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Disconnected GNN: Catalyst-Adsorbate separator #44

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Disconnected GNN: Catalyst-Adsorbate separator #44

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Commits on Jun 12, 2023

  1. no idea what I changed

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    AlvaroC-ML committed Jun 12, 2023
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Commits on Jun 13, 2023

  1. Created a file with disconnected gnn and an edge deleter

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  2. vectorized implementation of edge deleter

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Commits on Jun 14, 2023

  1. Changed config file to run faenet vs disconnected.

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    AlvaroC-ML committed Jun 14, 2023
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  2. Created new flag 'is_disconnected'

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    AlvaroC-ML committed Jun 14, 2023
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  3. Corrected some typos.

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    AlvaroC-ML committed Jun 14, 2023
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  4. Deleted disconnected model, as now it is a feature on data transforms… 

    …. Changed a config file to reflect this.
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    AlvaroC-ML committed Jun 14, 2023
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  5. Fixed problem that the function assumed there were no tag 0 vertices.

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    AlvaroC-ML committed Jun 14, 2023
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Commits on Jun 15, 2023

  1. Fixed a mistake where not all edge attributes are filtered

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    AlvaroC-ML committed Jun 15, 2023
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Commits on Jun 21, 2023

  1. Modified the is_disconnected flag to be a variable so it can be used … 

    …in yaml files. Also modified some yaml experiment files.
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    AlvaroC-ML committed Jun 21, 2023
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  2. fixed some typos

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    AlvaroC-ML committed Jun 21, 2023
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Commits on Jun 26, 2023

  1. Deleted disconnected model, and copied best configs to my experiments… 

    … folder
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  2. Added flag for only using a subset of the dataset with a unique datap… 

    …oint for every (catalyst, adsorbate, cell) tuple.
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  3. Added if statement in base trainer to use only the desired subset of … 

    …dataset for training purposes
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    AlvaroC-ML committed Jun 26, 2023
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  4. fixed some typos

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    AlvaroC-ML committed Jun 26, 2023
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Commits on Jun 28, 2023

  1. Fixed a bug when closing the dataset and modified config files to mak… 

    …e them easier to replicate
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Commits on Jul 3, 2023

  1. Added graph splitter. Still need to reindex edges to not cause errors… 

    … later.
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  2. Implemented: getting separate predictions for ads, cats. Their output… 

    …s get concatenated, and then passed through a 2-layer MLP to return a single value. Testing still needed.
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    AlvaroC-ML committed Jul 3, 2023
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Commits on Jul 5, 2023

  1. Middle point before implementing a needed modification to make skip_c… 

    …o=concat feature work.
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  2. Skip_co correctly implemented

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  3. Set it so using the disconnected model turns on the is_disconnected f… 

    …lag on
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Commits on Jul 7, 2023

  1. Changed the name of disconnected model to dependent as to make psace … 

    …for other types of disconnected models
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  2. Created a new dataset file where graphs will be split before transfor… 

    …ms are applied.
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  3. Implemented graph splitter. Currently debugging modification to data_… 

    …list_collater
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Commits on Jul 10, 2023

  1. Now that the new dataset is implemented, we correct so the dependent … 

    …model doesn't use it, and we start writing the independent model.
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Commits on Jul 11, 2023

  1. Renamed some models, started debugging a simplified version of model 3

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Commits on Jul 12, 2023

  1. Created debug file to debug from an interactive node

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  2. Finished implementing basic version of model indfaenet

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  3. Fixed small typo

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    AlvaroC-ML committed Jul 12, 2023
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  4. fixing bug

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Commits on Jul 13, 2023

  1. Bug of model 3 has been fixed.

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  2. Rewrote a line to make it nicer.

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Commits on Jul 14, 2023

  1. Finished implementing indfaenet

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Commits on Jul 17, 2023

  1. Implemented disconnected_mlp in indfaenet

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Commits on Jul 19, 2023

  1. Cleaned up some code, and set it ready for some hyperparameter tweaking

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  2. Deleted a wild point trace.

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    AlvaroC-ML committed Jul 19, 2023
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Commits on Jul 26, 2023

  1. Implemented a first version of the transformer

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  2. Changed implementation to a better one

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Commits on Jul 27, 2023

  1. Added positional encoding to allow the model to distinguish between a… 

    …dsorbate and catalysts inputs
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  2. Forgot to renable inference time calculation

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    AlvaroC-ML committed Jul 27, 2023
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  3. Modified training files.

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    AlvaroC-ML committed Jul 27, 2023
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Commits on Jul 28, 2023

  1. fixed typo in experiments folder

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  2. Started implementing transformer interaction faenet, init mostly done

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  3. Did good progress on the implementation of energy forward, modified b… 

    …ase trainer to make it easier to implement models like tifaenet/indfaenet. Now you just have to add it to a list in the initialization method.
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  4. Implemented everything up to the actual transformer block.

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Commits on Jul 30, 2023

  1. Finished implementation of transformer interactions, and will redo tr… 

    …aining on transformer combination to see if I can reduce the number of parameters
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  2. Changed initial learning rate for all dataset training

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  3. Made transformer larger

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  4. Readied an experiment

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Commits on Jul 31, 2023

  1. Started implementing a second type of transformer-like block.

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Commits on Aug 1, 2023

  1. Finished correcting a HUGE bug on attention based models.

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  2. Changed training file.

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Commits on Aug 4, 2023

  1. Improved the implementation of tifaenet to use sparse matrices. It st… 

    …ill isn't good.
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Commits on Aug 7, 2023

  1. Implemented attention tifaenet through sparse matrix. Now changing ba… 

    …ckend implementation of tifaenet so it uses heterogeneous graphs
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Commits on Aug 10, 2023

  1. Finished implementing heterogeneous graphs dataset. Most of the chang… 

    …es are simple changes in syntax throughout the code as heterogeneous graphs do not have the same syntax as homogeneous graphs in pytorch geometric.
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  2. Code worked fine. Implemented the requirement of specifying the versi… 

    …on of GAT. Training yaml files ready for submission.
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  3. fixed small typo

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  4. fixed a mistake in coding

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  5. Forgot a set_trace

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Commits on Aug 11, 2023

  1. Fixed mistake where version 2 wasn't being used. Added attention head… 

    …s to the GAT layer.
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  2. Small typo

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  3. Fixed another typo

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    AlvaroC-ML committed Aug 11, 2023
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  4. fixing some last mistakes

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  5. Forgot an ipdb set trace.

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Commits on Aug 14, 2023

  1. Testing the addition of edge weights to the graph model

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Commits on Aug 15, 2023

  1. forgot to remove a set trace

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  2. fixed typo

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  3. Better disconnected edge weights implemented

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Commits on Aug 17, 2023

  1. Last update before cleaning up code base.

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  2. Deleted sparse matrix implementation, which never ran fast enough to … 

    …even train in 15 hours.
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  3. Changed named of TIFaenet to AFaenet. ALSO I changed the largest z-in… 

    …dex from 25.0 to 20.0
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  4. Cleaned up the config files

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  5. Combined personalized datasets into one

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  6. Changed the name of tifaenet to afaenet

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Commits on Aug 18, 2023

  1. Data base cleaned, making sure results still make sense

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Commits on Aug 21, 2023

  1. Fixed and improved the implementation of indfaenet

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  2. Added other experiments to make sure they still work

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  3. Forgot to delete a set trace

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  4. Fixed some errors caused when using indfaenet

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Commits on Aug 22, 2023

  1. Fixed a small typo that affected the normal data mode

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Commits on Aug 23, 2023

  1. Forgot to uncomment the task part. I also didn't use the is_disconnec… 

    …ted flag correctly in the testing part
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Commits on Sep 3, 2023

  1. Comments added, removed a point trace.

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  2. modified a training file

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Commits on Sep 4, 2023

  1. Implemented all disconnected schnet models except for aschnet

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Commits on Sep 5, 2023

  1. Finished implementing aschnet and also made some modifications to the… 

    … way in which residual connections happen
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  2. Modified config files and a couple other updates

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  3. small mistake in config file

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  4. fixed a config file

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  5. prepared config files for jobs

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  6. modified afaenet slightly

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Commits on Sep 11, 2023

  1. Started implementing depgemnet

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  2. modified a config file

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  3. Corrected mistake in config file

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  4. implementing more

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  5. Finished implementing dep and ind gemnet

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  6. readied config files

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Commits on Sep 12, 2023

  1. About to start incorporating agemnet_oc

    @AlvaroC-ML
    AlvaroC-ML committed Sep 12, 2023
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  2. was implemented agemnet, need to stop for today and run tests

    @AlvaroC-ML
    AlvaroC-ML committed Sep 12, 2023
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Commits on Sep 13, 2023

  1. changing to implementing gemnet_t

    @AlvaroC-ML
    AlvaroC-ML committed Sep 13, 2023
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Commits on Sep 15, 2023

  1. fixed a mistake in aschnet

    @AlvaroC-ML
    AlvaroC-ML committed Sep 15, 2023
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  2. config file editing

    @AlvaroC-ML
    AlvaroC-ML committed Sep 15, 2023
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  3. debugging gemnet

    @AlvaroC-ML
    AlvaroC-ML committed Sep 15, 2023
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  4. readied gemnet for training

    @AlvaroC-ML
    AlvaroC-ML committed Sep 15, 2023
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  5. config mistake

    @AlvaroC-ML
    AlvaroC-ML committed Sep 15, 2023
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  6. tried to implement gemnet, didn't work. Now rerunning faenet with the… 

    … more standard config files
    @AlvaroC-ML
    AlvaroC-ML committed Sep 15, 2023
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Commits on Sep 16, 2023

  1. config file for dpp

    @AlvaroC-ML
    AlvaroC-ML committed Sep 16, 2023
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  2. implemented almost all varients of dimenetpp

    @AlvaroC-ML
    AlvaroC-ML committed Sep 16, 2023
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  3. IMPLEMENTED ALL DPP VARIANTS

    @AlvaroC-ML
    AlvaroC-ML committed Sep 16, 2023
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  4. modifications to config files

    @AlvaroC-ML
    AlvaroC-ML committed Sep 16, 2023
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Commits on Sep 17, 2023

  1. removed an ipdb

    @AlvaroC-ML
    AlvaroC-ML committed Sep 17, 2023
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Commits on Sep 20, 2023

  1. good config file included

    @AlvaroC-ML
    AlvaroC-ML committed Sep 20, 2023
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Commits on Sep 24, 2023

  1. Fixed dependent models, and attention model

    @AlvaroC-ML
    AlvaroC-ML committed Sep 24, 2023
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  2. fixed a mistake on two dep files

    @AlvaroC-ML
    AlvaroC-ML committed Sep 24, 2023
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Commits on Sep 25, 2023

  1. Changed independent models to have different dimentionalities

    @AlvaroC-ML
    AlvaroC-ML committed Sep 25, 2023
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Commits on Sep 26, 2023

  1. Fixed config files

    @AlvaroC-ML
    AlvaroC-ML committed Sep 26, 2023
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Commits on Oct 30, 2023

  1. reproduce results: new config

    @AlexDuvalinho
    AlexDuvalinho committed Oct 30, 2023
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  2. add debug file

    @AlexDuvalinho
    AlexDuvalinho committed Oct 30, 2023
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Commits on Nov 13, 2023

  1. 🧱 (base model): Make future-proof with **kwargs

    @vict0rsch
    vict0rsch committed Nov 13, 2023
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  2. ♻️ (utils): Import build_config from main

    @vict0rsch
    vict0rsch committed Nov 13, 2023
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  3. ✨ (utils): make_trainer_from_dir for gfn

    @vict0rsch
    vict0rsch committed Nov 13, 2023
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  4. ✨ (gfn): Import from #51

    @vict0rsch
    vict0rsch committed Nov 13, 2023
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  5. 🐛 (transforms): Fix GraphRewiring call to work with gfn

    @vict0rsch
    vict0rsch committed Nov 13, 2023
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  6. ♻️ (all): Blackify

    @vict0rsch
    vict0rsch committed Nov 13, 2023
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Commits on Nov 29, 2023

  1. Merge pull request #52 from RolnickLab/prepare-disconnected 

    Import changes to prepare for gfn
    @vict0rsch
    vict0rsch authored Nov 29, 2023
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  2. import changes from #48

    @vict0rsch
    vict0rsch committed Nov 29, 2023
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Commits on Jan 6, 2024

  1. Merge pull request #53 from RolnickLab/disconnected-per-ads-datasets 

    Disconnected per adsorbate dataset: import changes from #48
    @AlexDuvalinho
    AlexDuvalinho authored Jan 6, 2024
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  2. fine-tune / retrain depfaenet on per-ads-dataset

    @AlexDuvalinho
    AlexDuvalinho committed Jan 6, 2024
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  3. improve docu of continue_from_dir

    @AlexDuvalinho
    AlexDuvalinho committed Jan 6, 2024
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Commits on Jan 10, 2024

  1. fix setup

    @vict0rsch
    vict0rsch committed Jan 10, 2024
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Commits on Jan 16, 2024

  1. fix adsorbates filtering

    @vict0rsch
    vict0rsch committed Jan 16, 2024
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  2. fix ads filtering for val_ood_cat&both

    @vict0rsch
    vict0rsch committed Jan 16, 2024
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Commits on Jan 27, 2024

  1. config update

    @AlexDuvalinho
    AlexDuvalinho committed Jan 27, 2024
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  2. Merge branch 'disconnected_gnn' of https://github.com/RolnickLab/ocp … 

    …into disconnected_gnn
    @AlexDuvalinho
    AlexDuvalinho committed Jan 27, 2024
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Commits on Apr 16, 2024

  1. add ocdata

    @AlexDuvalinho
    AlexDuvalinho committed Apr 16, 2024
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