Miroslav Lzicar

Synthesis-on-demand libraries expose vast chemical spaces through reaction templates and compatible synthons, so the key question is which candidates to evaluate under a small oracle budget.

A CHEESE case study where 3D electrostatic similarity prioritized NS1, a tetrazolic neurosteroid candidate, before synthesis.

Neural thickets suggest that many task experts may lie dense around pretrained weights, but density does not mean those experts are easy to discover.

Make-on-demand design spaces are increasingly defined by reactions and synthons rather than enumerated molecules, which makes search, audit, and visualization a grounding problem.

A lightweight Python package for reaction-grounded synthon retrieval that stays intentionally simple: generic RDKit fingerprints combined with a binary OR.

A Wittgensteinian essay on chain-of-thought, state over tokens, form of life, and why reasoning traces are better understood as public marks with an operative role than as private language or transparent inner speech.

A Deep MedChem webinar on exploring ultra-large combinatorial chemical spaces with CHEESE SynthonGPT.

Final presentation from the 9th Advanced in silico Drug Design workshop 2026, covering our winning workflow for the DYRK1B virtual screening challenge.

Our team at Deep MedChem won the DYRK1B challenge at 9ADD 2026 with a CHEESE ShapeSim + LightGBM workflow.

A compact synthon-conditioned transformer for navigating makeable chemical space, grounded in vendor enumerations rather than hallucinated SMILES.

Introducing a cellular-automata-native benchmark, leaderboard, and dataset suite that scores reasoning systems on metadata-rich ARC-AGI style episodes.

A quick note on adapting ISONET’s Gumbel–Sinkhorn edge alignment to molecular substructure search, with links to the source notebook and paper.

CHEESE is a web-based shape and electrostatic search engine.

Ultra-lean BitBIRCH rewrite that clusters hundred-million scale molecular libraries with on-the-fly compression, optional C++ accelerators, and a batteries-included CLI.

There are two distinct technologies to search in databases of molecules.

A 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 quest…

An open-source React application that extracts all references from academic papers using DOI, converts them to 5000+ citation formats, and enables bulk downloads.

This is my billion-scale vector engine for 3D shape & electrostatic molecular similarity.

Web pages used to feel like the most boring part of programming—until I discovered React.

A 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.

Using 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.

In Frieren: Beyond Journey’s End, magic isn’t just a tool or a talent—it’s a reflection of character, circumstance, and culture history.

A talk at ACS Spring 2025 in San Diego

Visualisation of chemical spaces using CHEESE embeddings.

Fingerprints have long been the standard for representing molecules, but neural network embeddings are opening doors to new possibilities.

A novel approach to virtual screening using 3D shape and electrostatics in a vector space.

A novel approach to virtual screening using 3D shape and electrostatics in a vector space.

An app to predict ESP and RESP partial charges for small molecules.

I tried, and failed, to get ViTs to work on the ARC challenge.

A Glami webinar hosted by MITON on the topic of utilizing embeddings for drug discovery in billion-scale databases.

A ChemSpace Webinar on CHEESE embeddings

A Github Action to label issues based on their duration.

Grand Hotel Abyss, Stuart Jeffries' collective biography of the leading figures of the Frankfurt School, tells the story of critical theorists—mainly Jewish intellectuals of the early 20th century—who gathered around the Institute for Social Research, also

A review of Glass and Hall (2008), which argues that modern science is shifting from hypothesis falsification (Popper) towards data-driven model building.

Winkler’s book The Inmate of Jean Genet traces the fate of a remarkable outcast—criminal, prostitute, and homosexual—hailed as “the last accursed poet” and “the Orpheus of the gutter.”

An essay on the phenomenology of neural networks and the implications of inceptionism, submitted in partial fulfillment of the high school leaving examination.

A richer sandbox post that demonstrates Markdown, MDX, citations, images, tables, footnotes, and interactive components.