I'm passionate about applying Deep Learning & Artificial Intelligence to scientific domains, with a focus on Cheminformatics and Bioinformatics. Now I am a CTO, Co-Founder @ Deep MedChem and exploring innovative AI applications in drug discovery and medical chemistry.

• Chemical Embeddings Search Engine – Custom implemented disk-based vector database with 40B+ isometric embeddings of molecules trained using novel AI approach. The UI is written in React/Typescript, Vite, Express and Tailwind CSS. Read paper preprint
• Conformer Visualiser – An app for comparison of alignment of conformers
• DOI Reference Extractor @ references.mireklzicar.com – Enter a DOI to extract and download all references in your preferred citation format
• DNGPU Torch – Torch implementation of Neural GPU with Diagonal Recurrent Cells (ported from antique version of tensorflow)
• Neural Chomsky – Torch implementation of Neural Networks and the Chomsky Hierarchy (ported from Jax)
• Ketcher Docker @ ketcher.mireklzicar.com – A production-ready Vite-based application that embeds the Ketcher chemical structure editor with full iframe communication support.
• Issue Duration Labeller – Github Marketplace – Github Action for automatic labelling of issues based on time taken
• LineIndex – LineIndex provides lightning-fast random access to lines in large text files through efficient indexing. It's a pip package designed to handle very large files where you need to frequently access specific lines without reading the entire file.
• ESP and RESP partial charges – Streamlit app of computation of near DFT-quality ESP and RESP partial charges
• Modeller – Streamlit app allowing users to train custom AI models for ADMET property prediction and run inference at scale unmatched by competitors
• SynthonGPT @ technical report – A live prototype for diversity-oriented molecule search in ultra-large chemical spaces using a compact synthon-conditioned Transformer.
• OpenReview Paper Downloader – A CLI that downloads oral, spotlight, accepted, or rejected papers from OpenReview-hosted conferences into tidy decision-based folders.
• CellARC @ baselines @ paper – A synthetic benchmark for abstraction and reasoning built from multicolor 1D cellular automata, with reproducible dataset generation, baselines, and evaluation code.
• rdkit-fp – A fast CLI and Python package for parallel RDKit fingerprint generation, from beginner one-liners to staged large-scale pipelines.
• BitBIRCH-Lean – A memory-efficient toolkit for clustering huge molecular libraries; I contributed the bit packing that made it about 8x more memory efficient and 2x faster.
• codex_ntfy.sh – A small Bash hook that sends ntfy notifications when Codex finishes a turn, including the task title and formatted payload details.
• wfn2resp.py – A compact Psi4/RESP utility that computes RESP charges directly from saved Psi4 wavefunctions by generating ESP grids on van der Waals shells.
• Spanning Trees Search – Python project leveraging matrix methods in graph theory to efficiently enumerate spanning trees.
• Particle Swarm Optimization – C# project for visualisation of particle swarm optimization.
• Time Resolved X-ray Diffraction Crystallography – Work for ELI Beamlines under research group TREX at Department of Structural Dynamics
• mireklzicar.com – A personal blog written in Astro with plenty of cool features. Initial fork from Astro Sphere