Ecosyste.ms: Issues

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GitHub / chemprop/chemprop issues and pull requests

#807 - Add isort for sorting imports

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

#806 - [FEATURE]: Add option to make component order in multicomponent not matter

Issue - State: open - Opened by KnathanM 7 months ago - 13 comments
Labels: enhancement, mlpds

#804 - [TODO]: Add example notebook(s) for interoperability between chemprop and other libraries

Issue - State: closed - Opened by kevingreenman 7 months ago - 1 comment
Labels: mlpds, todo

#803 - V2: Fix reaction scaling

Pull Request - State: closed - Opened by hwpang 7 months ago - 4 comments

#802 - clean up column names

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

#801 - [TODO]: Add environment.yml installation instructions to docs

Issue - State: closed - Opened by kevingreenman 7 months ago - 2 comments
Labels: todo

#800 - [BUG]: Testing on SN2 Benchmark runs into issue with scaler

Issue - State: closed - Opened by am2145 7 months ago - 1 comment
Labels: bug

#799 - [QUESTION]: Re-training or New Training?

Issue - State: closed - Opened by spyda90 7 months ago - 2 comments
Labels: question

#798 - [BUG]: CI doesn't complain when notebooks fail

Issue - State: closed - Opened by KnathanM 7 months ago
Labels: bug

#797 - fix merge artifact

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

#796 - V2: Bug fix for hyperparameter optimization

Pull Request - State: closed - Opened by hwpang 7 months ago - 15 comments

#795 - Fix `get_column_names()`

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

#794 - [BUG]: Precision recall curve metric function name

Issue - State: closed - Opened by KnathanM 7 months ago
Labels: bug

#793 - [FEATURE]: Move --ignore-columns to common args

Issue - State: closed - Opened by KnathanM 7 months ago - 1 comment
Labels: enhancement

#792 - [FEATURE]: Cache in CLI

Issue - State: closed - Opened by KnathanM 7 months ago - 7 comments
Labels: enhancement

#790 - V2: Fix AUPRC + Add CLI tests for all available classification metrics

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

#789 - Add option of deterministic training

Pull Request - State: closed - Opened by am2145 7 months ago

#788 - Update --save-preds to save metric value to log and tidy up naming.

Pull Request - State: closed - Opened by am2145 7 months ago - 9 comments

#787 - V2: Remove outdated toml dependency

Pull Request - State: closed - Opened by hwpang 7 months ago

#786 - fix rev_edge_indexes

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

#785 - V2/update-branch-name

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

#784 - V2: update issue templates for the release of v2

Pull Request - State: closed - Opened by kevingreenman 7 months ago

#783 - [TODO]: Add Optuna support for hyperparameter optimization

Issue - State: closed - Opened by hwpang 7 months ago - 1 comment
Labels: enhancement, todo

#782 - [QUESTION]: How to further train a model based on a trained model

Issue - State: closed - Opened by hah2024 8 months ago - 3 comments
Labels: question

#781 - [QUESTION]: How to carry out hyperparameter optimization using codes

Issue - State: closed - Opened by hah2024 8 months ago - 4 comments
Labels: question

#780 - [BUG]: dtype mismatch when using attentive aggregation and bf16

Issue - State: closed - Opened by Rhys-McAlister 8 months ago - 1 comment
Labels: bug

#779 - V2/move task weights

Pull Request - State: closed - Opened by KnathanM 8 months ago - 6 comments

#778 - [v2] incorrect batching for graphs with empty edge sets

Issue - State: closed - Opened by davidegraff 8 months ago
Labels: bug

#776 - [TODO]: Run tests on M1

Issue - State: closed - Opened by KnathanM 8 months ago - 5 comments
Labels: todo

#775 - V2: read training arguments through config file

Pull Request - State: closed - Opened by hwpang 8 months ago - 4 comments

#774 - [QUESTION]: Hyperparameter using Optuna?

Issue - State: closed - Opened by spyda90 8 months ago - 5 comments
Labels: question

#773 - Update example notebooks to use pathlib

Pull Request - State: closed - Opened by am2145 8 months ago

#772 - V2: Add more example notebooks

Pull Request - State: closed - Opened by kevingreenman 8 months ago - 6 comments
Labels: mlpds

#771 - [TODO]: Standardize PR merge procedure.

Issue - State: closed - Opened by oscarwumit 8 months ago - 8 comments
Labels: todo

#770 - [TODO]: Better documentation for common Q&As and also for developers

Issue - State: closed - Opened by oscarwumit 8 months ago - 3 comments
Labels: todo

#769 - V2: Add fingerprints CLI

Pull Request - State: closed - Opened by shihchengli 8 months ago - 6 comments

#768 - V2/no with inference

Pull Request - State: closed - Opened by Olivierj23 8 months ago

#767 - Add a script to regenerate all example model files for test

Pull Request - State: closed - Opened by hwpang 8 months ago - 1 comment

#766 - changed w_t to buffer

Pull Request - State: closed - Opened by Olivierj23 8 months ago - 1 comment

#765 - Add environment.yml file for conda installation

Pull Request - State: closed - Opened by donerancl 8 months ago - 8 comments
Labels: enhancement

#764 - Tidy up float parameter default values

Pull Request - State: closed - Opened by am2145 8 months ago

#763 - [BUG]: Indexing error

Issue - State: closed - Opened by Rhys-McAlister 8 months ago - 12 comments
Labels: bug

#762 - [QUESTION]: Best way to run predictions in parallel

Issue - State: closed - Opened by asiomchen 8 months ago - 4 comments
Labels: question

#761 - V2: Convert from float64 to float32

Pull Request - State: closed - Opened by shihchengli 8 months ago - 4 comments

#760 - V2: Refactor `MLP` class and delegate encoding to `Predictor`

Pull Request - State: closed - Opened by shihchengli 8 months ago - 2 comments

#758 - remove repr mixin

Pull Request - State: closed - Opened by KnathanM 8 months ago - 1 comment

#757 - Refactor `MLP` class and delegate encoding to `Predictor`

Pull Request - State: closed - Opened by shihchengli 8 months ago - 3 comments

#756 - using pretraining in chemprop

Issue - State: closed - Opened by SoodabehGhaffari 8 months ago - 1 comment
Labels: question

#754 - [BUG]: MPNN.encoding() doesn't work

Issue - State: closed - Opened by shihchengli 8 months ago - 9 comments
Labels: bug

#752 - [BUG (RISK?)]: v2 relies on unsupported usage of scikit-learn

Issue - State: open - Opened by JacksonBurns 8 months ago - 3 comments
Labels: bug

#751 - [QUESTION]: Run train.py with 'mps' GPU

Issue - State: closed - Opened by Thanh-An-Pham 8 months ago - 4 comments
Labels: question

#750 - using multiple GPUs for speeding up chemprop hyperparameter optimization

Issue - State: closed - Opened by SoodabehGhaffari 8 months ago - 1 comment
Labels: question

#749 - add:pos_weights

Pull Request - State: closed - Opened by Furi5 8 months ago - 2 comments

#748 - [v2] [FEATURE]: eliminate `molecule_featurizer` input from `MoleculeDatapoint`

Issue - State: closed - Opened by davidegraff 8 months ago - 4 comments
Labels: enhancement

#747 - [v2] use generic types

Pull Request - State: closed - Opened by davidegraff 8 months ago - 1 comment

#745 - Fixed typo in README.md

Pull Request - State: closed - Opened by willspag 8 months ago

#744 - [QUESTION]: Hyperparameter optimisation in v2

Issue - State: closed - Opened by Rhys-McAlister 8 months ago - 1 comment
Labels: question

#743 - aggregation type

Issue - State: closed - Opened by SoodabehGhaffari 8 months ago - 1 comment
Labels: question

#742 - remove top level __init__.py

Pull Request - State: closed - Opened by c-w-feldmann 8 months ago - 2 comments

#741 - Fix load from checkpoint in python 3.12

Pull Request - State: closed - Opened by KnathanM 8 months ago - 3 comments

#740 - [BUG]: `num_workers`>0 hangs on Windows and sometimes MacOS.

Issue - State: closed - Opened by JacksonBurns 8 months ago - 3 comments
Labels: bug

#739 - overfitting in the ensemble of models

Issue - State: closed - Opened by SoodabehGhaffari 8 months ago - 1 comment
Labels: question

#737 - V2/feat/index file

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

#736 - [FEATURE]: Stub generation for V2

Issue - State: open - Opened by c-w-feldmann 8 months ago - 4 comments
Labels: enhancement

#735 - Question: How to use chemprop to convert SMILES into chemprop fingerprints only?

Issue - State: closed - Opened by jamesymwang 8 months ago - 3 comments
Labels: question

#734 - V2: Add CLI and tests for hyperparameter optimization

Pull Request - State: closed - Opened by hwpang 8 months ago - 11 comments

#733 - [v2]: Acceptance Testing for Numpy v2.0

Pull Request - State: closed - Opened by JacksonBurns 8 months ago - 9 comments

#732 - V2/fix and improve pyproject toml

Pull Request - State: open - Opened by c-w-feldmann 8 months ago - 7 comments

#731 - V2: consolidate `--checkpoint` CLI

Pull Request - State: closed - Opened by hwpang 8 months ago - 4 comments

#730 - V2: descriptors, {atom,bond} features, and atom descriptors for multicomponent

Pull Request - State: closed - Opened by hwpang 8 months ago - 4 comments

#728 - [QUESTION]: how to add atom-level features

Issue - State: closed - Opened by tom832 8 months ago - 4 comments
Labels: question

#727 - Extend saving of predictions to reaction and multi-component cases.

Pull Request - State: closed - Opened by am2145 8 months ago - 1 comment

#726 - V2: Improve saving and using of {input,output} scalers

Pull Request - State: closed - Opened by hwpang 8 months ago - 18 comments

#725 - fix the task names

Pull Request - State: closed - Opened by shihchengli 9 months ago
Labels: bug

#724 - [BUG]: supplied --constraints_path is not used during atom target predictions

Issue - State: closed - Opened by priabb 9 months ago - 3 comments
Labels: bug

#723 - update docker build `if` to use correct upstream branch name

Pull Request - State: closed - Opened by JacksonBurns 9 months ago

#722 - [FEATURE]: Extract atomic encodings before aggregating them into molecular encodings

Issue - State: open - Opened by zarkoivkovicc 9 months ago - 3 comments
Labels: enhancement

#721 - Use Factory to build metrics and features_generators

Pull Request - State: closed - Opened by KnathanM 9 months ago - 1 comment

#720 - remove macos and windows from v1 ci

Pull Request - State: closed - Opened by JacksonBurns 9 months ago - 2 comments

#719 - [TODO]: v2 `--show-individual-scores` implementation

Issue - State: closed - Opened by shihchengli 9 months ago - 4 comments
Labels: todo

#717 - hyperparameter tuning and cross validation

Issue - State: closed - Opened by SoodabehGhaffari 9 months ago
Labels: question

#716 - [FEATURE]: Revamp/Modularize CI

Issue - State: open - Opened by davidegraff 9 months ago - 2 comments
Labels: enhancement

#715 - Feature: create docker image and push to github registry

Pull Request - State: closed - Opened by xuyan-ru 9 months ago - 1 comment

#714 - [v2]: CI Overhaul (and make v2 actually _pass_ the CI)

Pull Request - State: closed - Opened by JacksonBurns 9 months ago - 51 comments

#713 - sklearn_train on chemprop

Issue - State: closed - Opened by SoodabehGhaffari 9 months ago - 1 comment
Labels: question

#712 - fix the `uncal_vars` for atom/bond property prediction

Pull Request - State: closed - Opened by shihchengli 9 months ago

#710 - [QUESTION]: should publish workflow depend on or be linked to successful tests?

Issue - State: open - Opened by kevingreenman 9 months ago - 2 comments
Labels: question, todo

#709 - [TODO]: use maintained alternative to bumpversion?

Issue - State: open - Opened by kevingreenman 9 months ago - 1 comment
Labels: todo

#708 - update training docs

Pull Request - State: closed - Opened by KnathanM 9 months ago

#707 - V2: Debug and add tests for various aggregation methods

Pull Request - State: closed - Opened by hwpang 9 months ago

#706 - revise dockerfile for chempropv2

Pull Request - State: closed - Opened by JacksonBurns 9 months ago - 9 comments