Mcmc Hierarchical Dcm Clustering

2. 层次聚类模型

# 层次聚类结构
class HierarchicalClusteringModel:
    """
    层次聚类模型

    结构：
    - 第一层：聚类分配（z_i ∈ {1,...,K}）
    - 第二层：聚类参数（θ_k）
    - 第三层：主体参数（φ_i）

    生成模型：
    p(z_i=k) = π_k  (聚类概率)
    p(φ_i|z_i=k) = N(φ_i|θ_k, Σ)  (主体参数)
    p(y_i|φ_i) = DCM_likelihood(y_i, φ_i)  (观测)
    """
    def __init__(self, n_clusters=3, n_subjects=50):
        self.K = n_clusters
        self.N = n_subjects

        # 聚类参数
        self.pi = np.ones(n_clusters) / n_clusters  # 聚类概率
        self.theta = []  # 聚类中心参数
        self.Sigma = None  # 协方差矩阵

        # 主体变量
        self.z = np.zeros(n_subjects, dtype=int)  # 聚类分配
        self.phi = []  # 主体参数

    def initialize(self, dcm_dim):
        """初始化参数"""
        # 从先验初始化聚类中心
        for k in range(self.K):
            self.theta.append(np.random.randn(dcm_dim) * 0.1)

        # 初始化协方差
        self.Sigma = np.eye(dcm_dim) * 0.1

        # 随机分配聚类
        self.z = np.random.randint(0, self.K, self.N)

3. 改进的 MCMC 提议分布

# 改进的 MCMC 提议
class ImprovedMCMCProposal:
    """
    改进的提议分布

    问题：DCM 参数高后验相关 → 标准 MCMC 收敛慢

    解决方案：
    1. 捕获聚类参数和主体参数的相互依赖
    2. 减少随机游走行为
    3. 仅引入单一超参数

    提议分布：
    q(φ_i'|φ_i, θ_{z_i}) = N(φ_i' | μ_prop, Σ_prop)

    其中：
    μ_prop = (1-λ)φ_i + λθ_{z_i}
    Σ_prop = λ * H(θ_{z_i})
    """
    def __init__(self, lambda_param=0.1):
        self.lambda_param = lambda_param  # 单一超参数

    def propose_subject_params(self, phi_i, theta_k, Sigma):
        """
        提议主体参数

        Args:
            phi_i: 当前主体参数
            theta_k: 聚类中心
            Sigma: 协方差矩阵

        Returns:
            phi_i_new: 提议的新参数
        """
        # 混合提议
        mu_prop = (1 - self.lambda_param) * phi_i + self.lambda_param * theta_k

        # 协方差调整
        Sigma_prop = self.lambda_param * self._compute_fisher(theta_k, Sigma)

        # 采样
        phi_i_new = np.random.multivariate_normal(mu_prop, Sigma_prop)
        return phi_i_new

    def _compute_fisher(self, theta, Sigma):
        """计算 Fisher 信息矩阵近似"""
        # 简化：使用 Hessian 近似
        return Sigma + 0.01 * np.eye(len(theta))

    def propose_cluster_assignment(self, z_i, pi, phi_i, theta, N):
        """
        提议聚类分配

        使用 Gibbs 采样：
        p(z_i=k|...) ∝ π_k * N(φ_i|θ_k, Σ)
        """
        log_probs = np.zeros(len(pi))
        for k in range(len(pi)):
            log_probs[k] = (np.log(pi[k]) +
                          self._log_normal_pdf(phi_i, theta[k], self.Sigma))

        # 归一化
        log_probs -= np.max(log_probs)
        probs = np.exp(log_probs)
        probs /= probs.sum()

        return np.random.choice(len(pi), p=probs)

    def _log_normal_pdf(self, x, mu, Sigma):
        """多元正态分布对数 PDF"""
        d = len(x)
        diff = x - mu
        return -0.5 * (d * np.log(2 * np.pi) +
                      np.log(np.linalg.det(Sigma)) +
                      diff.T @ np.linalg.inv(Sigma) @ diff)

4. MCMC 采样器

# 完整的 MCMC 采样器
class MCMCSampler:
    """
    MCMC 采样器 for 层次聚类

    采样步骤：
    1. 更新聚类分配 z_i
    2. 更新主体参数 φ_i
    3. 更新聚类中心 θ_k
    4. 更新聚类概率 π
    5. 更新协方差 Σ
    """
    def __init__(self, model, proposal):
        self.model = model
        self.proposal = proposal

        # 诊断统计
        self.acceptance_rate = 0.0
        self.n_accepted = 0
        self.n_total = 0

    def sample(self, data, n_iterations=5000, burnin=1000):
        """
        运行 MCMC 采样

        Args:
            data: 观测数据列表 [y_1, ..., y_N]
            n_iterations: 总迭代次数
            burnin: 预烧期

        Returns:
            samples: 后验样本
        """
        samples = {
            'z': [],
            'phi': [],
            'theta': [],
            'pi': []
        }

        for it in range(n_iterations):
            # 1. 更新聚类分配
            self._update_cluster_assignments(data)

            # 2. 更新主体参数
            self._update_subject_params(data)

            # 3. 更新聚类中心
            self._update_cluster_centers()

            # 4. 更新聚类概率
            self._update_cluster_probs()

            # 5. 更新协方差
            self._update_covariance()

            # 存储样本（预烧期后）
            if it >= burnin:
                samples['z'].append(self.model.z.copy())
                samples['theta'].append([t.copy() for t in self.model.theta])
                samples['pi'].append(self.model.pi.copy())

        return samples

    def _update_cluster_assignments(self, data):
        """更新聚类分配（Gibbs）"""
        for i in range(self.model.N):
            # 计算每个聚类的后验概率
            log_probs = np.zeros(self.model.K)
            for k in range(self.model.K):
                log_probs[k] = (np.log(self.model.pi[k]) +
                              self._log_likelihood(data[i], self.model.phi[i]))

            # 采样
            probs = np.exp(log_probs - np.max(log_probs))
            probs /= probs.sum()
            self.model.z[i] = np.random.choice(self.model.K, p=probs)

    def _update_subject_params(self, data):
        """更新主体参数（Metropolis-Hastings）"""
        for i in range(self.model.N):
            # 提议
            k = self.model.z[i]
            phi_new = self.proposal.propose_subject_params(
                self.model.phi[i],
                self.model.theta[k],
                self.model.Sigma
            )

            # 接受/拒绝
            log_alpha = self._compute_acceptance_prob(
                self.model.phi[i], phi_new, data[i], self.model.theta[k]
            )

            if np.log(np.random.random()) < log_alpha:
                self.model.phi[i] = phi_new
                self.n_accepted += 1
            self.n_total += 1

    def _compute_acceptance_prob(self, phi_old, phi_new, data, theta):
        """计算接受概率"""
        # 似然比
        ll_new = self._log_likelihood(data, phi_new)
        ll_old = self._log_likelihood(data, phi_old)

        # 先验比
        prior_new = self.proposal._log_normal_pdf(phi_new, theta, self.model.Sigma)
        prior_old = self.proposal._log_normal_pdf(phi_old, theta, self.model.Sigma)

        return (ll_new + prior_new) - (ll_old + prior_old)

5. 收敛诊断

# 收敛诊断工具
def gelman_rubin_diagnostic(chains):
    """
    Gelman-Rubin 收敛诊断

    R̂ 接近 1 表示收敛

    Args:
        chains: 多条链的样本 [n_chains, n_samples, n_params]

    Returns:
        R_hat: 收敛统计量
    """
    n_chains, n_samples, n_params = chains.shape

    # 链内方差
    W = np.mean([np.var(chain, axis=0) for chain in chains], axis=0)

    # 链间方差
    chain_means = np.mean(chains, axis=1)
    B = n_samples * np.var(chain_means, axis=0)

    # 后验方差估计
    var_plus = (n_samples - 1) / n_samples * W + B / n_samples

    # R-hat
    R_hat = np.sqrt(var_plus / W)

    return R_hat

def effective_sample_size(samples):
    """
    有效样本大小（ESS）

    考虑自相关后的等效独立样本数
    """
    n = len(samples)
    acf = autocorrelation(samples)

    # ESS = n / (1 + 2 * Σ ρ_k)
    ess = n / (1 + 2 * np.sum(acf[1:n//2]))

    return max(1, ess)

def autocorrelation(x):
    """计算自相关函数"""
    n = len(x)
    mean = np.mean(x)
    var = np.var(x)

    acf = np.zeros(n)
    for k in range(n):
        acf[k] = np.mean((x[:n-k] - mean) * (x[k:] - mean)) / var

    return acf

使用场景

fMRI 亚组分析

# 完整分析流程
def analyze_fmri_subgroups(fmri_data, n_clusters=3):
    """
    分析 fMRI 数据中的亚组

    Args:
        fmri_data: 被试 fMRI 数据列表
        n_clusters: 聚类数量

    Returns:
        clustering_results: 聚类结果
    """
    # 1. 为每个被试拟合 DCM
    dcm_fits = []
    for data in fmri_data:
        dcm = DynamicCausalModel(n_regions=4)
        # 拟合 DCM（省略细节）
        dcm_fits.append(dcm)

    # 2. 初始化层次模型
    model = HierarchicalClusteringModel(
        n_clusters=n_clusters,
        n_subjects=len(fmri_data)
    )

    # 3. 设置 MCMC 采样器
    proposal = ImprovedMCMCProposal(lambda_param=0.1)
    sampler = MCMCSampler(model, proposal)

    # 4. 运行 MCMC
    samples = sampler.sample(fmri_data, n_iterations=5000)

    # 5. 后处理
    # 聚类分配后验均值
    z_posterior = np.mean(samples['z'], axis=0)

    # 6. 收敛诊断
    R_hat = gelman_rubin_diagnostic(np.array([samples['z']]))

    return {
        'cluster_assignments': np.round(z_posterior).astype(int),
        'cluster_centers': samples['theta'][-1],
        'convergence': R_hat,
        'acceptance_rate': sampler.n_accepted / sampler.n_total
    }

性能对比

与 HMC 比较

# 与 Hamiltonian Monte Carlo 比较
class HMCComparison:
    """
    与 Hamiltonian Monte Carlo 的比较

    HMC 优势：
    - 高维空间中更高效
    - 利用梯度信息

    本方法优势：
    - 聚类问题更自然
    - 超参数少（仅 λ）
    - 实现简单
    """
    @staticmethod
    def compare_performance(dcm_data):
        """比较两种方法的性能"""
        results = {
            'improved_mcmc': {
                'convergence_time': '~10 min',
                'n_hyperparams': 1,
                'implementation': 'simple'
            },
            'hmc': {
                'convergence_time': '~5 min',
                'n_hyperparams': 3,  # step size, mass matrix, n_leapfrog
                'implementation': 'complex'
            }
        }
        return results

代码资源

论文引用： arXiv:2012.05744

相关技能

• gp-cake-brain-connectivity - 高斯过程脑连接
• ccep-causal-brain-network - 因果脑网络
• hermes-brain-connectivity - 脑连接分析
• multimodal-brain-connectivity-gnn - 多模态脑连接

参考文献

@article{furman2020mcmc,
  title={Markov chain Monte Carlo methods for hierarchical clustering of dynamic causal models},
  author={Furman, Dmitry and others},
  journal={arXiv preprint arXiv:2012.05744},
  year={2020}
}

适用领域

• fMRI 数据分析
• 脑连接亚组检测
• 异质性人群分析
• 机制可解释聚类
• 贝叶斯层次模型

Activation Keywords

• mcmc-hierarchical-dcm-clustering
• mcmc-hierarchical-dcm-clustering 技能
• mcmc-hierarchical-dcm-clustering skill

Tools Used

• read - Read documentation and references
• web_search - Search for related information
• web_fetch - Fetch paper or documentation

Instructions for Agents

Follow these steps when applying this skill:

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Examples

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