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Computational Chemistry
SELFIES representation of 2-Fluoroethenimine molecule

SELFIES (Self-Referencing Embedded Strings)

SELFIES is a 100% robust molecular string representation for ML, implemented in the open-source selfies Python library.

Computational Chemistry
Müller-Brown Potential Energy Surface showing the three minima and two saddle points

Implementing the Müller-Brown Potential in PyTorch

Guide to implementing the Müller-Brown potential in PyTorch, comparing analytical vs automatic differentiation with …

Computational Chemistry
Potential energy surface showing molecular conformation space with equilibrium and low energy conformations

DenoiseVAE: Adaptive Noise for Molecular Pre-training

Liu et al.'s ICLR 2025 paper introducing DenoiseVAE, which learns adaptive, atom-specific noise for better molecular …

Computational Chemistry
Adaptive grid merging visualization for benzene molecule showing multi-resolution spatial discretization

Beyond Atoms: 3D Space Modeling for Molecular Pretraining

Lu et al. introduce SpaceFormer, a Transformer that models entire 3D molecular space (not just atoms) for superior …

Computational Chemistry
Atomic structure of a spherical fullerene

Dark Side of Forces: Non-Conservative ML Force Models

Bigi et al. critique non-conservative force models in ML potentials, showing their simulation failures and proposing …

Computational Chemistry
Spherical harmonics visualization

Efficient DFT Hamiltonian Prediction via Adaptive Sparsity

Luo et al. introduce SPHNet, using adaptive sparsity to dramatically improve SE(3)-equivariant Hamiltonian prediction …

Computational Chemistry
Atomic structure of a spherical fullerene

Learning Smooth Interatomic Potentials with eSEN

Fu et al. propose energy conservation as a key MLIP diagnostic and introduce eSEN, bridging test accuracy and real …

Generative Modeling
Visualization of the VAE prior hole problem showing a ring-shaped aggregate posterior with an empty center where the Gaussian prior has highest density

Contrastive Learning for Variational Autoencoder Priors

Aneja et al.'s NeurIPS 2021 paper introducing Noise Contrastive Priors (NCPs) to address VAE's 'prior hole' problem with …

Computational Chemistry
Comparison of 2D molecular graph versus 3D conformer ensemble showing latanoprost molecule in multiple conformations

GEOM Dataset: 3D Molecular Conformer Generation

Learn how GEOM transforms 2D molecular graphs into dynamic 3D conformer ensembles for molecular machine learning …

Computational Chemistry
SELFIES robustness demonstration

Invalid SMILES Benefit Chemical Language Models: A Study

Skinnider (2024) shows that generating invalid SMILES actually improves chemical language model performance through …

Computational Chemistry
3D ball-and-stick model of butane molecule representing the structural isomer generation process

Synthetic Isomer Data Generation Pipeline

An end-to-end cheminformatics pipeline transforming 1D chemical formulas into 3D conformer datasets using graph …

Generative Modeling
Variational Autoencoder architecture diagram showing encoder, latent space, and decoder

Modern PyTorch Techniques for VAEs: A Hands-On Tutorial

Learn to implement VAEs in PyTorch: ELBO objective, reparameterization trick, loss scaling, and MNIST experiments on …