Differences in results between the old and new versions

[KnSun99]

New version:

Old version:

The code and the data are the same:
umap_model = umap.UMAP(n_components=2, n_neighbors=150, min_dist=0.051, metric='euclidean', n_jobs=-1, verbose=True)
reduction = umap_model.fit_transform(matrix)

Could you please guide me on how to adjust to obtain results similar to those of the old version?
Thank you

[KnSun99]

conda list:

channels:

• conda-forge
• defaults
  dependencies:
• aiodns=3.5.0=py312haa95532_0
• aiohappyeyeballs=2.6.1=py312haa95532_0
• aiohttp=3.12.15=py312h02ab6af_0
• aiosignal=1.4.0=py312haa95532_0
• alabaster=0.7.16=py312haa95532_0
• arrow=1.4.0=py312haa95532_0
• astroid=3.3.11=py312haa95532_0
• asttokens=3.0.0=py312haa95532_0
• asyncssh=2.17.0=py312haa95532_0
• atomicwrites=1.4.0=py_0
• attrs=25.4.0=py312haa95532_0
• autopep8=2.0.4=pyhd3eb1b0_0
• babel=2.16.0=py312haa95532_0
• bcrypt=4.3.0=py312h636fa0f_0
• beautifulsoup4=4.13.5=py312haa95532_0
• binaryornot=0.4.4=pyhd3eb1b0_1
• black=25.9.0=py312haa95532_0
• bleach=6.2.0=py312haa95532_0
• brotlicffi=1.0.9.2=py312h5da7b33_1
• bzip2=1.0.8=h0ad9c76_8
• c-ares=1.34.5=h731ff69_0
• ca-certificates=2025.10.5=h4c7d964_0
• cattrs=24.1.2=py312haa95532_0
• certifi=2025.10.5=pyhd8ed1ab_0
• cffi=2.0.0=py312h02ab6af_0
• chardet=5.2.0=py312haa95532_0
• charset-normalizer=3.3.2=pyhd3eb1b0_0
• click=8.2.1=py312haa95532_0
• cloudpickle=3.1.1=py312haa95532_0
• colorama=0.4.6=py312haa95532_0
• comm=0.2.1=py312haa95532_0
• cookiecutter=2.6.0=py312haa95532_1
• cryptography=46.0.2=py312h114bc41_0
• debugpy=1.8.16=py312h885b0b7_0
• decorator=5.2.1=py312haa95532_0
• defusedxml=0.7.1=pyhd3eb1b0_0
• deprecated=1.2.18=py312haa95532_0
• diff-match-patch=20200713=pyhd3eb1b0_0
• dill=0.4.0=py312haa95532_0
• docstring-to-markdown=0.17=py312haa95532_0
• docutils=0.21.2=py312haa95532_0
• executing=2.2.1=py312haa95532_0
• ezc3d=1.6.0=np2py312h6d06127_0
• flake8=7.1.1=py312haa95532_0
• frozenlist=1.8.0=py312h885b0b7_0
• fzf=0.55.0=h7d69c46_0
• icu=73.1=h6c2663c_0
• idna=3.7=py312haa95532_0
• imagesize=1.4.1=py312haa95532_0
• importlib-metadata=8.5.0=py312haa95532_0
• inflection=0.5.1=py312haa95532_1
• intervaltree=3.1.0=pyhd3eb1b0_0
• ipykernel=6.30.1=py312haa95532_0
• ipython=9.5.0=py312haa95532_0
• ipython_pygments_lexers=1.1.1=py312haa95532_0
• isort=6.1.0=py312haa95532_0
• jaraco.classes=3.4.0=py312haa95532_0
• jaraco.context=6.0.0=py312haa95532_0
• jaraco.functools=4.1.0=py312haa95532_0
• jedi=0.19.2=py312haa95532_0
• jellyfish=1.1.3=py312h8ecf97c_0
• jinja2=3.1.6=py312haa95532_0
• jpeg=9f=ha349fce_0
• jsonschema=4.25.0=py312haa95532_0
• jsonschema-specifications=2023.7.1=py312haa95532_0
• jupyter_client=8.6.3=py312haa95532_0
• jupyter_core=5.8.1=py312haa95532_0
• jupyterlab_pygments=0.3.0=py312haa95532_0
• keyring=25.6.0=py312haa95532_0
• krb5=1.20.1=h5b6d351_0
• libblas=3.9.0=35_h5709861_mkl
• libcblas=3.9.0=35_h2a3cdd5_mkl
• libclang13=14.0.6=default_h8e68704_2
• libexpat=2.7.1=hac47afa_0
• libffi=3.5.2=h52bdfb6_0
• libhwloc=2.12.1=default_h88281d1_1000
• libiconv=1.18=hc1393d2_2
• libkrb5=1.21.3=h885b0b7_4
• liblapack=3.9.0=35_hf9ab0e9_mkl
• liblzma=5.8.1=h2466b09_2
• liblzma-devel=5.8.1=h2466b09_2
• libpng=1.6.50=h46444df_0
• libpq=17.6=h652a1e2_0
• libsodium=1.0.20=h83e8143_0
• libspatialindex=1.9.3=h6c2663c_0
• libsqlite=3.50.4=hf5d6505_0
• libuv=1.48.0=h827c3e9_0
• libwinpthread=12.0.0.r4.gg4f2fc60ca=h57928b3_10
• libxml2=2.13.8=h741aa76_1
• libzlib=1.3.1=h2466b09_2
• llvm-openmp=21.1.4=hfa2b4ca_0
• lsprotocol=2025.0.0=py312haa95532_0
• lz4-c=1.9.4=h2bbff1b_1
• markdown-it-py=4.0.0=py312haa95532_0
• markupsafe=3.0.2=py312h827c3e9_0
• matplotlib-inline=0.1.7=py312haa95532_0
• mccabe=0.7.0=pyhd3eb1b0_0
• mdurl=0.1.2=py312haa95532_0
• mistune=3.1.2=py312haa95532_0
• mkl=2024.2.2=h57928b3_16
• more-itertools=10.8.0=py312haa95532_0
• multidict=6.7.0=py312h02ab6af_0
• mypy_extensions=1.0.0=py312haa95532_0
• nbclient=0.10.2=py312haa95532_0
• nbconvert=7.16.6=py312haa95532_0
• nbconvert-core=7.16.6=py312haa95532_0
• nbconvert-pandoc=7.16.6=py312haa95532_0
• nbformat=5.10.4=py312haa95532_0
• nest-asyncio=1.6.0=py312haa95532_0
• numpydoc=1.9.0=py312haa95532_0
• openssl=3.5.4=h725018a_0
• packaging=25.0=py312haa95532_1
• pandoc=3.8=haa95532_0
• pandocfilters=1.5.1=py312haa95532_0
• parso=0.8.4=py312haa95532_0
• pathspec=0.12.1=py312haa95532_0
• pexpect=4.9.0=py312haa95532_0
• pickleshare=0.7.5=pyhd3eb1b0_1003
• pip=25.2=pyh8b19718_0
• platformdirs=4.3.7=py312haa95532_0
• pluggy=1.5.0=py312haa95532_0
• ply=3.11=py312haa95532_1
• prompt-toolkit=3.0.52=py312haa95532_0
• prompt_toolkit=3.0.52=hd3eb1b0_0
• propcache=0.3.1=py312h827c3e9_0
• psutil=7.0.0=py312h02ab6af_0
• ptyprocess=0.7.0=pyhd3eb1b0_2
• pure_eval=0.2.3=py312haa95532_0
• pycares=4.10.0=py312he29e43d_0
• pycodestyle=2.12.1=py312haa95532_0
• pycparser=2.23=py312haa95532_0
• pydocstyle=6.3.0=py312haa95532_0
• pyflakes=3.2.0=py312haa95532_0
• pygithub=2.4.0=py312haa95532_0
• pygments=2.19.1=py312haa95532_0
• pyjwt=2.10.1=py312haa95532_0
• pylint=3.3.8=py312haa95532_0
• pylint-venv=3.0.3=py312haa95532_0
• pyls-spyder=0.4.0=pyhd3eb1b0_0
• pynacl=1.6.0=py312h581ae37_0
• pyqt=5.15.10=py312h5da7b33_1
• pyqt5-sip=12.13.0=py312h827c3e9_1
• pyqtwebengine=5.15.10=py312h5da7b33_1
• pysocks=1.7.1=py312haa95532_0
• python=3.12.12=h0159041_1_cpython
• python-dateutil=2.9.0post0=py312haa95532_2
• python-fastjsonschema=2.20.0=py312haa95532_0
• python-lsp-black=2.0.0=py312haa95532_1
• python-lsp-jsonrpc=1.1.2=pyhd3eb1b0_0
• python-lsp-ruff=2.3.0=py312haa95532_0
• python-lsp-server=1.13.1=py312hbc747e5_0
• python-slugify=8.0.4=py312haa95532_0
• python-tzdata=2025.2=pyhd3eb1b0_0
• python_abi=3.12=1_cp312
• pytokens=0.2.0=py312haa95532_0
• pytoolconfig=1.2.6=py312haa95532_0
• pyuca=1.2=py312haa95532_1
• pywin32=311=py312h885b0b7_0
• pywin32-ctypes=0.2.2=py312haa95532_0
• pyyaml=6.0.2=py312h827c3e9_0
• pyzmq=27.1.0=py312h7149c55_0
• qdarkstyle=3.2.3=pyhd3eb1b0_0
• qstylizer=0.2.2=py312haa95532_0
• qt-main=5.15.2=h19c9488_12
• qt-webengine=5.15.9=h5bd16bc_7
• qtawesome=1.4.0=py312haa95532_0
• qtconsole=5.7.0=py312haa95532_0
• qtconsole-base=5.7.0=pyha770c72_0
• qtpy=2.4.3=py312haa95532_0
• referencing=0.30.2=py312haa95532_0
• requests=2.32.5=py312haa95532_0
• rich=14.2.0=py312haa95532_0
• roman-numerals-py=3.1.0=py312haa95532_0
• rope=1.13.0=py312haa95532_0
• rpds-py=0.22.3=py312h636fa0f_0
• rtree=1.4.1=py312h1e5ca3c_0
• ruff=0.12.0=py312h1361809_0
• setuptools=80.9.0=pyhff2d567_0
• sip=6.7.12=py312h5da7b33_1
• six=1.17.0=py312haa95532_0
• snowballstemmer=3.0.1=py312haa95532_0
• sortedcontainers=2.4.0=pyhd3eb1b0_0
• soupsieve=2.5=py312haa95532_0
• sphinx=8.2.3=py312h827c3e9_0
• sphinxcontrib-applehelp=2.0.0=pyhd3eb1b0_1
• sphinxcontrib-devhelp=2.0.0=pyhd3eb1b0_0
• sphinxcontrib-htmlhelp=2.1.0=pyhd3eb1b0_0
• sphinxcontrib-jsmath=1.0.1=pyhd3eb1b0_0
• sphinxcontrib-qthelp=2.0.0=pyhd3eb1b0_1
• sphinxcontrib-serializinghtml=2.0.0=pyhd3eb1b0_0
• spyder=6.1.0=hd8ed1ab_0
• spyder-base=6.1.0=py312h2e8e312_0
• spyder-kernels=3.1.0=py312hbc747e5_0
• sqlite=3.50.2=hda9a48d_1
• stack_data=0.6.3=py312haa95532_0
• superqt=0.7.6=py312hdfb3b6f_0
• text-unidecode=1.3=pyhd3eb1b0_0
• textdistance=4.6.3=py312hbc747e5_1
• three-merge=0.1.1=pyhd3eb1b0_0
• tinycss2=1.4.0=py312haa95532_0
• tk=8.6.13=h2c6b04d_2
• tomlkit=0.13.2=py312haa95532_0
• tornado=6.5.1=py312h827c3e9_0
• traitlets=5.14.3=py312haa95532_0
• typing-extensions=4.15.0=py312haa95532_0
• typing_extensions=4.15.0=py312haa95532_0
• tzdata=2025b=h78e105d_0
• ucrt=10.0.26100.0=h57928b3_0
• ujson=5.10.0=py312h5da7b33_1
• urllib3=2.5.0=py312haa95532_0
• vc=14.3=h2b53caa_32
• vc14_runtime=14.44.35208=h818238b_32
• vcomp14=14.44.35208=h818238b_32
• vs2015_runtime=14.44.35208=h38c0c73_32
• watchdog=6.0.0=py312haa95532_0
• wcwidth=0.2.13=py312haa95532_0
• webencodings=0.5.1=py312haa95532_2
• whatthepatch=1.0.7=py312haa95532_0
• wheel=0.45.1=pyhd8ed1ab_1
• win_inet_pton=1.1.0=py312haa95532_0
• winloop=0.2.2=py312h913537a_0
• wrapt=1.17.0=py312h827c3e9_0
• xz=5.8.1=h208afaa_2
• xz-tools=5.8.1=h2466b09_2
• yaml=0.2.5=he774522_0
• yapf=0.43.0=py312haa95532_0
• yarl=1.18.0=py312h827c3e9_0
• zeromq=4.3.5=h6c54ac7_1
• zipp=3.21.0=py312haa95532_0
• zlib=1.3.1=h2466b09_2
• zstd=1.5.7=h56299aa_0
• pip:
  • absl-py==2.3.1
  • addict==2.4.0
  • astunparse==1.6.3
  • blosc2==3.10.2
  • c3d==0.6.0
  • contourpy==1.3.3
  • cycler==0.12.1
  • cython==3.1.6
  • daal==2025.9.0
  • filelock==3.19.1
  • flatbuffers==25.9.23
  • fonttools==4.60.1
  • fsspec==2025.9.0
  • gast==0.6.0
  • google-pasta==0.2.0
  • grpcio==1.76.0
  • h5py==3.15.1
  • imageio==2.37.2
  • joblib==1.5.2
  • keras==3.12.0
  • kiwisolver==1.4.9
  • lazy-loader==0.4
  • libclang==18.1.1
  • llvmlite==0.45.1
  • markdown==3.9
  • matplotlib==3.10.7
  • ml-dtypes==0.5.3
  • mpmath==1.3.0
  • msgpack==1.1.2
  • multiprocess==0.70.18
  • namex==0.1.0
  • narwhals==2.10.0
  • natsort==8.4.0
  • ndindex==1.10.0
  • networkx==3.5
  • numba==0.62.1
  • numexpr==2.14.1
  • numpy==2.3.5
  • opencv-python==4.12.0.88
  • opt-einsum==3.4.0
  • optree==0.17.0
  • pandas==2.3.3
  • pathos==0.3.4
  • pillow==11.3.0
  • plotly==6.3.1
  • pox==0.3.6
  • ppft==1.7.7
  • protobuf==6.33.0
  • py-cpuinfo==9.0.0
  • pynndescent==0.5.13
  • pyparsing==3.2.5
  • pytz==2025.2
  • scikit-image==0.25.2
  • scikit-learn==1.7.2
  • scikit-learn-intelex==2025.9.0
  • scipy==1.16.2
  • seaborn==0.13.2
  • sympy==1.14.0
  • tables==3.10.2
  • tbb==2022.3.0
  • tcmlib==1.4.1
  • tensorboard==2.20.0
  • tensorboard-data-server==0.7.2
  • tensorflow==2.20.0
  • termcolor==3.2.0
  • threadpoolctl==3.6.0
  • tifffile==2025.10.16
  • torch==2.8.0+cu128
  • torchaudio==2.8.0+cu128
  • torchvision==0.23.0+cu128
  • tqdm==4.67.1
  • umap-learn==0.5.9.post2
  • werkzeug==3.1.3

[lmcinnes]

I don't know which old version you are referring to. Not much has changed in layout optimization for a couple of semi-major versions, so it seems surprising that there would be this big a difference unless you were previously using version 0.3 or earlier.

[KnSun99]

The old version was 0.5.6.

However, upon my re-test, I found that it was not an issue with the umap version, but rather with the numba version.

I downgraded numba from version 0.62.1 to version 0.61.2, and then recalculated and everything returned to normal.
0.62.1 -> 0.61.2

Would it be necessary to update the umap version based on the new version of numba?