k d t = α m ( t ) − γ v ( t ) m ( t ) = 1 α [ d v ( t ) d t + γ v ( t ) ] \frac{ds_k}{dt}=-\beta kvs_k\\ \frac{de_k}{dt}=\beta kvs_k-\alpha e_k\\ \frac{di_k}{dt}=\alpha e_k-\gamma i_k\\ \frac{dr_k}{dt}=\gamma i_k\\ v(t)=\sum_{k=0}^\infin q_k i_k(t)\\ m(t)=\sum_{k=0}^\infin q_k e_k(t)\\ w(t)=\sum_{k=0}^\infin q_k r_k(t)\\ Take~the~derivative~of~ w(t)=\sum_{k=0}^\infin q_k r_k(t)\\ \frac{dw}{dt}=\sum_{k=0}^\infin q_k \frac{dr_k}{dt}=\gamma \sum_{k=0}^\infin q_ki_k=\gamma v(t)\\ \therefore v(t)=\frac{1}{\gamma}\frac{dw}{dt}\\ \frac{ds_k}{dt}=-\beta kvs_k\Leftrightarrow \frac{ds_k}{dt}=-\beta k\frac{1}{\gamma}\frac{dw}{dt}s_k\\ Take~the~derivative~of~ m(t)=\sum_{k=0}^\infin q_k e_k(t)\\ \frac{dm(t)}{dt}=\sum_{k=0}^\infin q_k \frac{de_k}{dt}=\beta k v \sum_{k=0}^\infin q_ks_k-\sum_{k=0}^\infin q_k \alpha e_k\\ =\beta k v \sum_{k=0}^\infin q_ks_k-\alpha m(t)\\ Take~the~derivative~of~ v(t)=\sum_{k=0}^\infin q_k i_k(t)\\ \frac{dv(t)}{dt}=\sum_{k=0}^\infin q_k \frac{di_k}{dt}= \alpha m(t)-\gamma v(t)\\ m(t)=\frac{1}{\alpha}[\frac{dv(t)}{dt}+\gamma v(t)]\\ dtdsk=βkvskdtdek=βkvskαekdtdik=αekγikdtdrk=γikv(t)=k=0qkik(t)m(t)=k=0qkek(t)w(t)=k=0qkrk(t)Take the derivative of w(t)=k=0qkrk(t)dtdw=k=0qkdtdrk=γk=0qkik=γv(t)v(t)=γ1dtdwdtdsk=βkvskdtdsk=βkγ1dtdwskTake the derivative of m(t)=k=0qkek(t)dtdm(t)=k=0qkdtdek=βkvk=0qkskk=0qkαek=βkvk=0qkskαm(t)Take the derivative of v(t)=k=0qkik(t)dtdv(t)=k=0qkdtdik=αm(t)γv(t)m(t)=α1[dtdv(t)+γv(t)]

We could solve these equation and get:

s k = s 0 e − β γ k w = s 0 [ e − β γ w ] k = s 0 [ u ( t ) ] k   w h e r e   u ( t ) = e − β γ w   w ( t ) = − γ β l n u s_k=s_0e^{-\frac{\beta}{\gamma}kw}\\ =s_0[e^{-\frac{\beta}{\gamma}w}]^k\\ =s_0[u(t)]^k~\\ where~u(t)=e^{-\frac{\beta}{\gamma}w}\\ ~w(t)=-\frac{\gamma}{\beta}ln u\\ sk=s0eγβkw=s0[eγβw]k=s0[u(t)]k where u(t)=eγβw w(t)=βγlnu

With s + e + i + r = 1 s+e +i+r=1 s+e+i+r=1, we could drive:

v ( t ) = ∑ k = 0 ∞ q k i k ( t ) = ∑ k = 0 ∞ q k ( 1 − r k − e k − s k ) = 1 − w ( t ) − m ( t ) − s 0 ∑ k = 0 ∞ q k u k = 1 + γ β l n u − m ( t ) − s 0 G 1 ( u ) ∴ m ( t ) = 1 + γ β l n u − s 0 G 1 ( u ) − v ( t ) ∵ m ( t ) = 1 α [ d v ( t ) d t + γ v ( t ) ] ∴ ( γ α + 1 ) v ( t ) + 1 α d v ( t ) d t = 1 + γ β l n u − s 0 G 1 ( u ) F o r   O D E   f u n c t i o n   d v d t + p ( t ) v = q ( t ) T h e   s o l u t i o n   i s   v ( t ) = e − ∫ p ( x ) d x C + e − ∫ p ( x ) d x ∫ q ( x ) e ∫ p ( x ) d x d x H e r e   p ( t ) = γ + α q ( t ) = [ 1 + γ β l n u − s 0 G 1 ( u ) ] α ∵ w ( t ) = − γ β l n u d w d t = γ v ( t ) ⇔ − γ β 1 u d u d t = − γ v ( t ) ∴ d u d t = β u v ( t ) = β u e − ∫ ( γ + α ) d x C + e − ∫ ( γ + α ) d x ∫ [ [ 1 + γ β l n u − s 0 G 1 ( u ) ] α ] e ∫ ( γ + α ) d x d x = C β u e − ( γ + α ) t + e − ( γ + α ) t ∫ [ [ 1 + γ β l n u ( t ) − s 0 G 1 ( u ( t ) ) ] α ] e ( γ + α ) t d t v(t)=\sum_{k=0}^\infin q_k i_k(t)\\ =\sum_{k=0}^\infin q_k(1-r_k-e_k-s_k)\\ =1-w(t)-m(t)-s_0\sum_{k=0}^\infin q_ku^k\\ =1+\frac{\gamma}{\beta}ln u-m(t)-s_0G_1(u)\\ \therefore m(t)=1+\frac{\gamma}{\beta}ln u-s_0G_1(u)-v(t)\\ \because m(t)=\frac{1}{\alpha}[\frac{dv(t)}{dt}+\gamma v(t)]\\ \therefore (\frac{\gamma}{\alpha}+1)v(t)+\frac{1}{\alpha}\frac{dv(t)}{dt}=1+\frac{\gamma}{\beta}ln u-s_0G_1(u)\\ For~ODE~function ~\frac{dv}{dt}+p(t)v=q(t)\\ The~solution~is~ v(t)=e^{-\int p(x)dx}C+e^{-\int p(x)dx}\int q(x)e^{\int p(x)dx}dx\\ Here~p(t)=\gamma+\alpha\\ q(t)=[1+\frac{\gamma}{\beta}ln u-s_0G_1(u)]\alpha\\\\ \because w(t)=-\frac{\gamma}{\beta}ln u\\ \frac{dw}{dt}=\gamma v(t)\Leftrightarrow -\frac{\gamma}{\beta}\frac{1}{u}\frac{du}{dt}=-\gamma v(t)\\ \therefore \frac{du}{dt}=\beta uv(t)\\ =\beta ue^{-\int (\gamma+\alpha)dx}C+e^{-\int(\gamma+\alpha)dx}\int [[1+\frac{\gamma}{\beta}ln u-s_0G_1(u)]\alpha]e^{\int (\gamma+\alpha)dx}dx\\ =C\beta ue^{-(\gamma+\alpha)t}+e^{-(\gamma+\alpha)t}\int [[1+\frac{\gamma}{\beta}ln u(t)-s_0G_1(u(t))]\alpha]e^{ (\gamma+\alpha)t}dt\\ v(t)=k=0qkik(t)=k=0qk(1rkeksk)=1w(t)m(t)s0k=0qkuk=1+βγlnum(t)s0G1(u)m(t)=1+βγlnus0G1(u)v(t)m(t)=α1[dtdv(t)+γv(t)](αγ+1)v(t)+α1dtdv(t)=1+βγlnus0G1(u)For ODE function dtdv+p(t)v=q(t)The solution is v(t)=ep(x)dxC+ep(x)dxq(x)ep(x)dxdxHere p(t)=γ+αq(t)=[1+βγlnus0G1(u)]αw(t)=βγlnudtdw=γv(t)βγu1dtdu=γv(t)dtdu=βuv(t)=βue(γ+α)dxC+e(γ+α)dx[[1+βγlnus0G1(u)]α]e(γ+α)dxdx=Cβue(γ+α)t+e(γ+α)t[[1+βγlnu(t)s0G1(u(t))]α]e(γ+α)tdt

Assume   s 0 = 1 ~s_0=1  s0=1:

d u d t = C β u e − ( γ + α ) t + e − ( γ + α ) t ∫ [ [ 1 + γ β l n u ( t ) − s 0 G 1 ( u ( t ) ) ] α ] e ( γ + α ) t d t s k ( t ) = u k s + e + i + r = 1 \frac{du}{dt}=C\beta ue^{-(\gamma+\alpha)t}+e^{-(\gamma+\alpha)t}\int [[1+\frac{\gamma}{\beta}ln u(t)-s_0G_1(u(t))]\alpha]e^{ (\gamma+\alpha)t}dt\\ s_k(t)=u^k\\ s+e +i+r=1 dtdu=Cβue(γ+α)t+e(γ+α)t[[1+βγlnu(t)s0G1(u(t))]α]e(γ+α)tdtsk(t)=uks+e+i+r=1

With the above equations, we could fit the lines of the rate of susceptible, infectious and recovered people and get the parameter estimation of γ \gamma γ , β \beta β, and α \alpha α. ( γ \gamma γ in the MGF method is just parameter for τ i \tau_i τi, since p ( τ ) d τ = γ e γ τ d τ p(\tau)d\tau=\gamma e^{\gamma \tau}d\tau p(τ)dτ=γeγτdτ, β \beta β is the T i j T_{ij} Tij which is simplified for the paired transmission, α \alpha α is the rate that exposed people become sick)

Here, we could rewrite the model of SEIR on network:
s k ( t ) = u ( t ) k d u d t = C β u e − ( γ + α ) t + e − ( γ + α ) t ∫ [ [ 1 + γ β l n u ( t ) − s 0 G 1 ( u ( t ) ) ] α ] e ( γ + α ) t d t d e k d t = k u ( t ) k − 1 d u d t − α e k d i k d t = α e k − γ i k d r k d t = γ i k s + e + i + r = 1 s_k(t)=u(t)^k\\ \frac{du}{dt}=C\beta ue^{-(\gamma+\alpha)t}+e^{-(\gamma+\alpha)t}\int [[1+\frac{\gamma}{\beta}ln u(t)-s_0G_1(u(t))]\alpha]e^{ (\gamma+\alpha)t}dt\\ \frac{de_k}{dt}=ku(t)^{k-1}\frac{du}{dt}-\alpha e_k\\ \frac{di_k}{dt}=\alpha e_k-\gamma i_k\\ \frac{dr_k}{dt}=\gamma i_k\\ s+e+i+r=1\\ sk(t)=u(t)kdtdu=Cβue(γ+α)t+e(γ+α)t[[1+βγlnu(t)s0G1(u(t))]α]e(γ+α)tdtdtdek=ku(t)k1dtduαekdtdik=αekγikdtdrk=γiks+e+i+r=1
Also, we could drive their iteration form with S = s N , E = e N , I = i N , R = r N S=sN, E=eN,I=iN, R=rN S=sN,E=eN,I=iN,R=rN and let c c c be the number of people one contact:
U n − α γ β l n U n + α G 1 ( U n ) = U n − 1 − α γ β l n U n − 1 + α G 1 ( U n − 1 ) + C β U n − 1 e − ( γ + α ) S n = U n k E n = E n − 1 + k U n − 1 ( t ) k − 1 [ C β U n − 1 e − ( γ + α ) + [ γ β l n U n − 1 − γ β l n U n − 2 − s 0 α [ G 1 ( U n − 1 ) − G 1 ( U n − 2 ) ] − α E n − 1 I n = I n − 1 + α E n − 1 − γ I n − 1 R n = R n − 1 + γ I n − 1 U_n-\frac{\alpha\gamma}{\beta}ln U_{n}+\alpha G_1(U_n)=U_{n-1}-\frac{\alpha\gamma}{\beta}ln U_{n-1}+\alpha G_1(U_{n-1})+C\beta U_{n-1}e^{-(\gamma+\alpha)}\\ S_n=U_n^k\\ E_n=E_{n-1}+kU_{n-1}(t)^{k-1}[C\beta U_{n-1}e^{-(\gamma+\alpha)}+ [\frac{\gamma}{\beta}ln U_{n-1}-\frac{\gamma}{\beta}ln U_{n-2}-s_0\alpha[G_1(U_{n-1})-G_1(U_{n-2})]-\alpha E_{n-1}\\ I_n=I_{n-1}+\alpha E_{n-1}-\gamma I_{n-1}\\ R_n=R_{n-1}+\gamma I_{n-1} UnβαγlnUn+αG1(Un)=Un1βαγlnUn1+αG1(Un1)+CβUn1e(γ+α)Sn=UnkEn=En1+kUn1(t)k1[CβUn1e(γ+α)+[βγlnUn1βγlnUn2s0α[G1(Un1)G1(Un2)]αEn1In=In1+αEn1γIn1Rn=Rn1+γIn1

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