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GitHub / chemprop/chemprop issues and pull requests

#1105 - Fix `tracking_metric` overwrite issue

Pull Request - State: open - Opened by shihchengli 5 days ago
Labels: bug, mlpds

#1104 - [v2 BUG]: dictionary update sequence element #0 has length 1; 2 is required

Issue - State: closed - Opened by AquifersBSIM 6 days ago - 2 comments
Labels: bug

#1103 - [v2 QUESTION]: how to train multiclass models with chemprop v2

Issue - State: open - Opened by hassanmohsin 7 days ago - 1 comment
Labels: question

#1102 - [v2 BUG]: Tracking metric gets overwritten when --num-replicates is greater than 1

Issue - State: open - Opened by am2145 8 days ago - 1 comment
Labels: bug, mlpds

#1101 - [v2 QUESTION]: no attribute 'R2Score'

Issue - State: closed - Opened by AquifersBSIM 8 days ago - 3 comments
Labels: question

#1098 - Fix batch size calculation for multicomponent

Pull Request - State: open - Opened by KnathanM 18 days ago

#1098 - Fix batch size calculation for multicomponent

Pull Request - State: open - Opened by KnathanM 18 days ago

#1097 - Set all transforms to train during validation

Pull Request - State: closed - Opened by KnathanM 18 days ago - 1 comment

#1097 - Set all transforms to train during validation

Pull Request - State: closed - Opened by KnathanM 18 days ago - 1 comment

#1096 - [v2 QUESTION]: predictions with v1_rdkit_2d_normalized

Issue - State: closed - Opened by yaosichao0915 18 days ago - 2 comments
Labels: question

#1095 - [v2 QUESTION]: How do I specify a specific GPU when I have multiple GPUs?

Issue - State: closed - Opened by yaosichao0915 19 days ago - 1 comment
Labels: question

#1095 - [v2 QUESTION]: How do I specify a specific GPU when I have multiple GPUs?

Issue - State: closed - Opened by yaosichao0915 19 days ago - 1 comment
Labels: question

#1094 - [v2 FEATURE]: Revise train_model to reduce complexity

Issue - State: open - Opened by twinbrian 22 days ago
Labels: enhancement

#1094 - [v2 FEATURE]: Revise train_model to reduce complexity

Issue - State: open - Opened by twinbrian 22 days ago
Labels: enhancement

#1093 - CLI - Include target values in saved predictions csv

Issue - State: open - Opened by KnathanM 22 days ago - 1 comment

#1093 - CLI - Include target values in saved predictions csv

Issue - State: open - Opened by KnathanM 22 days ago - 1 comment

#1092 - [v2 QUESTION]: multitask data spliting

Issue - State: closed - Opened by yaosichao0915 23 days ago - 2 comments
Labels: question

#1092 - [v2 QUESTION]: multitask data spliting

Issue - State: closed - Opened by yaosichao0915 23 days ago - 2 comments
Labels: question

#1091 - add more helpful warnings about the splitting api change

Pull Request - State: closed - Opened by JacksonBurns 25 days ago

#1091 - add more helpful warnings about the splitting api change

Pull Request - State: closed - Opened by JacksonBurns 25 days ago

#1090 - updated warning to logger

Pull Request - State: closed - Opened by twinbrian 26 days ago

#1089 - Atoms Dataset + Prediction

Pull Request - State: open - Opened by twinbrian 26 days ago

#1089 - Atoms Dataset + Prediction

Pull Request - State: open - Opened by twinbrian 26 days ago

#1087 - [v2 QUESTION]: How to incorporate x_d calculated under DFT theory in front of FNN layers

Issue - State: closed - Opened by yyyzzz111 27 days ago - 1 comment
Labels: question

#1086 - Fix: Splits file can have multiple splitting schemes

Pull Request - State: closed - Opened by KnathanM 27 days ago

#1086 - Fix: Splits file can have multiple splitting schemes

Pull Request - State: closed - Opened by KnathanM 27 days ago

#1084 - Add task weights to r2score

Pull Request - State: closed - Opened by KnathanM 29 days ago

#1084 - Add task weights to r2score

Pull Request - State: closed - Opened by KnathanM 29 days ago

#1083 - splits file is json

Pull Request - State: closed - Opened by KnathanM 30 days ago

#1082 - [v2 BUG]: MulticomponentMPNN 2.1.0 bug report

Issue - State: closed - Opened by Swordshinehjy 30 days ago - 3 comments
Labels: bug

#1081 - [v2 BUG]: Multitask metrics can only give an averaged score

Issue - State: closed - Opened by neuromaancer about 1 month ago - 9 comments
Labels: bug

#1081 - [v2 BUG]: Multitask metrics can only give an averaged score

Issue - State: closed - Opened by neuromaancer about 1 month ago - 9 comments
Labels: bug

#1080 - [v2 FEATURE]: An option to input a test set separately and use multiple `--num-folds` only for train/val split

Issue - State: open - Opened by yunsiechung about 1 month ago - 10 comments
Labels: enhancement, mlpds

#1080 - [v2 FEATURE]: An option to input a test set separately and use multiple `--num-folds` only for train/val split

Issue - State: open - Opened by yunsiechung about 1 month ago - 10 comments
Labels: enhancement, mlpds

#1079 - Initial Draft of `--canonicalize-smiles`

Pull Request - State: open - Opened by JacksonBurns about 1 month ago - 1 comment

#1078 - [v2 FEATURE]: Add an option to ignore chirality in input SMILES

Issue - State: open - Opened by yunsiechung about 1 month ago - 2 comments
Labels: enhancement, mlpds

#1078 - [v2 FEATURE]: Add an option to ignore chirality in input SMILES

Issue - State: open - Opened by yunsiechung about 1 month ago - 2 comments
Labels: enhancement, mlpds

#1076 - [v2 FEATURE]: More featurizers

Issue - State: open - Opened by KnathanM about 1 month ago - 1 comment
Labels: enhancement, mlpds

#1075 - [v2 FEATURE]: sklearn pipeline integration

Issue - State: open - Opened by KnathanM about 1 month ago
Labels: enhancement

#1074 - Fix: splits column is a string not a list

Pull Request - State: closed - Opened by KnathanM about 1 month ago - 2 comments

#1073 - [v2 BUG]: Bug with `--splits-column`

Issue - State: closed - Opened by yunsiechung about 1 month ago - 2 comments
Labels: bug, mlpds

#1072 - Cleanup the uncertainty modules

Pull Request - State: closed - Opened by shihchengli about 1 month ago

#1071 - Update uncertainty notebook

Pull Request - State: closed - Opened by shihchengli about 1 month ago - 1 comment

#1070 - Rename uncertainty estimator

Pull Request - State: closed - Opened by KnathanM about 1 month ago

#1069 - update train docs for v2.1

Pull Request - State: closed - Opened by KnathanM about 1 month ago

#1068 - [v2 FEATURE]: Add option for adaptive annealing coefficient to dirichlet loss

Issue - State: open - Opened by KnathanM about 1 month ago - 1 comment
Labels: enhancement

#1067 - Rerun notebooks for v2.1

Pull Request - State: closed - Opened by KnathanM about 1 month ago - 1 comment

#1066 - Multiclassdirichlet give uncertainty

Pull Request - State: closed - Opened by KnathanM about 1 month ago - 2 comments

#1065 - disable libuv with env var rather than avoiding latest torch

Pull Request - State: closed - Opened by JacksonBurns about 1 month ago - 1 comment

#1064 - Add ray to tests on python 3 12

Pull Request - State: closed - Opened by KnathanM about 1 month ago

#1062 - change installed torch version on windows actions again

Pull Request - State: closed - Opened by shihchengli about 1 month ago

#1061 - Adding Evidential, Mean-Variance (MVE), and Binary Dirichlet Uncertainty Predictors

Pull Request - State: closed - Opened by akshatzalte about 1 month ago - 3 comments

#1060 - .pt instead of .ckpt

Pull Request - State: closed - Opened by twinbrian about 1 month ago

#1058 - Disable batch norm by default, and reword CLI argument

Pull Request - State: closed - Opened by jonwzheng about 1 month ago - 2 comments

#1057 - Update pyproject.toml to exclude tests

Pull Request - State: closed - Opened by c-w-feldmann about 1 month ago

#1056 - [v2 BUG]: Installing chemproplocally fails

Issue - State: closed - Opened by c-w-feldmann about 1 month ago - 2 comments
Labels: bug

#1055 - Uncertainty regression calibrators (non-conformal)

Pull Request - State: closed - Opened by shihchengli about 1 month ago - 2 comments

#1054 - [v2 BUG]: model files do not work after v1_to_v2 conversion

Issue - State: open - Opened by dskarlov about 1 month ago - 12 comments
Labels: bug

#1053 - add isotonic calibrators

Pull Request - State: closed - Opened by KnathanM about 1 month ago

#1052 - [v2 QUESTION]: AttributeError in hyperparameter ptimization in multi-component tasks

Issue - State: closed - Opened by DengFeng-Zuo about 1 month ago - 4 comments
Labels: question

#1051 - Use pre-train output scaler to scale training data in CLI

Pull Request - State: closed - Opened by KnathanM about 1 month ago

#1050 - [v2 QUESTION]: ValueError reported when searching hyperparameter space

Issue - State: closed - Opened by DengFeng-Zuo about 1 month ago - 9 comments
Labels: question

#1048 - Added dry_run Flag

Pull Request - State: open - Opened by twinbrian about 2 months ago

#1047 - Example Notebook for Classification

Pull Request - State: closed - Opened by twinbrian about 2 months ago

#1046 - [v2 QUESTION]: invalid choice for molecule-featurizers

Issue - State: closed - Opened by xiongguoli about 2 months ago - 7 comments
Labels: question

#1045 - [v2 QUESTION]: RuntimeError in Predict

Issue - State: closed - Opened by xiongguoli about 2 months ago - 2 comments
Labels: question

#1044 - [v2 QUESTION]: Encounter errors when train models. Please help me.

Issue - State: closed - Opened by langcaijinjiangyan about 2 months ago - 1 comment
Labels: question

#1043 - Parallel Operation in Chemprop for hyperparameter optimization

Issue - State: closed - Opened by SoodabehGhaffari about 2 months ago - 1 comment
Labels: question

#1041 - Splits file docs

Pull Request - State: closed - Opened by KnathanM about 2 months ago - 4 comments

#1040 - [v2 FEATURE]: Integrate with torchserve

Issue - State: open - Opened by KnathanM about 2 months ago - 1 comment
Labels: enhancement

#1039 - [TODO]: Restart training from Checkpoint

Issue - State: open - Opened by KnathanM about 2 months ago
Labels: todo

#1038 - Update chemprop to v2.1

Pull Request - State: closed - Opened by KnathanM about 2 months ago - 7 comments

#1037 - Update multiclass data to be compatible with rdkit 2024.09.1

Pull Request - State: closed - Opened by jonwzheng about 2 months ago - 1 comment

#1036 - Example notebook for classification + dry_run flag draft

Pull Request - State: closed - Opened by twinbrian about 2 months ago - 3 comments

#1035 - [v2 QUESTION]: classification task

Issue - State: closed - Opened by Jameel9 about 2 months ago - 1 comment
Labels: question

#1034 - Fix `hpopting` Notebook and CLI for Windows

Pull Request - State: closed - Opened by JacksonBurns about 2 months ago - 3 comments

#1033 - [v2 QUESTION]: Hyperparameter Optimization Encountered FileNotFoundError

Issue - State: closed - Opened by xiongguoli about 2 months ago - 9 comments
Labels: question

#1032 - [v2 BUG]: Hyperparameter Optimization Encountered FileNotFoundError

Issue - State: closed - Opened by xiongguoli about 2 months ago - 1 comment
Labels: bug

#1031 - Weighted Training by Target and Data

Issue - State: closed - Opened by SoodabehGhaffari 2 months ago - 10 comments
Labels: question

#1030 - [v2 Example]: Classification example notebook

Issue - State: closed - Opened by KnathanM 2 months ago - 3 comments
Labels: enhancement

#1026 - [v2 BUG]: rdkit_2d can not be calculated in v2 version

Issue - State: closed - Opened by xiaoboy185 2 months ago - 1 comment
Labels: bug

#1025 - Add floor to spectral targets for positive targets

Pull Request - State: closed - Opened by KnathanM 2 months ago - 1 comment

#1024 - Remove task weights from state dict

Pull Request - State: closed - Opened by KnathanM 2 months ago - 1 comment

#1023 - Remove old validate-loss-function function

Pull Request - State: closed - Opened by KnathanM 2 months ago - 2 comments

#1022 - Refactor with torchmetrics

Pull Request - State: closed - Opened by KnathanM 2 months ago - 3 comments

#1021 - Test v2.1 dev branch

Pull Request - State: closed - Opened by KnathanM 2 months ago - 2 comments

#1018 - SSL Pretrain v2 featurization

Pull Request - State: open - Opened by jiali1025 2 months ago - 4 comments

#1017 - Fix `BinaryDirichletFFN` and `MulticlassDirichletFFN` predictors

Pull Request - State: closed - Opened by shihchengli 2 months ago - 7 comments