HiddenMarkovModels.jl | The Julia Language Ecosystem Directory

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HiddenMarkovModels.jl - v0.6.0

Published by github-actions[bot] 24 days ago

HiddenMarkovModels v0.6.0

Breaking changes

In-place single-sequence routines were hidden from the public API. Most user code will not be affected.

Performance improvements

Multithreading is now deactivated if seq_ends is passed as an NTuple. This helps remove overhead for very few sequences (especially for a single one).

Diff since v0.5.4

Merged pull requests:

Decompose forward function into initialize, predict, update (#105) (@THargreaves)
Update inference routines (#116) (@gdalle)

Closed issues:

Stop testing against HMMBase (#109)
Avoid @threads for a single sequence (#110)

HiddenMarkovModels.jl - v0.5.4

Published by github-actions[bot] 27 days ago

HiddenMarkovModels v0.5.4

Diff since v0.5.3

Merged pull requests:

Minor optimizations and simd (#108) (@gdalle)
Make HMMBase optional in the test suite (#111) (@gdalle)
Fix loglikelihood increase check in Baum-Welch (#112) (@gdalle)
Disable multithreading when seq_ends is passed as a tuple (#113) (@gdalle)
Bump version to 0.5.4 (#114) (@gdalle)
Improve code coverage (#115) (@gdalle)

Closed issues:

Avoid repeated transposition when using time-homogenous transition matrix (#106)

HiddenMarkovModels.jl - v0.5.3 Latest Release

Published by github-actions[bot] 5 months ago

HiddenMarkovModels v0.5.3

Diff since v0.5.2

Merged pull requests:

Allow heterogeneous distributions (#102) (@gdalle)

Closed issues:

Allow dist to be a Vector{Distribution{Univariate, Continuous}} in Baum Welch (#101)

HiddenMarkovModels.jl - v0.5.2

Published by github-actions[bot] 5 months ago

HiddenMarkovModels v0.5.2

Diff since v0.5.1

Merged pull requests:

Add JOSS citation (#98) (@gdalle)
Allow different types for elementwise log (#100) (@gdalle)

Closed issues:

Allow different types for transition matrix and elementwise log (#99)

HiddenMarkovModels.jl - v0.5.1

Published by github-actions[bot] 7 months ago

HiddenMarkovModels v0.5.1

Diff since v0.5.0

Merged pull requests:

Final benchmarks (#94) (@gdalle)
Fix benchmark reproducibility (#95) (@gdalle)
Remove precompilation (#97) (@gdalle)

Closed issues:

Benchmarks (#2)
Porting issues from HMMBase.jl (#92)

HiddenMarkovModels.jl - v0.5.0

Published by github-actions[bot] 8 months ago

HiddenMarkovModels v0.5.0

Diff since v0.4.1

See #93 for the user-facing changes

Merged pull requests:

Fix benchmarks (#90) (@gdalle)
Speed up viterbi (#93) (@gdalle)

HiddenMarkovModels.jl - v0.4.1

Published by github-actions[bot] 8 months ago

HiddenMarkovModels v0.4.1

Diff since v0.4.0

Merged pull requests:

Document fit! (#88) (@gdalle)

HiddenMarkovModels.jl - v0.4.0

Published by github-actions[bot] 8 months ago

HiddenMarkovModels v0.4.0

Diff since v0.3.1

Breaking changes

See the API reference for more details

Multiple sequences:

Revamped multiple sequence formatting: multiple sequences are concatenated for the input and for the output

Removals:

Removed alias HMMs for the package name
Removed everything related to (Abstract)MarkovChain
Removed PermutedHMM

Renamings:

initial_distribution(hmm) became initialization(hmm)
obs_distribution(hmm, i) became obs_distributions(hmm)
in baum_welch, check_loglikelihood_increasing became loglikelihood_increasing

Storage:

in ForwardBackwardStorage, ξ is now a vector of abstract matrices instead of a 3-dimensional array

Method signatures:

Revamped multiple sequence formatting: algorithm(hmm, obs_seqs, nb_seqs) became algorithm(hmm, obs_seq, [control_seq]; seq_ends).
Modified the arguments for in-place fitting: fit!(hmm, init_count, trans_count, obs_seq, state_marginals) became fit!(hmm, fb_storage, obs_seq, control_seq; seq_ends)

Return types;

Revamped multiple sequence formatting: results are now concatenated, and loglikelihoods are computed sequencewise

Merged pull requests:

Stdlib compat + Documenter v1 + bump to 0.3.1 (#54) (@gdalle)
Add TagBot workflow (#55) (@gdalle)
Move Python deps from pip to conda (#57) (@gdalle)
Fix docs benchmark (#58) (@gdalle)
Complete revamp (#59) (@gdalle)
Minor fixes (#60) (@gdalle)
Reactivate multithreaded BW (#62) (@gdalle)
Put benchmarks inside HMMBenchmark subpackage (#63) (@gdalle)
Move DependaBot (#64) (@gdalle)
Split (#66) (@gdalle)
Simplify docstrings (#67) (@gdalle)
Typo (#68) (@gdalle)
Benchmarks with Python updated (#69) (@gdalle)
More benchmarks (#70) (@gdalle)
Don't tune forward (#71) (@gdalle)
Threads (#72) (@gdalle)
Remove deps and fix Enzyme (#73) (@gdalle)
Remove pre 1.9 stuff (#74) (@gdalle)
Switch to StableRNGs (#75) (@gdalle)
Clean up benchmarks (#77) (@gdalle)
Add multithreading (#78) (@gdalle)
1 OpenBLAS thread (#79) (@gdalle)
Parallelize fitting (#80) (@gdalle)
Fairer Python benchmarks (#82) (@gdalle)
Format (#83) (@gdalle)
Correct benchmarks (#84) (@gdalle)
Add codecov token and documenter key (#85) (@gdalle)
Better docs and numerical stability (#87) (@gdalle)

Closed issues:

Chain rule (#3)
Benchmarks on different distributions (#8)
Add SIMD (#9)
Add links to (and comparisons with) other related packages (#14)
Make modification to allow support for Heterogeneous (Periodic) Hidden Markov Models (#52)
Clarify docs on the arguments of fit! (#53)
Fix benchmarks (#61)
MethodError Using baum_welch with MvLogNormal Emission Distributions (#76)
Test numerical stability (#86)