Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / chemprop/chemprop issues and pull requests

#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 3 months ago - 2 comments

#1018 - SSL Pretrain v2 featurization

Pull Request - State: open - Opened by jiali1025 3 months ago - 4 comments

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

Pull Request - State: closed - Opened by shihchengli 3 months ago - 7 comments

#1016 - change installed torch version on windows actions again

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

#1015 - [v2 QUESTION]: mat1 and mat2 shapes cannot be multiplied (64x300 and 2348x300)

Issue - State: closed - Opened by nevergreendd 3 months ago - 4 comments
Labels: question

#1013 - [v2 BUG]: Ray -- cluster resources not detected or are 0. Attempt #

Issue - State: closed - Opened by muammar 3 months ago - 4 comments
Labels: bug

#1012 - Add `miscalibration_area` and `ence` evaluators

Pull Request - State: closed - Opened by shihchengli 3 months ago

#1011 - Add `--class-balance` flag to `train` CLI

Pull Request - State: closed - Opened by shihchengli 3 months ago

#1010 - Add uncertainty quantification to the `predict` CLI

Pull Request - State: closed - Opened by shihchengli 3 months ago - 1 comment

#1009 - [TODO]: Add check inputs to SIDloss

Issue - State: open - Opened by am2145 3 months ago
Labels: todo

#1008 - [TODO]: Add normalization of spectra when training SpectralFFN() in v2

Issue - State: open - Opened by am2145 3 months ago
Labels: todo

#1007 - Add `--checkpoint` and `--freeze-encoder` flags in train CLI

Pull Request - State: closed - Opened by shihchengli 3 months ago - 1 comment

#1006 - [v2 QUESTION]: About smiles sting with multiple fragamets

Issue - State: closed - Opened by Rojina99 3 months ago - 4 comments
Labels: question

#1005 - V2 conformal evaluators

Pull Request - State: closed - Opened by shihchengli 3 months ago

#1004 - [v2 QUESTION]: weight-column exposed in API?

Issue - State: closed - Opened by dmoccia 3 months ago - 2 comments
Labels: question

#1003 - [v2 QUESTION]: How to apply optimized hyperparameters in training?

Issue - State: closed - Opened by llzhu 3 months ago - 3 comments
Labels: question

#1002 - [v2 FEATURE]: CLI dry run flag

Issue - State: open - Opened by KnathanM 3 months ago - 1 comment
Labels: enhancement

#1001 - fix no-header-rows in predict command error

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

#999 - [v2 QUESTION]: Load model for training

Issue - State: closed - Opened by sunhwan 3 months ago - 3 comments
Labels: question

#998 - V2: Fix `save-smiles-splits` not working with rxn. columns as column header

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

#997 - [v2 QUESTION]: Is there any example about two components with extra descriptors

Issue - State: closed - Opened by Swordshinehjy 3 months ago - 3 comments
Labels: question

#996 - [v2 QUESTION]: Moving chemprop data to gpu when using components with torch code

Issue - State: closed - Opened by Rhys-McAlister 3 months ago - 3 comments
Labels: question

#995 - Metrics overhaul using `torchmetrics`

Pull Request - State: closed - Opened by KnathanM 3 months ago - 5 comments

#994 - `v2.1` Feature: Replicates Instead of Cross Validation Folds

Pull Request - State: closed - Opened by JacksonBurns 3 months ago - 10 comments

#993 - Minor: Fix frzn-ffn-layers description and update doc for transfer learning

Pull Request - State: closed - Opened by oscarwumit 4 months ago - 1 comment

#991 - [v2 BUG]: MveFFN and EvidentialFFN do not work with Metrics/Loss fns

Issue - State: closed - Opened by AsaBarthMaron 4 months ago - 5 comments
Labels: bug

#989 - V2 conformal calibrators

Pull Request - State: closed - Opened by shihchengli 4 months ago

#988 - Define `task_weights` if it is `None` in `MulticlassClassificationFFN`

Pull Request - State: closed - Opened by shihchengli 4 months ago - 3 comments

#986 - Improve the docstring for uncertainty modules

Pull Request - State: closed - Opened by shihchengli 4 months ago - 3 comments

#985 - [v2 FEATURE]: using logging to handle logging messages in all the modules

Issue - State: closed - Opened by shihchengli 4 months ago
Labels: enhancement

#984 - Add NLL and Spearman Uncertainty Evaluators

Pull Request - State: closed - Opened by am2145 4 months ago - 2 comments

#983 - [WIP]: V2 uncertainty regression calibrators (non-conformal)

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

#982 - Switch docstring reference to numbers

Pull Request - State: open - Opened by KnathanM 4 months ago - 5 comments

#981 - [v2 FEATURE]: allow hpopt to work on multiple splits and ensemble models

Issue - State: open - Opened by shihchengli 4 months ago
Labels: enhancement

#980 - [v2 FEATURE]: allow multiple replicates for model training

Issue - State: closed - Opened by shihchengli 4 months ago
Labels: enhancement

#978 - Convert v1 models trained on GPU

Pull Request - State: closed - Opened by KnathanM 4 months ago - 3 comments

#977 - [v2 FEATURE]: Convert v0 model to v2

Issue - State: closed - Opened by KnathanM 4 months ago
Labels: enhancement

#976 - question about stereochemistry in the smiles

Issue - State: closed - Opened by SoodabehGhaffari 4 months ago - 3 comments
Labels: question

#975 - Refactor learning rate scheduler

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

#974 - [v2 QUESTION]: Is cross validation and num folds currently not complete in chemprop v2?

Issue - State: closed - Opened by davdma 4 months ago - 6 comments
Labels: question

#973 - Bug: Move `task_weights` to 'device' for MCC metrics

Pull Request - State: closed - Opened by YoochanMyung 4 months ago - 5 comments

#972 - [v2 QUESTION]: Classification model prediction output.

Issue - State: closed - Opened by isabelg-arcia 4 months ago - 1 comment
Labels: question

#970 - Add dropout and ensemble predictors for uncertainty

Pull Request - State: closed - Opened by joelnkn 4 months ago - 1 comment

#969 - [BUG] fix noam scheduler definition

Issue - State: closed - Opened by davidegraff 4 months ago - 12 comments

#968 - [TODO]: Problems with infinite training

Issue - State: closed - Opened by k-ujihara 4 months ago - 2 comments
Labels: todo

#967 - warn users when not using tensorboard logger

Pull Request - State: closed - Opened by JacksonBurns 4 months ago - 3 comments

#966 - [v2 BUG]: `TypeError` when manually specifying `--loss-function` as its default

Issue - State: closed - Opened by JacksonBurns 4 months ago - 3 comments
Labels: bug

#965 - [v2 QUESTION]: Getting ValueError on classification prediction

Issue - State: closed - Opened by isabelg-arcia 4 months ago - 3 comments
Labels: question

#964 - Fix docs building by pinning sphinx-argparse

Pull Request - State: closed - Opened by jonwzheng 4 months ago - 4 comments

#963 - add quantile regression

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

#961 - add platt calibrator

Pull Request - State: closed - Opened by KnathanM 4 months ago - 5 comments

#960 - [v2 BUG]: NaN target values set to 0.0 rather than being masked.

Issue - State: closed - Opened by joelnkn 5 months ago - 1 comment
Labels: bug

#959 - Place uncertainty into a separate dimension

Pull Request - State: closed - Opened by hwpang 5 months ago - 13 comments

#958 - Fix CGR featurizer behavior when bond features matrix is empty

Pull Request - State: closed - Opened by jonwzheng 5 months ago - 3 comments

#956 - [v2 BUG]:

Issue - State: closed - Opened by HHALee 5 months ago - 1 comment
Labels: bug

#955 - add transform tests

Pull Request - State: closed - Opened by KnathanM 5 months ago - 2 comments

#953 - Change the default verbose level to INFO

Pull Request - State: closed - Opened by shihchengli 5 months ago - 7 comments

#952 - Update batch norm freezing to freeze running stats

Pull Request - State: closed - Opened by joelnkn 5 months ago - 8 comments

#951 - transfer learning with Chemprop

Issue - State: closed - Opened by SoodabehGhaffari 5 months ago - 3 comments
Labels: question

#950 - Enable CPU prediction for GPU-trained models

Pull Request - State: closed - Opened by snaeppi 5 months ago - 3 comments

#949 - [v2 FEATURE]: Automatic device handling for loading trained models

Issue - State: closed - Opened by snaeppi 5 months ago - 1 comment
Labels: enhancement

#947 - Question about interpretation

Issue - State: closed - Opened by SoodabehGhaffari 5 months ago - 8 comments
Labels: question

#946 - change aggregation default to norm

Pull Request - State: closed - Opened by KnathanM 5 months ago

#945 - [v2 QUESTION]: Why does chemprop convert produce a ckpt file?

Issue - State: closed - Opened by KnathanM 5 months ago - 1 comment
Labels: question

#942 - Fix Issues in MCC Metrics and Loss Calculations

Pull Request - State: closed - Opened by shihchengli 5 months ago

#940 - [v2 BUG]: Binary-mcc not working as a --loss-function and --metrics

Issue - State: closed - Opened by ddgunizar 5 months ago - 9 comments
Labels: bug

#939 - Fix issue related to target column for fingerprint

Pull Request - State: closed - Opened by hwpang 5 months ago

#938 - V2: Add Shapley Value notebook for interpretability

Pull Request - State: open - Opened by oscarwumit 5 months ago - 1 comment

#937 - V2: Uncertainty implementation

Pull Request - State: closed - Opened by shihchengli 5 months ago - 2 comments

#936 - Move ignore columns to common

Pull Request - State: closed - Opened by hwpang 5 months ago - 2 comments

#935 - Improve predict CLI for saving multitask prediction

Pull Request - State: closed - Opened by hwpang 5 months ago

#934 - [v1 QUESTION]: Conformal prediction in and out sets

Issue - State: closed - Opened by soulios 5 months ago - 9 comments
Labels: question

#933 - [v2 QUESTION]: Getting D-MPNN Embedding without target values

Issue - State: closed - Opened by haiqzhu 5 months ago - 2 comments
Labels: question

#932 - add devcontainer

Pull Request - State: open - Opened by kevingreenman 5 months ago - 3 comments
Labels: enhancement

#931 - Use mol.GetBonds() instead of for loop

Pull Request - State: closed - Opened by KnathanM 5 months ago - 1 comment

#930 - Move features_generators processing step into process_common_args

Pull Request - State: closed - Opened by hwpang 5 months ago - 2 comments

#929 - [v2 BUG]: no features generators in predict.py

Issue - State: closed - Opened by jsanders802 5 months ago - 3 comments
Labels: bug

#928 - Set Ray Train's trainer resources to 0

Pull Request - State: closed - Opened by hwpang 5 months ago

#927 - Make fingerprint CLI consistent with predict CLI

Pull Request - State: closed - Opened by hwpang 5 months ago - 3 comments

#926 - How do I implement V_d into a trainer?

Issue - State: closed - Opened by AquifersBSIM 5 months ago - 6 comments

#925 - mat1 and mat2 shapes cannot be multiplied (64x2348 and 300x300)

Issue - State: closed - Opened by AquifersBSIM 5 months ago - 6 comments

#924 - Add Monte Carlo Tree search notebook for interpretability

Pull Request - State: closed - Opened by hwpang 5 months ago - 12 comments

#923 - [v2 Feature] Implement Shapley value analysis

Pull Request - State: closed - Opened by oscarwumit 5 months ago - 9 comments
Labels: enhancement

#922 - Change the installed numpy version in pyproject

Pull Request - State: closed - Opened by shihchengli 5 months ago - 1 comment

#921 - [v2 better design?]: Function override can cause unexpected and unclear featurization behavior

Issue - State: open - Opened by oscarwumit 5 months ago - 10 comments
Labels: enhancement, todo

#920 - Add `--show-individual-scores` CLI flag

Pull Request - State: closed - Opened by shihchengli 6 months ago

#919 - Save individual and average predictions into different files

Pull Request - State: closed - Opened by shihchengli 6 months ago