Implementing the Müller-Brown Potential in PyTorch
Guide to implementing the Müller-Brown potential in PyTorch, comparing analytical vs automatic differentiation with …
Machine-Learning
DenoiseVAE: Learning Molecule-Adaptive Noise Distributions for Denoising-based 3D Molecular Pre-training
Liu et al.'s ICLR 2025 paper introducing DenoiseVAE, which learns adaptive, atom-specific noise for better molecular …...
Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling
Lu et al. introduce SpaceFormer, a Transformer that models entire 3D molecular space—not just atoms—for superior …...
The Dark Side of the Forces: Assessing Non-Conservative Force Models for Atomistic Machine Learning
Bigi et al. critique non-conservative force models in ML potentials, showing their simulation failures and proposing …...
A Contrastive Learning Approach for Training Variational Autoencoder Priors
Dai et al.'s NeurIPS 2021 paper introducing Noise Contrastive Priors (NCPs) to address VAE's 'prior hole' problem with …...
GEOM Dataset: 3D Molecular Conformer Generation
Learn how GEOM transforms 2D molecular graphs into dynamic 3D conformer ensembles for molecular machine learning …
3D Steerable CNNs: Learning Rotationally Equivariant Features in Volumetric Data
Weiler et al.'s NeurIPS 2018 paper introducing SE(3)-equivariant CNNs for volumetric data using group theory and …...
LLMs for Page Stream Segmentation
Enhanced TABME benchmark for page stream segmentation, creating TABME++, showing fine-tuned decoder-based LLMs …...
Invalid SMILES are Beneficial Rather than Detrimental to Chemical Language Models
Skinnider's 2024 Nature Machine Intelligence paper demonstrates that the ability to generate invalid SMILES is actually …...
Modern PyTorch Techniques for VAEs: A Hands-On Tutorial
A VAE tutorial using modern PyTorch: torch.distributions, BCEWithLogits, KL Warmup, and a hands-on guide to tuning the …
Can You Hear the Shape of a Molecule? (Part Three)
Supervised learning reveals hidden eigenvalue patterns that clustering missed, testing k-NN and logistic regression on …
Can You Hear the Shape of a Molecule? (Part Two)
Clustering analysis reveals why Coulomb matrix eigenvalues struggle with larger alkanes, using Dunn Index and silhouette …