Add auto-marginalization implementation to the main package #385

sunxd3 · 2025-08-23T11:00:28Z

No description provided.

github-actions · 2025-08-23T11:02:25Z

JuliaBUGS.jl documentation for PR #385 is available at:
https://TuringLang.github.io/JuliaBUGS.jl/previews/PR385/

codecov · 2025-08-23T15:04:10Z

Codecov Report

❌ Patch coverage is 88.75740% with 38 lines in your changes missing coverage. Please review.
✅ Project coverage is 83.64%. Comparing base (53fd7bb) to head (f6002b3).

Files with missing lines	Patch %	Lines
JuliaBUGS/src/model/evaluation.jl	84.79%	33 Missing ⚠️
JuliaBUGS/src/model/bugsmodel.jl	97.77%	2 Missing ⚠️
JuliaBUGS/src/model/logdensityproblems.jl	90.00%	2 Missing ⚠️
JuliaBUGS/src/model/abstractppl.jl	90.90%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #385      +/-   ##
==========================================
+ Coverage   83.26%   83.64%   +0.37%     
==========================================
  Files          31       31              
  Lines        3759     4066     +307     
==========================================
+ Hits         3130     3401     +271     
- Misses        629      665      +36

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github-actions

Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

JuliaFormatter

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/test/model/frontier_cache_hmm.jl

Line 72 in 0445a28

    
           println("[FrontierCacheTest] Computing minimal keys (states-first)..."); flush(stdout)

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/test/model/frontier_cache_hmm.jl

Line 107 in 0445a28

    
           println("[FrontierCacheTest] Evaluating logp with interleaved order..."); flush(stdout)

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/test/model/frontier_cache_hmm.jl

Line 114 in 0445a28

    
           println("[FrontierCacheTest] Evaluating logp with states-first order..."); flush(stdout)

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/test/model/frontier_cache_hmm.jl

Line 125 in 0445a28

println("[FrontierCacheTest] Done evaluations, comparing..."); flush(stdout)

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

github-actions · 2025-09-02T02:54:03Z

Benchmark results on macOS (aarch64)

BridgeStan not found at location specified by $BRIDGESTAN environment variable, downloading version 2.6.2 to /Users/runner/.bridgestan/bridgestan-2.6.2
Done!

Stan results:

Model	Parameters	Density Time (µs)	Density+Gradient Time (µs)
rats	65	5.5084	8.014
pumps	12	0.901031	1.04
bones	13	81.416	92.709
oxford	244	10.479	13.041
epil	303	34.709	42.4585
lsat	1006	110.0	159.417
schools	133	245.792	389.438
beetles	2	0.745958	0.861133
air	5	0.909935	1.01696

JuliaBUGS Mooncake results:

Model	Parameters	Density Time (µs)	Density+Gradient Time (µs)
rats	65	1.22646	7.59733
pumps	12	0.463379	1.83336
bones	33	49.291	272.666
oxford	244	19.834	55.791
epil	303	7.44433	36.792
lsat	1006	51.209	224.125
schools	133	113.271	811.375
beetles	2	0.872485	3.82812
air	5	0.263636	1.14668

Benchmark results on Ubuntu (x64)

BridgeStan not found at location specified by $BRIDGESTAN environment variable, downloading version 2.6.2 to /home/runner/.bridgestan/bridgestan-2.6.2
Done!

Stan results:

Model	Parameters	Density Time (µs)	Density+Gradient Time (µs)
rats	65	5.1616	7.544
pumps	12	0.959133	1.14135
bones	13	70.651	88.094
oxford	244	14.3365	18.365
epil	303	28.994	35.536
lsat	1006	161.811	204.375
schools	133	552.785	789.442
beetles	2	0.844529	0.980167
air	5	0.656909	0.802333

JuliaBUGS Mooncake results:

Model	Parameters	Density Time (µs)	Density+Gradient Time (µs)
rats	65	1.9336	13.7505
pumps	12	0.597857	2.49736
bones	33	48.14	366.894
oxford	244	23.694	74.759
epil	303	10.8205	55.212
lsat	1006	89.957	364.499
schools	133	104.359	1082.84
beetles	2	1.08704	4.73217
air	5	0.339368	1.30624

coveralls · 2025-09-23T12:53:41Z

Pull Request Test Coverage Report for Build 17946143376

Details

300 of 338 (88.76%) changed or added relevant lines in 4 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage increased (+0.4%) to 83.645%

Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
JuliaBUGS/src/model/abstractppl.jl	10	11	90.91%
JuliaBUGS/src/model/bugsmodel.jl	88	90	97.78%
JuliaBUGS/src/model/logdensityproblems.jl	18	20	90.0%
JuliaBUGS/src/model/evaluation.jl	184	217	84.79%

Totals
Change from base Build 17946015706:	0.4%
Covered Lines:	3401
Relevant Lines:	4066

💛 - Coveralls

github-actions

Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

JuliaFormatter

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmm_correctness_sweep.jl

Line 114 in 2d7a51b

logp, logp_ref = run_case(K=K, T=T, seed=seed)

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmm_gradient_check.jl

Line 38 in 2d7a51b

eps = try parse(Float64, get(ENV, "AGC_EPS", "1e-5")) catch; 1e-5 end

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmm_gradient_check.jl

Line 109 in 2d7a51b

    
           sim = simulate_hmm(rng, T, K; init_probs=init_probs, transition=transition, means=means_true, sigmas=sigmas_true)

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmm_gradient_check.jl

Line 111 in 2d7a51b

    
           mu_prior_mean, mu_prior_std, logsigma_prior_mean, logsigma_prior_std = priors_from_truth(means_true, sigmas_true)

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmm_gradient_check.jl

Lines 114 to 122 in 2d7a51b

    
           T = T, 
        
           K = K, 
        
           y = sim.y, 
        
           init_probs = init_probs, 
        
           transition = transition, 
        
           mu_prior_mean = mu_prior_mean, 
        
           mu_prior_std = mu_prior_std, 
        
           logsigma_prior_mean = logsigma_prior_mean, 
        
           logsigma_prior_std = logsigma_prior_std,

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmm_gradient_check.jl

Line 157 in 2d7a51b

    
           logp, max_abs_diff, max_rel_diff = run_case(seed, K, T; ϵ=eps, verbose=(verbose && is_single))

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmm_marginal_logp.jl

Lines 69 to 70 in 2d7a51b

    
           rng = MersenneTwister(get(ENV, "AM_SEED", "1") |> x -> parse(Int, x)) 
        
           T = get(ENV, "AM_T", "50") |> x -> parse(Int, x)

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmm_marginal_logp.jl

Line 77 in 2d7a51b

    
           sim = simulate_hmm(rng, T; init_probs=init_probs, transition=transition, means=means, sigmas=sigmas)

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmm_marginal_logp.jl

Lines 81 to 87 in 2d7a51b

    
           T = T, 
        
           K = K, 
        
           y = sim.obs, 
        
           init_probs = init_probs, 
        
           transition = transition, 
        
           means = means, 
        
           sigmas = sigmas,

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmm_scaling_bench.jl

Line 40 in 2d7a51b

trials = try parse(Int, get(ENV, "AS_TRIALS", "5")) catch; 5 end

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmm_scaling_bench.jl

Line 42 in 2d7a51b

    
           function simulate_hmm(rng::AbstractRNG, T::Int, K::Int; init_probs, transition, means, sigmas)

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JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmm_scaling_bench.jl

Line 97 in 2d7a51b

    
           sim = simulate_hmm(rng, T, K; init_probs=init_probs, transition=transition, means=means, sigmas=sigmas)

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmm_scaling_bench.jl

Lines 101 to 107 in 2d7a51b

    
           T = T, 
        
           K = K, 
        
           y = sim.obs, 
        
           init_probs = init_probs, 
        
           transition = transition, 
        
           means = means, 
        
           sigmas = sigmas,

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmm_scaling_bench.jl

Line 129 in 2d7a51b

    
           mean_time, logp, max_f, mean_f, sum_f = bench_case(K=K, T=T, seed=seed, trials=trials)

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmt_order_comparison.jl

Lines 20 to 24 in 2d7a51b

    
           B = try parse(Int, get(ENV, "AHMT_B", "2")) catch; 2 end 
        
           depth = try parse(Int, get(ENV, "AHMT_DEPTH", "8")) catch; 8 end 
        
           K = try parse(Int, get(ENV, "AHMT_K", "4")) catch; 4 end 
        
           seed = try parse(Int, get(ENV, "AHMT_SEED", "1")) catch; 1 end 
        
           trials = try parse(Int, get(ENV, "AHMT_TRIALS", "10")) catch; 10 end

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmt_order_comparison.jl

Line 26 in 2d7a51b

    
           cost_thresh = try parse(Float64, get(ENV, "AHMT_COST_THRESH", "1.0e8")) catch; 1.0e8 end

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmt_order_comparison.jl

Line 57 in 2d7a51b

    
           function simulate_hmt(rng::AbstractRNG, B::Int, depth::Int, K::Int; init_probs, transition, means, sigmas)

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmt_order_comparison.jl

Line 87 in 2d7a51b

    
           sim = simulate_hmt(rng, B, depth, K; init_probs=init_probs, transition=transition, means=means, sigmas=sigmas)

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmt_order_comparison.jl

Lines 91 to 100 in 2d7a51b

    
           B = B, 
        
           depth = depth, 
        
           N = N, 
        
           K = K, 
        
           y = sim.y, 
        
           init_probs = init_probs, 
        
           transition = transition, 
        
           means = means, 
        
           sigmas = sigmas, 
        
           parent = parent,

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmt_order_comparison.jl

Lines 113 to 117 in 2d7a51b

    
           "dfs"        => () -> make_model_with_order(model, build_hmt_dfs_order(model; B_hint=B)), 
        
           "bfs"        => () -> make_model_with_order(model, build_hmt_bfs_order(model)), 
        
           "random_dfs" => () -> make_model_with_order(model, build_hmt_dfs_order(model; B_hint=B, rng=MersenneTwister(seed+1), randomized=true)), 
        
           "min_fill"   => () -> make_model_with_order(model, build_min_fill_order(model; rng=MersenneTwister(seed+2), num_restarts=3)), 
        
           "min_degree" => () -> make_model_with_order(model, build_min_degree_order(model; rng=MersenneTwister(seed+3), num_restarts=3)),

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/scripts/hmt_order_comparison.jl

Lines 138 to 140 in 2d7a51b

    
           ) ( 
        
               isnan(logp) ? "NA" : @sprintf("%.12f", logp) 
        
           )

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Lines 47 to 48 in 2d7a51b

    
           i = try parse(Int, s[3:end-1]) catch; -1 end 
        
           if i > 0; z_idxs[i] = j; else; push!(other, j); end

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JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Lines 50 to 51 in 2d7a51b

    
           i = try parse(Int, s[3:end-1]) catch; -1 end 
        
           if i > 0; y_idxs[i] = j; else; push!(other, j); end

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 62 in 2d7a51b

if yi != 0; push!(order, yi); end

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JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 93 in 2d7a51b

inner = replace(s[3:end-1], " " => "")

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JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

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           c = try parse(Int, parts[1]) catch; -1 end 
        
           t = try parse(Int, parts[2]) catch; -1 end

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JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 134 in 2d7a51b

inner = replace(s[3:end-1], " " => "")

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JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Lines 137 to 138 in 2d7a51b

    
           c = try parse(Int, parts[1]) catch; -1 end 
        
           t = try parse(Int, parts[2]) catch; -1 end

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JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 185 in 2d7a51b

if placed[i]; return; end

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JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 198 in 2d7a51b

    
           ps = [p for p in st_parents[j] if gd.is_discrete_finite_vals[p] && !gd.is_observed_vals[p]]

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JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 274 in 2d7a51b

return

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JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 309 in 2d7a51b

    
           gd2 = JModel.GraphEvaluationData{typeof(gd.node_function_vals),typeof(gd.loop_vars_vals)}(

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JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 340 in 2d7a51b

i = try parse(Int, s[3:end-1]) catch; -1 end

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 347 in 2d7a51b

i = try parse(Int, s[3:end-1]) catch; -1 end

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 384 in 2d7a51b

inner = replace(s[3:end-1], " " => "")

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Lines 387 to 388 in 2d7a51b

    
           c = try parse(Int, parts[1]) catch; -1 end 
        
           t = try parse(Int, parts[2]) catch; -1 end

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JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 396 in 2d7a51b

i = try parse(Int, s[3:end-1]) catch; -1 end

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 441 in 2d7a51b

i = try parse(Int, s[3:end-1]) catch; -1 end

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 503 in 2d7a51b

i = try parse(Int, s[3:end-1]) catch; -1 end

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 560 in 2d7a51b

    
           if gd.is_discrete_finite_vals[i] && !gd.is_observed_vals[i] && gd.is_stochastic_vals[i]

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 575 in 2d7a51b

for k in (i+1):length(disc_parents)

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JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 598 in 2d7a51b

for j in (i+1):length(neighbors_vec)

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JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 619 in 2d7a51b

for j in (i+1):length(neighbors_vec)

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JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 683 in 2d7a51b

    
           test_model = make_model_with_order(model, build_eval_order_from_discrete_order(model, order))

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 758 in 2d7a51b

    
           test_model = make_model_with_order(model, build_eval_order_from_discrete_order(model, order))

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JuliaBUGS.jl/JuliaBUGS/src/model/abstractppl.jl

Line 626 in 2d7a51b

    
           @warn "Failed to precompute auto-marginalization caches; falling back to graph evaluation" exception=(err, catch_backtrace())

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/src/model/evaluation.jl

Line 576 in 2d7a51b

branch_loglikelihoods = Vector{typeof(lik_val)}(undef, length(possible_values))

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/src/model/evaluation.jl

Line 584 in 2d7a51b

    
           log_joint_total = LogExpFunctions.logsumexp(total_logpriors .+ branch_loglikelihoods)

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/test/model/auto_marginalization.jl

Lines 723 to 729 in 2d7a51b

    
           data = ( 
        
               K=2, 
        
               w=[0.3, 0.7], 
        
               delta=[0.0, 2.0], 
        
               sigma=1.0, 
        
               y=1.5, 
        
           )

github-actions · 2025-09-30T05:20:09Z

JuliaBUGS/experiments/scripts/fhmm_order_comparison.jl

+C = try parse(Int, get(ENV, "AFH_C", "2")) catch; 2 end
+K = try parse(Int, get(ENV, "AFH_K", "4")) catch; 4 end
+T = try parse(Int, get(ENV, "AFH_T", "100")) catch; 100 end
+seed = try parse(Int, get(ENV, "AFH_SEED", "1")) catch; 1 end
+trials = try parse(Int, get(ENV, "AFH_TRIALS", "10")) catch; 10 end


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

C = try parse(Int, get(ENV, "AFH_C", "2")) catch; 2 end

K = try parse(Int, get(ENV, "AFH_K", "4")) catch; 4 end

T = try parse(Int, get(ENV, "AFH_T", "100")) catch; 100 end

seed = try parse(Int, get(ENV, "AFH_SEED", "1")) catch; 1 end

trials = try parse(Int, get(ENV, "AFH_TRIALS", "10")) catch; 10 end

C = try

parse(Int, get(ENV, "AFH_C", "2"))

catch

; 2

end

K = try

parse(Int, get(ENV, "AFH_K", "4"))

catch

; 4

end

T = try

parse(Int, get(ENV, "AFH_T", "100"))

catch

; 100

end

seed = try

parse(Int, get(ENV, "AFH_SEED", "1"))

catch

; 1

end

trials = try

parse(Int, get(ENV, "AFH_TRIALS", "10"))

catch

; 10

end

github-actions · 2025-09-30T05:20:09Z

JuliaBUGS/experiments/scripts/fhmm_order_comparison.jl

+seed = try parse(Int, get(ENV, "AFH_SEED", "1")) catch; 1 end
+trials = try parse(Int, get(ENV, "AFH_TRIALS", "10")) catch; 10 end
+mode = lowercase(get(ENV, "AFH_MODE", "frontier"))  # frontier | timed
+cost_thresh = try parse(Float64, get(ENV, "AFH_COST_THRESH", "1.0e8")) catch; 1.0e8 end


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

cost_thresh = try parse(Float64, get(ENV, "AFH_COST_THRESH", "1.0e8")) catch; 1.0e8 end

cost_thresh = try

parse(Float64, get(ENV, "AFH_COST_THRESH", "1.0e8"))

catch

; 1.0e8

end

github-actions · 2025-09-30T05:20:09Z

JuliaBUGS/experiments/scripts/fhmm_order_comparison.jl

+    return init_probs, transition, mu, sigma_y
+end
+
+function simulate_fhmm(rng::AbstractRNG, C::Int, K::Int, T::Int; init_probs, transition, mu, sigma_y)


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

function simulate_fhmm(rng::AbstractRNG, C::Int, K::Int, T::Int; init_probs, transition, mu, sigma_y)

function simulate_fhmm(

rng::AbstractRNG, C::Int, K::Int, T::Int; init_probs, transition, mu, sigma_y

)

github-actions · 2025-09-30T05:20:09Z

JuliaBUGS/experiments/scripts/fhmm_order_comparison.jl

+# Simulate data
+rng = MersenneTwister(seed)
+init_probs, transition, mu, sigma_y = default_fhmm_params(C, K)
+sim = simulate_fhmm(rng, C, K, T; init_probs=init_probs, transition=transition, mu=mu, sigma_y=sigma_y)


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

sim = simulate_fhmm(rng, C, K, T; init_probs=init_probs, transition=transition, mu=mu, sigma_y=sigma_y)

sim = simulate_fhmm(

rng, C, K, T; init_probs=init_probs, transition=transition, mu=mu, sigma_y=sigma_y

)

github-actions · 2025-09-30T05:20:09Z

JuliaBUGS/experiments/scripts/fhmm_order_comparison.jl

+    C = C,
+    K = K,
+    T = T,
+    y = sim.y,
+    init_probs = init_probs,
+    transition = transition,
+    mu = mu,
+    sigma_y = sigma_y,


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

C = C,

K = K,

T = T,

y = sim.y,

init_probs = init_probs,

transition = transition,

mu = mu,

sigma_y = sigma_y,

C=C,

K=K,

T=T,

y=sim.y,

init_probs=init_probs,

transition=transition,

mu=mu,

sigma_y=sigma_y,

github-actions · 2025-09-30T05:20:12Z

JuliaBUGS/experiments/scripts/hdphmm_gradient_check.jl

+        T = T,
+        K = K,
+        y = y,
+        alpha = α,
+        gamma = γ,
+        kappa = κ,
+        mu0 = m0,
+        mu0_std = s0,
+        logsigma0 = ℓ0,
+        logsigma0_std = τ0,


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

T = T,

K = K,

y = y,

alpha = α,

gamma = γ,

kappa = κ,

mu0 = m0,

mu0_std = s0,

logsigma0 = ℓ0,

logsigma0_std = τ0,

T=T,

K=K,

y=y,

alpha=α,

gamma=γ,

kappa=κ,

mu0=m0,

mu0_std=s0,

logsigma0=ℓ0,

logsigma0_std=τ0,

github-actions · 2025-09-30T05:20:12Z

JuliaBUGS/experiments/scripts/hdphmm_gradient_check.jl

+end
+
+for seed in seeds, K in Ks, T in Ts
+    logp, max_abs_diff, max_rel_diff = run_case(seed, K, T; α=alpha, γ=gamma, κ=kappa, ϵ=eps, verbose=(verbose && is_single))


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

logp, max_abs_diff, max_rel_diff = run_case(seed, K, T; α=alpha, γ=gamma, κ=kappa, ϵ=eps, verbose=(verbose && is_single))

logp, max_abs_diff, max_rel_diff = run_case(

seed, K, T; α=alpha, γ=gamma, κ=kappa, ϵ=eps, verbose=(verbose && is_single)

)

github-actions · 2025-09-30T05:20:12Z

JuliaBUGS/experiments/scripts/hmm_correctness_sweep.jl

+using LogDensityProblems
+using LogExpFunctions: logsumexp
+
+function simulate_hmm(rng::AbstractRNG, T::Int, K::Int; init_probs, transition, means, sigmas)


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

function simulate_hmm(rng::AbstractRNG, T::Int, K::Int; init_probs, transition, means, sigmas)

function simulate_hmm(

rng::AbstractRNG, T::Int, K::Int; init_probs, transition, means, sigmas

)

github-actions · 2025-09-30T05:20:12Z

JuliaBUGS/experiments/scripts/hmm_correctness_sweep.jl

+function run_case(; K::Int, T::Int, seed::Int)
+    rng = MersenneTwister(seed)
+    init_probs, transition, means, sigmas = default_params(K)
+    sim = simulate_hmm(rng, T, K; init_probs=init_probs, transition=transition, means=means, sigmas=sigmas)


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

sim = simulate_hmm(rng, T, K; init_probs=init_probs, transition=transition, means=means, sigmas=sigmas)

sim = simulate_hmm(

rng, T, K; init_probs=init_probs, transition=transition, means=means, sigmas=sigmas

)

github-actions · 2025-09-30T05:20:12Z

JuliaBUGS/experiments/scripts/hmm_correctness_sweep.jl

+        T = T,
+        K = K,
+        y = sim.obs,
+        init_probs = init_probs,
+        transition = transition,
+        means = means,
+        sigmas = sigmas,


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

T = T,

K = K,

y = sim.obs,

init_probs = init_probs,

transition = transition,

means = means,

sigmas = sigmas,

T=T,

K=K,

y=sim.obs,

init_probs=init_probs,

transition=transition,

means=means,

sigmas=sigmas,

github-actions

Remaining comments which cannot be posted as a review comment to avoid GitHub Rate Limit

JuliaFormatter

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 274 in aec0159

return

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 309 in aec0159

    
           gd2 = JModel.GraphEvaluationData{typeof(gd.node_function_vals),typeof(gd.loop_vars_vals)}(

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 340 in aec0159

i = try parse(Int, s[3:end-1]) catch; -1 end

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 347 in aec0159

i = try parse(Int, s[3:end-1]) catch; -1 end

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 384 in aec0159

inner = replace(s[3:end-1], " " => "")

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Lines 387 to 388 in aec0159

    
           c = try parse(Int, parts[1]) catch; -1 end 
        
           t = try parse(Int, parts[2]) catch; -1 end

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 396 in aec0159

i = try parse(Int, s[3:end-1]) catch; -1 end

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 441 in aec0159

i = try parse(Int, s[3:end-1]) catch; -1 end

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 503 in aec0159

i = try parse(Int, s[3:end-1]) catch; -1 end

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 560 in aec0159

    
           if gd.is_discrete_finite_vals[i] && !gd.is_observed_vals[i] && gd.is_stochastic_vals[i]

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 575 in aec0159

for k in (i+1):length(disc_parents)

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 598 in aec0159

for j in (i+1):length(neighbors_vec)

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 619 in aec0159

for j in (i+1):length(neighbors_vec)

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 683 in aec0159

    
           test_model = make_model_with_order(model, build_eval_order_from_discrete_order(model, order))

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/experiments/utils.jl

Line 758 in aec0159

    
           test_model = make_model_with_order(model, build_eval_order_from_discrete_order(model, order))

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/src/model/abstractppl.jl

Line 626 in aec0159

    
           @warn "Failed to precompute auto-marginalization caches; falling back to graph evaluation" exception=(err, catch_backtrace())

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/src/model/evaluation.jl

Line 576 in aec0159

branch_loglikelihoods = Vector{typeof(lik_val)}(undef, length(possible_values))

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/src/model/evaluation.jl

Line 584 in aec0159

    
           log_joint_total = LogExpFunctions.logsumexp(total_logpriors .+ branch_loglikelihoods)

[JuliaFormatter] _{reported by reviewdog 🐶}

JuliaBUGS.jl/JuliaBUGS/test/model/auto_marginalization.jl

Lines 723 to 729 in aec0159

    
           data = ( 
        
               K=2, 
        
               w=[0.3, 0.7], 
        
               delta=[0.0, 2.0], 
        
               sigma=1.0, 
        
               y=1.5, 
        
           )

github-actions · 2025-09-30T07:01:28Z

JuliaBUGS/experiments/scripts/hmm_correctness_sweep.jl

+@printf "# HMM correctness sweep\n"
+@printf "# seed,K,T,logp_autmarg,logp_forward,diff\n"
+for seed in seed_vals, K in Ks, T in Ts
+    logp, logp_ref = run_case(K=K, T=T, seed=seed)


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

logp, logp_ref = run_case(K=K, T=T, seed=seed)

logp, logp_ref = run_case(; K=K, T=T, seed=seed)

github-actions · 2025-09-30T07:01:28Z

JuliaBUGS/experiments/scripts/hmm_gradient_check.jl

+    isempty(xs) ? [50] : xs
+end
+
+eps = try parse(Float64, get(ENV, "AGC_EPS", "1e-5")) catch; 1e-5 end


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

eps = try parse(Float64, get(ENV, "AGC_EPS", "1e-5")) catch; 1e-5 end

eps = try

parse(Float64, get(ENV, "AGC_EPS", "1e-5"))

catch

; 1e-5

end

github-actions · 2025-09-30T07:01:28Z

JuliaBUGS/experiments/scripts/hmm_gradient_check.jl

+        transition[k, k] = diag
+    end
+    means_true, sigmas_true = default_hmm_params(K)
+    sim = simulate_hmm(rng, T, K; init_probs=init_probs, transition=transition, means=means_true, sigmas=sigmas_true)


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

sim = simulate_hmm(rng, T, K; init_probs=init_probs, transition=transition, means=means_true, sigmas=sigmas_true)

sim = simulate_hmm(

rng,

T,

K;

init_probs=init_probs,

transition=transition,

means=means_true,

sigmas=sigmas_true,

)

github-actions · 2025-09-30T07:01:28Z

JuliaBUGS/experiments/scripts/hmm_gradient_check.jl

+    means_true, sigmas_true = default_hmm_params(K)
+    sim = simulate_hmm(rng, T, K; init_probs=init_probs, transition=transition, means=means_true, sigmas=sigmas_true)
+
+    mu_prior_mean, mu_prior_std, logsigma_prior_mean, logsigma_prior_std = priors_from_truth(means_true, sigmas_true)


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

mu_prior_mean, mu_prior_std, logsigma_prior_mean, logsigma_prior_std = priors_from_truth(means_true, sigmas_true)

mu_prior_mean, mu_prior_std, logsigma_prior_mean, logsigma_prior_std = priors_from_truth(

means_true, sigmas_true

)

github-actions · 2025-09-30T07:01:28Z

JuliaBUGS/experiments/scripts/hmm_gradient_check.jl

+        T = T,
+        K = K,
+        y = sim.y,
+        init_probs = init_probs,
+        transition = transition,
+        mu_prior_mean = mu_prior_mean,
+        mu_prior_std = mu_prior_std,
+        logsigma_prior_mean = logsigma_prior_mean,
+        logsigma_prior_std = logsigma_prior_std,


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

T = T,

K = K,

y = sim.y,

init_probs = init_probs,

transition = transition,

mu_prior_mean = mu_prior_mean,

mu_prior_std = mu_prior_std,

logsigma_prior_mean = logsigma_prior_mean,

logsigma_prior_std = logsigma_prior_std,

T=T,

K=K,

y=sim.y,

init_probs=init_probs,

transition=transition,

mu_prior_mean=mu_prior_mean,

mu_prior_std=mu_prior_std,

logsigma_prior_mean=logsigma_prior_mean,

logsigma_prior_std=logsigma_prior_std,

github-actions · 2025-09-30T07:01:31Z

JuliaBUGS/experiments/utils.jl

+                c = try parse(Int, parts[1]) catch; -1 end
+                t = try parse(Int, parts[2]) catch; -1 end


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

c = try parse(Int, parts[1]) catch; -1 end

t = try parse(Int, parts[2]) catch; -1 end

c = try

parse(Int, parts[1])

catch

; -1

end

t = try

parse(Int, parts[2])

catch

; -1

end

github-actions · 2025-09-30T07:01:31Z

JuliaBUGS/experiments/utils.jl

+    for (j, vn) in enumerate(gd.sorted_nodes)
+        s = string(vn)
+        if startswith(s, "z[")
+            inner = replace(s[3:end-1], " " => "")


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

inner = replace(s[3:end-1], " " => "")

inner = replace(s[3:(end - 1)], " " => "")

github-actions · 2025-09-30T07:01:31Z

JuliaBUGS/experiments/utils.jl

+                c = try parse(Int, parts[1]) catch; -1 end
+                t = try parse(Int, parts[2]) catch; -1 end


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

c = try parse(Int, parts[1]) catch; -1 end

t = try parse(Int, parts[2]) catch; -1 end

c = try

parse(Int, parts[1])

catch

; -1

end

t = try

parse(Int, parts[2])

catch

; -1

end

github-actions · 2025-09-30T07:01:31Z

JuliaBUGS/experiments/utils.jl

+
+    function place_with_dependencies(vn)
+        i = pos[vn]
+        if placed[i]; return; end


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

if placed[i]; return; end

if placed[i]

;

return nothing;

end

github-actions · 2025-09-30T07:01:31Z

JuliaBUGS/experiments/utils.jl

+    obs_nodes = [i for i in 1:n if gd.is_stochastic_vals[i] && gd.is_observed_vals[i]]
+    obs_disc_parents = Dict{Int,Vector{Int}}()
+    for j in obs_nodes
+        ps = [p for p in st_parents[j] if gd.is_discrete_finite_vals[p] && !gd.is_observed_vals[p]]


[JuliaFormatter] _{reported by reviewdog 🐶}

Suggested change

ps = [p for p in st_parents[j] if gd.is_discrete_finite_vals[p] && !gd.is_observed_vals[p]]

ps = [

p for

p in st_parents[j] if gd.is_discrete_finite_vals[p] && !gd.is_observed_vals[p]

]

add auto-marginalization implementation to the main package

38e4efe

github-actions bot assigned sunxd3 Aug 23, 2025

sunxd3 added 4 commits August 23, 2025 13:25

format

a5aeb6b

add import

b4eb8d5

import Exponential distribution

fbfac76

using LogExpFunctions in tests

3c0504e

sunxd3 added 6 commits August 23, 2025 19:56

test on GMM

6b1206e

fix some errors

7243c23

add hmm sanity check

2bc9e4b

format some example files

ad90ec8

fix error

6de0807

add sampling tests

0445a28

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sunxd3 and others added 11 commits August 29, 2025 15:22

formatting

f06e2f1

Update JuliaBUGS/test/model/auto_marginalization_sampling.jl

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Update JuliaBUGS/test/model/auto_marginalization.jl

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Update JuliaBUGS/test/model/auto_marginalization.jl

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Merge branch 'main' into sunxd/auto_marginalization

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fix test error

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stop using invokelatest

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fix test errors

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Merge branch 'main' into sunxd/auto_marginalization

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Update bugsmodel.jl

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add experiment package

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example

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sunxd3 and others added 4 commits September 23, 2025 13:19

chore: revert example formatting changes

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	T = T,
	K = K,
	y = sim.y,
	init_probs = init_probs,
	transition = transition,
	mu_prior_mean = mu_prior_mean,
	mu_prior_std = mu_prior_std,
	logsigma_prior_mean = logsigma_prior_mean,
	logsigma_prior_std = logsigma_prior_std,

	rng = MersenneTwister(get(ENV, "AM_SEED", "1") \|> x -> parse(Int, x))
	T = get(ENV, "AM_T", "50") \|> x -> parse(Int, x)

	T = T,
	K = K,
	y = sim.obs,
	init_probs = init_probs,
	transition = transition,
	means = means,
	sigmas = sigmas,

	B = try parse(Int, get(ENV, "AHMT_B", "2")) catch; 2 end
	depth = try parse(Int, get(ENV, "AHMT_DEPTH", "8")) catch; 8 end
	K = try parse(Int, get(ENV, "AHMT_K", "4")) catch; 4 end
	seed = try parse(Int, get(ENV, "AHMT_SEED", "1")) catch; 1 end
	trials = try parse(Int, get(ENV, "AHMT_TRIALS", "10")) catch; 10 end

	B = B,
	depth = depth,
	N = N,
	K = K,
	y = sim.y,
	init_probs = init_probs,
	transition = transition,
	means = means,
	sigmas = sigmas,
	parent = parent,

	"dfs" => () -> make_model_with_order(model, build_hmt_dfs_order(model; B_hint=B)),
	"bfs" => () -> make_model_with_order(model, build_hmt_bfs_order(model)),
	"random_dfs" => () -> make_model_with_order(model, build_hmt_dfs_order(model; B_hint=B, rng=MersenneTwister(seed+1), randomized=true)),
	"min_fill" => () -> make_model_with_order(model, build_min_fill_order(model; rng=MersenneTwister(seed+2), num_restarts=3)),
	"min_degree" => () -> make_model_with_order(model, build_min_degree_order(model; rng=MersenneTwister(seed+3), num_restarts=3)),

	i = try parse(Int, s[3:end-1]) catch; -1 end
	if i > 0; z_idxs[i] = j; else; push!(other, j); end

	i = try parse(Int, s[3:end-1]) catch; -1 end
	if i > 0; y_idxs[i] = j; else; push!(other, j); end

	c = try parse(Int, parts[1]) catch; -1 end
	t = try parse(Int, parts[2]) catch; -1 end

	logp, logp_ref = run_case(K=K, T=T, seed=seed)
	logp, logp_ref = run_case(; K=K, T=T, seed=seed)

	inner = replace(s[3:end-1], " " => "")
	inner = replace(s[3:(end - 1)], " " => "")

Add auto-marginalization implementation to the main package #385

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Benchmark results on macOS (aarch64)

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JuliaBUGS Mooncake results:

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