t-SNE Kernel Crash

### Describe the bug

TSNE `fit_transform` leads in rare cases to a Kernel crash. I was able to reproduce it locally on my Mac, on Google Colab as well as in a GitHub Actions pipeline (Ubuntu). 

The error message doesn't mention a specific reason:
`[error] Disposing session as kernel process died ExitCode: undefined, Reason:`

I came across this while working on this pull request: https://github.com/JohT/code-graph-analysis-pipeline/pull/148

### Steps/Code to Reproduce

Link to Google Colab with a detailed reproducer: https://drive.google.com/file/d/1l7sLOkE8vkfNcY57iVJ7YdpbQk1x0cTT/view?usp=drive_link

```python
import pandas as pd
import numpy as np
from sklearn.manifold import TSNE

import sklearn
sklearn.show_versions()

# HashGNN embeddings (dict, 64 dimensions) of a very small Graph with only 4 nodes
# Something about this data will cause the t-SNE algorithm to crash the Kernel
hashGNN_embeddings = {'projectName': {0: 'react-router', 1: 'react-router-dom', 2: 'react-router-native', 3: 'react-router-dom', 4: 'router'}, 'embedding': {0: [0.0, -0.4330126941204071, -0.4330126941204071, 0.21650634706020355, -0.21650634706020355, -0.4330126941204071, 0.4330126941204071, 0.0, -1.0825317353010178, -0.21650634706020355, -0.21650634706020355, 0.6495190411806107, 0.8660253882408142, 0.21650634706020355, -0.21650634706020355, -0.4330126941204071, 0.21650634706020355, -0.4330126941204071, -0.8660253882408142, 0.4330126941204071, 0.21650634706020355, 0.8660253882408142, 0.0, 0.4330126941204071, 0.21650634706020355, 0.21650634706020355, -0.21650634706020355, 0.0, 0.0, 0.0, -0.21650634706020355, 0.4330126941204071, 1.0825317353010178, -0.4330126941204071, 0.21650634706020355, 1.0825317353010178, -0.4330126941204071, 1.0825317353010178, 0.0, -0.8660253882408142, 0.21650634706020355, 0.8660253882408142, 0.0, 0.21650634706020355, 0.21650634706020355, 0.0, 0.21650634706020355, 0.6495190411806107, 0.6495190411806107, 0.0, -0.6495190411806107, 0.21650634706020355, -0.4330126941204071, 0.4330126941204071, 0.21650634706020355, 0.6495190411806107, -0.6495190411806107, 0.4330126941204071, 0.6495190411806107, 0.0, 0.4330126941204071, 0.0, 0.21650634706020355, 0.4330126941204071], 1: [0.0, -0.4330126941204071, -0.4330126941204071, 0.21650634706020355, -0.21650634706020355, -0.4330126941204071, 0.4330126941204071, 0.0, -1.0825317353010178, -0.21650634706020355, -0.21650634706020355, 0.6495190411806107, 0.8660253882408142, 0.21650634706020355, -0.21650634706020355, -0.4330126941204071, 0.21650634706020355, -0.4330126941204071, -0.8660253882408142, 0.4330126941204071, 0.21650634706020355, 0.8660253882408142, 0.0, 0.4330126941204071, 0.21650634706020355, 0.21650634706020355, -0.21650634706020355, 0.0, 0.0, 0.0, -0.21650634706020355, 0.4330126941204071, 1.0825317353010178, -0.4330126941204071, 0.21650634706020355, 1.0825317353010178, -0.4330126941204071, 1.0825317353010178, 0.0, -0.8660253882408142, 0.21650634706020355, 0.8660253882408142, 0.0, 0.21650634706020355, 0.21650634706020355, 0.0, 0.21650634706020355, 0.6495190411806107, 0.6495190411806107, 0.0, -0.6495190411806107, 0.21650634706020355, -0.4330126941204071, 0.4330126941204071, 0.21650634706020355, 0.6495190411806107, -0.6495190411806107, 0.4330126941204071, 0.6495190411806107, 0.0, 0.4330126941204071, 0.0, 0.21650634706020355, 0.4330126941204071], 2: [0.0, -0.4330126941204071, -0.4330126941204071, 0.21650634706020355, -0.21650634706020355, -0.4330126941204071, 0.4330126941204071, 0.0, -1.0825317353010178, -0.21650634706020355, -0.21650634706020355, 0.6495190411806107, 0.8660253882408142, 0.21650634706020355, -0.21650634706020355, -0.4330126941204071, 0.21650634706020355, -0.4330126941204071, -0.8660253882408142, 0.4330126941204071, 0.21650634706020355, 0.8660253882408142, 0.0, 0.4330126941204071, 0.21650634706020355, 0.21650634706020355, -0.21650634706020355, 0.0, 0.0, 0.0, -0.21650634706020355, 0.4330126941204071, 1.0825317353010178, -0.4330126941204071, 0.21650634706020355, 1.0825317353010178, -0.4330126941204071, 1.0825317353010178, 0.0, -0.8660253882408142, 0.21650634706020355, 0.8660253882408142, 0.0, 0.21650634706020355, 0.21650634706020355, 0.0, 0.21650634706020355, 0.6495190411806107, 0.6495190411806107, 0.0, -0.6495190411806107, 0.21650634706020355, -0.4330126941204071, 0.4330126941204071, 0.21650634706020355, 0.6495190411806107, -0.6495190411806107, 0.4330126941204071, 0.6495190411806107, 0.0, 0.4330126941204071, 0.0, 0.21650634706020355, 0.4330126941204071], 3: [0.0, -0.4330126941204071, -0.4330126941204071, 0.21650634706020355, -0.21650634706020355, -0.4330126941204071, 0.4330126941204071, 0.0, -1.0825317353010178, -0.21650634706020355, -0.21650634706020355, 0.6495190411806107, 0.8660253882408142, 0.21650634706020355, -0.21650634706020355, -0.4330126941204071, 0.21650634706020355, -0.4330126941204071, -0.8660253882408142, 0.4330126941204071, 0.21650634706020355, 0.8660253882408142, 0.0, 0.4330126941204071, 0.21650634706020355, 0.21650634706020355, -0.21650634706020355, 0.0, 0.0, 0.0, -0.21650634706020355, 0.4330126941204071, 1.0825317353010178, -0.4330126941204071, 0.21650634706020355, 1.0825317353010178, -0.4330126941204071, 1.0825317353010178, 0.0, -0.8660253882408142, 0.21650634706020355, 0.8660253882408142, 0.0, 0.21650634706020355, 0.21650634706020355, 0.0, 0.21650634706020355, 0.6495190411806107, 0.6495190411806107, 0.0, -0.6495190411806107, 0.21650634706020355, -0.4330126941204071, 0.4330126941204071, 0.21650634706020355, 0.6495190411806107, -0.6495190411806107, 0.4330126941204071, 0.6495190411806107, 0.0, 0.4330126941204071, 0.0, 0.21650634706020355, 0.4330126941204071], 4: [0.0, -0.4330126941204071, -0.4330126941204071, 0.21650634706020355, -0.21650634706020355, -0.4330126941204071, 0.4330126941204071, 0.0, -1.0825317353010178, -0.21650634706020355, -0.21650634706020355, 0.6495190411806107, 0.8660253882408142, 0.21650634706020355, -0.21650634706020355, -0.4330126941204071, 0.21650634706020355, -0.4330126941204071, -0.8660253882408142, 0.4330126941204071, 0.21650634706020355, 0.8660253882408142, 0.0, 0.4330126941204071, 0.21650634706020355, 0.21650634706020355, -0.21650634706020355, 0.0, 0.0, 0.0, -0.21650634706020355, 0.4330126941204071, 1.0825317353010178, -0.4330126941204071, 0.21650634706020355, 1.0825317353010178, -0.4330126941204071, 1.0825317353010178, 0.0, -0.8660253882408142, 0.21650634706020355, 0.8660253882408142, 0.0, 0.21650634706020355, 0.21650634706020355, 0.0, 0.21650634706020355, 0.6495190411806107, 0.6495190411806107, 0.0, -0.6495190411806107, 0.21650634706020355, -0.4330126941204071, 0.4330126941204071, 0.21650634706020355, 0.6495190411806107, -0.6495190411806107, 0.4330126941204071, 0.6495190411806107, 0.0, 0.4330126941204071, 0.0, 0.21650634706020355, 0.4330126941204071]}}
embeddings = pd.DataFrame.from_dict(hashGNN_embeddings)
embeddings_as_numpy_array = np.array(embeddings.embedding.to_list())
tsne = TSNE(n_components=2, perplexity=3.0, verbose=1, random_state=50)

# ----> The next line will cause the Kernel crash with the following message:
#       "[error] Disposing session as kernel process died ExitCode: undefined, Reason:"
two_dimension_node_embeddings = tsne.fit_transform(embeddings_as_numpy_array)
```

### Expected Results

No Kernel crash.

### Actual Results

```json
{
	"name": "",
	"message": "",
	"stack": "The Kernel crashed while executing code in the current cell or a previous cell. 
Please review the code in the cell(s) to identify a possible cause of the failure. 
Click <a href='https://aka.ms/vscodeJupyterKernelCrash'>here</a> for more info. 
View Jupyter <a href='command:jupyter.viewOutput'>log</a> for further details."
}
```

### Versions

```shell
System:
    python: 3.11.9 | packaged by conda-forge | (main, Apr 19 2024, 18:34:54) [Clang 16.0.6 ]
executable: /opt/homebrew/Caskroom/miniforge/base/envs/tsne-bug-reproducer-environment/bin/python
   machine: macOS-14.4.1-arm64-arm-64bit

Python dependencies:
      sklearn: 1.5.0
          pip: 24.0
   setuptools: 70.0.0
        numpy: 1.23.5
        scipy: 1.13.1
       Cython: None
       pandas: 1.5.3
   matplotlib: 3.6.3
       joblib: 1.4.2
threadpoolctl: 3.5.0

Built with OpenMP: True

threadpoolctl info:
       user_api: blas
   internal_api: openblas
    num_threads: 8
         prefix: libopenblas
       filepath: /opt/homebrew/Caskroom/miniforge/base/envs/tsne-bug-reproducer-environment/lib/libopenblas.0.dylib
        version: 0.3.27
threading_layer: openmp
   architecture: VORTEX

       user_api: openmp
   internal_api: openmp
    num_threads: 8
         prefix: libomp
       filepath: /opt/homebrew/Caskroom/miniforge/base/envs/tsne-bug-reproducer-environment/lib/libomp.dylib
        version: None
```

COMMENT:
Thanks for the reproducing snippet, this is a duplicate of https://github.com/scikit-learn/scikit-learn/issues/28368, there is a bit more information there, so I am going to close this issue.

Note for other maintainers: I can reproduce on Linux so this is not OSX specific and this is not a regression in 1.5 since this existed already in 1.4.

Labels: Bug, Needs Triage