- techAug 14, 20256 min readEnumerative vs. Synthon-Based Molecule SearchThere are two distinct technologies to search in databases of molecules. This post explains both with intuitive LEGO illustrations and presents a practical guide on when to use each.
- techAug 08, 202510 min readDo Stereoisomers Cause Leakage? A Closer Look at the LIT-PCBA AuditA recent paper claims an established virtual screening benchmark to be 'fundamentally compromised' due to 'egregious data leakage, rampant duplication, and pervasive analog redundancy', rendering it 'unfit for its intended purpose' and 'calling into question previous results based on its use'. The catch: the authors canonicalized to non-isomeric SMILES, effectively collapsing stereoisomers into duplicates.
- techJun 22, 20258 min readDOI Reference Extractor: Open-Source Tool for Effortless Literature ReviewsAn open-source React application that extracts all references from academic papers using DOI, converts them to 5000+ citation formats, and enables bulk downloads. Built with OpenCitations API and modern web technologies.
- techJun 16, 20252 min readCHEESE Search: A Billion-Scale Vector Molecular SearchThis is my billion-scale vector engine for 3D shape & electrostatic molecular similarity. It turns ligand-based screening into nearest-neighbour lookups—so you can *search, rank, and visualise* huge chemical spaces in seconds.
- techJun 13, 202510 min readMy Flight from Flask to React, via Streamlit and DashWeb pages used to feel like the most boring part of programming—until I discovered React. In this post I reflect on my coding journey from the backend to the frontend.
- techJun 07, 20254 min readKetcher Docker: Production-Ready Chemical Structure EditorA dockerized deployment of EPAM's Ketcher chemical structure editor with iframe communication API, React 19, and production-ready configuration for seamless integration into web applications.
- cultureMay 21, 20256 min readOn the Contents of This Blog (May 2025)Some notes on which texts are published here or not, why, and what the plans are.
- techMay 18, 20254 min readMemecoins as a Vanity Fair: only 1 in 10 000 Solana tokens clears a basic rug‑checkUsing on‑chain metadata for every token minted on Solana in February 2025, we show that fewer than 0.01 % of fresh meme‑coins meet even the loosest criteria for legitimacy.
- cultureMay 17, 20257 min readIt Didn’t Have to Be Magic—Yet You Chose It: On the Purpose of Magic in FrierenIn Frieren: Beyond Journey’s End, magic isn’t just a tool or a talent—it’s a reflection of character, circumstance, and culture history. From obsession and duty to chance and inheritance, the reasons characters become mages are as varied as the spells they wield. This piece collects dialogue excerpts from the anime’s first season to show how magic, for each mage, holds a different meaning—and often, no single explanation.
- talksMar 25, 20251 min readACS Spring: 3D Shape and Electrostatic Virtual Screening in a Vector SpaceA talk at ACS Spring 2025 in San Diego
- techNov 18, 20241 min readExplorer of Chemical SpacesVisualisation of chemical spaces using CHEESE embeddings.
- techNov 13, 202412 min readWhat Can Neural Network Embeddings Do That Fingerprints Can’t?Fingerprints have long been the standard for representing molecules, but neural network embeddings are opening doors to new possibilities. This post explores where these AI-driven representations excel, from better capturing molecular similarity with metrics to addressing modalities that traditional fingerprints often miss.
- talksNov 05, 20241 min readInteractive Molecular Space Exploration with AIA novel approach to virtual screening using 3D shape and electrostatics in a vector space.
- techSep 17, 20241 min readDFT quality Electrostatics with AIAn app to predict ESP and RESP partial charges for small molecules.
- techAug 31, 20242 min readAbstraction and Reasoning with Vision TransformersI tried, and failed, to get ViTs to work on the ARC challenge.
- talksMar 31, 20241 min readUtilizing Embeddings for Drug Discovery in Billion-Scale DatabasesA Glami webinar hosted by MITON on the topic of utilizing embeddings for drug discovery in billion-scale databases.
- talksAug 11, 20231 min readMolecular Search in AI Learned Chemical Similarity SpaceA ChemSpace Webinar on CHEESE embeddings
- techJun 20, 20231 min readIssue Duration LabellerA Github Action to label issues based on their duration.
