1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
use std::collections::BTreeMap;

use special::Gamma as _;

use crate::consts::HALF_LN_2PI;
use crate::data::{
    extract_stat, extract_stat_then, DataOrSuffStat, GaussianSuffStat,
};
use crate::dist::{Gaussian, NormalInvGamma};
use crate::gaussian_prior_geweke_testable;
use crate::test::GewekeTestable;
use crate::traits::*;

#[inline]
fn ln_z(v: f64, a: f64, b: f64) -> f64 {
    // -(a * b.ln() - 0.5 * v.ln() - a.ln_gamma().0)
    let p1 = v.ln().mul_add(0.5, a.ln_gamma().0);
    -b.ln().mul_add(a, -p1)
}

// XXX: Check out section 6.3 from Kevin Murphy's paper
// https://www.cs.ubc.ca/~murphyk/Papers/bayesGauss.pdf
#[allow(clippy::clippy::many_single_char_names)]
fn posterior_from_stat(
    nig: &NormalInvGamma,
    stat: &GaussianSuffStat,
) -> NormalInvGamma {
    let n = stat.n() as f64;

    let (m, v, a, b) = nig.params();

    let v_inv = v.recip();

    let vn_inv = v_inv + n;
    let vn = vn_inv.recip();
    // let mn = (v_inv * m + stat.sum_x()) * vn;
    let mn = v_inv.mul_add(m, stat.sum_x()) / vn_inv;
    // let an = a + 0.5 * n;
    let an = n.mul_add(0.5, a);
    // let bn = b + 0.5 * (m * m * v_inv + stat.sum_x_sq() - mn * mn * vn_inv);
    let p1 = (m * m).mul_add(v_inv, stat.sum_x_sq());
    let bn = (-mn * mn).mul_add(vn_inv, p1).mul_add(0.5, b);

    NormalInvGamma::new(mn, vn, an, bn).expect("Invalid posterior params.")
}

impl ConjugatePrior<f64, Gaussian> for NormalInvGamma {
    type Posterior = Self;
    type LnMCache = f64;
    type LnPpCache = (GaussianSuffStat, f64);
    // type LnPpCache = NormalInvGamma;

    fn posterior(&self, x: &DataOrSuffStat<f64, Gaussian>) -> Self {
        extract_stat_then(
            x,
            || GaussianSuffStat::new(),
            |stat: GaussianSuffStat| posterior_from_stat(&self, &stat),
        )
    }

    #[inline]
    fn ln_m_cache(&self) -> Self::LnMCache {
        ln_z(self.v, self.a, self.b)
    }

    fn ln_m_with_cache(
        &self,
        cache: &Self::LnMCache,
        x: &DataOrSuffStat<f64, Gaussian>,
    ) -> f64 {
        extract_stat_then(
            x,
            || GaussianSuffStat::new(),
            |stat: GaussianSuffStat| {
                let post = posterior_from_stat(&self, &stat);
                let n = stat.n() as f64;
                let lnz_n = ln_z(post.v, post.a, post.b);
                lnz_n - cache - n * HALF_LN_2PI
                // lnz_n - cache - n * HALF_LN_PI - n*LN_2
            },
        )
    }

    #[inline]
    fn ln_pp_cache(
        &self,
        x: &DataOrSuffStat<f64, Gaussian>,
    ) -> Self::LnPpCache {
        let stat = extract_stat(&x, || GaussianSuffStat::new());
        let post_n = posterior_from_stat(&self, &stat);
        let lnz_n = ln_z(post_n.v, post_n.a, post_n.b);
        (stat, lnz_n)
    }

    fn ln_pp_with_cache(&self, cache: &Self::LnPpCache, y: &f64) -> f64 {
        let mut stat = cache.0.clone();
        let lnz_n = cache.1;

        stat.observe(y);
        let post_m = posterior_from_stat(&self, &stat);

        let lnz_m = ln_z(post_m.v, post_m.a, post_m.b);

        -HALF_LN_2PI + lnz_m - lnz_n
    }
}

gaussian_prior_geweke_testable!(NormalInvGamma, Gaussian);

#[cfg(test)]
mod test {
    use super::*;
    use crate::consts::LN_2PI;

    const TOL: f64 = 1E-12;

    #[test]
    fn geweke() {
        use crate::test::GewekeTester;

        let mut rng = rand::thread_rng();
        let pr = NormalInvGamma::new(0.1, 1.2, 0.5, 1.8).unwrap();
        let n_passes = (0..5)
            .map(|_| {
                let mut tester = GewekeTester::new(pr.clone(), 20);
                tester.run_chains(5_000, 20, &mut rng);
                if tester.eval(0.025).is_ok() {
                    1u8
                } else {
                    0u8
                }
            })
            .sum::<u8>();
        assert!(n_passes > 1);
    }

    // Random reference I found using the same source
    // https://github.com/JuliaStats/ConjugatePriors.jl/blob/master/src/normalinversegamma.jl
    fn ln_f_ref(gauss: &Gaussian, nig: &NormalInvGamma) -> f64 {
        let (m, v, a, b) = nig.params();
        let mu = gauss.mu();
        let sigma = gauss.sigma();
        let sig2 = sigma * sigma;
        let lz_inv = a * b.ln() - a.ln_gamma().0 - 0.5 * (v.ln() + LN_2PI);
        lz_inv
            - 0.5 * sig2.ln()
            - (a + 1.) * sig2.ln()
            - b / sig2
            - 0.5 / (sig2 * v) * (mu - m).powi(2)
    }

    fn post_params(
        xs: &Vec<f64>,
        m: f64,
        v: f64,
        a: f64,
        b: f64,
    ) -> (f64, f64, f64, f64) {
        let n = xs.len() as f64;
        let sum_x: f64 = xs.iter().sum();
        let sum_x_sq: f64 = xs.iter().map(|&x| x * x).sum();

        let v_inv = v.recip();
        let vn_inv = v_inv + n;
        let vn = vn_inv.recip();
        let mn = (v_inv * m + sum_x) * vn;
        let an = a + n / 2.0;
        let bn = b + 0.5 * (m * m * v_inv + sum_x_sq - mn * mn * vn_inv);
        // let bn = 0.5*(sum_x_sq - n.recip()*sum_x*sum_x);
        // let bn = (1.0 + n/(2.0 * a)) * (a*b + sum_x_sq - n.recip()*sum_x + (n/v)/(v_inv + n)*(m - sum_x/n).powi(2));

        (mn, vn, an, bn)
    }

    // XXX: Implemented this directly against the Kevin Murphy whitepaper. Makes
    // things a little easier to understand compared to using the sufficient
    // statistics and traits and all that. Still possible for this to be wrong,
    // but if this matches what's in the code AND the DPGMM example (at
    // examples/dpgmm.rs) words with the NormalInvGamma prior, then we should be
    // good to go.
    fn alternate_ln_marginal(
        xs: &Vec<f64>,
        m: f64,
        v: f64,
        a: f64,
        b: f64,
    ) -> f64 {
        let n = xs.len() as f64;
        let (_, vn, an, bn) = post_params(xs, m, v, a, b);

        let numer = 0.5 * vn.ln() + a * b.ln() + an.ln_gamma().0;
        let denom =
            0.5 * v.ln() + an * bn.ln() + a.ln_gamma().0 + (n / 2.0) * LN_2PI;

        numer - denom
    }

    #[test]
    fn ln_f_vs_reference() {
        let (m, v, a, b) = (0.0, 1.2, 2.3, 3.4);
        let nig = NormalInvGamma::new(m, v, a, b).unwrap();
        let mut rng = rand::thread_rng();
        for _ in 0..100 {
            let gauss = nig.draw(&mut rng);
            let ln_f = nig.ln_f(&gauss);
            let reference = ln_f_ref(&gauss, &nig);
            assert::close(reference, ln_f, TOL);
        }
    }

    #[test]
    fn ln_m_vs_reference() {
        let (m, v, a, b) = (0.0, 1.2, 2.3, 3.4);
        let xs = vec![1.0, 2.0, 3.0, 4.0, 5.0];
        let reference = alternate_ln_marginal(&xs, m, v, a, b);
        let nig = NormalInvGamma::new(m, v, a, b).unwrap();
        let ln_m = nig.ln_m(&DataOrSuffStat::<f64, Gaussian>::from(&xs));

        assert::close(reference, ln_m, TOL);
    }

    #[test]
    fn ln_m_vs_monte_carlo() {
        use crate::misc::logsumexp;

        let n_samples = 1_000_000;
        let xs = vec![1.0, 2.0, 3.0, 4.0, 5.0, 6.0];

        let (m, v, a, b) = (1.0, 2.2, 3.3, 4.4);
        let nig = NormalInvGamma::new(m, v, a, b).unwrap();
        let ln_m = nig.ln_m(&DataOrSuffStat::<f64, Gaussian>::from(&xs));
        // let ln_m = alternate_ln_marginal(&xs, m, v, a, b);

        let mc_est = {
            let ln_fs: Vec<f64> = nig
                .sample_stream(&mut rand::thread_rng())
                .take(n_samples)
                .map(|gauss: Gaussian| {
                    xs.iter().map(|x| gauss.ln_f(x)).sum::<f64>()
                })
                .collect();
            logsumexp(&ln_fs) - (n_samples as f64).ln()
        };
        // high error tolerance. MC estimation is not the most accurate...
        assert::close(ln_m, mc_est, 1e-2);
    }

    #[test]
    fn ln_m_vs_importance() {
        use crate::dist::Gamma;
        use crate::misc::logsumexp;

        let n_samples = 1_000_000;
        let xs = vec![1.0, 2.0, 3.0, 4.0, 5.0, 6.0];

        let (m, v, a, b) = (1.0, 2.2, 3.3, 4.4);
        let nig = NormalInvGamma::new(m, v, a, b).unwrap();
        let ln_m = nig.ln_m(&DataOrSuffStat::<f64, Gaussian>::from(&xs));

        let mc_est = {
            let mut rng = rand::thread_rng();
            let pr_m = Gaussian::new(1.0, 8.0).unwrap();
            let pr_s = Gamma::new(2.0, 0.4).unwrap();
            let ln_fs: Vec<f64> = (0..n_samples)
                .map(|_| {
                    let mu: f64 = pr_m.draw(&mut rng);
                    let var: f64 = pr_s.draw(&mut rng);
                    let gauss = Gaussian::new(mu, var.sqrt()).unwrap();
                    let ln_f = xs.iter().map(|x| gauss.ln_f(x)).sum::<f64>();
                    ln_f + nig.ln_f(&gauss) - pr_m.ln_f(&mu) - pr_s.ln_f(&var)
                })
                .collect();
            logsumexp(&ln_fs) - (n_samples as f64).ln()
        };
        // high error tolerance. MC estimation is not the most accurate...
        assert::close(ln_m, mc_est, 1e-2);
    }

    #[test]
    fn ln_pp_vs_monte_carlo() {
        use crate::misc::logsumexp;

        let n_samples = 1_000_000;
        let xs = vec![1.0, 2.0, 3.0, 4.0, 5.0, 6.0];

        let y: f64 = -0.3;
        let (m, v, a, b) = (1.0, 2.2, 3.3, 4.4);
        let nig = NormalInvGamma::new(m, v, a, b).unwrap();
        let post = nig.posterior(&DataOrSuffStat::<f64, Gaussian>::from(&xs));
        let ln_pp = nig.ln_pp(&y, &DataOrSuffStat::<f64, Gaussian>::from(&xs));
        // let ln_m = alternate_ln_marginal(&xs, m, v, a, b);

        let mc_est = {
            let ln_fs: Vec<f64> = post
                .sample_stream(&mut rand::thread_rng())
                .take(n_samples)
                .map(|gauss: Gaussian| gauss.ln_f(&y))
                .collect();
            logsumexp(&ln_fs) - (n_samples as f64).ln()
        };
        // high error tolerance. MC estimation is not the most accurate...
        assert::close(ln_pp, mc_est, 1e-2);
    }

    #[test]
    fn ln_pp_vs_ln_m_single() {
        let y: f64 = -0.3;
        let (m, v, a, b) = (0.0, 1.2, 2.3, 3.4);
        let nig = NormalInvGamma::new(m, v, a, b).unwrap();
        let ln_pp = nig.ln_pp(&y, &DataOrSuffStat::None);
        let ln_m = nig.ln_m(&DataOrSuffStat::from(&vec![y]));
        assert::close(ln_pp, ln_m, TOL);
    }

    #[test]
    fn ln_pp_vs_t() {
        use crate::dist::StudentsT;

        let xs = vec![1.0, 2.0, 3.0, 4.0, 5.0];
        let y: f64 = -0.3;
        let (m, v, a, b) = (0.0, 1.2, 2.3, 3.4);
        // let (m, v, a, b) = (0.0, 1.0, 1.0, 1.0);
        let (mn, vn, an, bn) = post_params(&xs, m, v, a, b);

        let ln_f_t = {
            // fit into non-shifted-and-scaled T using the parameterization in
            // 10.6 of the Kevin Murphy's whitepaper
            let t = StudentsT::new(2.0 * an).unwrap();
            let t_scale = bn * (1.0 + vn) / an;
            let t_shift = mn;
            let y_adj = (y - t_shift) / t_scale.sqrt();

            t.ln_f(&y_adj) - 0.5 * t_scale.ln()
        };

        let ln_pp = {
            let nig = NormalInvGamma::new(m, v, a, b).unwrap();
            let ln_pp =
                nig.ln_pp(&y, &DataOrSuffStat::<f64, Gaussian>::from(&xs));
            ln_pp
        };
        assert::close(ln_f_t, ln_pp, TOL);
    }
}