Merge pull request #201 from WenjieDu/wdu_dev

Refactor algorithms' module structure, enable customized loss function in SAITS, enable GP-VAE to run on CUDA
WenjieDu · Oct 9, 2023 · 6a2107c · 6a2107c
2 parents 164175f + 60b42c9
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diff --git a/README.md b/README.md
@@ -191,9 +191,12 @@ and we are pursuing to publish it in prestigious academic venues, e.g. JMLR (tra
 [Machine Learning Open Source Software](https://www.jmlr.org/mloss/)). If you use PyPOTS in your work,
 please cite it as below and 🌟star this repository to make others notice this library. 🤗
 
+There are scientific research projects using PyPOTS and referencing in their papers.
+Here is [an incomplete list of them](https://scholar.google.com/scholar?as_ylo=2022&q=%E2%80%9CPyPOTS%E2%80%9D&hl=en>).
+
 ``` bibtex
 @article{du2023PyPOTS,
-title={{PyPOTS: A Python Toolbox for Data Mining on Partially-Observed Time Series}},
+title={{PyPOTS: a Python toolbox for data mining on Partially-Observed Time Series}},
 author={Wenjie Du},
 year={2023},
 eprint={2305.18811},
@@ -204,11 +207,25 @@ doi={10.48550/arXiv.2305.18811},
 }
 ```
 
+> Wenjie Du. (2023).
+> PyPOTS: a Python toolbox for data mining on Partially-Observed Time Series.
+> arXiv, abs/2305.18811.https://arxiv.org/abs/2305.18811
+
 or
 
+``` bibtex
+@inproceedings{du2023PyPOTS,
+title={{PyPOTS: a Python toolbox for data mining on Partially-Observed Time Series}},
+booktitle={9th SIGKDD workshop on Mining and Learning from Time Series (MiLeTS'23)},
+author={Wenjie Du},
+year={2023},
+url={https://arxiv.org/abs/2305.18811},
+}
+```
+
 > Wenjie Du. (2023).
-> PyPOTS: A Python Toolbox for Data Mining on Partially-Observed Time Series.
-> arXiv, abs/2305.18811. https://doi.org/10.48550/arXiv.2305.18811
+> PyPOTS: a Python toolbox for data mining on Partially-Observed Time Series.
+> In *9th SIGKDD workshop on Mining and Learning from Time Series (MiLeTS'23)*. https://arxiv.org/abs/2305.18811
 
 
 ## ❖ Contribution

diff --git a/docs/index.rst b/docs/index.rst
@@ -133,6 +133,8 @@ Task                           Type             Algorithm
 ============================== ================ =========================================================================  ====== =========
 Imputation                     Neural Network   SAITS (Self-Attention-based Imputation for Time Series)                    2022   :cite:`du2023SAITS`
 Imputation                     Neural Network   Transformer                                                                2017   :cite:`vaswani2017Transformer`, :cite:`du2023SAITS`
+Imputation                     Neural Network   US-GAN                                                                     2021   :cite:`miao2021SSGAN`
+Imputation                     Neural Network   GP-VAE                                                                     2020   :cite:`fortuin2020GPVAEDeep`
 Imputation, Classification     Neural Network   BRITS (Bidirectional Recurrent Imputation for Time Series)                 2018   :cite:`cao2018BRITS`
 Imputation                     Neural Network   M-RNN (Multi-directional Recurrent Neural Network)                         2019   :cite:`yoon2019MRNN`
 Imputation                     Naive            LOCF (Last Observation Carried Forward)                                    /      /
@@ -159,7 +161,7 @@ please cite it as below and 🌟star `PyPOTS repository <https://github.com/Wenj
    :linenos:
 
    @article{du2023PyPOTS,
-   title={{PyPOTS: A Python Toolbox for Data Mining on Partially-Observed Time Series}},
+   title={{PyPOTS: a Python toolbox for data mining on Partially-Observed Time Series}},
    author={Wenjie Du},
    year={2023},
    eprint={2305.18811},
@@ -169,12 +171,32 @@ please cite it as below and 🌟star `PyPOTS repository <https://github.com/Wenj
    doi={10.48550/arXiv.2305.18811},
    }
 
-or
+..
 
    Wenjie Du. (2023).
-   PyPOTS: A Python Toolbox for Data Mining on Partially-Observed Time Series.
+   PyPOTS: a Python toolbox for data mining on Partially-Observed Time Series.
    arXiv, abs/2305.18811. https://doi.org/10.48550/arXiv.2305.18811
 
+or
+
+.. code-block:: bibtex
+   :linenos:
+
+   @inproceedings{du2023PyPOTS,
+   title={{PyPOTS: a Python toolbox for data mining on Partially-Observed Time Series}},
+   booktitle={9th SIGKDD workshop on Mining and Learning from Time Series (MiLeTS'23)},
+   author={Wenjie Du},
+   year={2023},
+   url={https://arxiv.org/abs/2305.18811},
+   }
+
+..
+
+   Wenjie Du. (2023).
+   PyPOTS: a Python toolbox for data mining on Partially-Observed Time Series.
+   In *9th SIGKDD workshop on Mining and Learning from Time Series (MiLeTS'23)*. https://arxiv.org/abs/2305.18811
+
+
 
 ❖ Contribution
 ^^^^^^^^^^^^^^^

diff --git a/docs/model_api.rst b/docs/model_api.rst
@@ -1,7 +1,7 @@
 Model API Cheatsheet
 =======================
 
-pypots.base module
+pypots.base
 ------------------
 
 .. automodule:: pypots.base
@@ -10,7 +10,7 @@ pypots.base module
    :show-inheritance:
    :inherited-members:
 
-pypots.imputation.base module
+pypots.imputation.base
 -----------------------------
 
 .. automodule:: pypots.imputation.base
@@ -19,7 +19,7 @@ pypots.imputation.base module
    :show-inheritance:
    :inherited-members:
 
-pypots.classification.base module
+pypots.classification.base
 ---------------------------------
 
 .. automodule:: pypots.classification.base
@@ -28,7 +28,7 @@ pypots.classification.base module
    :show-inheritance:
    :inherited-members:
 
-pypots.clustering.base module
+pypots.clustering.base
 -----------------------------
 
 .. automodule:: pypots.clustering.base
@@ -37,7 +37,7 @@ pypots.clustering.base module
    :show-inheritance:
    :inherited-members:
 
-pypots.forecasting.base module
+pypots.forecasting.base
 ------------------------------
 
 .. automodule:: pypots.forecasting.base

diff --git a/docs/pypots.classification.rst b/docs/pypots.classification.rst
@@ -1,7 +1,7 @@
 pypots.classification package
 =============================
 
-pypots.classification.brits module
+pypots.classification.brits
 ----------------------------------
 
 .. automodule:: pypots.classification.brits
@@ -10,7 +10,7 @@ pypots.classification.brits module
    :show-inheritance:
    :inherited-members:
 
-pypots.classification.grud module
+pypots.classification.grud
 ---------------------------------
 
 .. automodule:: pypots.classification.grud
@@ -19,7 +19,7 @@ pypots.classification.grud module
    :show-inheritance:
    :inherited-members:
 
-pypots.classification.raindrop module
+pypots.classification.raindrop
 -------------------------------------
 
 .. automodule:: pypots.classification.raindrop

diff --git a/docs/pypots.clustering.rst b/docs/pypots.clustering.rst
@@ -1,7 +1,7 @@
 pypots.clustering package
 =========================
 
-pypots.clustering.crli module
+pypots.clustering.crli
 -----------------------------
 
 .. automodule:: pypots.clustering.crli
@@ -10,7 +10,7 @@ pypots.clustering.crli module
    :show-inheritance:
    :inherited-members:
 
-pypots.clustering.vader module
+pypots.clustering.vader
 ------------------------------
 
 .. automodule:: pypots.clustering.vader

diff --git a/docs/pypots.data.rst b/docs/pypots.data.rst
@@ -1,7 +1,7 @@
 pypots.data package
 ===================
 
-pypots.data.base module
+pypots.data.base
 -----------------------
 
 .. automodule:: pypots.data.base
@@ -10,7 +10,7 @@ pypots.data.base module
    :show-inheritance:
    :inherited-members:
 
-pypots.data.saving module
+pypots.data.saving
 -----------------------------
 
 .. automodule:: pypots.data.saving
@@ -19,7 +19,7 @@ pypots.data.saving module
    :show-inheritance:
    :inherited-members:
 
-pypots.data.generating module
+pypots.data.generating
 -----------------------------
 
 .. automodule:: pypots.data.generating
@@ -28,7 +28,7 @@ pypots.data.generating module
    :show-inheritance:
    :inherited-members:
 
-pypots.data.load\_preprocessing module
+pypots.data.load\_preprocessing
 --------------------------------------
 
 .. automodule:: pypots.data.load_preprocessing
@@ -37,7 +37,7 @@ pypots.data.load\_preprocessing module
    :show-inheritance:
    :inherited-members:
 
-pypots.data.load\_specific\_datasets module
+pypots.data.load\_specific\_datasets
 -------------------------------------------
 
 .. automodule:: pypots.data.load_specific_datasets
@@ -46,7 +46,7 @@ pypots.data.load\_specific\_datasets module
    :show-inheritance:
    :inherited-members:
 
-pypots.data.utils module
+pypots.data.utils
 ------------------------
 
 .. automodule:: pypots.data.utils

diff --git a/docs/pypots.forecasting.rst b/docs/pypots.forecasting.rst
@@ -1,7 +1,7 @@
 pypots.forecasting package
 ==========================
 
-pypots.forecasting.bttf module
+pypots.forecasting.bttf
 ------------------------------
 
 .. automodule:: pypots.forecasting.bttf

diff --git a/docs/pypots.imputation.rst b/docs/pypots.imputation.rst
@@ -1,7 +1,7 @@
 pypots.imputation package
 =========================
 
-pypots.imputation.saits module
+pypots.imputation.saits
 ------------------------------
 
 .. automodule:: pypots.imputation.saits
@@ -10,7 +10,7 @@ pypots.imputation.saits module
    :show-inheritance:
    :inherited-members:
 
-pypots.imputation.transformer module
+pypots.imputation.transformer
 ------------------------------------
 
 .. automodule:: pypots.imputation.transformer
@@ -19,7 +19,7 @@ pypots.imputation.transformer module
    :show-inheritance:
    :inherited-members:
 
-pypots.imputation.usgan module
+pypots.imputation.usgan
 ------------------------------
 
 .. automodule:: pypots.imputation.usgan
@@ -28,7 +28,7 @@ pypots.imputation.usgan module
    :show-inheritance:
    :inherited-members:
 
-pypots.imputation.gpvae module
+pypots.imputation.gpvae
 ------------------------------
 
 .. automodule:: pypots.imputation.gpvae
@@ -37,7 +37,7 @@ pypots.imputation.gpvae module
    :show-inheritance:
    :inherited-members:
 
-pypots.imputation.brits module
+pypots.imputation.brits
 ------------------------------
 
 .. automodule:: pypots.imputation.brits
@@ -46,7 +46,7 @@ pypots.imputation.brits module
    :show-inheritance:
    :inherited-members:
 
-pypots.imputation.mrnn module
+pypots.imputation.mrnn
 ------------------------------
 
 .. automodule:: pypots.imputation.mrnn
@@ -55,7 +55,7 @@ pypots.imputation.mrnn module
    :show-inheritance:
    :inherited-members:
 
-pypots.imputation.locf module
+pypots.imputation.locf
 -----------------------------
 
 .. automodule:: pypots.imputation.locf

diff --git a/docs/pypots.optim.rst b/docs/pypots.optim.rst
@@ -1,7 +1,7 @@
 pypots.optim package
 ====================
 
-pypots.optim.adam module
+pypots.optim.adam
 ------------------------
 
 .. automodule:: pypots.optim.adam
@@ -10,7 +10,7 @@ pypots.optim.adam module
    :show-inheritance:
    :inherited-members:
 
-pypots.optim.adamw module
+pypots.optim.adamw
 -------------------------
 
 .. automodule:: pypots.optim.adamw
@@ -19,7 +19,7 @@ pypots.optim.adamw module
    :show-inheritance:
    :inherited-members:
 
-pypots.optim.adagrad module
+pypots.optim.adagrad
 ---------------------------
 
 .. automodule:: pypots.optim.adagrad
@@ -28,7 +28,7 @@ pypots.optim.adagrad module
    :show-inheritance:
    :inherited-members:
 
-pypots.optim.rmsprop module
+pypots.optim.rmsprop
 ---------------------------
 
 .. automodule:: pypots.optim.rmsprop
@@ -37,7 +37,7 @@ pypots.optim.rmsprop module
    :show-inheritance:
    :inherited-members:
 
-pypots.optim.sgd module
+pypots.optim.sgd
 -----------------------
 
 .. automodule:: pypots.optim.sgd
@@ -46,7 +46,7 @@ pypots.optim.sgd module
    :show-inheritance:
    :inherited-members:
 
-pypots.optim.base module
+pypots.optim.base
 ------------------------
 
 .. automodule:: pypots.optim.base
@@ -55,7 +55,7 @@ pypots.optim.base module
    :show-inheritance:
    :inherited-members:
 
-pypots.optim.lr_scheduler module
+pypots.optim.lr_scheduler
 ------------------------------
 
 .. automodule:: pypots.optim.lr_scheduler