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PHATE #210

Merged
merged 45 commits into from
Dec 21, 2024
Merged

PHATE #210

merged 45 commits into from
Dec 21, 2024

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edyoshikun
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  • Adding support for PHATE
  • Adding reviewed Alishba's scripts for ALFI.

ziw-liu and others added 22 commits November 8, 2024 09:47
@ziw-liu
translation: fix validation loss aggregation (#202)
db80819
@edyoshikun
exposing prefetch and persistent worker (#203)
820c805
@alishbaimran
metrics for dynamic, smoothness and docstrings
a73b9a0
@alishbaimran
updated metrics and plots for distance
79db1e4
@alishbaimran
fixed CI test cases
42cf756
@edyoshikun
nexnt loss prototype
0a23fc4
@edyoshikun
fix bug with z_scale_range in hcs datamodule. If the value is an int …
f2d75cd 
…this does not work.
@edyoshikun
exclude the negative pair from dataloader and forward pass
aa74eff
@edyoshikun
adding option using pytorch-metric-learning implementation
771d33d 
and modifying previous to match same input args
@edyoshikun
removing our implementation of NTXentLoss and using pytorch metric
46974bc
@edyoshikun
ruff
1fde4ab
@edyoshikun
prototype for phate and umap plot
3f8363d
@edyoshikun
- proofreading the calculations
26ebe74 
- removing unecessary calls to ALFI script
- simplifying code to re-use functions
@ziw-liu @edyoshikun
methods to rank nearest neighbors in embeddings
7a3b036
@ziw-liu @edyoshikun
example script to plot state change of a single track
3992d9d
@ziw-liu @edyoshikun
test using scaled features
cae8290
@edyoshikun
phate embeddings
30f4246
@edyoshikun
removing dataframe from the compute_phate
356c15d 
adding docstring
@edyoshikun
adding phate to the prediction writer and moving it as dependency.
57abb19
@edyoshikun
changing the phate defaults in the prediction writer.
19fdcf2
@edyoshikun
ruff
1ee8af1
@edyoshikun
fixing bug in phate in predict writer
14b7368
ziw-liu
ziw-liu reviewed Nov 21, 2024
View reviewed changes
pyproject.toml Outdated Show resolved Hide resolved
@edyoshikun edyoshikun changed the title Phate PHATE Nov 27, 2024
@Soorya19Pradeep
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@edyoshikun , can we add the calculation and storage of PHATE in the predictions in this PR?

edyoshikun and others added 12 commits December 18, 2024 16:32
@edyoshikun
nexnt loss prototype
b75ddd1
@edyoshikun
exclude the negative pair from dataloader and forward pass
98b36de
@edyoshikun
adding option using pytorch-metric-learning implementation
5bc2ff6 
and modifying previous to match same input args
@edyoshikun
removing our implementation of NTXentLoss and using pytorch metric
472be4e
@edyoshikun
ruff
66b3899
@ziw-liu @edyoshikun
remove blank line diff
9cc35cf
@ziw-liu @edyoshikun
remove blank line diff
3c96f13
@edyoshikun
simplying the engine
d3d4715
@ziw-liu @edyoshikun
explicit target shape argument in the HCS data module
70dfb5d
@ziw-liu @edyoshikun
Revert "explicit target shape argument in the HCS data module"
a845847 
This reverts commit 464d4c9.
@ziw-liu @edyoshikun
Explicit target shape argument in the HCS data module (#212)
a6e2318 
* explicit target shape argument in the HCS data module

* update docstring

* update test cases
@edyoshikun
Gradio example (#158)
fa74b0d 
* initial demo

* using the predict_step

* modifying paths to chkpt and example pngs

* updating gradio as the one on Huggingface
@edyoshikun edyoshikun merged commit 3475223 into ntxent_loss Dec 21, 2024
4 checks passed
@edyoshikun edyoshikun deleted the phate branch December 21, 2024 22:33
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@ziw-liu ziw-liu ziw-liu left review comments

@Soorya19Pradeep Soorya19Pradeep Awaiting requested review from Soorya19Pradeep

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4 participants
@edyoshikun @Soorya19Pradeep @ziw-liu @alishbaimran