The goal of precision oncology is to select more effective treatments or beneficial drugs for patients. The transcription of ‘‘hidden responders’’ which precision oncology often fails to identify for patients is important for revealing responsive molecular states. Recently, a RAS pathway activation detection method based on machine learning and a nature-inspired deep RAS activation pan-cancer has been proposed. However, we note that the activating gene variations found in KRAS, HRAS and NRAS vary substantially across cancers. Besides, the ability of a machine learning classifier to detect which KRAS, HRAS and NRAS gain of function mutations or copy number alterations causes the RAS pathway activation is not clear. Here, we proposed a deep neural network framework for deciphering and identifying pan-cancer RAS pathway activation (DIPRAS). DIPRAS brings a new insight into deciphering and identifying the pan-cancer RAS pathway activation from a deeper perspective. In addition, we further revealed the identification and characterization of RAS aberrant pathway activity through gene ontological enrichment and pathological analysis. The source code is available by the URL https://github.com/zhaoyw456/DIPRAS.
Citation: Jianting Gong, Yingwei Zhao, Xiantao Heng, Yongbing Chen, Pingping Sun, Fei He, Zhiqiang Ma, Zilin Ren. Deciphering and identifying pan-cancer RAS pathway activation based on graph autoencoder and ClassifierChain[J]. Electronic Research Archive, 2023, 31(8): 4951-4967. doi: 10.3934/era.2023253
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The goal of precision oncology is to select more effective treatments or beneficial drugs for patients. The transcription of ‘‘hidden responders’’ which precision oncology often fails to identify for patients is important for revealing responsive molecular states. Recently, a RAS pathway activation detection method based on machine learning and a nature-inspired deep RAS activation pan-cancer has been proposed. However, we note that the activating gene variations found in KRAS, HRAS and NRAS vary substantially across cancers. Besides, the ability of a machine learning classifier to detect which KRAS, HRAS and NRAS gain of function mutations or copy number alterations causes the RAS pathway activation is not clear. Here, we proposed a deep neural network framework for deciphering and identifying pan-cancer RAS pathway activation (DIPRAS). DIPRAS brings a new insight into deciphering and identifying the pan-cancer RAS pathway activation from a deeper perspective. In addition, we further revealed the identification and characterization of RAS aberrant pathway activity through gene ontological enrichment and pathological analysis. The source code is available by the URL https://github.com/zhaoyw456/DIPRAS.
Boundary value problems with p-Laplace operator Δpu=div(|∇u|p−2∇u) arise in many different areas of applied mathematics and physics, such as non-Newtonian fluids, reaction-diffusion problems, non-linear elasticity, etc. But little is known about the p-Laplace operator cases (p≠2) compared to the vast amount of knowledge for the Laplace operator (p=2). In this paper, we discuss the existence of positive radial solution for the p-Laplace boundary value problem (BVP)
{−Δpu=K(|x|)f(u),x∈Ω,∂u∂n=0,x∈∂Ω,lim|x|→∞u(x)=0, | (1.1) |
in the exterior domain Ω={x∈RN:|x|>r0}, where N≥2, r0>0, 1<p<N, ∂u∂n is the outward normal derivative of u on ∂Ω, K:[r0,∞)→R+ is a coefficient function, f:R+→R is a nonlinear function. Throughout this paper, we assume that the following conditions hold:
(A1) K∈C([r0,∞),R+) and 0<∫∞r0rN−1K(r)dr<∞;
(A2) f∈C(R+,R+);
For the special case of p=2, namely the Laplace boundary value problem
{−Δu=K(|x|)f(u),x∈Ω,∂u∂n=0,x∈∂Ω,lim|x|→∞u(x)=0, | (1.2) |
the existence of positive radial solutions has been discussed by many authors, see [1,2,3,4,5,6,7]. The authors of references[1,2,3,4,5,6] obtained some existence results by using upper and lower solutions method, priori estimates technique and fixed point index theory. In [7], the present author built an eigenvalue criteria of existing positive radial solutions. The eigenvalue criterion is related to the principle eigenvalue λ1 of the corresponding radially symmetric Laplace eigenvalue problem (EVP)
{−Δu=λK(|x|)u,x∈Ω,∂u∂n=0,x∈∂Ω,u=u(|x|),lim|x|→∞u(|x|)=0. | (1.3) |
Specifically, if f satisfies one of the following eigenvalue conditions:
(H1) f0<λ1, f∞>λ1;
(H2) f∞<λ1, f0>λ1,
the BVP(1.2) has a classical positive radial solution, where
f0=lim infu→0+f(u)u,f0=lim supu→0+f(u)u,f∞=lim infu→∞f(u)u,f∞=lim supu→∞f(u)u. |
See [7,Theorem 1.1]. This criterion first appeared in a boundary value problem of second-order ordinary differential equations, and built by Zhaoli Liu and Fuyi Li in [8]. Then it was extended to general boundary value problems of ordinary differential equations, See [9,10]. In [11,12], the radially symmetric solutions of the more general Hessian equations are discussed.
The purpose of this paper is to establish a similar existence result of positive radial solution of BVP (1.1). Our results are related to the principle eigenvalue λp,1 of the radially symmetric p-Laplce eigenvalue problem (EVP)
{−Δpu=λK(|x|)|u|p−2u,x∈Ω,∂u∂n=0,x∈∂Ω,u=u(|x|),lim|x|→∞u(|x|)=0. | (1.4) |
Different from EVP (1.3), EVP (1.4) is a nonlinear eigenvalue problem, and the spectral theory of linear operators is not applicable to it. In Section 2 we will prove that EVP (1.4) has a minimum positive real eigenvalue λp,1, see Lemma 2.3. For BVP (1.1), we conjecture that eigenvalue criteria is valid if f0, f0, f∞ and f∞ is replaced respectively by
fp0=lim infu→0+f(u)up−1,fp0=lim supu→0+f(u)up−1,fp∞=lim infu→∞f(u)up−1,fp∞=lim supu→∞f(u)up−1. | (1.5) |
But now we can only prove a weaker version of it: In second inequality of (H1) and (H2), λp,1 needs to be replaced by the larger number
B=[∫10Ψ(∫1stp−1a(t)dt)ds]−(p−1), | (1.6) |
where a∈C+(0,1] is given by (2.4) and Ψ∈C(R) is given by (2.7). Our result is as follows:
Theorem 1.1. Suppose that Assumptions (A1) and (A2) hold. If the nonlinear function f satisfies one of the the following conditions:
(H1)∗ fp0<λp,1, fp∞>B;
(H2)∗ fp∞<λp,1, fp0>B,
then BVP (1.1) has at least one classical positive radial solution.
As an example of the application of Theorem 1.1, we consider the following p-Laplace boundary value problem
{−Δpu=K(|x|)|u|γ,x∈Ω,∂u∂n=0,x∈∂Ω,lim|x|→∞u(x)=0. | (1.7) |
Corresponding to BVP (1.1), f(u)=|u|γ. If γ>p−1, by (1.5) fp0=0, fp∞=+∞, and (H1) holds. If 0<γ<p−1, then fp∞=0, fp0=+∞, and (H2) holds. Hence, by Theorem 1.1 we have
Corollary 1. Let K:[r0,∞)→R+ satisfy Assumption (A1), γ>0 and γ≠p−1. Then BVP (1.7) has a positive radial solution.
The proof of Theorem 1.1 is based on the fixed point index theory in cones, which will be given in Section 3. Some preliminaries to discuss BVP (1.1) are presented in Section 2.
For the radially symmetric solution u=u(|x|) of BVP (1.1), setting r=|x|, since
−Δpu=div(|∇u|p−2∇u)=−(|u′(r)|p−2u′(r))′−N−1r|u′(r)|p−2u′(r), |
BVP (1.1) becomes the ordinary differential equation BVP in [r0,∞)
{−(|u′(r)|p−2u′(r))′−N−1r|u′(r)|p−2u′(r)=K(r)f(u(r)),r∈[r0,∞),u′(r0)=0,u(∞)=0, | (2.1) |
where u(∞)=limr→∞u(r).
Let q>1 be the constant satisfying 1p+1q=1. To solve BVP (2.1), make the variable transformations
t=(r0r)(q−1)(N−p),r=r0t−1/(q−1)(N−p),v(t)=u(r(t)), | (2.2) |
Then BVP (2.1) is converted to the ordinary differential equation BVP in (0,1]
{−(|v′(t)|p−2v′(t))′=a(t)f(v(t)),t∈(0,1],v(0)=0,v′(1)=0, | (2.3) |
where
a(t)=rq(N−1)(t)(q−1)p(N−p)pr0q(N−p)K(r(t)),t∈(0,1]. | (2.4) |
BVP (2.3) is a quasilinear ordinary differential equation boundary value problem with singularity at t=0. A solution v of BVP (2.3) means that v∈C1[0,1] such that |v′|p−2v′∈C1(0,1] and it satisfies the Eq (2.3). Clearly, if v is a solution of BVP (2.3), then u(r)=v(t(r)) is a solution of BVP (2.1) and u(|x|) is a classical radial solution of BVP (1.1). We discuss BVP (2.3) to obtain positive radial solutions of BVP (1.1).
Let I=[0,1] and R+=[0,+∞). Let C(I) denote the Banach space of all continuous function v(t) on I with norm ‖v‖C=maxt∈I|v(t)|, C1(I) denote the Banach space of all continuous differentiable function on I. Let C+(I) be the cone of all nonnegative functions in C(I).
To discuss BVP (2.3), we first consider the corresponding simple boundary value problem
{−(|v′(t)|p−2v′(t))′=a(t)h(t),t∈(0,1],v(0)=0,v′(1)=0, | (2.5) |
where h∈C+(I) is a given function. Let
Φ(v)=|v|p−2v=|v|p−1sgnv,v∈R, | (2.6) |
then w=Φ(v) is a strictly monotone increasing continuous function on R and its inverse function
Φ−1(w):=Ψ(w)=|w|q−1sgnw,w∈R, | (2.7) |
is also a strictly monotone increasing continuous function.
Lemma 2.1. For every h∈C(I), BVP (2.5) has a unique solution v:=Sh∈C1(I). Moreover, the solution operator S:C(I)→C(I) is completely continuous and has the homogeneity
S(νh)=νq−1Sh,h∈C(I),ν≥0. | (2.8) |
Proof. By (2.4) and Assumption (A1), the coefficient a(t)∈C+(0,1] and satisfies
∫10a(t)dt=1[(q−1)(N−p)]p−1r0N−p∫∞r0rN−1K(r)dr<∞. | (2.9) |
Hence a∈L(I).
For every h∈C(I), we verify that
v(t)=∫t0Ψ(∫1sa(τ)h(τ)dτ)ds:=Sh(t),t∈I | (2.10) |
is a unique solution of BVP (2.5). Since the function G(s):=∫1sa(τ)h(τ)dτ∈C(I), from (2.10) it follows that v∈C1(I) and
v′(t)=Ψ(∫1ta(τ)h(τ)dτ),t∈I. | (2.11) |
Hence,
|v′(t)|p−2v′(t)=Φ(v′(t))=∫1ta(τ)h(τ)dτ,t∈I. |
This means that (|v′(t)|p−2v′(t)∈C1(0,1] and
(|v′(t)|p−2v′(t))′=−a(t)h(t),t∈(0,1], |
that is, v is a solution of BVP (2.5).
Conversely, if v is a solution of BVP (2.5), by the definition of the solution of BVP (2.5), it is easy to show that v can be expressed by (2.10). Hence, BVP (2.5) has a unique solution v=Sh.
By (2.10) and the continuity of Ψ, the solution operator S:C(I)→C(I) is continuous. Let D⊂C(I) be bounded. By (2.10) and (2.11) we can show that S(D) and its derivative set {v′|v∈S(D)} are bounded sets in C(I). By the Ascoli-Arzéla theorem, S(D) is a precompact subset of C(I). Thus, S:C(I)→C(I) is completely continuous.
By the uniqueness of solution of BVP (2.5), we easily verify that the solution operator S satisfies (2.8).
Lemma 2.2. If h∈C+(I), then the solution v=Sh of LBVP (2.5) satisfies: ‖v‖c=v(1), v(t)≥t‖v‖C for every t∈I.
Proof. Let h∈C+(I) and v=Sh. By (2.10) and (2.11), for every t∈I v(t)≥0 and v′(t)≥0. Hence, v(t) is a nonnegative monotone increasing function and ‖v‖C=maxt∈Iv(t)=v(1). From (2.11) and the monotonicity of Ψ, we notice that v′(t) is a monotone decreasing function on I. For every t∈(0,1), by Lagrange's mean value theorem, there exist ξ1∈(0,t) and ξ2∈(t,1), such that
(1−t)v(t)=(1−t)(v(t)−v(0))=v′(ξ1)t(1−t)≥v′(t)t(1−t),tv(t)=tv(1)−t(v(1)−v(t))=tv(1)−tv′(ξ2)(1−t)≥tv(1)−v′(t)t(1−t). |
Hence
v(t)=tv(t)+(1−t)v(t)≥tv(1)=t‖v‖C. |
Obviously, when t=0 or 1, this inequality also holds. The proof is completed.
Consider the radially symmetric p-Laplace eigenvalue problem EVP (1.3). We have
Lemma 2.3. EVP (1.4) has a minimum positive real eigenvalue λp,1, and λp,1 has a radially symmetric positive eigenfunction.
Proof. For the radially symmetric eigenvalue problem EVP (1.4), writing r=|x| and making the variable transformations of (2.2), it is converted to the one-dimensional weighted p-Laplace eigenvalue problem (EVP)
{−(|v′(t)|p−2v′(t))′=λa(t)|v(t)|p−2v(t),t∈(0,1],v(0)=0,v′(1)=0, | (2.12) |
where v(t)=u(r(t)). Clearly, λ∈R is an eigenvalue of EVP (1.4) if and only if it is an eigenvalue of EVP (2.12). By (2.4) and (2.9), a∈C+(0,1]∩L(I) and ∫10a(s)ds>0. This guarantees that EVP (2.12) has a minimum positive real eigenvalue λp,1, which given by
λp,1=inf{∫10|w′(t)|pdt∫10a(t)wp(t)dt|w∈C1(I),w(0)=0,w′(1)=0,∫10a(t)wp(t)dt≠0}. | (2.13) |
Moreover, λp,1 is simple and has a positive eigenfunction ϕ∈C+(I)∩C1(I). See [13, Theorem 5], [14, Theorem 1.1] or [15, Theorem 1.2]. Hence, λp,1 is also the minimum positive real eigenvalue of EVP (1.4), and ϕ((r0/|x|)(q−1)(N−p)) is corresponding positive eigenfunction.
Now we consider BVP (2.3). Define a closed convex cone K of C(I) by
K={v∈C(I)|v(t)≥t‖v‖C,t∈I}. | (2.14) |
By Lemma 2.2, S(C+(I))⊂K. Let f∈C(R+,R+), and define a mapping F:K→C+(I) by
F(v)(t):=f(v(t)),t∈I. | (2.15) |
Then F:K→C+(I) is continuous and it maps every bounded subset of K into a bounded subset of C+(I). Define the composite mapping by
A=S∘F. | (2.16) |
Then A:K→K is completely continuous by the complete continuity of the operator S:C+(I)→K. By the definitions of S and K, the positive solution of BVP (2.3) is equivalent to the nonzero fixed point of A.
Let E be a Banach space and K⊂E be a closed convex cone in E. Assume D is a bounded open subset of E with boundary ∂D, and K∩D≠∅. Let A:K∩¯D→K be a completely continuous mapping. If Av≠v for every v∈K∩∂D, then the fixed point index i(A,K∩D,K) is well defined. One important fact is that if i(A,K∩D,K)≠0, then A has a fixed point in K∩D. In next section, we will use the following two lemmas in [16,17] to find the nonzero fixed point of the mapping A defined by (2.16).
Lemma 2.4. Let D be a bounded open subset of E with 0∈D, and A:K∩¯D→K a completely continuous mapping. If μAv≠v for every v∈K∩∂D and 0<μ≤1, then i(A,K∩D,K)=1.
Lemma 2.5. Let D be a bounded open subset of E with 0∈D, and A:K∩¯D→K a completely continuous mapping. If ‖Av‖≥‖v‖ and Av≠v for every v∈K∩∂D, then i(A,K∩D,K)=0.
Proof of Theorem 1.1. We only consider the case that (H1)* holds, and the case that (H2)* holds can be proved by a similar way.
Let K⊂C(I) be the closed convex cone defined by (2.14) and A:K→K be the completely continuous mapping defined by (2.16). If v∈K is a nontrivial fixed point of A, then by the definitions of S and A, v(t) is a positive solution of BVP (2.3) and u=v(r0N−2/|x|N−2) is a classical positive radial solution of BVP (1.1). Let 0<R1<R2<+∞ and set
D1={v∈C(I):‖v‖C<R1},D2={v∈C(I):‖v‖C<R2}. | (3.1) |
We prove that A has a fixed point in K∩(¯D2∖D1) when R1 is small enough and R2 large enough.
Since fp0<λp,1, by the definition of fp0, there exist ε∈(0,λp,1) and δ>0, such that
f(u)≤(λp,1−ε)up−1,0≤u≤δ. | (3.2) |
Choosing R1∈(0,δ), we prove that A satisfies the condition of Lemma 2.4 in K∩∂D1, namely
μAv≠v,∀v∈K∩∂D1,0<μ≤1. | (3.3) |
In fact, if (3.3) does not hold, there exist v0∈K∩∂D1 and 0<μ0≤1 such that μ0Av0=v0. By the homogeneity of S, v0=μ0S(F(v0))=S(μ0p−1F(v0)). By the definition of S, v0 is the unique solution of BVP (2.5) for h=μ0p−1F(v0)∈C+(I). Hence, v0∈C1(I) satisfies the differential equation
{−(|v′0(t)|p−2v0′(t))′=μ0p−1a(t)f(v0(t)),t∈(0,1],v0(0)=0,v0′(1)=0. | (3.4) |
Since v0∈K∩∂D1, by the definitions of K and D1,
0≤v0(t)≤‖v0‖C=R1<δ,t∈I. |
Hence by (3.2),
f(v0(t))≤(λp,1−ε)v0p−1(t),t∈I. |
By this inequality and Eq (3.4), we have
−(|v′0(t)|p−2v0′(t))′≤μ0p−1(λp,1−ε)a(t)v0p−1(t),t∈(0,1]. |
Multiplying this inequality by v0(t) and integrating on (0,1], then using integration by parts for the left side, we have
∫10|v′0(t)|pdt≤μ0p−1(λp,1−ε)∫10a(t)v0p(t)dt≤(λp,1−ε)∫10a(t)v0p(t)dt. | (3.5) |
Since v0∈K∩∂D, by the definition of K,
∫10a(t)v0p(t)dt≥‖v0‖Cp∫10tpa(t)dt=R1p∫10tpa(t)dt>0. |
Hence, by (2.13) and (3.5) we obtain that
λp,1≤∫10|v′0(t)|pdt∫10a(t)v0p(t)dt≤λp,1−ε, |
which is a contradiction. This means that (3.3) holds, namely A satisfies the condition of Lemma 2.4 in K∩∂D1. By Lemma 2.4, we have
i(A,K∩D1,K)=1. | (3.6) |
On the other hand, by the definition (1.6) of B, we have
B<[∫1σΨ(∫1stp−1a(t)dt)ds]−(p−1)→B(σ→0+),σ∈(0,1). | (3.7) |
Since fp∞>B, by (3.7) there exists σ0∈(0,1), such that
B0:=[∫1σ0Ψ(∫1stp−1a(t)dt)ds]−(p−1)<fp∞. | (3.8) |
By this inequality and the definition of fp∞, there exists H>0 such that
f(u)>B0up−1,u>H. | (3.9) |
Choosing R2>max{δ,H/σ0}, we show that
‖Av‖C≥‖v‖C,v∈K∩∂D2. | (3.10) |
For ∀v∈K∩∂D2 and t∈[σ0,1], by the definitions of K and D2
v(t)≥t‖v‖C≥σ0R2>H. |
By this inequality and (3.9),
f(v(t))>B0vp−1(t)≥B0‖v‖p−1Ctp−1,t∈[σ0,1]. | (3.11) |
Since Av=S(F(v)), by the expression (2.10) of the solution operator S and (3.11), noticing (p−1)(q−1)=1, we have
‖Av‖C≥Av(1)=∫10Ψ(∫1sa(t)f(v(t))dt)ds≥∫1σ0Ψ(∫1sa(t)f(v(t))dt)ds≥∫1σ0Ψ(∫1sa(t)B0‖v‖p−1Ctp−1dt)ds=Bq−10‖v‖C∫1σ0Ψ(∫1stp−1a(t)dt)ds=‖v‖C. |
Namely, (3.10) holds. Suppose A has no fixed point on ∂D2. Then by (3.10), A satisfies the condition of Lemma 2.5 in K∩∂D2. By Lemma 2.5, we have
i(A,K∩D2,K)=0. | (3.12) |
By the additivity of fixed point index, (3.6) and (3.11), we have
i(A,K∩(D2∖¯D1),K)=i(A,K∩D2,K)−i(A,K∩D1,K)=−1. |
Hence A has a fixed point in K∩(D2∖¯D1).
The proof of Theorem 1.1 is complete.
The authors would like to express sincere thanks to the reviewers for their helpful comments and suggestions. This research was supported by National Natural Science Foundations of China (No.12061062, 11661071).
The authors declare that they have no competing interests.
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