Charlles Abreu

CUDA tests failing

1

The `ExampleForce` tests fail in the CUDA platform when executing the following line: https://github.com/openmm/openmmexampleplugin/blob/6340817d2c53105c0cb8c862d83653b7ebc079db/platforms/common/src/CommonExampleKernels.cpp#L83 I compiled both OpenMM and this plugin with the same GCC compiler (version 11.2.0) and CudaToolkit...

## Description When setting velocities from temperature, remove the COM component from the physical velocities and set vy=vz=0 for extra particles. Optionally split velocities (like done for positions) when rettrieving...

Fixes multiple quantile regression bugs

3

This PR solves the following issues (#1228): * Fixes tensor dimension mismatch in quantile uncertainty estimator. * Allows prediction with QuantileFFN models when no uncertainty method is specified. * Removes...

Refactor multi-hot featurizers

2

## Description This PR restructures the multi-hot featurizers for atoms, bonds, and molecular graphs. The changes do not alter the default behavior of the current featurizers but improve readability and...

Implements v1-to-v2 conversion of checkpoint files with uncertainty-handling models

3

## Summary This PR enables the conversion of Chemprop v1 checkpoint files that include uncertainty quantification (UQ) models, addressing the issue reported in [#1222](https://github.com/chemprop/chemprop/issues/1222). ### Key Improvements 1. **Support for...

The following command should be sufficient to train a quantile regression model with $\alpha=0.317$: ``` chemprop train \ --data-path tests/data/regression.csv \ --output-dir train_example \ --task-type regression-quantile \ --alpha 0.317 ```...

The quantile regression loss function is registered in v1 as `quantile_interval`: https://github.com/chemprop/chemprop/blob/02c760216ec03488b69b41abe184589b9c996d74/chemprop/train/loss_functions.py#L25 In addition, there is a registered quantile metric in v1: https://github.com/chemprop/chemprop/blob/02c760216ec03488b69b41abe184589b9c996d74/chemprop/train/metrics.py#L49-L50 However, there is no registered quantile metric...

Bugs related to quantile regression: ### 1. Uncertainty estimator raises exception The quantile regression uncertainty estimator raises an exception: ``` ValueError: not enough values to unpack (expected 2, got 1)...

## Description OpenMM's StateDataReported has changed. This PR updates the UFEDMM's counterpart accordingly.

# Add Duck-Typed RDKit Molecule Implementation with C++ Integration > **⚠️ Experimental Implementation - Draft PR** > This is an experimental implementation exploring performance optimization through duck-typed molecular objects. Opening...