Generative Modeling
Diagram comparing standard stochastic sampling (gradient blocked) vs the reparameterization trick (gradient flows)

Auto-Encoding Variational Bayes (VAE Paper Summary)

Summary of Kingma & Welling's foundational VAE paper introducing the reparameterization trick and variational …...

Generative Modeling
Flowchart comparing VAE and IWAE computation showing the key difference in where averaging occurs relative to the log operation

Importance Weighted Autoencoders (IWAE Paper Summary)

Summary of Burda, Grosse & Salakhutdinov's ICLR 2016 paper introducing Importance Weighted Autoencoders for tighter …...

Generative Modeling
MNIST digit samples generated from a Variational Autoencoder latent space

Importance Weighted Autoencoders: Beyond the Standard VAE

The key difference between multi-sample VAEs and IWAEs: how log-of-averages creates a tighter bound on log-likelihood.

Computational Chemistry

Recent Advances in the SELFIES Library (2023)

Major updates to the SELFIES library, improved performance, expanded chemistry support, and new customization features....

Computational Chemistry

SELFIES: The Original Paper (Krenn et al. 2020)

The 2020 paper introducing SELFIES, the 100% robust molecular representation that solves SMILES validity problems in ML.

Computational Chemistry

GTR-CoT: Graph Traversal as Visual Chain of Thought for Molecular Structure Recognition

GTR-CoT uses graph traversal chain-of-thought reasoning to improve optical chemical structure recognition....

Computational Chemistry

SubGrapher: Visual Fingerprinting of Chemical Structures

SubGrapher creates molecular fingerprints from images via functional group segmentation, enabling retrieval without full …...

Computational Chemistry
The transformation from a 2D chemical structure image to a SMILES representation

What is Optical Chemical Structure Recognition (OCSR)?

A micro-review of Optical Chemical Structure Recognition (OCSR), from rule-based systems to modern AI models.

Computational Chemistry

αExtractor: Automatic Chemical Information Extraction from Biomedical Literature

αExtractor uses ResNet-Transformer to extract chemical structures from literature images, including noisy and hand-drawn …...

Computational Chemistry

Img2Mol: Accurate SMILES Recognition from Molecular Graphical Depictions

Clevert et al.'s two-stage CNN approach for converting molecular images to SMILES using CDDD embeddings and extensive …...

Computational Chemistry

MolNexTR: A Generalized Deep Learning Model for Molecular Image Recognition

Chen et al.'s dual-stream encoder approach for robust molecular structure recognition from diverse real-world images …...

Computational Chemistry

MolParser: End-to-end Visual Recognition of Molecule Structures in the Wild

MolParser converts molecular images from scientific documents to machine-readable formats using E-SMILES....