Biosecurity retrieval compendium — ESM-2 homology cliff analysis, 5 papers, 4 pre-registrations, 9360 per-cell results, SHA-256 manifest

This paper has been published on Interdisciplinary Sciences: Computational Life Sciences.

Code for processing FASTA files into batched, tokenized, and padded sequences, and training FlashAttention-based implementations of ESM-2

A Graph Neural Network (Siamese GATv2) pipeline using ESM-2 embeddings to map the Dengue NS1–Human interactome. Discovered a novel link between NS1 and Carbonic Anhydrases.

Graph-based Protein-Peptide Interaction Predictor. Reranking candidates using ESM-2 embeddings and Graph Neural Networks (GNN) on PROPEDIA data.

ML classifier for genome-editing enzymes, assigning nuclease/recombinase/transposase classes that predicts mechanism class and flags IS110-family composite recombinases overlooked by existing tools.

Bioinformatics capstone of the UoA DI 'Software Development for Algorithmic Problems' trilogy. Protein remote-homolog search on SwissProt-50k via ESM-2 embeddings + 6 ANN methods (brute, LSH, Hypercube, IVF-Flat, IVF-PQ, Neural LSH), benchmarked against BLAST.

Programmable genome‑writing knowledge graph and GNN toolkit for DNA‑modifying enzymes, combining CRISPR/CAST/Fanzor annotations with ESM‑2 embeddings, GraphSAGE/GAT link prediction, and an editor‑selection API for gene‑editing use cases.

A hybrid C++/Python pipeline for remote protein homology detection, coupling ESM-2 language model embeddings with custom Neural-LSH for scalable approximate nearest neighbor search.

ProteinFlex is a comprehensive platform for protein structure analysis and drug discovery, leveraging advanced AI and machine learning techniques. The platform combines state-of-the-art protein structure prediction with interactive visualization and sophisticated drug discovery tools.

Empirical dual-use risk assessment of protein language models (ESM-2) and structure-based design tools (ProteinMPNN)