예제 #1
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def fit_lds_model(Xs, Xtest, D, N_samples=100):
    model = MultinomialLDS(K,
                           D,
                           init_dynamics_distn=GaussianFixed(mu=np.zeros(D),
                                                             sigma=1 *
                                                             np.eye(D)),
                           dynamics_distn=AutoRegression(nu_0=D + 1,
                                                         S_0=1 * np.eye(D),
                                                         M_0=np.zeros((D, D)),
                                                         K_0=1 * np.eye(D)),
                           sigma_C=0.01)

    for X in Xs:
        model.add_data(X)

    model.resample_parameters()

    init_results = (0, model, model.log_likelihood(),
                    model.heldout_log_likelihood(Xtest, M=1),
                    model.predictive_log_likelihood(Xtest, M=1000))

    def resample():
        tic = time.time()
        model.resample_model()
        toc = time.time() - tic

        return toc, None, model.log_likelihood(), \
            model.heldout_log_likelihood(Xtest, M=1), \
            model.predictive_log_likelihood(Xtest, M=1000)

    times, samples, lls, test_lls, pred_lls = \
        map(np.array, zip(*([init_results] + [resample() for _ in progprint_xrange(N_samples)])))
    timestamps = np.cumsum(times)

    return Results(lls, test_lls, pred_lls, samples, timestamps)
예제 #2
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파일: dna_lds.py 프로젝트: fivejjs/pgmult
def fit_lds_model(Xs, Xtest, D, N_samples=100):
    model = MultinomialLDS(K, D,
        init_dynamics_distn=GaussianFixed(mu=np.zeros(D), sigma=1*np.eye(D)),
        dynamics_distn=AutoRegression(nu_0=D+1,S_0=1*np.eye(D),M_0=np.zeros((D,D)),K_0=1*np.eye(D)),
        sigma_C=0.01
        )

    for X in Xs:
        model.add_data(X)

    model.resample_parameters()

    init_results = (0, model, model.log_likelihood(),
                    model.heldout_log_likelihood(Xtest, M=1),
                    model.predictive_log_likelihood(Xtest, M=1000))

    def resample():
        tic = time.time()
        model.resample_model()
        toc = time.time() - tic

        return toc, None, model.log_likelihood(), \
            model.heldout_log_likelihood(Xtest, M=1), \
            model.predictive_log_likelihood(Xtest, M=1000)

    times, samples, lls, test_lls, pred_lls = \
        map(np.array, zip(*([init_results] + [resample() for _ in progprint_xrange(N_samples)])))
    timestamps = np.cumsum(times)

    return Results(lls, test_lls, pred_lls, samples, timestamps)
예제 #3
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파일: ap_lds.py 프로젝트: yinsenm/pgmult
def fit_lds_model(Xs, Xtest, D, N_samples=100):
    Nx = len(Xs)
    assert len(Xtest) == Nx

    model = MultinomialLDS(K,
                           D,
                           init_dynamics_distn=GaussianFixed(mu=np.zeros(D),
                                                             sigma=1 *
                                                             np.eye(D)),
                           dynamics_distn=AutoRegression(nu_0=D + 1,
                                                         S_0=1 * np.eye(D),
                                                         M_0=np.zeros((D, D)),
                                                         K_0=1 * np.eye(D)),
                           sigma_C=1.)

    for X in Xs:
        model.add_data(X)

    model.resample_parameters()

    compute_pred_ll = lambda: sum([
        model.predictive_log_likelihood(Xt, data_index=i, M=10)[0]
        for i, Xt in enumerate(Xtest)
    ])

    init_results = (
        0,
        None,
        model.log_likelihood(),
        # model.heldout_log_likelihood(Xtest, M=1),
        np.nan,
        compute_pred_ll())

    def resample():
        tic = time.time()
        model.resample_model()
        toc = time.time() - tic

        return toc, None, model.log_likelihood(), \
            np.nan,\
            compute_pred_ll()

    times, samples, lls, test_lls, pred_lls = \
        list(map(np.array, list(zip(*([init_results] +
            [resample() for _ in progprint_xrange(N_samples, perline=5)])))))
    timestamps = np.cumsum(times)

    return Results(lls, test_lls, pred_lls, samples, timestamps)
예제 #4
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def fit_lds_model(Xs, Xtest, N_samples=100):
    model = MultinomialLDS(K,
                           D,
                           init_dynamics_distn=Gaussian(mu_0=np.zeros(D),
                                                        sigma_0=np.eye(D),
                                                        kappa_0=1.0,
                                                        nu_0=D + 1.0),
                           dynamics_distn=AutoRegression(nu_0=D + 1,
                                                         S_0=np.eye(D),
                                                         M_0=np.zeros((D, D)),
                                                         K_0=np.eye(D)),
                           sigma_C=1)

    for X in Xs:
        model.add_data(X)
    data = model.data_list[0]

    samples = []
    lls = []
    test_lls = []
    mc_test_lls = []
    pis = []
    psis = []
    zs = []
    timestamps = [time.time()]
    for smpl in progprint_xrange(N_samples):
        model.resample_model()
        timestamps.append(time.time())

        samples.append(model.copy_sample())
        # TODO: Use log_likelihood() to marginalize over z
        lls.append(model.log_likelihood())
        # test_lls.append(model.heldout_log_likelihood(Xtest, M=50)[0])
        mc_test_lls.append(model._mc_heldout_log_likelihood(Xtest, M=1)[0])
        pis.append(model.pi(data))
        psis.append(model.psi(data))
        zs.append(data["states"].stateseq)

    lls = np.array(lls)
    test_lls = np.array(test_lls)
    pis = np.array(pis)
    psis = np.array(psis)
    zs = np.array(zs)
    timestamps = np.array(timestamps)
    timestamps -= timestamps[0]
    return model, lls, test_lls, mc_test_lls, pis, psis, zs, timestamps
예제 #5
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def fit_lds_model(Xs, Xtest, N_samples=100):
    model = MultinomialLDS(K, D,
        init_dynamics_distn=Gaussian(mu_0=np.zeros(D), sigma_0=np.eye(D), kappa_0=1.0, nu_0=D+1.0),
        dynamics_distn=AutoRegression(nu_0=D+1,S_0=np.eye(D),M_0=np.zeros((D,D)),K_0=np.eye(D)),
        sigma_C=1
        )

    for X in Xs:
        model.add_data(X)
    data = model.data_list[0]

    samples = []
    lls = []
    test_lls = []
    mc_test_lls = []
    pis = []
    psis = []
    zs = []
    timestamps = [time.time()]
    for smpl in progprint_xrange(N_samples):
        model.resample_model()
        timestamps.append(time.time())

        samples.append(model.copy_sample())
        # TODO: Use log_likelihood() to marginalize over z
        lls.append(model.log_likelihood())
        # test_lls.append(model.heldout_log_likelihood(Xtest, M=50)[0])
        mc_test_lls.append(model._mc_heldout_log_likelihood(Xtest, M=1)[0])
        pis.append(model.pi(data))
        psis.append(model.psi(data))
        zs.append(data["states"].stateseq)

    lls = np.array(lls)
    test_lls = np.array(test_lls)
    pis = np.array(pis)
    psis = np.array(psis)
    zs = np.array(zs)
    timestamps = np.array(timestamps)
    timestamps -= timestamps[0]
    return model, lls, test_lls, mc_test_lls, pis, psis, zs, timestamps
예제 #6
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파일: ap_lds.py 프로젝트: fivejjs/pgmult
def fit_lds_model(Xs, Xtest, D, N_samples=100):
    Nx = len(Xs)
    assert len(Xtest) == Nx

    model = MultinomialLDS(K, D,
        init_dynamics_distn=GaussianFixed(mu=np.zeros(D), sigma=1*np.eye(D)),
        dynamics_distn=AutoRegression(nu_0=D+1,S_0=1*np.eye(D),M_0=np.zeros((D,D)),K_0=1*np.eye(D)),
        sigma_C=1.
        )

    for X in Xs:
        model.add_data(X)

    model.resample_parameters()

    compute_pred_ll = lambda: sum([model.predictive_log_likelihood(Xt, data_index=i, M=10)[0]
                                   for i,Xt in enumerate(Xtest)])

    init_results = (0, None, model.log_likelihood(),
                    # model.heldout_log_likelihood(Xtest, M=1),
                    np.nan,
                    compute_pred_ll())

    def resample():
        tic = time.time()
        model.resample_model()
        toc = time.time() - tic

        return toc, None, model.log_likelihood(), \
            np.nan,\
            compute_pred_ll()

    times, samples, lls, test_lls, pred_lls = \
        map(np.array, zip(*([init_results] +
            [resample() for _ in progprint_xrange(N_samples, perline=5)])))
    timestamps = np.cumsum(times)

    return Results(lls, test_lls, pred_lls, samples, timestamps)
예제 #7
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testmodel.add_data(data["x"])
testdata = testmodel.data_list[0]

N_samples = 100
samples = []
lls = []
pis = []
psis = []
zs = []
for smpl in range(N_samples):
    print("Iteration ", smpl)
    testmodel.resample_model()

    samples.append(testmodel.copy_sample())
    lls.append(testmodel.log_likelihood())
    pis.append(testmodel.pi(testdata))
    psis.append(testmodel.psi(testdata))
    zs.append(testdata["states"].stateseq)

lls = np.array(lls)
pis = np.array(pis)

psis = np.array(psis)
psi_mean = psis[N_samples // 2:, ...].mean(0)
psi_std = psis[N_samples // 2:, ...].std(0)

zs = np.array(zs)
z_mean = zs[N_samples // 2:, ...].mean(0)
z_std = zs[N_samples // 2:, ...].std(0)
예제 #8
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testmodel.add_data(data["x"])
testdata = testmodel.data_list[0]

N_samples = 100
samples = []
lls = []
pis = []
psis = []
zs = []
for smpl in xrange(N_samples):
    print("Iteration ", smpl)
    testmodel.resample_model()

    samples.append(testmodel.copy_sample())
    lls.append(testmodel.log_likelihood())
    pis.append(testmodel.pi(testdata))
    psis.append(testmodel.psi(testdata))
    zs.append(testdata["states"].stateseq)

lls = np.array(lls)
pis = np.array(pis)

psis = np.array(psis)
psi_mean = psis[N_samples//2:,...].mean(0)
psi_std = psis[N_samples//2:,...].std(0)

zs = np.array(zs)
z_mean = zs[N_samples//2:,...].mean(0)
z_std = zs[N_samples//2:,...].std(0)