Releases: gdalle/HiddenMarkovModels.jl
Releases · gdalle/HiddenMarkovModels.jl
v0.5.3
v0.5.2
v0.5.1
v0.5.0
v0.4.1
Contributors
gdalle
Assets 2
v0.4.0
HiddenMarkovModels v0.4.0
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
HMMsfor the package name - Removed everything related to
(Abstract)MarkovChain - Removed
PermutedHMM
Renamings:
initial_distribution(hmm)becameinitialization(hmm)obs_distribution(hmm, i)becameobs_distributions(hmm)- in
baum_welch,check_loglikelihood_increasingbecameloglikelihood_increasing
Storage:
- in
ForwardBackwardStorage,ξis now a vector of abstract matrices instead of a 3-dimensional array
Method signatures:
- Revamped multiple sequence formatting:
algorithm(hmm, obs_seqs, nb_seqs)becamealgorithm(hmm, obs_seq, [control_seq]; seq_ends). - Modified the arguments for in-place fitting:
fit!(hmm, init_count, trans_count, obs_seq, state_marginals)becamefit!(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)
Contributors
gdalle
Assets 2
v0.3.1
v0.3.0
What's Changed
- Update docs-benchmark.yml by @gdalle in #27
- Allow manual build of docs with benchmarks by @gdalle in #28
- Fix image display in README by @gdalle in #29
- Replace citation bib with citation cff by @gdalle in #30
- Remove rtol in Baum-Welch by @gdalle in #31
- Upgrades all around by @gdalle in #32
- Working reverse AD and more efficient forward-backward by @gdalle in #33
- Better docs and tests by @gdalle in #34
- Fix_docs by @gdalle in #35
- Fix benchmark suite definition by @gdalle in #37
- Switch judge order by @gdalle in #39
- Compensate PythonCall overhead by @gdalle in #40
- Finish tutorials by @gdalle in #41
- Improve sparse and logarithmic testing by @gdalle in #42
- Fix benchmarks by @gdalle in #43
- Joss paper by @gdalle in #44
- Activate benchmarks on push to main by @gdalle in #45
- Remove outdated info on benchmarks by @gdalle in #46
- Fix_ci_again by @gdalle in #47
- Warning for empty benchmarks by @gdalle in #48
- fix spaces by @gdalle in #49
Full Changelog: v0.2.2...v0.3.0
Contributors
gdalle