An Introduction to Systems Biology from a Machine Learning Perspective <span>II</span>

$$\newcommand{\tk}[1]{} \newcommand{\Amatrix}{\mathbf{A}} \newcommand{\KL}[2]{\text{KL}\left( #1\,\|\,#2 \right)} \newcommand{\Kaast}{\kernelMatrix_{\mathbf{ \ast}\mathbf{ \ast}}} \newcommand{\Kastu}{\kernelMatrix_{\mathbf{ \ast} \inducingVector}} \newcommand{\Kff}{\kernelMatrix_{\mappingFunctionVector \mappingFunctionVector}} \newcommand{\Kfu}{\kernelMatrix_{\mappingFunctionVector \inducingVector}} \newcommand{\Kuast}{\kernelMatrix_{\inducingVector \bf\ast}} \newcommand{\Kuf}{\kernelMatrix_{\inducingVector \mappingFunctionVector}} \newcommand{\Kuu}{\kernelMatrix_{\inducingVector \inducingVector}} \newcommand{\Kuui}{\Kuu^{-1}} \newcommand{\Qaast}{\mathbf{Q}_{\bf \ast \ast}} \newcommand{\Qastf}{\mathbf{Q}_{\ast \mappingFunction}} \newcommand{\Qfast}{\mathbf{Q}_{\mappingFunctionVector \bf \ast}} \newcommand{\Qff}{\mathbf{Q}_{\mappingFunctionVector \mappingFunctionVector}} \newcommand{\aMatrix}{\mathbf{A}} \newcommand{\aScalar}{a} \newcommand{\aVector}{\mathbf{a}} \newcommand{\acceleration}{a} \newcommand{\bMatrix}{\mathbf{B}} \newcommand{\bScalar}{b} \newcommand{\bVector}{\mathbf{b}} \newcommand{\basisFunc}{\phi} \newcommand{\basisFuncVector}{\boldsymbol{ \basisFunc}} \newcommand{\basisFunction}{\phi} \newcommand{\basisLocation}{\mu} \newcommand{\basisMatrix}{\boldsymbol{ \Phi}} \newcommand{\basisScalar}{\basisFunction} \newcommand{\basisVector}{\boldsymbol{ \basisFunction}} \newcommand{\activationFunction}{\phi} \newcommand{\activationMatrix}{\boldsymbol{ \Phi}} \newcommand{\activationScalar}{\basisFunction} \newcommand{\activationVector}{\boldsymbol{ \basisFunction}} \newcommand{\bigO}{\mathcal{O}} \newcommand{\binomProb}{\pi} \newcommand{\cMatrix}{\mathbf{C}} \newcommand{\cbasisMatrix}{\hat{\boldsymbol{ \Phi}}} \newcommand{\cdataMatrix}{\hat{\dataMatrix}} \newcommand{\cdataScalar}{\hat{\dataScalar}} \newcommand{\cdataVector}{\hat{\dataVector}} \newcommand{\centeredKernelMatrix}{\mathbf{ \MakeUppercase{\centeredKernelScalar}}} \newcommand{\centeredKernelScalar}{b} \newcommand{\centeredKernelVector}{\centeredKernelScalar} \newcommand{\centeringMatrix}{\mathbf{H}} \newcommand{\chiSquaredDist}[2]{\chi_{#1}^{2}\left(#2\right)} \newcommand{\chiSquaredSamp}[1]{\chi_{#1}^{2}} \newcommand{\conditionalCovariance}{\boldsymbol{ \Sigma}} \newcommand{\coregionalizationMatrix}{\mathbf{B}} \newcommand{\coregionalizationScalar}{b} \newcommand{\coregionalizationVector}{\mathbf{ \coregionalizationScalar}} \newcommand{\covDist}[2]{\text{cov}_{#2}\left(#1\right)} \newcommand{\covSamp}[1]{\text{cov}\left(#1\right)} \newcommand{\covarianceScalar}{c} \newcommand{\covarianceVector}{\mathbf{ \covarianceScalar}} \newcommand{\covarianceMatrix}{\mathbf{C}} \newcommand{\covarianceMatrixTwo}{\boldsymbol{ \Sigma}} \newcommand{\croupierScalar}{s} \newcommand{\croupierVector}{\mathbf{ \croupierScalar}} \newcommand{\croupierMatrix}{\mathbf{ \MakeUppercase{\croupierScalar}}} \newcommand{\dataDim}{p} \newcommand{\dataIndex}{i} \newcommand{\dataIndexTwo}{j} \newcommand{\dataMatrix}{\mathbf{Y}} \newcommand{\dataScalar}{y} \newcommand{\dataSet}{\mathcal{D}} \newcommand{\dataStd}{\sigma} \newcommand{\dataVector}{\mathbf{ \dataScalar}} \newcommand{\decayRate}{d} \newcommand{\degreeMatrix}{\mathbf{ \MakeUppercase{\degreeScalar}}} \newcommand{\degreeScalar}{d} \newcommand{\degreeVector}{\mathbf{ \degreeScalar}} \newcommand{\diag}[1]{\text{diag}\left(#1\right)} \newcommand{\diagonalMatrix}{\mathbf{D}} \newcommand{\diff}[2]{\frac{\text{d}#1}{\text{d}#2}} \newcommand{\diffTwo}[2]{\frac{\text{d}^2#1}{\text{d}#2^2}} \newcommand{\displacement}{x} \newcommand{\displacementVector}{\textbf{\displacement}} \newcommand{\distanceMatrix}{\mathbf{ \MakeUppercase{\distanceScalar}}} \newcommand{\distanceScalar}{d} \newcommand{\distanceVector}{\mathbf{ \distanceScalar}} \newcommand{\eigenvaltwo}{\ell} \newcommand{\eigenvaltwoMatrix}{\mathbf{L}} \newcommand{\eigenvaltwoVector}{\mathbf{l}} \newcommand{\eigenvalue}{\lambda} \newcommand{\eigenvalueMatrix}{\boldsymbol{ \Lambda}} \newcommand{\eigenvalueVector}{\boldsymbol{ \lambda}} \newcommand{\eigenvector}{\mathbf{ \eigenvectorScalar}} \newcommand{\eigenvectorMatrix}{\mathbf{U}} \newcommand{\eigenvectorScalar}{u} \newcommand{\eigenvectwo}{\mathbf{v}} \newcommand{\eigenvectwoMatrix}{\mathbf{V}} \newcommand{\eigenvectwoScalar}{v} \newcommand{\entropy}[1]{\mathcal{H}\left(#1\right)} \newcommand{\errorFunction}{E} \newcommand{\expDist}[2]{\left\langle#1\right\rangle_{#2}} \newcommand{\expSamp}[1]{\left\langle#1\right\rangle} \newcommand{\expectation}[1]{\left\langle #1 \right\rangle } \newcommand{\expectationDist}[2]{\left\langle #1 \right\rangle _{#2}} \newcommand{\expectedDistanceMatrix}{\mathcal{D}} \newcommand{\eye}{\mathbf{I}} \newcommand{\fantasyDim}{r} \newcommand{\fantasyMatrix}{\mathbf{ \MakeUppercase{\fantasyScalar}}} \newcommand{\fantasyScalar}{z} \newcommand{\fantasyVector}{\mathbf{ \fantasyScalar}} \newcommand{\featureStd}{\varsigma} \newcommand{\gammaCdf}[3]{\mathcal{GAMMA CDF}\left(#1|#2,#3\right)} \newcommand{\gammaDist}[3]{\mathcal{G}\left(#1|#2,#3\right)} \newcommand{\gammaSamp}[2]{\mathcal{G}\left(#1,#2\right)} \newcommand{\gaussianDist}[3]{\mathcal{N}\left(#1|#2,#3\right)} \newcommand{\gaussianSamp}[2]{\mathcal{N}\left(#1,#2\right)} \newcommand{\uniformDist}[3]{\mathcal{U}\left(#1|#2,#3\right)} \newcommand{\uniformSamp}[2]{\mathcal{U}\left(#1,#2\right)} \newcommand{\given}{|} \newcommand{\half}{\frac{1}{2}} \newcommand{\heaviside}{H} \newcommand{\hiddenMatrix}{\mathbf{ \MakeUppercase{\hiddenScalar}}} \newcommand{\hiddenScalar}{h} \newcommand{\hiddenVector}{\mathbf{ \hiddenScalar}} \newcommand{\identityMatrix}{\eye} \newcommand{\inducingInputScalar}{z} \newcommand{\inducingInputVector}{\mathbf{ \inducingInputScalar}} \newcommand{\inducingInputMatrix}{\mathbf{Z}} \newcommand{\inducingScalar}{u} \newcommand{\inducingVector}{\mathbf{ \inducingScalar}} \newcommand{\inducingMatrix}{\mathbf{U}} \newcommand{\inlineDiff}[2]{\text{d}#1/\text{d}#2} \newcommand{\inputDim}{q} \newcommand{\inputMatrix}{\mathbf{X}} \newcommand{\inputScalar}{x} \newcommand{\inputSpace}{\mathcal{X}} \newcommand{\inputVals}{\inputVector} \newcommand{\inputVector}{\mathbf{ \inputScalar}} \newcommand{\iterNum}{k} \newcommand{\kernel}{\kernelScalar} \newcommand{\kernelMatrix}{\mathbf{K}} \newcommand{\kernelScalar}{k} \newcommand{\kernelVector}{\mathbf{ \kernelScalar}} \newcommand{\kff}{\kernelScalar_{\mappingFunction \mappingFunction}} \newcommand{\kfu}{\kernelVector_{\mappingFunction \inducingScalar}} \newcommand{\kuf}{\kernelVector_{\inducingScalar \mappingFunction}} \newcommand{\kuu}{\kernelVector_{\inducingScalar \inducingScalar}} \newcommand{\lagrangeMultiplier}{\lambda} \newcommand{\lagrangeMultiplierMatrix}{\boldsymbol{ \Lambda}} \newcommand{\lagrangian}{L} \newcommand{\laplacianFactor}{\mathbf{ \MakeUppercase{\laplacianFactorScalar}}} \newcommand{\laplacianFactorScalar}{m} \newcommand{\laplacianFactorVector}{\mathbf{ \laplacianFactorScalar}} \newcommand{\laplacianMatrix}{\mathbf{L}} \newcommand{\laplacianScalar}{\ell} \newcommand{\laplacianVector}{\mathbf{ \ell}} \newcommand{\latentDim}{q} \newcommand{\latentDistanceMatrix}{\boldsymbol{ \Delta}} \newcommand{\latentDistanceScalar}{\delta} \newcommand{\latentDistanceVector}{\boldsymbol{ \delta}} \newcommand{\latentForce}{f} \newcommand{\latentFunction}{u} \newcommand{\latentFunctionVector}{\mathbf{ \latentFunction}} \newcommand{\latentFunctionMatrix}{\mathbf{ \MakeUppercase{\latentFunction}}} \newcommand{\latentIndex}{j} \newcommand{\latentScalar}{z} \newcommand{\latentVector}{\mathbf{ \latentScalar}} \newcommand{\latentMatrix}{\mathbf{Z}} \newcommand{\learnRate}{\eta} \newcommand{\lengthScale}{\ell} \newcommand{\rbfWidth}{\ell} \newcommand{\likelihoodBound}{\mathcal{L}} \newcommand{\likelihoodFunction}{L} \newcommand{\locationScalar}{\mu} \newcommand{\locationVector}{\boldsymbol{ \locationScalar}} \newcommand{\locationMatrix}{\mathbf{M}} \newcommand{\variance}[1]{\text{var}\left( #1 \right)} \newcommand{\mappingFunction}{f} \newcommand{\mappingFunctionMatrix}{\mathbf{F}} \newcommand{\mappingFunctionTwo}{g} \newcommand{\mappingFunctionTwoMatrix}{\mathbf{G}} \newcommand{\mappingFunctionTwoVector}{\mathbf{ \mappingFunctionTwo}} \newcommand{\mappingFunctionVector}{\mathbf{ \mappingFunction}} \newcommand{\scaleScalar}{s} \newcommand{\mappingScalar}{w} \newcommand{\mappingVector}{\mathbf{ \mappingScalar}} \newcommand{\mappingMatrix}{\mathbf{W}} \newcommand{\mappingScalarTwo}{v} \newcommand{\mappingVectorTwo}{\mathbf{ \mappingScalarTwo}} \newcommand{\mappingMatrixTwo}{\mathbf{V}} \newcommand{\maxIters}{K} \newcommand{\meanMatrix}{\mathbf{M}} \newcommand{\meanScalar}{\mu} \newcommand{\meanTwoMatrix}{\mathbf{M}} \newcommand{\meanTwoScalar}{m} \newcommand{\meanTwoVector}{\mathbf{ \meanTwoScalar}} \newcommand{\meanVector}{\boldsymbol{ \meanScalar}} \newcommand{\mrnaConcentration}{m} \newcommand{\naturalFrequency}{\omega} \newcommand{\neighborhood}[1]{\mathcal{N}\left( #1 \right)} \newcommand{\neilurl}{http://inverseprobability.com/} \newcommand{\noiseMatrix}{\boldsymbol{ E}} \newcommand{\noiseScalar}{\epsilon} \newcommand{\noiseVector}{\boldsymbol{ \epsilon}} \newcommand{\noiseStd}{\sigma} \newcommand{\norm}[1]{\left\Vert #1 \right\Vert} \newcommand{\normalizedLaplacianMatrix}{\hat{\mathbf{L}}} \newcommand{\normalizedLaplacianScalar}{\hat{\ell}} \newcommand{\normalizedLaplacianVector}{\hat{\mathbf{ \ell}}} \newcommand{\numActive}{m} \newcommand{\numBasisFunc}{m} \newcommand{\numComponents}{m} \newcommand{\numComps}{K} \newcommand{\numData}{n} \newcommand{\numFeatures}{K} \newcommand{\numHidden}{h} \newcommand{\numInducing}{m} \newcommand{\numLayers}{\ell} \newcommand{\numNeighbors}{K} \newcommand{\numSequences}{s} \newcommand{\numSuccess}{s} \newcommand{\numTasks}{m} \newcommand{\numTime}{T} \newcommand{\numTrials}{S} \newcommand{\outputIndex}{j} \newcommand{\paramVector}{\boldsymbol{ \theta}} \newcommand{\parameterMatrix}{\boldsymbol{ \Theta}} \newcommand{\parameterScalar}{\theta} \newcommand{\parameterVector}{\boldsymbol{ \parameterScalar}} \newcommand{\partDiff}[2]{\frac{\partial#1}{\partial#2}} \newcommand{\precisionScalar}{j} \newcommand{\precisionVector}{\mathbf{ \precisionScalar}} \newcommand{\precisionMatrix}{\mathbf{J}} \newcommand{\pseudotargetScalar}{\widetilde{y}} \newcommand{\pseudotargetVector}{\mathbf{ \pseudotargetScalar}} \newcommand{\pseudotargetMatrix}{\mathbf{ \widetilde{Y}}} \newcommand{\rank}[1]{\text{rank}\left(#1\right)} \newcommand{\rayleighDist}[2]{\mathcal{R}\left(#1|#2\right)} \newcommand{\rayleighSamp}[1]{\mathcal{R}\left(#1\right)} \newcommand{\responsibility}{r} \newcommand{\rotationScalar}{r} \newcommand{\rotationVector}{\mathbf{ \rotationScalar}} \newcommand{\rotationMatrix}{\mathbf{R}} \newcommand{\sampleCovScalar}{s} \newcommand{\sampleCovVector}{\mathbf{ \sampleCovScalar}} \newcommand{\sampleCovMatrix}{\mathbf{s}} \newcommand{\scalarProduct}[2]{\left\langle{#1},{#2}\right\rangle} \newcommand{\sign}[1]{\text{sign}\left(#1\right)} \newcommand{\sigmoid}[1]{\sigma\left(#1\right)} \newcommand{\singularvalue}{\ell} \newcommand{\singularvalueMatrix}{\mathbf{L}} \newcommand{\singularvalueVector}{\mathbf{l}} \newcommand{\sorth}{\mathbf{u}} \newcommand{\spar}{\lambda} \newcommand{\trace}[1]{\text{tr}\left(#1\right)} \newcommand{\BasalRate}{B} \newcommand{\DampingCoefficient}{C} \newcommand{\DecayRate}{D} \newcommand{\Displacement}{X} \newcommand{\LatentForce}{F} \newcommand{\Mass}{M} \newcommand{\Sensitivity}{S} \newcommand{\basalRate}{b} \newcommand{\dampingCoefficient}{c} \newcommand{\mass}{m} \newcommand{\sensitivity}{s} \newcommand{\springScalar}{\kappa} \newcommand{\springVector}{\boldsymbol{ \kappa}} \newcommand{\springMatrix}{\boldsymbol{ \mathcal{K}}} \newcommand{\tfConcentration}{p} \newcommand{\tfDecayRate}{\delta} \newcommand{\tfMrnaConcentration}{f} \newcommand{\tfVector}{\mathbf{ \tfConcentration}} \newcommand{\velocity}{v} \newcommand{\sufficientStatsScalar}{g} \newcommand{\sufficientStatsVector}{\mathbf{ \sufficientStatsScalar}} \newcommand{\sufficientStatsMatrix}{\mathbf{G}} \newcommand{\switchScalar}{s} \newcommand{\switchVector}{\mathbf{ \switchScalar}} \newcommand{\switchMatrix}{\mathbf{S}} \newcommand{\tr}[1]{\text{tr}\left(#1\right)} \newcommand{\loneNorm}[1]{\left\Vert #1 \right\Vert_1} \newcommand{\ltwoNorm}[1]{\left\Vert #1 \right\Vert_2} \newcommand{\onenorm}[1]{\left\vert#1\right\vert_1} \newcommand{\twonorm}[1]{\left\Vert #1 \right\Vert} \newcommand{\vScalar}{v} \newcommand{\vVector}{\mathbf{v}} \newcommand{\vMatrix}{\mathbf{V}} \newcommand{\varianceDist}[2]{\text{var}_{#2}\left( #1 \right)} \newcommand{\vecb}[1]{\left(#1\right):} \newcommand{\weightScalar}{w} \newcommand{\weightVector}{\mathbf{ \weightScalar}} \newcommand{\weightMatrix}{\mathbf{W}} \newcommand{\weightedAdjacencyMatrix}{\mathbf{A}} \newcommand{\weightedAdjacencyScalar}{a} \newcommand{\weightedAdjacencyVector}{\mathbf{ \weightedAdjacencyScalar}} \newcommand{\onesVector}{\mathbf{1}} \newcommand{\zerosVector}{\mathbf{0}} $$