Home

Blog Posts

Technical articles on machine learning, computational chemistry, and scientific computing with deep dives into methodologies and practical implementations.
Generative Modeling

Importance Weighted Autoencoders: Beyond the Standard VAE

Learn the crucial difference between multi-sample VAEs and Importance Weighted Autoencoders (IWAEs). Explore how …

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), tracing its evolution from rule-based systems to …

Computational Chemistry
SELFIES strings guarantee 100% valid molecules - even when generated randomly

Converting SELFIES Strings to 2D Molecular Images

Learn how to visualize SELFIES molecular representations and explore their unique advantages through random sampling, …

Computational Chemistry
Aspirin molecular structure generated from SMILES string

Converting SMILES Strings to 2D Molecular Images

Learn how to create 2D molecular images from SMILES strings using RDKit and PIL, with proper formatting and legends.

Scientific Computing
Comparison of exponential sampling methods showing histograms from both inverse transform and von Neumann methods overlaid with the theoretical exponential distribution

Exponential Random Number Generation: Two Classic Algorithms Compared

Compare inverse transform sampling and von Neumann's rejection method for exponential random numbers with Python …

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 …

Scientific Computing
Velocity Autocorrelation Function showing the signature negative region characteristic of liquid dynamics and the cage effect discovered by Rahman

Replicating Rahman's 1964 Liquid Argon Simulation

Recreating the foundational 1964 molecular dynamics simulation with modern Python and LAMMPS, testing whether Rahman's …...

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 …

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

Modern PyTorch Techniques for VAEs: A Hands-On Tutorial

A comprehensive guide to implementing Variational Autoencoders (VAEs) in PyTorch. Covers the ELBO objective, …

Computational Chemistry
Comparison chart showing k-NN significantly outperforming logistic regression for molecular classification across different alkane sizes

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 …

Computational Chemistry
Charts showing Dunn Index, distance metrics, and computation time analysis revealing clustering performance degradation with molecular size

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 …

Natural Language Processing
Word vector illustration showing text classification and NLP concepts

Sarcasm Detection with Transformers: A Cautionary Tale

Learn how dataset bias can lead to misleading results in NLP: a sarcasm detection model that actually learned to …