Hi, I was looking in the code to check how does HSNE initialize embeddings for dimensionality reduction.

I understand that t-SNE is used at the end of the day but which type of initialization does it use? PCA, random?

Checking the outputs and code I believe it is not random. Am I right?

Hi, I was reading the HSNE article.

1. How can I use the library to generate an interpolation based on a hierarchy level?
2. How can I project an HSNE scale to plot, for example, using pyplot?

Thank you!

Hi nptsne team,

I'm having some trouble getting nptsne to import (see below for error).

This seems to be due to a requirement for a high version of GLIBC (2.29), which isn't directly available through apt-get for my system (the max version available currently is 2.24).

If there's any way I might be able to work around this, that would be great, as manually updating GLIBC is difficult in my computing environment.

Thanks! -Lucas

lucasg@graybuck-ide:/home/lucas.graybuck/nptsne_leiden_testing$ miniconda/envs/r-reticulate-9530452876/bin/python
Python 3.7.3 (default, Mar 27 2019, 22:11:17) 
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import nptsne
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/lucas.graybuck/nptsne_leiden_testing/miniconda/envs/r-reticulate-9530452876/lib/python3.7/site-packages/nptsne/__init__.py", line 1, in <module>
    from .nptsne import *
ImportError: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.29' not found (required by /home/lucas.graybuck/nptsne_leiden_testing/miniconda/envs/r-reticulate-9530452876/lib/python3.7/site-packages/nptsne/./libpng16.so.16)
>>> quit()
lucasg@graybuck-ide:/home/lucas.graybuck/nptsne_leiden_testing$ sudo apt-cache policy libc6
libc6:
  Installed: 2.24-11+deb9u4
  Candidate: 2.24-11+deb9u4
  Version table:
 *** 2.24-11+deb9u4 500
        500 http://deb.debian.org/debian stretch/main amd64 Packages
        100 /var/lib/dpkg/status
     2.24-11+deb9u1 500
        500 http://security.debian.org stretch/updates/main amd64 Packages

Github readme still points to the github pages doc (biovault.github.io/nptsne) and the PyPI links old nptsne 1.0.0 doc (bldrvnlw.readthedocs.io) Update to https://nptsne.readthedocs.io/en/release-1.1.0

Hi, I'm trying to install the latest version (1.2.0, bb49bb6aa1bdde4c4e39652e1ae331fecdf2c782). When I run pip install -v -e . it fails with cmake exit status 1. The problem is in the following cmake call:

cmake /home/vpetukhov/build/nptsne  -DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/home/vpetukhov/build/nptsne/src/nptsne/libs -DPYTHON_EXECUTABLE=/home/vpetukhov/local/miniconda3/envs/viaduct/bin/python -DCMAKE_BUILD_TYPE=Release -DTEMP_LIBS_DIR=/tmp/cibwlibsdir -DLIBCXX=libstdc++ -DNPTSNE_BUILD_WITH_CONAN=ON

It fails with a certificate error:

ERROR: HTTPSConnectionPool(host='lkeb-artifactory.lumc.nl', port=443): Max retries exceeded with url: /artifactory/api/conan/conan-local/v1/ping (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1123)')))

And if I disable SSL validation with conan remote update conan-biovault https://lkeb-artifactory.lumc.nl/artifactory/api/conan/conan-local False, the new error is:

ERROR: HDILib/1.2.4@lkeb/testing: option 'shared' doesn't exist Possible options are []

Here are full cmake logs for enabled and disabled ssl.

Hi, I work with high-dimensional data (hundreds of dimensions), and it requires using cosine distance. However, TextureTsne has Euclidean distance hardcoded. Could you please make it configurable?

New features in HDILib (changing metrics and user generated pre-calculated metrics) are not accessible in nptsne 1.1.0 . Please make a new release soon.

Original report

When creating a conda environment, 3.8.1 was the default, so at first I was wondering why it didn't work
3:06
Now, I'm not super familiar with the sub-versioning of python and package distribution, so I don't know if 3.8.1 should work when 3.8 is supported
3:10
Mhm, but I'm a little confused:
3:12
If I create a conda environment without specifying the python version, it defaults to 3.8.1 and pip install nptsne does not work (ERROR: Could not find a version that satisfies the requirement nptsne (from versions: none)
ERROR: No matching distribution found for nptsne) but when I create an environment and explicitly define the python version to be 3.8.1, it works just fine

python testhsnelouvain.py

Traceback (most recent call last): File "testhsnelouvain.py", line 5, in import community as community_louvain File "C:\Users\bvanlew\Anaconda3\envs\p37hsnedemo\lib\site-packages\community_init_.py", line 9, in from .community_louvain import ( File "C:\Users\bvanlew\Anaconda3\envs\p37hsnedemo\lib\site-packages\community\community_louvain.py", line 12, in import networkx as nx File "C:\Users\bvanlew\Anaconda3\envs\p37hsnedemo\lib\site-packages\networkx_init_.py", line 112, in import networkx.generators File "C:\Users\bvanlew\Anaconda3\envs\p37hsnedemo\lib\site-packages\networkx\generators_init_.py", line 8, in from networkx.generators.community import * File "C:\Users\bvanlew\Anaconda3\envs\p37hsnedemo\lib\site-packages\networkx\generators\community.py", line 20, in from scipy.special import zeta as zeta File "C:\Users\bvanlew\Anaconda3\envs\p37hsnedemo\lib\site-packages\scipy_init.py", line 136, in from . import distributor_init File "C:\Users\bvanlew\Anaconda3\envs\p37hsnedemo\lib\site-packages\scipy_distributor_init.py", line 61, in WinDLL(os.path.abspath(filename)) File "C:\Users\bvanlew\Anaconda3\envs\p37hsnedemo\lib\ctypes_init.py", line 364, in init self._handle = _dlopen(self._name, mode) OSError: [WinError 126] The specified module could not be found